An Introduction to Microbiomes

  1. Apprill, A. (2017). Marine Animal Microbiomes: Toward Understanding Host–Microbiome Interactions in a Changing Ocean. Frontiers in Marine Science, 4, 222.
  2. Arif, I., Batool, M., & Schenk, P. M. (2020). Plant Microbiome Engineering: Expected Benefits for Improved Crop Growth and Resilience. Trends in Biotechnology, 38(12), 1385–1396.
  3. Backhed F, Fraser CM, Ringel Y, Sanders ME, Sartor RB, Sherman PM, et al. Defining a healthy human gut microbiome: current concepts, future directions, and clinical applications. Cell Host Microbe. 2012;12:611–22.
  4. Baedke, J., Fábregas-Tejeda, A., & Nieves Delgado, A. (2020). The holobiont concept before Margulis. Journal of Experimental Zoology Part B: Molecular and Developmental Evolution, 334(3), 149–155.
  5. Bashiardes S, Zilberman-Schapira G, Elinav E. Use of Metatranscriptomics in Microbiome Research. Bioinformatics and Biology Insights. January 2016. doi:10.4137/BBI.S34610
  6. Berg, G., Rybakova, D., Fischer, D. et al. Microbiome definition re-visited: old concepts and new challenges. Microbiome 8, 103 (2020).
  7. Busby PE, Soman C, Wagner MR, Friesen ML, Kremer J, Bennett A, et al. (2017) Research priorities for harnessing plant microbiomes in sustainable agriculture. PLoS Biol 15(3): e2001793.
  8. Clapp M, Aurora N, Herrera L, Bhatia M, Wilen E, Wakefield S. Gut Microbiota’s Effect on Mental Health: The Gut-Brain Axis. Clinics and Practice. 2017; 7(4):131-136.
  9. Cryan, J. F., O’Riordan, K. J., Cowan, C. S. M., Sandhu, K. v, Bastiaanssen, T. F. S., Boehme, M., Codagnone, M. G., Cussotto, S., Fulling, C., Golubeva, A. v, Guzzetta, K. E., Jaggar, M., Long-Smith, C. M., Lyte, J. M., Martin, J. A., Molinero-Perez, A., Moloney, G., Morelli, E., Morillas, E., … Dinan, T. G. (2019). The Microbiota-Gut-Brain Axis. Physiological Reviews, 99(4), 1877–2013.
  10. Diakite, A., Dubourg, G., Dione, N. et al. Optimization and standardization of the culturomics technique for human microbiome exploration. Sci Rep 10, 9674 (2020).
  11. Elhady, A., Adss, S., Hallmann, J., & Heuer, H. (2018). Rhizosphere Microbiomes Modulated by Pre-crops Assisted Plants in Defense Against Plant-Parasitic Nematodes. Frontiers in Microbiology, 9, 1133.
  12. Daliri, E. B., Wei, S., Oh, D. H., & Lee, B. H. (2017). The human microbiome and metabolomics: Current concepts and applications. Critical reviews in food science and nutrition57(16), 3565–3576.
  13. Foster, J. A., Rinaman, L., & Cryan, J. F. (2017). Stress & the gut-brain axis: Regulation by the microbiome. Neurobiology of Stress, 7, 124–136.
  14. Garrett W. S. (2015). Cancer and the microbiota. Science (New York, N.Y.)348(6230), 80–86.
  15. Gilbert, J. A., Blaser, M. J., Caporaso, J. G., Jansson, J. K., Lynch, S. v, & Knight, R. (2018). Current understanding of the human microbiome. Nature Medicine, 24(4), 392–400.
  16. Grice, E., Segre, J. The skin microbiome. Nat Rev Microbiol 9, 244–253 (2011).
  17. Hannula, S., Morriën, E., de Hollander, M. et al. Shifts in rhizosphere fungal community during secondary succession following abandonment from agriculture. ISME J 11, 2294–2304 (2017).
  18. Hernández-Álvarez, C., García-Oliva, F., Cruz-Ortega, R., Romero, M. F., Barajas, H. R., Piñero, D., & Alcaraz, L. D. (2022). Squash root microbiome transplants and metagenomic inspection for in situ arid adaptations. Science of The Total Environment, 805, 150136.
  19. Hirt, H. (2020). Healthy soils for healthy plants for healthy humans. EMBO Reports, 21(8), e51069.
  20. Hsiao, E. Y., McBride, S. W., Hsien, S., Sharon, G., Hyde, E. R., McCue, T., Codelli, J. A., Chow, J., Reisman, S. E., Petrosino, J. F., Patterson, P. H., & Mazmanian, S. K. (2013). Microbiota modulate behavioral and physiological abnormalities associated with neurodevelopmental disorders. Cell155(7), 1451–1463.
  21. Lin, H., He, Q. Y., Shi, L., Sleeman, M., Baker, M. S., & Nice, E. C. (2019). Proteomics and the microbiome: pitfalls and potential. Expert review of proteomics16(6), 501–511.
  22. Human Microbiome Project / Program Initiatives. The NIH Common Fund. Retrieved 9 September 2021.
  23. Huttenhower C, Gevers D, Knight R, Abubucker S, Badger JH, Chinwalla AT, Creasy HH, Earl AM, FitzGerald MG, Fulton RS, et al. Human Microbiome Project Consortium (2012). Structure, function and diversity of the healthy human microbiome. Nature486(7402), 207–214.
  24. Integrative HMP (iHMP) Research Network Consortium (2014). The Integrative Human Microbiome Project: dynamic analysis of microbiome-host omics profiles during periods of human health and disease. Cell host & microbe16(3), 276–289.
  25. Jandhyala SM, Talukdar R, Subramanyam C, Vuyyuru H, Sasikala M, Nageshwar Reddy D. Role of the normal gut microbiota. World J Gastroenterol. 2015 Aug 7;21(29):8787-803. doi: 10.3748/wjg.v21.i29.8787. PMID: 26269668; PMCID: PMC4528021.
  26. Jansson, J. K., & Hofmockel, K. S. (2018). The soil microbiome—from metagenomics to metaphenomics. Current Opinion in Microbiology, 43, 162–168.
  27. Jiang, D., Armour, C. R., Hu, C., Mei, M., Tian, C., Sharpton, T. J., & Jiang, Y. (2019). Microbiome Multi-Omics Network Analysis: Statistical Considerations, Limitations, and Opportunities. Frontiers in genetics10, 995.
  28. Lederberg J, Mccray AT. `Ome Sweet `Omics–A genealogical treasury of words. The Scientist. 2001;15(7):8–8.
  29. Levkovich T, Poutahidis T, Smillie C, Varian BJ, Ibrahim YM, Lakritz JR, et al. (2013) Probiotic Bacteria Induce a ‘Glow of Health’. PLoS ONE 8(1): e53867.
  30. Lloyd-Price, J., Abu-Ali, G. & Huttenhower, C. The healthy human microbiome. Genome Med 8, 51 (2016).
  31. Marchesi, J. R., & Ravel, J. (2015). The vocabulary of microbiome research: a proposal. Microbiome3, 31.
  32. Margulis L. Symbiosis as a source of evolutionary innovation: speciation and morphogenesis. In: Cambridge MA MLFR, editor. Symbiogenesis and Symbionticism: MIT Press; 1991. p. 1–14.
  33. NIH Human Microbiome Project – About the Human Microbiome. Retrieved 9 September 2021.
  34. O’Neill, C.A., Monteleone, G., McLaughlin, J.T. and Paus, R. (2016), The gut-skin axis in health and disease: A paradigm with therapeutic implications. BioEssays, 38: 1167-1176.
  35. Petersen, C., & Round, J. L. (2014). Defining dysbiosis and its influence on host immunity and disease. Cellular microbiology16(7), 1024–1033.
  36. Pratama, A. A., & van Elsas, J. D. (2018). The ‘Neglected’ Soil Virome – Potential Role and Impact. Trends in Microbiology, 26(8), 649–662.
  37. Rosenberg, E. and Zilber-Rosenberg, I. (2011), Symbiosis and development: The hologenome concept. Birth Defects Research Part C: Embryo Today: Reviews, 93: 56-66.
  38. Saleem, M., Hu, J., & Jousset, A. (2019). More Than the Sum of Its Parts: Microbiome Biodiversity as a Driver of Plant Growth and Soil Health. Annual Review of Ecology, Evolution, and Systematics, 50(1), 145–168.
  39. Salem I, Ramser A, Isham N and Ghannoum MA (2018) The Gut Microbiome as a Major Regulator of the Gut-Skin Axis. Front. Microbiol. 9:1459. doi: 10.3389/fmicb.2018.01459
  40. Sender R, Fuchs S, Milo R (2016) Revised Estimates for the Number of Human and Bacteria Cells in the Body. PLoS Biol 14(8): e1002533.
  41. Simon, JC., Marchesi, J.R., Mougel, C. et al. Host-microbiota interactions: from holobiont theory to analysis. Microbiome 7, 5 (2019).
  42. The Integrative HMP (iHMP) Research Network Consortium. The Integrative Human Microbiome Project. Nature 569, 641–648 (2019).
  43. Trompette, A., Gollwitzer, E. S., Yadava, K., Sichelstiel, A. K., Sprenger, N., Ngom-Bru, C., Blanchard, C., Junt, T., Nicod, L. P., Harris, N. L., & Marsland, B. J. (2014). Gut microbiota metabolism of dietary fiber influences allergic airway disease and hematopoiesis. Nature medicine20(2), 159–166.
  44. Turnbaugh, P., Ley, R., Hamady, M. et al. The Human Microbiome Project. Nature 449, 804–810 (2007).
  45. Whipps J, Lewis K, Cooke R. Mycoparasitism and plant disease control. In: Burge M, editor. Fungi Biol Control Syst. Manchester University Press; 1988. p. 161-187.
  46. Zhong, W., Yian, G., Ville-Petri, F., A, K. G., Yangchun, X., Qirong, S., & Alexandre, J. (2021). Initial soil microbiome composition and functioning predetermine future plant health. Science Advances, 5(9), eaaw0759.

Analyzing Microbiomes

  1. Allaband, C., McDonald, D., Vázquez-Baeza, Y., Minich, J. J., Tripathi, A., Brenner, D. A., Loomba, R., Smarr, L., Sandborn, W. J., Schnabl, B., Dorrestein, P., Zarrinpar, A., & Knight, R. (2019). Microbiome 101: Studying, Analyzing, and Interpreting Gut Microbiome Data for Clinicians. Clinical Gastroenterology and Hepatology, 17(2), 218–230.
  2. Bashiardes, S., Zilberman-Schapira, G., & Elinav, E. (2016). Use of Metatranscriptomics in Microbiome Research. Bioinformatics and Biology Insights, 10, BBI.S34610.
  3. Bauermeister, A., Mannochio-Russo, H., Costa-Lotufo, L. v, Jarmusch, A. K., & Dorrestein, P. C. (2021). Mass spectrometry-based metabolomics in microbiome investigations. Nature Reviews Microbiology.
  4. Bharti, R., & Grimm, D. G. (2021). Current challenges and best-practice protocols for microbiome analysis. Briefings in Bioinformatics, 22(1), 178–193.
  5. Caporaso, J. G., Lauber, C. L., Costello, E. K., Berg-Lyons, D., Gonzalez, A., Stombaugh, J., Knights, D., Gajer, P., Ravel, J., Fierer, N., Gordon, J. I., & Knight, R. (2011). Moving pictures of the human microbiome. Genome Biology, 12(5), R50.
  6. Chen, I.-M. A., Chu, K., Palaniappan, K., Ratner, A., Huang, J., Huntemann, M., Hajek, P., Ritter, S., Varghese, N., Seshadri, R., Roux, S., Woyke, T., Eloe-Fadrosh, E. A., Ivanova, N. N., & Kyrpides, N. C. (2021). The IMG/M data management and analysis system v.6.0: new tools and advanced capabilities. Nucleic Acids Research, 49(D1), D751–D763.
  7. Chong, J., Liu, P., Zhou, G., & Xia, J. (2020). Using MicrobiomeAnalyst for comprehensive statistical, functional, and meta-analysis of microbiome data. Nature Protocols, 15(3), 799–821.
  8. Costello, E. K., L, L. C., Micah, H., Noah, F., I, G. J., & Rob, K. (2009). Bacterial Community Variation in Human Body Habitats Across Space and Time. Science, 326(5960), 1694–1697.
  9. de Cárcer, D. A., Cuív, P. Ó., Wang, T., Kang, S., Worthley, D., Whitehall, V., Gordon, I., McSweeney, C., Leggett, B., & Morrison, M. (2011). Numerical ecology validates a biogeographical distribution and gender-based effect on mucosa-associated bacteria along the human colon. The ISME Journal, 5(5), 801–809.
  10. Dhariwal, A., Chong, J., Habib, S., King, I. L., Agellon, L. B., & Xia, J. (2017). MicrobiomeAnalyst: a web-based tool for comprehensive statistical, visual and meta-analysis of microbiome data. Nucleic Acids Research, 45(W1), W180–W188.
  11. Eckburg, P. B., Bik, E. M., Bernstein, C. N., Purdom, E., Dethlefsen, L., Sargent, M., Gill, S. R., Nelson, K. E., & Relman, D. A. (2005). Diversity of the Human Intestinal Microbial Flora. Science, 308(5728), 1635–1638.
  12. Findley, K., & Grice, E. A. (2014). The Skin Microbiome: A Focus on Pathogens and Their Association with Skin Disease. PLOS Pathogens, 10(11), e1004436-.
  13. Franzosa, E. A., Morgan, X. C., Segata, N., Waldron, L., Reyes, J., Earl, A. M., Giannoukos, G., Boylan, M. R., Ciulla, D., Gevers, D., Izard, J., Garrett, W. S., Chan, A. T., & Huttenhower, C. (2014). Relating the metatranscriptome and metagenome of the human gut. Proceedings of the National Academy of Sciences, 111(22), E2329.
  14. Giannoukos, G., Ciulla, D. M., Huang, K., Haas, B. J., Izard, J., Levin, J. Z., Livny, J., Earl, A. M., Gevers, D., Ward, D. v, Nusbaum, C., Birren, B. W., & Gnirke, A. (2012). Efficient and robust RNA-seq process for cultured bacteria and complex community transcriptomes. Genome Biology, 13(3), r23.
  15. Gloor, G. B., Wu, J. R., Pawlowsky-Glahn, V., & Egozcue, J. J. (2016). It’s all relative: analyzing microbiome data as compositions. Annals of Epidemiology, 26(5), 322–329.
  16. Gonzalez, A., Navas-Molina, J. A., Kosciolek, T., McDonald, D., Vázquez-Baeza, Y., Ackermann, G., DeReus, J., Janssen, S., Swafford, A. D., Orchanian, S. B., Sanders, J. G., Shorenstein, J., Holste, H., Petrus, S., Robbins-Pianka, A., Brislawn, C. J., Wang, M., Rideout, J. R., Bolyen, E., … Knight, R. (2018). Qiita: rapid, web-enabled microbiome meta-analysis. Nature Methods, 15(10), 796–798.
  17. Gosalbes, M. J., Durbán, A., Pignatelli, M., Abellan, J. J., Jiménez-Hernández, N., Pérez-Cobas, A. E., Latorre, A., & Moya, A. (2011). Metatranscriptomic Approach to Analyze the Functional Human Gut Microbiota. PLOS ONE, 6(3), e17447-.
  18. Iorio, A., Biazzo, M., Gardini, S., Muda, A. O., Perno, C. F., Dallapiccola, B., & Putignani, L. (2022). Cross-correlation of virome–bacteriome–host–metabolome to study respiratory health. Trends in Microbiology, 30(1), 34–46.
  19. Jiang, D., Armour, C. R., Hu, C., Mei, M., Tian, C., Sharpton, T. J., & Jiang, Y. (2019). Microbiome Multi-Omics Network Analysis: Statistical Considerations, Limitations, and Opportunities. Frontiers in Genetics, 10.
  20. Lagier, J.-C., Armougom, F., Million, M., Hugon, P., Pagnier, I., Robert, C., Bittar, F., Fournous, G., Gimenez, G., Maraninchi, M., Trape, J.-F., Koonin, E. v, la Scola, B., & Raoult, D. (2012). Microbial culturomics: paradigm shift in the human gut microbiome study. Clinical Microbiology and Infection, 18(12), 1185–1193.
  21. Lee-Sarwar KA, Lasky-Su J, Kelly RS, Litonjua AA, Weiss ST. Metabolome–Microbiome Crosstalk and Human Disease. Metabolites. 2020; 10(5):181.
  22. Markowitz, V. M., Ivanova, N. N., Szeto, E., Palaniappan, K., Chu, K., Dalevi, D., Chen, I.-M. A., Grechkin, Y., Dubchak, I., Anderson, I., Lykidis, A., Mavromatis, K., Hugenholtz, P., & Kyrpides, N. C. (2008). IMG/M: a data management and analysis system for metagenomes. Nucleic Acids Research, 36(suppl_1), D534–D538.
  23. McDonald, D., Embriette, H., W, D. J., T, M. J., Antonio, G., Gail, A., A, A. A., Bahar, B., Caitriona, B., Yingfeng, C., Lindsay, D. G., C, D. P., R, D. R., K, F. A., James, G., A, G. J., Grant, G., L, G. J., Philip, H., … Beau, G. (2018). American Gut: an Open Platform for Citizen Science Microbiome Research. MSystems, 3(3), e00031-18.
  24. Mitchell, A. L., Almeida, A., Beracochea, M., Boland, M., Burgin, J., Cochrane, G., Crusoe, M. R., Kale, V., Potter, S. C., Richardson, L. J., Sakharova, E., Scheremetjew, M., Korobeynikov, A., Shlemov, A., Kunyavskaya, O., Lapidus, A., & Finn, R. D. (2020). MGnify: the microbiome analysis resource in 2020. Nucleic Acids Research, 48(D1), D570–D578.
  25. Nkrumah-Elie, Y., Elie, M., & Reisdorph, N. (2018). Chapter 14 – Systems Biology Approaches to Asthma Management. In S. J. Szefler, F. Holguin, & M. E. Wechsler (Eds.), Personalizing Asthma Management for the Clinician (pp. 151–160). Elsevier.
  26. Rivera-Pinto, J., Egozcue, J. J., Pawlowsky-Glahn, V., Paredes, R., Noguera-Julian, M., Calle, M. L., & Catherine, L. (2022). Balances: a New Perspective for Microbiome Analysis. MSystems, 3(4), e00053-18.
  27. Sajulga, R., Easterly, C., Riffle, M., Mesuere, B., Muth, T., Mehta, S., Kumar, P., Johnson, J., Gruening, B. A., Schiebenhoefer, H., Kolmeder, C. A., Fuchs, S., Nunn, B. L., Rudney, J., Griffin, T. J., & Jagtap, P. D. (2020). Survey of metaproteomics software tools for functional microbiome analysis. PLOS ONE, 15(11), e0241503-.
  28. Sarhan, M. S., Hamza, M. A., Youssef, H. H., Patz, S., Becker, M., ElSawey, H., Nemr, R., Daanaa, H.-S. A., Mourad, E. F., Morsi, A. T., Abdelfadeel, M. R., Abbas, M. T., Fayez, M., Ruppel, S., & Hegazi, N. A. (2019). Culturomics of the plant prokaryotic microbiome and the dawn of plant-based culture media – A review. Journal of Advanced Research, 19, 15–27.
  29. Schiebenhoefer, H., van den Bossche, T., Fuchs, S., Renard, B. Y., Muth, T., & Martens, L. (2019). Challenges and promise at the interface of metaproteomics and genomics: an overview of recent progress in metaproteogenomic data analysis. Expert Review of Proteomics, 16(5), 375–390.
  30. Seng, P., Drancourt, M., Gouriet, F., la Scola, B., Fournier, P.-E., Rolain, J. M., & Raoult, D. (2009). Ongoing Revolution in Bacteriology: Routine Identification of Bacteria by Matrix-Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry. Clinical Infectious Diseases, 49(4), 543–551.
  31. Shakya, M., Lo, C.-C., & Chain, P. S. G. (2019). Advances and Challenges in Metatranscriptomic Analysis. Frontiers in Genetics, 10.
  32. Wang, M., Carver, J. J., Phelan, V. v, Sanchez, L. M., Garg, N., Peng, Y., Nguyen, D. D., Watrous, J., Kapono, C. A., Luzzatto-Knaan, T., Porto, C., Bouslimani, A., Melnik, A. v, Meehan, M. J., Liu, W.-T., Crüsemann, M., Boudreau, P. D., Esquenazi, E., Sandoval-Calderón, M., … Bandeira, N. (2016). Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking. Nature Biotechnology, 34(8), 828–837.
  33. Watrous, J., Roach, P., Alexandrov, T., Heath, B. S., Yang, J. Y., Kersten, R. D., van der Voort, M., Pogliano, K., Gross, H., Raaijmakers, J. M., Moore, B. S., Laskin, J., Bandeira, N., & Dorrestein, P. C. (2012). Mass spectral molecular networking of living microbial colonies. Proceedings of the National Academy of Sciences, 109(26), E1743.

Human Health and Disease

  1. Dąbrowska, K., & Witkiewicz, W. (2016). Correlations of Host Genetics and Gut Microbiome Composition. Frontiers in Microbiology, 7, 1357.
  2. Kates, A. E., Jarrett, O., Skarlupka, J. H., Sethi, A., Duster, M., Watson, L., Suen, G., Poulsen, K., & Safdar, N. (2020). Household Pet Ownership and the Microbial Diversity of the Human Gut Microbiota. Frontiers in Cellular and Infection Microbiology, 10, 73.
  3. Kiecolt-Glaser, J. K., Wilson, S. J., & Madison, A. (2019). Marriage and Gut (Microbiome) Feelings: Tracing Novel Dyadic Pathways to Accelerated Aging. Psychosomatic Medicine, 81(8), 704–710.
  4. Knights, D., Lassen, K. G., & Xavier, R. J. (2013). Advances in inflammatory bowel disease pathogenesis: linking host genetics and the microbiome. Gut, 62(10), 1505.
  5. Kurilshikov, A., Wijmenga, C., Fu, J., & Zhernakova, A. (2017). Host Genetics and Gut Microbiome: Challenges and Perspectives. Trends in Immunology, 38(9), 633–647.
  6. Martinez J., Showering, A., Oke, C., Jones, R. T., & Logan, J. G. (2020) Differential attraction in mosquito–human interactions and implications for disease control. Phil. Trans. R. Soc. B. Biol. Sci, 376(1818), 20190811.
  7. Rothschild, D., Weissbrod, O., Barkan, E., Kurilshikov, A., Korem, T., Zeevi, D., Costea, P. I., Godneva, A., Kalka, I. N., Bar, N., Shilo, S., Lador, D., Vila, A. V., Zmora, N., Pevsner-Fischer, M., Israeli, D., Kosower, N., Malka, G., Wolf, B. C., … Segal, E. (2018). Environment dominates over host genetics in shaping human gut microbiota. Nature, 555(7695), 210–215.
  8. Si, J., Lee, S., Park, J. M., Sung, J., & Ko, G. (2015). Genetic associations and shared environmental effects on the skin microbiome of Korean twins. BMC Genomics, 16(1), 992.
  9. Silverman, G. J., Azzouz, D. F., & Alekseyenko, A. v. (2019). Systemic Lupus Erythematosus and dysbiosis in the microbiome: cause or effect or both? Current Opinion in Immunology, 61, 80–85.
  10. Tabrett, A., & Horton, M. W. (2020). The influence of host genetics on the microbiome. F1000Research, 9, F1000 Faculty Rev-84.
  11. Woo, T. E., & Sibley, C. D. (2020). The emerging utility of the cutaneous microbiome in the treatment of acne and atopic dermatitis. Journal of the American Academy of Dermatology, 82(1), 222–228.

The Gut Microbiome

  1. Abulizi, N., Quin, C., Brown, K., Chan, Y. K., Gill, S. K., & Gibson, D. L. (2019). Gut Mucosal Proteins and Bacteriome Are Shaped by the Saturation Index of Dietary Lipids. Nutrients, 11(2).
  2. Arbuckle, M. R., McClain, M. T., Rubertone, M. v, Scofield, R. H., Dennis, G. J., James, J. A., & Harley, J. B. (2003). Development of Autoantibodies before the Clinical Onset of Systemic Lupus Erythematosus. New England Journal of Medicine, 349(16), 1526–1533.
  3. Baker, S. S., Faden, H., Sayej, W., Patel, R., & Baker, R. D. (2010). Increasing Incidence of Community-Associated Atypical Clostridium difficile Disease in Children. Clinical Pediatrics, 49(7), 644–647.
  4. Becattini, S., Taur, Y., & Pamer, E. G. (2016). Antibiotic-Induced Changes in the Intestinal Microbiota and Disease. Trends in Molecular Medicine, 22(6), 458–478.
  5. Benson L, Song X, Campos J, Singh N. Changing epidemiology of Clostridium difficile-associated disease in children. Infect Control Hosp Epidemiol. 2007 Nov;28(11):1233-5. doi: 10.1086/520732. Epub 2007 Aug 27. PMID: 17926272.
  6. Boulangé, C. L., Neves, A. L., Chilloux, J., Nicholson, J. K., & Dumas, M.-E. (2016). Impact of the gut microbiota on inflammation, obesity, and metabolic disease. Genome Medicine, 8(1), 42.
  7. Camacho-Ortiz, A., Gutiérrez-Delgado, E. M., Garcia-Mazcorro, J. F., Mendoza-Olazarán, S., Martínez-Meléndez, A., Palau-Davila, L., Baines, S. D., Maldonado-Garza, H., & Garza-González, E. (2017). Randomized clinical trial to evaluate the effect of fecal microbiota transplant for initial Clostridium difficile infection in intestinal microbiome. PLOS ONE, 12(12), e0189768-.
  8. Cammarota, G., Masucci, L., Ianiro, G., Bibbò, S., Dinoi, G., Costamagna, G., Sanguinetti, M., & Gasbarrini, A. (2015). Randomised clinical trial: faecal microbiota transplantation by colonoscopy vs. vancomycin for the treatment of recurrent Clostridium difficile infection. Alimentary Pharmacology & Therapeutics, 41(9), 835–843.
  9. Cani, P. D., Amar, J., Iglesias, M. A., Poggi, M., Knauf, C., Bastelica, D., Neyrinck, A. M., Fava, F., Tuohy, K. M., Chabo, C., Waget, A., Delmée, E., Cousin, B., Sulpice, T., Chamontin, B., Ferrières, J., Tanti, J.-F., Gibson, G. R., Casteilla, L., … Burcelin, R. (2007). Metabolic Endotoxemia Initiates Obesity and Insulin Resistance. Diabetes, 56(7), 1761.
  10. Clooney, A. G., Sutton, T. D. S., Shkoporov, A. N., Holohan, R. K., Daly, K. M., O’Regan, O., Ryan, F. J., Draper, L. A., Plevy, S. E., Ross, R. P., & Hill, C. (2019). Whole-Virome Analysis Sheds Light on Viral Dark Matter in Inflammatory Bowel Disease. Cell Host & Microbe, 26(6), 764-778.e5.
  11. Costello, M.-E., Ciccia, F., Willner, D., Warrington, N., Robinson, P. C., Gardiner, B., Marshall, M., Kenna, T. J., Triolo, G., & Brown, M. A. (2015). Brief Report: Intestinal Dysbiosis in Ankylosing Spondylitis. Arthritis & Rheumatology, 67(3), 686–691.
  12. Davenport, E. R., Mizrahi-Man, O., Michelini, K., Barreiro, L. B., Ober, C., & Gilad, Y. (2014). Seasonal Variation in Human Gut Microbiome Composition. PLOS ONE, 9(3), e90731-.
  13. David, L. A., Maurice, C. F., Carmody, R. N., Gootenberg, D. B., Button, J. E., Wolfe, B. E., Ling, A. v, Devlin, A. S., Varma, Y., Fischbach, M. A., Biddinger, S. B., Dutton, R. J., & Turnbaugh, P. J. (2014). Diet rapidly and reproducibly alters the human gut microbiome. Nature, 505(7484), 559–563.
  14. de Bandt, J.-P., Waligora-Dupriet, A.-J., & Butel, M.-J. (2011). Intestinal microbiota in inflammation and insulin resistance: relevance to humans. Current Opinion in Clinical Nutrition & Metabolic Care, 14(4).
  15. DeFilipp, Z., Bloom, P. P., Torres Soto, M., Mansour, M. K., Sater, M. R. A., Huntley, M. H., Turbett, S., Chung, R. T., Chen, Y.-B., & Hohmann, E. L. (2019). Drug-Resistant E. coli Bacteremia Transmitted by Fecal Microbiota Transplant. New England Journal of Medicine, 381(21), 2043–2050.
  16. Everard, A., & Cani, P. D. (2013). Diabetes, obesity and gut microbiota. Best Practice & Research Clinical Gastroenterology, 27(1), 73–83.
  17. Forbes, J. D., Bernstein, C. N., Tremlett, H., van Domselaar, G., & Knox, N. C. (2019). A Fungal World: Could the Gut Mycobiome Be Involved in Neurological Disease? Frontiers in Microbiology, 9, 3249.
  18. Fujimoto, K., Kimura, Y., Allegretti, J. R., Yamamoto, M., Zhang, Y., Katayama, K., Tremmel, G., Kawaguchi, Y., Shimohigoshi, M., Hayashi, T., Uematsu, M., Yamaguchi, K., Furukawa, Y., Akiyama, Y., Yamaguchi, R., Crowe, S. E., Ernst, P. B., Miyano, S., Kiyono, H., … Uematsu, S. (2021). Functional Restoration of Bacteriomes and Viromes by Fecal Microbiota Transplantation. Gastroenterology, 160(6), 2089-2102.e12.
  19. Gaulke, C. A., & Sharpton, T. J. (2018). The influence of ethnicity and geography on human gut microbiome composition. Nature Medicine, 24(10), 1495–1496.
  20. George, R. H., Symonds, J. M., Dimock, F., Brown, J. D., Arabi, Y., Shinagawa, N., Keighley, M. R., Alexander-Williams, J., & Burdon, D. W. (1978). Identification of Clostridium difficile as a cause of pseudomembranous colitis. British Medical Journal, 1(6114), 695.
  21. Giongo, A., Gano, K. A., Crabb, D. B., Mukherjee, N., Novelo, L. L., Casella, G., Drew, J. C., Ilonen, J., Knip, M., Hyöty, H., Veijola, R., Simell, T., Simell, O., Neu, J., Wasserfall, C. H., Schatz, D., Atkinson, M. A., & Triplett, E. W. (2011). Toward defining the autoimmune microbiome for type 1 diabetes. The ISME Journal, 5(1), 82–91.
  22. Gu, Y., Zhou, G., Qin, X., Huang, S., Wang, B., & Cao, H. (2019). The Potential Role of Gut Mycobiome in Irritable Bowel Syndrome. Frontiers in Microbiology, 10, 1894.
  23. Halfvarson, J., Brislawn, C. J., Lamendella, R., Vázquez-Baeza, Y., Walters, W. A., Bramer, L. M., D’Amato, M., Bonfiglio, F., McDonald, D., Gonzalez, A., McClure, E. E., Dunklebarger, M. F., Knight, R., & Jansson, J. K. (2017). Dynamics of the human gut microbiome in inflammatory bowel disease. Nature Microbiology, 2(5), 17004.
  24. He, M., Miyajima, F., Roberts, P., Ellison, L., Pickard, D. J., Martin, M. J., Connor, T. R., Harris, S. R., Fairley, D., Bamford, K. B., D’Arc, S., Brazier, J., Brown, D., Coia, J. E., Douce, G., Gerding, D., Kim, H. J., Koh, T. H., Kato, H., … Lawley, T. D. (2013). Emergence and global spread of epidemic healthcare-associated Clostridium difficile. Nature Genetics, 45(1), 109–113.
  25. Hensgens, M. P. M., Keessen, E. C., Squire, M. M., Riley, T. v, Koene, M. G. J., de Boer, E., Lipman, L. J. A., & Kuijper, E. J. (2012). Clostridium difficile infection in the community: a zoonotic disease? Clinical Microbiology and Infection, 18(7), 635–645.
  26. Hoarau, G., Mukherjee, P. K., Gower-Rousseau, C., Hager, C., Chandra, J., Retuerto, M. A., Neut, C., Vermeire, S., Clemente, J., Colombel, J. F., Fujioka, H., Poulain, D., Sendid, B., Ghannoum, M. A., & A, B. R. (2021). Bacteriome and Mycobiome Interactions Underscore Microbial Dysbiosis in Familial Crohn’s Disease. MBio, 7(5), e01250-16.
  27. Jackson, M. A., Verdi, S., Maxan, M.-E., Shin, C. M., Zierer, J., Bowyer, R. C. E., Martin, T., Williams, F. M. K., Menni, C., Bell, J. T., Spector, T. D., & Steves, C. J. (2018). Gut microbiota associations with common diseases and prescription medications in a population-based cohort. Nature Communications, 9(1), 2655.
  28. Jin, D., Wu, S., Zhang, Y., Lu, R., Xia, Y., Dong, H., & Sun, J. (2015). Lack of Vitamin D Receptor Causes Dysbiosis and Changes the Functions of the Murine Intestinal Microbiome. Clinical Therapeutics, 37(5), 996-1009.e7.
  29. Johanesen, P. A., Mackin, K. E., Hutton, M. L., Awad, M. M., Larcombe, S., Amy, J. M., & Lyras, D. (2015). Disruption of the Gut Microbiome: Clostridium difficile Infection and the Threat of Antibiotic Resistance. Genes, 6(4), 1347–1360.
  30. Johnson, K. V.-A. (2020). Gut microbiome composition and diversity are related to human personality traits. Human Microbiome Journal, 15, 100069.
  31. Kho, Z. Y., & Lal, S. K. (2018). The Human Gut Microbiome – A Potential Controller of Wellness and Disease. Frontiers in Microbiology, 9, 1835.
  32. Kim, S. K., Guevarra, R. B., Kim, Y. T., Kwon, J., Kim, H., Cho, J. H., Kim, H. B., & Lee, J. H. (2019). Role of Probiotics in Human Gut Microbiome-Associated Diseases. Journal of Microbiology and Biotechnology, 29(9), 1335–1340.
  33. Larsen, N., Vogensen, F. K., van den Berg, F. W. J., Nielsen, D. S., Andreasen, A. S., Pedersen, B. K., Al-Soud, W. A., Sørensen, S. J., Hansen, L. H., & Jakobsen, M. (2010). Gut Microbiota in Human Adults with Type 2 Diabetes Differs from Non-Diabetic Adults. PLOS ONE, 5(2), e9085-.
  34. Leber, A., Viladomiu, M., Hontecillas, R., Abedi, V., Philipson, C., Hoops, S., Howard, B., & Bassaganya-Riera, J. (2015). Systems Modeling of Interactions between Mucosal Immunity and the Gut Microbiome during Clostridium difficile Infection. PLOS ONE, 10(7), e0134849-.
  35. Lee, Y. K., Menezes, J. S., Umesaki, Y., & Mazmanian, S. K. (2011). Proinflammatory T-cell responses to gut microbiota promote experimental autoimmune encephalomyelitis. Proceedings of the National Academy of Sciences, 108(Supplement 1), 4615.
  36. Magne, F., Gotteland, M., Gauthier, L., Zazueta, A., Pesoa, S., Navarrete, P., & Balamurugan, R. (2020). The Firmicutes/Bacteroidetes Ratio: A Relevant Marker of Gut Dysbiosis in Obese Patients? Nutrients, 12(5).
  37. Martinez-Gili, L., McDonald, J. a K., Liu, Z., Kao, D., Allegretti, J. R., Monaghan, T. M., Barker, G. F., Miguéns Blanco, J., Williams, H. R. T., Holmes, E., Thursz, M. R., Marchesi, J. R., & Mullish, B. H. (2020). Understanding the mechanisms of efficacy of fecal microbiota transplant in treating recurrent Clostridioides difficile infection and beyond: the contribution of gut microbial-derived metabolites. Gut Microbes, 12(1), 1810531.
  38. Mattila, E., Uusitalo–Seppälä, R., Wuorela, M., Lehtola, L., Nurmi, H., Ristikankare, M., Moilanen, V., Salminen, K., Seppälä, M., Mattila, P. S., Anttila, V., & Arkkila, P. (2012). Fecal Transplantation, Through Colonoscopy, Is Effective Therapy for Recurrent Clostridium difficile Infection. Gastroenterology, 142(3), 490–496.
  39. McDermott, A. J., & Huffnagle, G. B. (2014). The microbiome and regulation of mucosal immunity. Immunology, 142(1), 24–31.
  40. McQuade, J. L., Ologun, G. O., Arora, R., & Wargo, J. A. (2020). Gut Microbiome Modulation Via Fecal Microbiota Transplant to Augment Immunotherapy in Patients with Melanoma or Other Cancers. Current Oncology Reports, 22(7), 74.
  41. Mikuls, T. R., Thiele, G. M., Deane, K. D., Payne, J. B., O’Dell, J. R., Yu, F., Sayles, H., Weisman, M. H., Gregersen, P. K., Buckner, J. H., Keating, R. M., Derber, L. A., Robinson, W. H., Holers, V. M., & Norris, J. M. (2012). Porphyromonas gingivalis and disease-related autoantibodies in individuals at increased risk of rheumatoid arthritis. Arthritis & Rheumatism, 64(11), 3522–3530.
  42. Monaco, C. L., Gootenberg, D. B., Zhao, G., Handley, S. A., Ghebremichael, M. S., Lim, E. S., Lankowski, A., Baldridge, M. T., Wilen, C. B., Flagg, M., Norman, J. M., Keller, B. C., Luévano, J. M., Wang, D., Boum, Y., Martin, J. N., Hunt, P. W., Bangsberg, D. R., Siedner, M. J., … Virgin, H. W. (2016). Altered Virome and Bacterial Microbiome in Human Immunodeficiency Virus-Associated Acquired Immunodeficiency Syndrome. Cell Host & Microbe, 19(3), 311–322.
  43. Musso, G., Gambino, R., & Cassader, M. (2011). Interactions Between Gut Microbiota and Host Metabolism Predisposing to Obesity and Diabetes. Annual Review of Medicine, 62(1), 361–380.
  44. Nagpal, R., & Yadav, H. (2017). Bacterial Translocation from the Gut to the Distant Organs: An Overview. Annals of Nutrition and Metabolism, 71(suppl 1)(Suppl. 1), 11–16.
  45. Nagpal, R., Newman, T. M., Wang, S., Jain, S., Lovato, J. F., & Yadav, H. (2018). Obesity-Linked Gut Microbiome Dysbiosis Associated with Derangements in Gut Permeability and Intestinal Cellular Homeostasis Independent of Diet. Journal of Diabetes Research, 2018, 3462092.
  46. Norman, J. M., Handley, S. A., Baldridge, M. T., Droit, L., Liu, C. Y., Keller, B. C., Kambal, A., Monaco, C. L., Zhao, G., Fleshner, P., Stappenbeck, T. S., McGovern, D. P. B., Keshavarzian, A., Mutlu, E. A., Sauk, J., Gevers, D., Xavier, R. J., Wang, D., Parkes, M., & Virgin, H. W. (2015). Disease-Specific Alterations in the Enteric Virome in Inflammatory Bowel Disease. Cell, 160(3), 447–460.
  47. Ouwehand, A. C., Kirjavainen, P. v, Grönlund, M.-M., Isolauri, E., & Salminen, S. J. (1999). Adhesion of probiotic micro-organisms to intestinal mucus. International Dairy Journal, 9(9), 623–630.
  48. Qin, X., Gu, Y., Liu, T., Wang, C., Zhong, W., Wang, B., & Cao, H. (2021). Gut mycobiome: A promising target for colorectal cancer. Biochimica et Biophysica Acta (BBA) – Reviews on Cancer, 1875(1), 188489.
  49. Reyes, A., Blanton, L. v, Cao, S., Zhao, G., Manary, M., Trehan, I., Smith, M. I., Wang, D., Virgin, H. W., Rohwer, F., & Gordon, J. I. (2015). Gut DNA viromes of Malawian twins discordant for severe acute malnutrition. Proceedings of the National Academy of Sciences, 112(38), 11941.
  50. Rogers, M. A. M., & Aronoff, D. M. (2016). The influence of non-steroidal anti-inflammatory drugs on the gut microbiome. Clinical Microbiology and Infection, 22(2), 178.e1-178.e9.
  51. Rouphael, N. G., O’Donnell, J. A., Bhatnagar, J., Lewis, F., Polgreen, P. M., Beekmann, S., Guarner, J., Killgore, G. E., Coffman, B., Campbell, J., Zaki, S. R., & McDonald, L. C. (2008). Clostridium difficile–associated diarrhea: an emerging threat to pregnant women. American Journal of Obstetrics and Gynecology, 198(6), 635.e1-635.e6.
  52. Shi, N., Li, N., Duan, X., & Niu, H. (2017). Interaction between the gut microbiome and mucosal immune system. Military Medical Research, 4(1), 14.
  53. Shkoporov, A. N., & Hill, C. (2019). Bacteriophages of the Human Gut: The “Known Unknown” of the Microbiome. Cell Host & Microbe, 25(2), 195–209.
  54. Sohail, M. U., Althani, A., Anwar, H., Rizzi, R., & Marei, H. E. (2017). Role of the Gastrointestinal Tract Microbiome in the Pathophysiology of Diabetes Mellitus. Journal of Diabetes Research, 2017, 9631435.
  55. Stewart, D. B., Wright, J., Maria, F., McLimans, C. J., Vasily, T., Isabella, A., Owen, B., Hoi-Tong, W., Jeff, B., Rebecca, D., Regina, L., & Rosa, K.-B. (2021). Integrated Meta-omics Reveals a Fungus-Associated Bacteriome and Distinct Functional Pathways in Clostridioides difficile Infection. MSphere, 4(4), e00454-19.
  56. Turnbaugh, P. J., Bäckhed, F., Fulton, L., & Gordon, J. I. (2008). Diet-Induced Obesity Is Linked to Marked but Reversible Alterations in the Mouse Distal Gut Microbiome. Cell Host & Microbe, 3(4), 213–223.
  57. Xu, F., Fu, Y., Sun, T., Jiang, Z., Miao, Z., Shuai, M., Gou, W., Ling, C., Yang, J., Wang, J., Chen, Y., & Zheng, J.-S. (2020). The interplay between host genetics and the gut microbiome reveals common and distinct microbiome features for complex human diseases. Microbiome, 8(1), 145.
  58. Xu, Z., & Knight, R. (2015). Dietary effects on human gut microbiome diversity. British Journal of Nutrition, 113(S1), S1–S5. 10.1017/S0007114514004127
  59. Yan, A., Butcher, J., Mack, D., & Stintzi, A. (2020). Virome Sequencing of the Human Intestinal Mucosal–Luminal Interface. Frontiers in Cellular and Infection Microbiology, 10, 593.
  60. Yatsunenko, T., Rey, F. E., Manary, M. J., Trehan, I., Dominguez-Bello, M. G., Contreras, M., Magris, M., Hidalgo, G., Baldassano, R. N., Anokhin, A. P., Heath, A. C., Warner, B., Reeder, J., Kuczynski, J., Caporaso, J. G., Lozupone, C. A., Lauber, C., Clemente, J. C., Knights, D., … Gordon, J. I. (2012). Human gut microbiome viewed across age and geography. Nature, 486(7402), 222–227.
  61. Zhang, F., Zuo, T., Yeoh, Y. K., Cheng, F. W. T., Liu, Q., Tang, W., Cheung, K. C. Y., Yang, K., Cheung, C. P., Mo, C. C., Hui, M., Chan, F. K. L., Li, C.-K., Chan, P. K. S., & Ng, S. C. (2021). Longitudinal dynamics of gut bacteriome, mycobiome and virome after fecal microbiota transplantation in graft-versus-host disease. Nature Communications, 12(1), 65.
  62. Zou, Y., Ju, X., Chen, W., Yuan, J., Wang, Z., Aluko, R. E., & He, R. (2020). Rice bran attenuated obesity via alleviating dyslipidemia, browning of white adipocytes and modulating gut microbiota in high-fat diet-induced obese mice. Food & Function, 11(3), 2406–2417.

The Oral Microbiome

  1. Aas, J. A., Paster, B. J., Stokes, L. N., Ingar, O., & Dewhirst, F. E. (2005). Defining the Normal Bacterial Flora of the Oral Cavity. Journal of Clinical Microbiology, 43(11), 5721–5732.
  2. Abnet, C. C., Qiao, Y.-L., Dawsey, S. M., Dong, Z.-W., Taylor, P. R., & Mark, S. D. (2005). Tooth loss is associated with increased risk of total death and death from upper gastrointestinal cancer, heart disease, and stroke in a Chinese population-based cohort. International Journal of Epidemiology, 34(2), 467–474.
  3. Acs, G., Shulman, R., Ng, M. W., & Chussid, S. (1999). The effect of dental rehabilitation on the body weight of children with early childhood caries. Pediatric dentistry21(2), 109–113.
  4. Al-hebshi, N. N., Alharbi, F. A., Mahri, M., & Chen, T. (2017). Differences in the Bacteriome of Smokeless Tobacco Products with Different Oral Carcinogenicity: Compositional and Predicted Functional Analysis. Genes, 8(4), 106.
  5. Al-hebshi, N. N., Nasher, A. T., Maryoud, M. Y., Homeida, H. E., Chen, T., Idris, A. M., & Johnson, N. W. (2017). Inflammatory bacteriome featuring Fusobacterium nucleatum and Pseudomonas aeruginosa identified in association with oral squamous cell carcinoma. Scientific Reports, 7(1), 1834.
  6. Amerongen, A. V. N., & Veerman, E. C. I. (2002). Saliva – the defender of the oral cavity. Oral Diseases, 8(1), 12–22.
  7. Avila, M., Ojcius, D. M., & Yilmaz, Ö. (2009). The Oral Microbiota: Living with a Permanent Guest. DNA and Cell Biology, 28(8), 405–411.
  8. Bakhti, S. Z., & Latifi-Navid, S. (2021). Oral microbiota and Helicobacter pylori in gastric carcinogenesis: what do we know and where next? BMC Microbiology, 21(1), 71.
  9. Benabdelkader, S., Andreani, J., Gillet, A., Terrer, E., Pignoly, M., Chaudet, H., Aboudharam, G., & la Scola, B. (2019). Specific clones of Trichomonas tenax are associated with periodontitis. PLOS ONE, 14(3), e0213338-.
  10. Blostein, F., Foote, S., Salzman, E., McNeil, D. W., Marazita, M. L., Martin, E. T., & Foxman, B. (2021). Associations Between Salivary Bacteriome Diversity and Salivary Human Herpesvirus Detection in Early Childhood: A Prospective Cohort Study. Journal of the Pediatric Infectious Diseases Society, 10(8), 856–863.
  11. Chalabi, M., Moghim, S., Mogharehabed, A., Najafi, F., & Rezaie, F. (2008). EBV and CMV in chronic periodontitis: a prevalence study. Archives of Virology, 153(10), 1917.
  12. Chhour, K. L., Nadkarni, M. A., Byun, R., Martin, F. E., Jacques, N. A., & Hunter, N. (2005). Molecular Analysis of Microbial Diversity in Advanced Caries. Journal of Clinical Microbiology, 43(2), 843–849.
  13. Chrysanthakopoulos, N. A., & Chrysanthakopoulos, P. A. (2016). Association between indices of clinically-defined periodontitis and self-reported history of systemic medical conditions. Journal of Investigative and Clinical Dentistry, 7(1), 27–36.
  14. Corby, P. M., Lyons-Weiler, J., Bretz, W. A., Hart, T. C., Aas, J. A., Boumenna, T., Goss, J., Corby, A. L., Junior, H. M., Weyant, R. J., & Paster, B. J. (2005). Microbial Risk Indicators of Early Childhood Caries. Journal of Clinical Microbiology, 43(11), 5753–5759.
  15. Costalonga, M., & Herzberg, M. C. (2014). The oral microbiome and the immunobiology of periodontal disease and caries. Immunology Letters, 162(2, Part A), 22–38.
  16. Cross, B. W., & Ruhl, S. (2018). Glycan recognition at the saliva – oral microbiome interface. Cellular Immunology, 333, 19–33.
  17. Cui, J., Cui, H., Yang, M., Du, S., Li, J., Li, Y., Liu, L., Zhang, X., & Li, S. (2019). Tongue coating microbiome as a potential biomarker for gastritis including precancerous cascade. Protein & Cell, 10(7), 496–509.
  18. Davenport, E. R. (2017). Tooth Be Told, Genetics Influences Oral Microbiome. Cell Host & Microbe, 22(3), 251–253.
  19. Dewhirst, F. E., Tuste, C., Jacques, Paster, B. J., Tanner, A. C. R., Wen-Han, Y., Abirami, L., & Wade, W. G. (2010). The Human Oral Microbiome. Journal of Bacteriology, 192(19), 5002–5017.
  20. Duran-Pinedo, A. E., & Frias-Lopez, J. (2015). Beyond microbial community composition: functional activities of the oral microbiome in health and disease. Microbes and Infection, 17(7), 505–516.
  21. Eren, A. M., Borisy, G. G., Huse, S. M., & Mark Welch, J. L. (2014). Oligotyping analysis of the human oral microbiome. Proceedings of the National Academy of Sciences, 111(28), E2875.
  22. Filoche, S., Wong, L., & Sissons, C. H. (2009). Oral Biofilms: Emerging Concepts in Microbial Ecology. Journal of Dental Research, 89(1), 8–18.
  23. Fitzpatrick, S. G., & Katz, J. (2010). The association between periodontal disease and cancer: A review of the literature. Journal of Dentistry, 38(2), 83–95.
  24. Flemmig, T. F., & Beikler, T. (2011). Control of oral biofilms. Periodontology 2000, 55(1), 9–15.
  25. Fukui, Y., Aoki, K., Ishii, Y., & Tateda, K. (2018). The palatine tonsil bacteriome, but not the mycobiome, is altered in HIV infection. BMC Microbiology, 18(1), 127.
  26. Gao, Z., Kang, Y., Yu, J., & Ren, L. (2014). Human Pharyngeal Microbiome May Play A Protective Role in Respiratory Tract Infections. Genomics, Proteomics & Bioinformatics, 12(3), 144–150.
  27. Ghannoum, M. A., Jurevic, R. J., Mukherjee, P. K., Cui, F., Sikaroodi, M., Naqvi, A., & Gillevet, P. M. (2010). Characterization of the Oral Fungal Microbiome (Mycobiome) in Healthy Individuals. PLOS Pathogens, 6(1), e1000713-.
  28. Gopinath, D., Wie, C. C., Banerjee, M., Thangavelu, L., Kumar R, P., Nallaswamy, D., Botelho, M. G., & Johnson, N. W. (2021). Compositional profile of mucosal bacteriome of smokers and smokeless tobacco users. Clinical Oral Investigations.
  29. Grassl, N., Kulak, N. A., Pichler, G., Geyer, P. E., Jung, J., Schubert, S., Sinitcyn, P., Cox, J., & Mann, M. (2016). Ultra-deep and quantitative saliva proteome reveals dynamics of the oral microbiome. Genome Medicine, 8(1), 44.
  30. Griffen, A. L., Beall, C. J., Campbell, J. H., Firestone, N. D., Kumar, P. S., Yang, Z. K., Podar, M., & Leys, E. J. (2012). Distinct and complex bacterial profiles in human periodontitis and health revealed by 16S pyrosequencing. The ISME Journal, 6(6), 1176–1185.
  31. Gross, E. L., Leys, E. J., Gasparovich, E. R., Firestone, N. D., Swartzbaum, J. A., Janies, D. A., Asnani, K., & Griffen, A. L. (2010). Bacterial 16S Sequence Analysis of Severe Caries in Young Permanent Teeth. Journal of Clinical Microbiology, 48(11), 4121–4128.
  32. Hajishengallis, G., & Lamont, R. J. (2012). Beyond the red complex and into more complexity: the polymicrobial synergy and dysbiosis (PSD) model of periodontal disease etiology. Molecular Oral Microbiology, 27(6), 409–419.
  33. Han, S., Chen, Y., Hu, J., & Ji, Z. (2014). Tongue images and tongue coating microbiome in patients with colorectal cancer. Microbial Pathogenesis, 77, 1–6.
  34. Haubek, D. (2010). The highly leukotoxic JP2 clone of Aggregatibacter actinomycetemcomitans: Evolutionary aspects, epidemiology and etiological role in aggressive periodontitis. APMIS, 118.
  35. Hong, B. Y., Hoare, A., Cardenas, A., Dupuy, A. K., Choquette, L., Salner, A. L., Schauer, P. K., Hegde, U., Peterson, D. E., Dongari-Bagtzoglou, A., Strausbaugh, L. D., & Diaz, P. I. (2020). The Salivary Mycobiome Contains 2 Ecologically Distinct Mycotypes. Journal of Dental Research, 99(6), 730–738.
  36. Horz, H.-P., & Conrads, G. (2007). Diagnosis and anti-infective therapy of periodontitis. Expert Review of Anti-Infective Therapy, 5(4), 703–715.
  37. Ioannidou, E., & Swede, H. (2011). Disparities in Periodontitis Prevalence among Chronic Kidney Disease Patients. Journal of Dental Research, 90(6), 730–734.
  38. Jeffcoat, M. K., Jeffcoat, R. L., Gladowski, P. A., Bramson, J. B., & Blum, J. J. (2014). Impact of Periodontal Therapy on General Health: Evidence from Insurance Data for Five Systemic Conditions. American Journal of Preventive Medicine, 47(2), 166–174.
  39. Jiang, B., Liang, X., Chen, Y., Ma, T., Liu, L., Li, J., Jiang, R., Chen, T., Zhang, X., & Li, S. (2012). Integrating next-generation sequencing and traditional tongue diagnosis to determine tongue coating microbiome. Scientific Reports, 2(1), 936.
  40. Jorth, P., Turner, K. H., Gumus, P., Nizam, N., Buduneli, N., & Whitely, M. (2014). Metatranscriptomics of the Human Oral Microbiome during Health and Disease. MBio, 5(2), e01012-14.
  41. Kamio, N., Imai, K., Shimizu, K., Cueno, M. E., Tamura, M., Saito, Y., & Ochiai, K. (2015). Neuraminidase-producing oral mitis group streptococci potentially contribute to influenza viral infection and reduction in antiviral efficacy of zanamivir. Cellular and Molecular Life Sciences, 72(2), 357–366.
  42. Kolenbrander, P. E., Palmer, R. J., Jr, Rickard, A. H., Jakubovics, N. S., Chalmers, N. I., & Diaz, P. I. (2006). Bacterial interactions and successions during plaque development. Periodontology 200042, 47–79.
  43. Koo, H., & Bowen, W. H. (2014). Candida albicans and Streptococcus mutans: a potential synergistic alliance to cause virulent tooth decay in children. Future Microbiology, 9(12), 1295–1297.
  44. Kori, J. A., Saleem, F., Ullah, S., & Azim, M. K. (2020). Characterization of Oral bacteriome dysbiosis in type 2 diabetic patients. MedRxiv, 2020.04.09.20052613.
  45. Kumaraswamy, K. L., & Vidya, M. (2011). Human papilloma virus and oral infections: An update. Journal of Cancer Research and Therapeutics, 7(2), 120-127.
  46. Kurkivuori, J., Salaspuro, V., Kaihovaara, P., Kari, K., Rautemaa, R., Grönroos, L., Meurman, J. H., & Salaspuro, M. (2007). Acetaldehyde production from ethanol by oral streptococci. Oral Oncology, 43(2), 181–186.
  47. Lepp, P. W., Brinig, M. M., Ouverney, C. C., Palm, K., Armitage, G. C., & Relman, D. A. (2004). Methanogenic Archaea and human periodontal disease. Proceedings of the National Academy of Sciences of the United States of America, 101(16), 6176.
  48. Li, Y., Wang, K., Zhang, B., Tu, Q., Yao, Y., Cui, B., Ren, B., He, J., Shen, X., van Nostrand, J. D., Zhou, J., Shi, W., Xiao, L., Lu, C., & Zhou, X. (2019). Salivary mycobiome dysbiosis and its potential impact on bacteriome shifts and host immunity in oral lichen planus. International Journal of Oral Science, 11(2), 13.
  49. Lim, Y., Totsika, M., Morrison, M., & Punyadeera, C. (2017). The saliva microbiome profiles are minimally affected by collection method or DNA extraction protocols. Scientific Reports, 7(1), 8523.
  50. Lin, M., Li, X., Wang, J., Cheng, C., Zhang, T., Han, X., Song, Y., Wang, Z., & Wang, S. (2020). Saliva Microbiome Changes in Patients With Periodontitis With and Without Chronic Obstructive Pulmonary Disease. Frontiers in Cellular and Infection Microbiology, 10, 124.
  51. Ling, Z., Kong, J., Jia, P., Wei, C., Wang, Y., Pan, Z., Huang, W., Li, L., Chen, H., & Xiang, C. (2010). Analysis of Oral Microbiota in Children with Dental Caries by PCR-DGGE and Barcoded Pyrosequencing. Microbial Ecology, 60(3), 677–690.
  52. Listgarten, M. A. (1986). Pathogenesis of periodontitis. Journal of Clinical Periodontology, 13(5), 418–425.
  53. Liu, B., Faller, L. L., Klitgord, N., Mazumdar, V., Ghodsi, M., Sommer, D. D., Gibbons, T. R., Treangen, T. J., Chang, Y.-C., Li, S., Stine, O. C., Hasturk, H., Kasif, S., Segrè, D., Pop, M., & Amar, S. (2012). Deep Sequencing of the Oral Microbiome Reveals Signatures of Periodontal Disease. PLOS ONE, 7(6), e37919-.
  54. Loesche, W. J., & Grenier, E. (1976). Detection of Streptococcus mutans in plaque samples by the direct fluorescent antibody test. Journal of dental research55, A87–A93.
  55. Low, W., Tan, S., & Schwartz, S. (1999). The effect of severe caries on the quality of life in young children. Pediatric Dentistry, 21(6), 325–326.
  56. Lu, H., Ren, Z., Li, A., Li, J., Xu, S., Zhang, H., Jiang, J., Yang, J., Luo, Q., Zhou, K., Zheng, S., & Li, L. (2019). Tongue coating microbiome data distinguish patients with pancreatic head cancer from healthy controls. Journal of Oral Microbiology, 11(1), 1563409.
  57. Mager, D. L., Haffajee, A. D., Devlin, P. M., Norris, C. M., Posner, M. R., & Goodson, J. M. (2005). The salivary microbiota as a diagnostic indicator of oral cancer: A descriptive, non-randomized study of cancer-free and oral squamous cell carcinoma subjects. Journal of Translational Medicine, 3(1), 27.
  58. Mandel, I. D. (1987). The Functions of Saliva. Journal of Dental Research, 66(1_suppl), 623–627.
  59. Marsh, P. D., Do, T., Beighton, D., & Devine, D. A. (2016). Influence of saliva on the oral microbiota. Periodontology 2000, 70(1), 80–92.
  60. Martínez, A., Kuraji, R., & Kapila, Y. L. (2021). The human oral virome: Shedding light on the dark matter. Periodontology 2000, 87(1), 282–298.
  61. Matarazzo, F., Ribeiro, A. C., Feres, M., Faveri, M., & Mayer, M. P. A. (2011). Diversity and quantitative analysis of Archaea in aggressive periodontitis and periodontally healthy subjects. Journal of Clinical Periodontology, 38(7), 621–627.
  62. McIlvanna, E., Linden, G. J., Craig, S. G., Lundy, F. T., & James, J. A. (2021). Fusobacterium nucleatum and oral cancer: a critical review. BMC Cancer, 21(1), 1212.
  63. Michaud, D. S., Fu, Z., Shi, J., & Chung, M. (2017). Periodontal Disease, Tooth Loss, and Cancer Risk. Epidemiologic Reviews, 39(1), 49–58.
  64. Miller E. H., Annavajhala, M. K., Chong, A. M., Park, H., Nobel, Y. R., Soroush, A., Blackett, J. W., Krigel, A., Phipps, M. M., Freedberg, D. E., Zucker, J., Sano, E. D., Uhlemann, E. C., & Abrams, J. A.(2021). Oral Microbiome Alterations and SARS-CoV-2 Saliva Viral Load in Patients with COVID-19. Microbiology Spectrum, 9(2), e00055-21.
  65. Mohammed, M. M. A., al Kawas, S., & Al-Qadhi, G. (2021). Tongue-coating microbiome as a cancer predictor: A scoping review. Archives of Oral Biology, 132, 105271.
  66. Mukherjee, P. K., Wang, H., Retuerto, M., Zhang, H., Burkey, B., Ghannoum, M. A., & Eng, C. (2017). Bacteriome and mycobiome associations in oral tongue cancer. Oncotarget, 8(57), 97273–97289.
  67. Munson, M. A., Banerjee, A., Watson, T. F., & Wade, W. G. (2004). Molecular Analysis of the Microflora Associated with Dental Caries. Journal of Clinical Microbiology, 42(7), 3023–3029.
  68. Ng, E., Tay, J. R. H., Balan, P., Ong, M. M. A., Bostanci, N., Belibasakis, G. N., & Seneviratne, C. J. (2021). Metagenomic sequencing provides new insights into the subgingival bacteriome and aetiopathology of periodontitis. Journal of Periodontal Research, 56(2), 205–218.
  69. Parahitiyawa, N. B., Scully, C., Leung, W. K., Yam, W. C., Jin, L. J., & Samaranayake, L. P. (2010). Exploring the oral bacterial flora: current status and future directions. Oral Diseases, 16(2), 136–145.
  70. Peters, B. A., Wu, J., Pei, Z., Yang, L., Purdue, M. P., Freedman, N. D., Jacobs, E. J., Gapstur, S. M., Hayes, R. B., & Ahn, J. (2017). Oral Microbiome Composition Reflects Prospective Risk for Esophageal Cancers. Cancer Research, 77(23), 6777.
  71. Peterson, S. N., Snesrud, E., Liu, J., Ong, A. C., Kilian, M., Schork, N. J., & Bretz, W. (2013). The Dental Plaque Microbiome in Health and Disease. PLOS ONE, 8(3), e58487-.
  72. Pihlstrom, B. L., Michalowicz, B. S., & Johnson, N. W. (2005). Periodontal diseases. The Lancet, 366(9499), 1809–1820.
  73. Pushalkar, S., Ji, X., Li, Y., Estilo, C., Yegnanarayana, R., Singh, B., Li, X., & Saxena, D. (2012). Comparison of oral microbiota in tumor and non-tumor tissues of patients with oral squamous cell carcinoma. BMC Microbiology, 12(1), 144.
  74. Rôças, I. N., Siqueira, J. F., Jr, Santos, K. R., & Coelho, A. M. (2001). “Red complex” (Bacteroides forsythus, Porphyromonas gingivalis, and Treponema denticola) in endodontic infections: a molecular approach. Oral surgery, oral medicine, oral pathology, oral radiology, and endodontics91(4), 468–471.
  75. Sajid, M., Srivastava, S., Joshi, L., & Bharadwaj, M. (2021). Impact of smokeless tobacco-associated bacteriome in oral carcinogenesis. Anaerobe, 70, 102400.
  76. Sampaio-Maia, B., Caldas, I. M., Pereira, M. L., Pérez-Mongiovi, D., & Araujo, R. (2016). Chapter Four – The Oral Microbiome in Health and Its Implication in Oral and Systemic Diseases. In S. Sariaslani & G. Michael Gadd (Eds.), Advances in Applied Microbiology (Vol. 97, pp. 171–210). Academic Press.
  77. Sato, N., Kakuta, M., Hasegawa, T., Yamaguchi, R., Uchino, E., Kobayashi, W., Sawada, K., Tamura, Y., Tokuda, I., Murashita, K., Nakaji, S., Imoto, S., Yanagita, M., & Okuno, Y. (2020). Metagenomic analysis of bacterial species in tongue microbiome of current and never smokers. Npj Biofilms and Microbiomes, 6(1), 11.
  78. Sato, Y., Yamagishi, J., Yamashita, R., Shinozaki, N., Ye, B., Yamada, T., Yamamoto, M., Nagasaki, M., & Tsuboi, A. (2015). Inter-Individual Differences in the Oral Bacteriome Are Greater than Intra-Day Fluctuations in Individuals. PLOS ONE, 10(6), e0131607-.
  79. Scannapieco, F. A. (1994). Saliva-Bacterium Interactions in Oral Microbial Ecology. Critical Reviews in Oral Biology & Medicine, 5(3), 203–248.
  80. Scher, J. U., Bretz, W. A., & Abramson, S. B. (2014). Periodontal disease and subgingival microbiota as contributors for rheumatoid arthritis pathogenesis: modifiable risk factors? Current Opinion in Rheumatology, 26(4), 424–429.
  81. Segata, N., Haake, S. K., Mannon, P., Lemon, K. P., Waldron, L., Gevers, D., Huttenhower, C., & Izard, J. (2012). Composition of the adult digestive tract bacterial microbiome based on seven mouth surfaces, tonsils, throat and stool samples. Genome Biology, 13(6), R42.
  82. Selwitz, R. H., Ismail, A. I., & Pitts, N. B. (2007). Dental caries. The Lancet, 369(9555), 51–59.
  83. Seymour, G. J., Ford, P. J., Cullinan, M. P., Leishman, S., & Yamazaki, K. (2007). Relationship between periodontal infections and systemic disease. Clinical Microbiology and Infection, 13(s4), 3–10.
  84. Shi, B., Chang, M., Martin, J., Mitreva, M., Lux, R., Klokkevold, P., Sodergren, E., Weinstock, G. M., Haake, S. K., & Li, H. (2021). Dynamic Changes in the Subgingival Microbiome and Their Potential for Diagnosis and Prognosis of Periodontitis. MBio, 6(1), e01926-14.
  85. Socransky, S. S., & Haffajee, A. D. (2005). Periodontal microbial ecology. Periodontology 2000, 38(1), 135–187.
  86. Socransky, S. S., Haffajee, A. D., Cugini, M. A., Smith, C., & Kent Jr., R. L. (1998). Microbial complexes in subgingival plaque. Journal of Clinical Periodontology, 25(2), 134–144.
  87. Springer, S. A., & Gagneux, P. (2013). Glycan Evolution in Response to Collaboration, Conflict, and Constraint *. Journal of Biological Chemistry, 288(10), 6904–6911.
  88. Takahashi, N., Washio, J., & Mayanagi, G. (2010). Metabolomics of Supragingival Plaque and Oral Bacteria. Journal of Dental Research, 89(12), 1383–1388.
  89. Teles, R. P., Gursky, L. C., Faveri, M., Rosa, E. A., Teles, F. R. F., Feres, M., Socransky, S. S., & Haffajee, A. D. (2010). Relationships between subgingival microbiota and GCF biomarkers in generalized aggressive periodontitis. Journal of Clinical Periodontology, 37(4), 313–323.
  90. Tribble, G. D., Angelov, N., Weltman, R., Wang, B.-Y., Eswaran, S. v, Gay, I. C., Parthasarathy, K., Dao, D.-H. v, Richardson, K. N., Ismail, N. M., Sharina, I. G., Hyde, E. R., Ajami, N. J., Petrosino, J. F., & Bryan, N. S. (2019). Frequency of Tongue Cleaning Impacts the Human Tongue Microbiome Composition and Enterosalivary Circulation of Nitrate. Frontiers in Cellular and Infection Microbiology, 9, 39.
  91. van der Meulen, T. A., Harmsen, H. J. M., Bootsma, H., Liefers, S. C., Vich Vila, A., Zhernakova, A., Fu, J., Wijmenga, C., Spijkervet, F. K. L., Kroese, F. G. M., & Vissink, A. (2018). Dysbiosis of the buccal mucosa microbiome in primary Sjögren’s syndrome patients. Rheumatology, 57(12), 2225–2234.
  92. Van Essche, M., Quirynen, M., Sliepen, I., Loozen, G., Boon, N., van Eldere, J., & Teughels, W. (2011). Killing of anaerobic pathogens by predatory bacteria. Molecular Oral Microbiology, 26(1), 52–61.
  93. Vartoukian, S. R., Palmer, R. M., & Wade, W. G. (2009). Diversity and Morphology of Members of the Phylum “Synergistetes” in Periodontal Health and Disease. Applied and Environmental Microbiology, 75(11), 3777–3786.
  94. Wade, W. G. (2013). The oral microbiome in health and disease. Pharmacological Research, 69(1), 137–143.
  95. Wang, L., Ganly, I. (2014). The oral microbiome and oral cancer. Clinics in Laboratory Medicine, 34, 711–719.
  96. Wang, T.-F., Jen, I.-A., Chou, C., & Lei, Y.-P. (2014). Effects of periodontal therapy on metabolic control in patients with type 2 diabetes mellitus and periodontal disease: a meta-analysis. Medicine, 93(28), e292–e292.
  97. Wantland, W. W., Wantland, E. M., Remo, J. W., & Winquist, D. L. (1958). Studies on Human Mouth Protozoa. Journal of Dental Research, 37(5), 949–950.
  98. Welch, J. L., Utter, D. R., Rossetti, B. J., Mark Welch, D. B., Eren, A. M., & Borisy, G. G. (2014). Dynamics of tongue microbial communities with single-nucleotide resolution using oligotyping. Frontiers in Microbiology, 5, 568.
  99. Wilbert, S. A., Mark Welch, J. L., & Borisy, G. G. (2020). Spatial Ecology of the Human Tongue Dorsum Microbiome. Cell Reports, 30(12), 4003-4015.e3.
  100. Willis, J. R., & Gabaldón, T. (2020). The Human Oral Microbiome in Health and Disease: From Sequences to Ecosystems. Microorganisms, 8(2).
  101. Xiao, J., Grier, A., Faustoferri, R. C., Alzoubi, S., Gill, A. L., Feng, C., Liu, Y., Quivey, R. G., Kopycka-Kedzierawski, D. T., Koo, H., & Gill, S. R. (2018). Association between Oral Candida and Bacteriome in Children with Severe ECC. Journal of Dental Research, 97(13), 1468–1476.
  102. Zarco, M. F., Vess, T. J., & Ginsburg, G. S. (2012). The oral microbiome in health and disease and the potential impact on personalized dental medicine. Oral Diseases, 18(2), 109–120.
  103. Zhou, X., Han, J., Liu, Z., Song, Y., Wang, Z., & Sun, Z. (2014). Effects of periodontal treatment on lung function and exacerbation frequency in patients with chronic obstructive pulmonary disease and chronic periodontitis: A 2-year pilot randomized controlled trial. Journal of Clinical Periodontology, 41(6), 564–572.
  104. Zuo, Y., Whitbeck, J. C., Haila, G. J., Hakim, A. A., Rothlauf, P. W., Eisenberg, R. J., Cohen, G. H., & Krummenacher, C. (2019). Saliva enhances infection of gingival fibroblasts by herpes simplex virus 1. PLOS ONE, 14(10), e0223299-.

The Skin Microbiome

  1. Bek-Thomsen, M., Lomholt, H. B., & Kilian, M. (2008). Acne is Not Associated with Yet-Uncultured Bacteria. Journal of Clinical Microbiology, 46(10), 3355–3360.
  2. Belkaid, Y., & Harrison, O. J. (2017). Homeostatic Immunity and the Microbiota. Immunity, 46(4), 562–576.
  3. Bierber, T. (2008). Mechanisms of disease: atopic dermatitis. N Engl J Med358, 358-1483.
  4. Blicharz, L., Rudnicka, L., & Samochocki, Z. (2019). Staphylococcus aureus: an underestimated factor in the pathogenesis of atopic dermatitis? Postepy Dermatologii i Alergologii, 36(1), 11–17.
  5. Byrd, A. L., Belkaid, Y., & Segre, J. A. (2018). The human skin microbiome. Nature Reviews Microbiology, 16(3), 143–155.
  6. Capone, K. A., Dowd, S. E., Stamatas, G. N., & Nikolovski, J. (2011). Diversity of the Human Skin Microbiome Early in Life. Journal of Investigative Dermatology, 131(10), 2026–2032.
  7. Casas, C., Paul, C., Lahfa, M., Livideanu, B., Lejeune, O., Alvarez-Georges, S., Saint-Martory, C., Degouy, A., Mengeaud, V., Ginisty, H., Durbise, E., Schmitt, A. M., & Redoulès, D. (2012). Quantification of Demodex folliculorum by PCR in rosacea and its relationship to skin innate immune activation. Experimental Dermatology, 21(12), 906–910.
  8. Cogen, A. L., Yamasaki, K., Sanchez, K. M., Dorschner, R. A., Lai, Y., MacLeod, D. T., Torpey, J. W., Otto, M., Nizet, V., Kim, J. E., & Gallo, R. L. (2010). Selective Antimicrobial Action Is Provided by Phenol-Soluble Modulins Derived from Staphylococcus epidermidis, a Normal Resident of the Skin. Journal of Investigative Dermatology, 130(1), 192–200.
  9. Dominguez-Bello, M. G., Costello, E. K., Contreras, M., Magris, M., Hidalgo, G., Fierer, N., & Knight, R. (2010). Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns. Proceedings of the National Academy of Sciences, 107(26), 11971.
  10. Dreno, B., Martin, R., Moyal, D., Henley, J. B., Khammari, A., & Seité, S. (2017). Skin microbiome and acne vulgaris: Staphylococcus, a new actor in acne. Experimental Dermatology, 26(9), 798–803.
  11. Fahlén, A., Engstrand, L., Baker, B. S., Powles, A., & Fry, L. (2012). Comparison of bacterial microbiota in skin biopsies from normal and psoriatic skin. Archives of Dermatological Research, 304(1), 15–22.
  12. Findley, K., & Grice, E. A. (2014). The Skin Microbiome: A Focus on Pathogens and Their Association with Skin Disease. PLOS Pathogens, 10(11), e1004436-.
  13. Findley, K., Oh, J., Yang, J., Conlan, S., Deming, C., Meyer, J. A., Schoenfeld, D., Nomicos, E., Park, M., Becker, J., Benjamin, B., Blakesley, R., Bouffard, G., Brooks, S., Coleman, H., Dekhtyar, M., Gregory, M., Guan, X., Gupta, J., … Program, N. I. H. I. S. C. C. S. (2013). Topographic diversity of fungal and bacterial communities in human skin. Nature, 498(7454), 367–370.
  14. Fitz-Gibbon, S., Tomida, S., Chiu, B.-H., Nguyen, L., Du, C., Liu, M., Elashoff, D., Erfe, M. C., Loncaric, A., Kim, J., Modlin, R. L., Miller, J. F., Sodergren, E., Craft, N., Weinstock, G. M., & Li, H. (2013). Propionibacterium acnes Strain Populations in the Human Skin Microbiome Associated with Acne. Journal of Investigative Dermatology, 133(9), 2152–2160.
  15. Forton, F. M. N. (2012). Papulopustular rosacea, skin immunity and Demodex: pityriasis folliculorum as a missing link. Journal of the European Academy of Dermatology and Venereology, 26(1), 19–28.
  16. Forton, F., & Seys, B. (1993). Density of Demodex folliculorum in rosacea: a case-control study using standardized skin-surface biopsy. British Journal of Dermatology, 128(6), 650–659.
  17. Gao, Z., Tseng, C., Strober, B. E., Pei, Z., & Blaser, M. J. (2008). Substantial Alterations of the Cutaneous Bacterial Biota in Psoriatic Lesions. PLOS ONE, 3(7), e2719-.
  18. Gardiner M, Vicaretti M, Sparks J, Bansal S, Bush S, Liu M, Darling A, Harry E, Burke CM. (2017). A longitudinal study of the diabetic skin and wound microbiome. PeerJ 5:e3543
  19. Georgala, S., Katoulis, A. C., Kylafis, G. D., Koumantaki-Mathioudaki, E., Georgala, C., & Aroni, K. (2001). Increased density of Demodex folliculorum and evidence of delayed hypersensitivity reaction in subjects with papulopustular rosacea. Journal of the European Academy of Dermatology and Venereology, 15(5), 441–444.
  20. Grice, E. A., & Segre, J. A. (2011). The skin microbiome. Nature Reviews Microbiology, 9(4), 244–253.
  21. Grice, E. A., Kong, H. H., Conlan, S., Deming, C. B., Davis, J., Young, A. C., Nisc Comparative Sequencing Program, Bouffard, G. G., Blakesley, R. W., Muray, P. R., Green, E. D., Turner, M. L., & Segre, J. A. (2009). Topographical and Temporal Diversity of the Human Skin Microbiome. Science, 324(5931), 1190–1192.
  22. Iwase, T., Uehara, Y., Shinji, H., Tajima, A., Seo, H., Takada, K., Agata, T., & Mizunoe, Y. (2010). Staphylococcus epidermidis Esp inhibits Staphylococcus aureus biofilm formation and nasal colonization. Nature, 465(7296), 346–349.
  23. Kalan, L. R., Meisel, J. S., Loesche, M. A., Horwinski, J., Soaita, I., Chen, X., Uberoi, A., Gardner, S. E., & Grice, E. A. (2019). Strain- and Species-Level Variation in the Microbiome of Diabetic Wounds Is Associated with Clinical Outcomes and Therapeutic Efficacy. Cell Host & Microbe, 25(5), 641-655.e5.
  24. Kennedy, E. A., Connolly, J., Hourihane, J. O., Fallon, P. G., McLean, W. H. I., Murray, D., Jo, J.-H., Segre, J. A., Kong, H. H., & Irvine, A. D. (2017). Skin microbiome before development of atopic dermatitis: Early colonization with commensal staphylococci at 2 months is associated with a lower risk of atopic dermatitis at 1 year. Journal of Allergy and Clinical Immunology, 139(1), 166–172.
  25. Koller, B., Müller-Wiefel, A. S., Rupec, R., Korting, H. C., & Ruzicka, T. (2011). Chitin Modulates Innate Immune Responses of Keratinocytes. PLOS ONE, 6(2), e16594-.
  26. Kong, H. H. (2011). Skin microbiome: genomics-based insights into the diversity and role of skin microbes. Trends in Molecular Medicine, 17(6), 320–328.
  27. Kong, H. H., Oh, J., Deming, C., Conlan, S., Grice, E. A., Beatson, M. A., Nomicos, E., Polley, E. C., Komarow, H. D., Program, N. C. S., Murray, P. R., Turner, M. L., & Segre, J. A. (2012). Temporal shifts in the skin microbiome associated with disease flares and treatment in children with atopic dermatitis. Genome Research, 22(5), 850–859.
  28. Kuhbacher, A., Burger-Kentischer, A., & Rupp, S. (2017). Interaction of Candida species with the skin. Microorganisms5(2), 32.
  29. Lacey, N., Delaney, S., Kavanagh, K., & Powell, F. C. (2007). Mite-related bacterial antigens stimulate inflammatory cells in rosacea. British Journal of Dermatology, 157(3), 474–481.
  30. Lacey, N., Kavanagh, K., & Tseng, S. C. G. (2009). Under the lash: Demodex mites in human diseases. The Biochemist, 31(4), 20–24.
  31. Lacey, N., Ní Raghallaigh, S., & Powell, F. C. (2011). Demodex mites – commensals, parasites or mutualistic organisms? Dermatology, 222(2), 128-30. doi:
  32. McKelvey, K., Xue, M., Whitmont, K., Shen, K., Cooper, A., & Jackson, C. (2012). Potential anti-inflammatory treatments for chronic wounds. Wound Practice & Research: Journal of the Australian Wound Management Association, 20(2), 86–89.
  33. Naik, S., Bouladoux, N., Linehan, J. L., Han, S.-J., Harrison, O. J., Wilhelm, C., Conlan, S., Himmelfarb, S., Byrd, A. L., Deming, C., Quinones, M., Brenchley, J. M., Kong, H. H., Tussiwand, R., Murphy, K. M., Merad, M., Segre, J. A., & Belkaid, Y. (2015). Commensal–dendritic-cell interaction specifies a unique protective skin immune signature. Nature, 520(7545), 104–108.
  34. Naik, S., Bouladoux, N., Wilhelm, C., Molloy, M. J., Salcedo, R., Kastenmuller, W., Deming, C., Quinones, M., Koo, L., Conlan, S., Spencer, S., Hall, J. A., Dzutsev, A., Kong, H., Campbell, D. J., Trinchieri, G., Segre, J. A., & Belkaid, Y. (2012). Compartmentalized control of skin immunity by resident commensals. Science (New York, N.Y.)337(6098), 1115–1119.
  35. Nakamura, Y., Oscherwitz, J., Cease, K. B., Chan, S. M., Muñoz-Planillo, R., Hasegawa, M., Villaruz, A. E., Cheung, G. Y. C., McGavin, M. J., Travers, J. B., Otto, M., Inohara, N., & Núñez, G. (2013). Staphylococcus δ-toxin induces allergic skin disease by activating mast cells. Nature, 503(7476), 397–401.
  36. Nakatsuji, T., Chen, T. H., Two, A. M., Chun, K. A., Narala, S., Geha, R. S., Hata, T. R., & Gallo, R. L. (2016). Staphylococcus aureus Exploits Epidermal Barrier Defects in Atopic Dermatitis to Trigger Cytokine Expression. Journal of Investigative Dermatology, 136(11), 2192–2200.
  37. Niebuhr, M., Gathmann, M., Scharonow, H., Mamerow, D., Mommert, S., Balaji, H., & Werfel, T. (2011). Staphylococcal Alpha-Toxin Is a Strong Inducer of Interleukin-17 in Humans. Infection and Immunity, 79(4), 1615–1622.
  38. Norlind, R. (1955). Significance of infections in origin of psoriasis. Acta Rheumatol Scand1, 135-44.
  39. Oh, J., Byrd, A. L., Park, M., Kong, H. H., & Segre, J. A. (2016). Temporal Stability of the Human Skin Microbiome. Cell, 165(4), 854–866.
  40. Oh, J., Freeman, A. F., Program, N. C. S., Park, M., Sokolic, R., Candotti, F., Holland, S. M., Segre, J. A., & Kong, H. H. (2013). The altered landscape of the human skin microbiome in patients with primary immunodeficiencies. Genome Research, 23(12), 2103–2114.
  41. Otto, M. (2009). Staphylococcus epidermidis — the “accidental” pathogen. Nature Reviews Microbiology, 7(8), 555–567.
  42. Otto, M. (2012). Molecular basis of Staphylococcus epidermidis infections. Seminars in Immunopathology, 34(2), 201–214.
  43. Owen, C. M., Chalmers, R., O’Sullivan, T., & Griffiths, C. E.M. (2000) Antistreptococcal interventions for guttate and chronic plaque psoriasis. Cochrane Database of Systematic Reviews, 2. Art. No.: CD001976. DOI: 10.1002/14651858.CD001976.
  44. PrabhuDas, M., Adkins, B., Gans, H., King, C., Levy, O., Ramilo, O., & Siegrist, C.-A. (2011). Challenges in infant immunity: implications for responses to infection and vaccines. Nature Immunology, 12(3), 189–194.
  45. Price, L. B., Liu, C. M., Melendez, J. H., Frankel, Y. M., Engelthaler, D., Aziz, M., Bowers, J., Rattray, R., Ravel, J., Kingsley, C., Keim, P. S., Lazarus, G. S., & Zenilman, J. M. (2009). Community Analysis of Chronic Wound Bacteria Using 16S rRNA Gene-Based Pyrosequencing: Impact of Diabetes and Antibiotics on Chronic Wound Microbiota. PLOS ONE, 4(7), e6462-.
  46. Schommer, N. N., & Gallo, R. L. (2013). Structure and function of the human skin microbiome. Trends in Microbiology, 21(12), 660–668.
  47. Statnikov, A., Alekseyenko, A. v, Li, Z., Henaff, M., Perez-Perez, G. I., Blaser, M. J., & Aliferis, C. F. (2013). Microbiomic Signatures of Psoriasis: Feasibility and Methodology Comparison. Scientific Reports, 3(1), 2620.
  48. Verbanic, S., Shen, Y., Lee, J., Deacon, J. M., & Chen, I. A. (2020). Microbial predictors of healing and short-term effect of debridement on the microbiome of chronic wounds. Npj Biofilms and Microbiomes, 6(1), 21.
  49. Weyrich, L. S., Dixit, S., Farrer, A. G., Cooper, A. J., & Cooper, A. J. (2015). The skin microbiome: Associations between altered microbial communities and disease. Australasian Journal of Dermatology, 56(4), 268–274.
  50. Williams, M. R., & Gallo, R. L. (2015). The Role of the Skin Microbiome in Atopic Dermatitis. Current Allergy and Asthma Reports, 15(11), 65.
  51. Wolcott, R., Costerton, J. W., Raoult, D., & Cutler, S. J. (2013). The polymicrobial nature of biofilm infection. Clinical Microbiology and Infection, 19(2), 107–112.

The Respiratory Microbiome

  1. Abreu, N. A., Nagalingam, N. A., Song, Y., Roediger, F. C., Pletcher, S. D., Goldberg, A. N., & Lynch, S. V. (2012). Sinus Microbiome Diversity Depletion and Corynebacterium tuberculostearicum Enrichment Mediates Rhinosinusitis. Science Translational Medicine, 4(151), 151ra124-151ra124.
  2. Beck, J. M., Schloss, P. D., Venkataraman, A., Twigg, H., Jablonski, K. A., Bushman, F. D., Campbell, T. B., Charlson, E. S., Collman, R. G., Crothers, K., Curtis, J. L., Drews, K. L., Flores, S. C., Fontenot, A. P., Foulkes, M. A., Frank, I., Ghedin, E., Huang, L., Lynch, S. v, … Young, V. B. (2015). Multicenter Comparison of Lung and Oral Microbiomes of HIV-infected and HIV-uninfected Individuals. American Journal of Respiratory and Critical Care Medicine, 192(11), 1335–1344.
  3. Biesbroek, G., Tsivtsivadze, E., Sanders, E. A. M., Montijn, R., Veenhoven, R. H., Keijser, B. J. F., & Bogaert, D. (2014). Early Respiratory Microbiota Composition Determines Bacterial Succession Patterns and Respiratory Health in Children. American Journal of Respiratory and Critical Care Medicine, 190(11), 1283–1292.
  4. Bosch, A. A. T. M., Levin, E., van Houten, M. A., Hasrat, R., Kalkman, G., Biesbroek, G., de Steenhuijsen Piters, W. A. A., de Groot, P.-K. C. M., Pernet, P., Keijser, B. J. F., Sanders, E. A. M., & Bogaert, D. (2016). Development of Upper Respiratory Tract Microbiota in Infancy is Affected by Mode of Delivery. EBioMedicine, 9, 336–345.
  5. Bousbia, S., Papazian, L., Saux, P., Forel, J. M., Auffray, J.-P., Martin, C., Raoult, D., & la Scola, B. (2012). Repertoire of Intensive Care Unit Pneumonia Microbiota. PLOS ONE, 7(2), e32486-.
  6. Carmody, L. A., Zhao, J., Schloss, P. D., Petrosino, J. F., Murray, S., Young, V. B., Li, J. Z., & LiPuma, J. J. (2013). Changes in Cystic Fibrosis Airway Microbiota at Pulmonary Exacerbation. Annals of the American Thoracic Society, 10(3), 179–187.
  7. Chalmers, J. D., Taylor, J. K., Mandal, P., Choudhury, G., Singanayagam, A., Akram, A. R., & Hill, A. T. (2011). Validation of the Infectious Diseases Society of America/American Thoratic Society Minor Criteria for Intensive Care Unit Admission in Community-Acquired Pneumonia Patients Without Major Criteria or Contraindications to Intensive Care Unit Care. Clinical Infectious Diseases, 53(6), 503–511.
  8. Charlson, E. S., Diamond, J. M., Bittinger, K., Fitzgerald, A. S., Yadav, A., Haas, A. R., Bushman, F. D., & Collman, R. G. (2012). Lung-enriched Organisms and Aberrant Bacterial and Fungal Respiratory Microbiota after Lung Transplant. American Journal of Respiratory and Critical Care Medicine, 186(6), 536–545.
  9. Cui, L., Morris, A., Huang, L., Beck, J. M., Twigg, H. L., von Mutius, E., & Ghedin, E. (2014). The Microbiome and the Lung. Annals of the American Thoracic Society, 11(Supplement 4), S227–S232.
  10. de Steenhuijsen Piters, W. A. A., Huijskens, E. G. W., Wyllie, A. L., Biesbroek, G., van den Bergh, M. R., Veenhoven, R. H., Wang, X., Trzciński, K., Bonten, M. J., Rossen, J. W. A., Sanders, E. A. M., & Bogaert, D. (2016). Dysbiosis of upper respiratory tract microbiota in elderly pneumonia patients. The ISME Journal, 10(1), 97–108.
  11. Denning, D. W., Pashley, C., Hartl, D., Wardlaw, A., Godet, C., del Giacco, S., Delhaes, L., & Sergejeva, S. (2014). Fungal allergy in asthma–state of the art and research needs. Clinical and Translational Allergy, 4(1), 14.
  12. Dickson, R. P., & Huffnagle, G. B. (2015). The Lung Microbiome: New Principles for Respiratory Bacteriology in Health and Disease. PLOS Pathogens, 11(7), e1004923-.
  13. Dickson, R. P., Martinez, F. J., & Huffnagle, G. B. (2014). The role of the microbiome in exacerbations of chronic lung diseases. The Lancet, 384(9944), 691–702.
  14. Dominguez-Bello, M. G., Costello, E. K., Contreras, M., Magris, M., Hidalgo, G., Fierer, N., & Knight, R. (2010). Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns. Proceedings of the National Academy of Sciences, 107(26), 11971.
  15. Durack, J., Boushey, H. A., & Lynch, S. v. (2016). Airway Microbiota and the Implications of Dysbiosis in Asthma. Current Allergy and Asthma Reports, 16(8), 52.
  16. Fall, T., Lundholm, C., Örtqvist, A. K., Fall, K., Fang, F., Hedhammar, Å., Kämpe, O., Ingelsson, E., & Almqvist, C. (2015). Early Exposure to Dogs and Farm Animals and the Risk of Childhood Asthma. JAMA Pediatrics, 169(11), e153219–e153219.
  17. File, T. M. (2003). Community-acquired pneumonia. The Lancet, 362(9400), 1991–2001.
  18. Fujimura, K. E., Johnson, C. C., Ownby, D. R., Cox, M. J., Brodie, E. L., Havstad, S. L., Zoratti, E. M., Woodcroft, K. J., Bobbitt, K. R., Wegienka, G., Boushey, H. A., & Lynch, S. v. (2010). Man’s best friend? The effect of pet ownership on house dust microbial communities. The Journal of Allergy and Clinical Immunology, 126(2), 410-412.e4123.
  19. Fukata, M., & Arditi, M. (2013). The role of pattern recognition receptors in intestinal inflammation. Mucosal Immunology, 6(3), 451–463.
  20. Hakansson, A. P., Orihuela, C. J., & Bogaert, D. (2018). Bacterial-Host Interactions: Physiology and Pathophysiology of Respiratory Infection. Physiological Reviews, 98(2), 781–811.
  21. Hamilos, D. L. (2019). Biofilm Formations in Pediatric Respiratory Tract Infection. Current Infectious Disease Reports, 21(2), 6.
  22. Hanada, S., Pirzadeh, M., Carver, K. Y., & Deng, J. C. (2018). Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia. Frontiers in Immunology, 9, 2640.
  23. Hilty, M., Burke, C., Pedro, H., Cardenas, P., Bush, A., Bossley, C., Davies, J., Ervine, A., Poulter, L., Pachter, L., Moffatt, M. F., & Cookson, W. O. C. (2010). Disordered Microbial Communities in Asthmatic Airways. PLOS ONE, 5(1), e8578-.
  24. Høiby, N., Ciofu, O., & Bjarnsholt, T. (2010). Pseudomonas aeruginosa biofilms in cystic fibrosis. Future Microbiology, 5(11), 1663–1674.
  25. Huang, Y. J., & Boushey, H. A. (2015). The microbiome in asthma. Journal of Allergy and Clinical Immunology, 135(1), 25–30.
  26. Huang, Y. J., Sethi, S., Murphy, T., Nariya, S., Boushey, H. A., & Lynch, S. V. (2014). Airway microbiome dynamics in exacerbations of chronic obstructive pulmonary disease. Journal of clinical microbiology52(8), 2813–2823.
  27. Iwai, S., Huang, D., Fong, S., Jarlsberg, L. G., Worodria, W., Yoo, S., Cattamanchi, A., Davis, J. L., Kaswabuli, S., Segal, M., Huang, L., & Lynch, S. v. (2014). The Lung Microbiome of Ugandan HIV-Infected Pneumonia Patients Is Compositionally and Functionally Distinct from That of San Franciscan Patients. PLOS ONE, 9(4), e95726-.
  28. Jain, S., Self, W. H., Wunderink, R. G., Fakhran, S., Balk, R., Bramley, A. M., Reed, C., Grijalva, C. G., Anderson, E. J., Courtney, D. M., Chappell, J. D., Qi, C., Hart, E. M., Carroll, F., Trabue, C., Donnelly, H. K., Williams, D. J., Zhu, Y., Arnold, S. R., … Finelli, L. (2015). Community-Acquired Pneumonia Requiring Hospitalization among U.S. Adults. New England Journal of Medicine, 373(5), 415–427.
  29. Keogh, R. H., & Stanojevic, S. (2018). A guide to interpreting estimated median age of survival in cystic fibrosis patient registry reports. Journal of Cystic Fibrosis, 17(2), 213–217.
  30. Khalkhali, H. R., Oshnouei, S., Salarilak, S., Rahimi Rad, M., Karamyar, M., & Khashabi, J. (2014). Effects of antibiotic consumption on children 2-8 years of age developing asthma. Epidemiology and Health, 36, e2014006–e2014006.
  31. Krone, C. L., Biesbroek, G., Trzciński, K., Sanders, E. A. M., & Bogaert, D. (2014). Respiratory microbiota dynamics following Streptococcus pneumoniae acquisition in young and elderly mice. Infection and Immunity, 82(4), 1725–1731.
  32. Mallia, P., Message, S. D., Gielen, V., Contoli, M., Gray, K., Kebadze, T., Aniscenko, J., Laza-Stanca, V., Edwards, M. R., Slater, L., Papi, A., Stanciu, L. A., Kon, O. M., Johnson, M., & Johnston, S. L. (2011). Experimental Rhinovirus Infection as a Human Model of Chronic Obstructive Pulmonary Disease Exacerbation. American Journal of Respiratory and Critical Care Medicine, 183(6), 734–742.
  33. Mika, M., Mack, I., Korten, I., Qi, W., Aebi, S., Frey, U., Latzin, P., & Hilty, M. (2015). Dynamics of the nasal microbiota in infancy: A prospective cohort study. Journal of Allergy and Clinical Immunology, 135(4), 905-912.e11.
  34. Millares, L., Ferrari, R., Gallego, M., Garcia-Nuñez, M., Pérez-Brocal, V., Espasa, M., Pomares, X., Monton, C., Moya, A., & Monsó, E. (2014). Bronchial microbiome of severe COPD patients colonised by Pseudomonas aeruginosa. European Journal of Clinical Microbiology & Infectious Diseases, 33(7), 1101–1111.
  35. Nguyen, L. D. N., Deschaght, P., Merlin, S., Loywick, A., Audebert, C., van Daele, S., Viscogliosi, E., Vaneechoutte, M., & Delhaes, L. (2016). Effects of Propidium Monoazide (PMA) Treatment on Mycobiome and Bacteriome Analysis of Cystic Fibrosis Airways during Exacerbation. PLOS ONE, 11(12), e0168860-.
  36. Nguyen, L. D. N., Viscogliosi, E., & Delhaes, L. (2015). The lung mycobiome: an emerging field of the human respiratory microbiome. Frontiers in Microbiology, 6, 89.
  37. Ober, C., & Yao, T.-C. (2011). The genetics of asthma and allergic disease: a 21st century perspective. Immunological Reviews, 242(1), 10–30.
  38. Orazi, G., & O’Toole, G. A. (2021). Pseudomonas aeruginosa Alters Staphylococcus aureus Sensitivity to Vancomycin in a Biofilm Model of Cystic Fibrosis Infection. MBio, 8(4), e00873-17.
  39. Ownby, D. R., Johnson, C. C., & Peterson, E. L. (2002). Exposure to Dogs and Cats in the First Year of Life and Risk of Allergic Sensitization at 6 to 7 Years of Age. JAMA, 288(8), 963–972.
  40. Pashley, C. H., Fairs, A., Free, R. C., & Wardlaw, A. J. (2012). DNA analysis of outdoor air reveals a high degree of fungal diversity, temporal variability, and genera not seen by spore morphology. Fungal Biology, 116(2), 214–224.
  41. Pettigrew, M. M., Tanner, W., & Harris, A. D. (2021). The Lung Microbiome and Pneumonia. The Journal of Infectious Diseases, 223(Supplement_3), S241–S245.
  42. Popgeorgiev, N., Temmam, S., Raoult, D., & Desnues, C. (2013). Describing the Silent Human Virome with an Emphasis on Giant Viruses. Intervirology, 56(6), 395–412.
  43. Prescott, S. L. (2013). Early-life environmental determinants of allergic diseases and the wider pandemic of inflammatory noncommunicable diseases. Journal of Allergy and Clinical Immunology, 131(1), 23–30.
  44. Price, K. E., Hampton, T. H., Gifford, A. H., Dolben, E. L., Hogan, D. A., Morrison, H. G., Sogin, M. L., & O’Toole, G. A. (2013). Unique microbial communities persist in individual cystic fibrosis patients throughout a clinical exacerbation. Microbiome, 1(1), 27.
  45. Ramos-Sevillano, E., Wade, W. G., Mann, A., Gilbert, A., Lambkin-Williams, R., Killingley, B., Nguyen-Van-Tam, J. S., & Tang, C. M. (2019). The Effect of Influenza Virus on the Human Oropharyngeal Microbiome. Clinical Infectious Diseases, 68(12), 1993–2002.
  46. Rohde, G., Wiethege, A., Borg, I., Kauth, M., Bauer, T. T., Gillissen, A., Bufe, A., & Schultze-Werninghaus, G. (2003). Respiratory viruses in exacerbations of chronic obstructive pulmonary disease requiring hospitalisation: a case-control study. Thorax, 58(1), 37.
  47. SEEMUNGAL, T., HARPER-OWEN, R., BHOWMIK, A., MORIC, I., SANDERSON, G., MESSAGE, S., MacCALLUM, P., MEADE, T. W., JEFFRIES, D. J., JOHNSTON, S. L., & WEDZICHA, J. A. (2001). Respiratory Viruses, Symptoms, and Inflammatory  Markers in Acute Exacerbations and Stable Chronic  Obstructive Pulmonary Disease. American Journal of Respiratory and Critical Care Medicine, 164(9), 1618–1623.
  48. Shilts, M. H., Rosas-Salazar, C., Tovchigrechko, A., Larkin, E. K., Torralba, M., Akopov, A., Halpin, R., Peebles, R. S., Moore, M. L., Anderson, L. J., Nelson, K. E., Hartert, T. v, & Das, S. R. (2016). Minimally Invasive Sampling Method Identifies Differences in Taxonomic Richness of Nasal Microbiomes in Young Infants Associated with Mode of Delivery. Microbial Ecology, 71(1), 233–242.
  49. Stearns, J. C., Davidson, C. J., McKeon, S., Whelan, F. J., Fontes, M. E., Schryvers, A. B., Bowdish, D. M. E., Kellner, J. D., & Surette, M. G. (2015). Culture and molecular-based profiles show shifts in bacterial communities of the upper respiratory tract that occur with age. The ISME Journal, 9(5), 1246–1259.
  50. Sze, M. A., Dimitriu, P. A., Suzuki, M., McDonough, J. E., Campbell, J. D., Brothers, J. F., Erb-Downward, J. R., Huffnagle, G. B., Hayashi, S., Elliott, W. M., Cooper, J., Sin, D. D., Lenburg, M. E., Spira, A., Mohn, W. W., & Hogg, J. C. (2015). Host Response to the Lung Microbiome in Chronic Obstructive Pulmonary Disease. American Journal of Respiratory and Critical Care Medicine, 192(4), 438–445.
  51. Teo, S. M., Mok, D., Pham, K., Kusel, M., Serralha, M., Troy, N., Holt, B. J., Hales, B. J., Walker, M. L., Hollams, E., Bochkov, Y. A., Grindle, K., Johnston, S. L., Gern, J. E., Sly, P. D., Holt, P. G., Holt, K. E., & Inouye, M. (2015). The Infant Nasopharyngeal Microbiome Impacts Severity of Lower Respiratory Infection and Risk of Asthma Development. Cell Host & Microbe, 17(5), 704–715.
  52. Teo, S. M., Mok, D., Pham, K., Kusel, M., Serralha, M., Troy, N., Holt, B. J., Hales, B. J., Walker, M. L., Hollams, E., Bochkov, Y. A., Grindle, K., Johnston, S. L., Gern, J. E., Sly, P. D., Holt, P. G., Holt, K. E., & Inouye, M. (2015). The Infant Nasopharyngeal Microbiome Impacts Severity of Lower Respiratory Infection and Risk of Asthma Development. Cell Host & Microbe, 17(5), 704–715.
  53. Underhill, D. M., & Iliev, I. D. (2014). The mycobiota: interactions between commensal fungi and the host immune system. Nature Reviews Immunology, 14(6), 405–416.
  54. Unger, S. A., & Bogaert, D. (2017). The respiratory microbiome and respiratory infections. Journal of Infection, 74, S84–S88.
  55. Urb, M., Snarr, B. D., Wojewodka, G., Lehoux, M., Lee, M. J., Ralph, B., Divangahi, M., King, I. L., McGovern, T. K., Martin, J. G., Fraser, R., Radzioch, D., & Sheppard, D. C. (2015). Evolution of the Immune Response to Chronic Airway Colonization with Aspergillus fumigatus Hyphae. Infection and immunity83(9), 3590–3600.
  56. Valley, T. S., Sjoding, M. W., Ryan, A. M., Iwashyna, T. J., & Cooke, C. R. (2015). Association of Intensive Care Unit Admission With Mortality Among Older Patients With Pneumonia. JAMA, 314(12), 1272–1279.
  57. van Woerden, H. C., Gregory, C., Brown, R., Marchesi, J. R., Hoogendoorn, B., & Matthews, I. P. (2013). Differences in fungi present in induced sputum samples from asthma patients and non-atopic controls: a community based case control study. BMC Infectious Diseases, 13(1), 69.
  58. Wang, Z., Bafadhel, M., Haldar, K., Spivak, A., Mayhew, D., Miller, B. E., Tal-Singer, R., Johnston, S. L., Ramsheh, M. Y., Barer, M. R., Brightling, C. E., & Brown, J. R. (2016). Lung microbiome dynamics in COPD exacerbations. European Respiratory Journal, 47(4), 1082.
  59. Wardlaw, T., Salama, P., Johansson, E. W., & Mason, E. (2006). Pneumonia: the leading killer of children. The Lancet, 368(9541), 1048–1050.
  60. Watson, R. L., de Koff, E. M., & Bogaert, D. (2019). Characterising the respiratory microbiome. European Respiratory Journal, 53(2), 1801711.
  61. Willner, D., Furlan, M., Haynes, M., Schmieder, R., Angly, F. E., Silva, J., Tammadoni, S., Nosrat, B., Conrad, D., & Rohwer, F. (2009). Metagenomic Analysis of Respiratory Tract DNA Viral Communities in Cystic Fibrosis and Non-Cystic Fibrosis Individuals. PLOS ONE, 4(10), e7370-.
  62. Zaura, E., Nicu, E. A., Krom, B. P., & Keijser, B. J. F. (2014). Acquiring and maintaining a normal oral microbiome: current perspective. Frontiers in Cellular and Infection Microbiology, 4, 85.
  63. Zhao, J., Schloss, P. D., Kalikin, L. M., Carmody, L. A., Foster, B. K., Petrosino, J. F., Cavalcoli, J. D., VanDevanter, D. R., Murray, S., Li, J. Z., Young, V. B., & LiPuma, J. J. (2012). Decade-long bacterial community dynamics in cystic fibrosis airways. Proceedings of the National Academy of Sciences, 109(15), 5809.
  64. Zhou, F., Yu, T., Du, R., Fan, G., Liu, Y., Liu, Z., Xiang, J., Wang, Y., Song, B., Gu, X., Guan, L., Wei, Y., Li, H., Wu, X., Xu, J., Tu, S., Zhang, Y., Chen, H., & Cao, B. (2020). Clinical course and risk factors for mortality of adult inpatients with COVID-19 in Wuhan, China: a retrospective cohort study. The Lancet, 395(10229), 1054–1062.

The Vaginal Microbiome

  1. Aagaard, K., Ma, J., Antony, K. M., Ganu, R., Petrosino, J., & Versalovic, J. (2014). The Placenta Harbors a Unique Microbiome. Science Translational Medicine, 6(237), 237ra65-237ra65.
  2. Aagaard, K., Riehle, K., Ma, J., Segata, N., Mistretta, T.-A., Coarfa, C., Raza, S., Rosenbaum, S., van den Veyver, I., Milosavljevic, A., Gevers, D., Huttenhower, C., Petrosino, J., & Versalovic, J. (2012). A Metagenomic Approach to Characterization of the Vaginal Microbiome Signature in Pregnancy. PLOS ONE, 7(6), e36466-.
  3. Abou Chacra, L., & Fenollar, F. (2021). Exploring the global vaginal microbiome and its impact on human health. Microbial Pathogenesis, 160, 105172.
  4. Albert, A. Y. K., Chaban, B., Wagner, E. C., Schellenberg, J. J., Links, M. G., van Schalkwyk, J., Reid, G., Hemmingsen, S. M., Hill, J. E., Money, D., & Group, V. R. (2015). A Study of the Vaginal Microbiome in Healthy Canadian Women Utilizing cpn60-Based Molecular Profiling Reveals Distinct Gardnerella Subgroup Community State Types. PLOS ONE, 10(8), e0135620-.
  5. Allonsius, C. N., Vandenheuvel, D., Oerlemans, E. F. M., Petrova, M. I., Donders, G. G. G., Cos, P., Delputte, P., & Lebeer, S. (2019). Inhibition of Candida albicans morphogenesis by chitinase from Lactobacillus rhamnosus GG. Scientific Reports, 9(1), 2900.
  6. Amabebe, E., & Anumba, D. O. C. (2018). The Vaginal Microenvironment: The Physiologic Role of Lactobacilli. Frontiers in Medicine, 5, 181.
  7. Amsel, R., Totten, P. A., Spiegel, C. A., Chen, K. C. S., Eschenbach, D., & Holmes, K. K. (1983). Nonspecific vaginitis: Diagnostic criteria and microbial and epidemiologic associations. The American Journal of Medicine, 74(1), 14–22.
  8. Anahtar, M. N., Byrne, E. H., Doherty, K. E., Bowman, B. A., Yamamoto, H. S., Soumillon, M., Padavattan, N., Ismail, N., Moodley, A., Sabatini, M. E., Ghebremichael, M. S., Nusbaum, C., Huttenhower, C., Virgin, H. W., Ndung’u, T., Dong, K. L., Walker, B. D., Fichorova, R. N., & Kwon, D. S. (2015). Cervicovaginal Bacteria Are a Major Modulator of Host Inflammatory Responses in the Female Genital Tract. Immunity, 42(5), 965–976.
  9. Auriemma, R. S., Scairati, R., del Vecchio, G., Liccardi, A., Verde, N., Pirchio, R., Pivonello, R., Ercolini, D., & Colao, A. (2021). The Vaginal Microbiome: A Long Urogenital Colonization Throughout Woman Life. Frontiers in Cellular and Infection Microbiology, 11, 613.
  10. AVONTS, D., SERCU, M., HEYERICK, P., VANDERMEEREN, I., MEHEUS, A., & PIOT, P. (1990). Incidence of Uncomplicated Genital Infections in Women Using Oral Contraception or an Intrauterine Device: A Prospective Study. Sexually Transmitted Diseases, 17(1), 23–29.
  11. Belay, N., Mukhopadhyay, B., E, C. de M., Galask, R., & Daniels, L. (1990). Methanogenic bacteria in human vaginal samples. Journal of Clinical Microbiology, 28(7), 1666–1668.
  12. Boskey, E. R., Cone, R. A., Whaley, K. J., & Moench, T. R. (2001). Origins of vaginal acidity: high d/l lactate ratio is consistent with bacteria being the primary source. Human Reproduction, 16(9), 1809–1813.
  13. Bradford, L. L., & Ravel, J. (2017). The vaginal mycobiome: A contemporary perspective on fungi in women’s health and diseases. Virulence, 8(3), 342–351.
  14. Bradshaw, C. S., & Sobel, J. D. (2016). Current Treatment of Bacterial Vaginosis—Limitations and Need for Innovation. The Journal of Infectious Diseases, 214(suppl_1), S14–S20.
  15. Brotman, R. M., Klebanoff, M. A., Nansel, T. R., Yu, K. F., Andrews, W. W., Zhang, J., & Schwebke, J. R. (2010). Bacterial vaginosis assessed by gram stain and diminished colonization resistance to incident gonococcal, chlamydial, and trichomonal genital infection. The Journal of infectious diseases202(12), 1907–1915.
  16. Calzolari, E., Masciangelo, R., Milite, V., & Verteramo, R. (2000). Bacterial vaginosis and contraceptive methods. International Journal of Gynecology & Obstetrics, 70(3), 341–346.
  17. Ceccarani, C., Foschi, C., Parolin, C., D’Antuono, A., Gaspari, V., Consolandi, C., Laghi, L., Camboni, T., Vitali, B., Severgnini, M., & Marangoni, A. (2019). Diversity of vaginal microbiome and metabolome during genital infections. Scientific Reports, 9(1), 14095.
  18. Chee, W. J. Y., Chew, S. Y., & Than, L. T. L. (2020). Vaginal microbiota and the potential of Lactobacillus derivatives in maintaining vaginal health. Microbial Cell Factories, 19(1), 203.
  19. Cherpes, T. L., Meyn, L. A., Krohn, M. A., Lurie, J. G., & Hillier, S. L. (2003). Association between acquisition of herpes simplex virus type 2 in women and bacterial vaginosis. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America37(3), 319–325.
  20. Chew, S. Y., & Than, L. T. L. (2016). Vulvovaginal candidosis: contemporary challenges and the future of prophylactic and therapeutic approaches. Mycoses, 59(5), 262–273.
  21. Chu, D. M., Ma, J., Prince, A. L., Antony, K. M., Seferovic, M. D., & Aagaard, K. M. (2017). Maturation of the infant microbiome community structure and function across multiple body sites and in relation to mode of delivery. Nature Medicine, 23(3), 314–326.
  22. Collado, M. C., Rautava, S., Aakko, J., Isolauri, E., & Salminen, S. (2016). Human gut colonisation may be initiated in utero by distinct microbial communities in the placenta and amniotic fluid. Scientific Reports, 6(1), 23129.
  23. de Seta, F., Campisciano, G., Zanotta, N., Ricci, G., & Comar, M. (2019). The Vaginal Community State Types Microbiome-Immune Network as Key Factor for Bacterial Vaginosis and Aerobic Vaginitis. Frontiers in Microbiology, 10, 2451.
  24. de Seta, F., Lonnee-Hoffmann, R., Campisciano, G., Comar, M., Verstraelen, H., Vieira-Baptista, P., Ventolini, G., & Lev-Sagie, A. (2022). The Vaginal Microbiome: III. The Vaginal Microbiome in Various Urogenital Disorders. Journal of Lower Genital Tract Disease, 26(1).
  25. Diop, K., Dufour, J.-C., Levasseur, A., & Fenollar, F. (2019). Exhaustive repertoire of human vaginal microbiota. Human Microbiome Journal, 11, 100051.
  26. Donders, G. G. G., Bosmans, E., Dekeersmaecker, A., Vereecken, A., van Bulck, B., & Spitz, B. (2000). Pathogenesis of abnormal vaginal bacterial flora. American Journal of Obstetrics and Gynecology, 182(4), 872–878.
  27. Eriksen B. (1999). A randomized, open, parallel-group study on the preventive effect of an estradiol-releasing vaginal ring (Estring) on recurrent urinary tract infections in postmenopausal women. American journal of obstetrics and gynecology180(5), 1072–1079.
  28. Fan, W., Kan, H., Liu, H. Y., Wang, T. L., He, Y. N., Zhang, M., Li, Y. X., Li, Y. J., Meng, W., Li, Q., Hu, A. Q., & Zheng, Y. J. (2022). Association between Human Genetic Variants and the Vaginal Bacteriome of Pregnant Women. MSystems, 6(4), e00158-21.
  29. Farage, M. A., Miller, K. W., & Sobel, J. D. (2010). Dynamics of the Vaginal Ecosystem—Hormonal Influences. Infectious Diseases: Research and Treatment, 3, IDRT.S3903.
  30. Feehily, C., Crosby, D., Walsh, C. J., Lawton, E. M., Higgins, S., McAuliffe, F. M., & Cotter, P. D. (2020). Shotgun sequencing of the vaginal microbiome reveals both a species and functional potential signature of preterm birth. Npj Biofilms and Microbiomes, 6(1), 50.
  31. Fettweis, J. M., Brooks, J. P., Serrano, M. G., Sheth, N. U., Girerd, P. H., Edwards, D. J., Strauss, J. F., Consortium, T. V. M., Jefferson, K. K., & Buck, G. A. (2014). Differences in vaginal microbiome in African American women versus women of European ancestry. Microbiology (Reading, England), 160(Pt 10), 2272–2282.
  32. Fettweis, J. M., Serrano, M. G., Brooks, J. P., Edwards, D. J., Girerd, P. H., Parikh, H. I., Huang, B., Arodz, T. J., Edupuganti, L., Glascock, A. L., Xu, J., Jimenez, N. R., Vivadelli, S. C., Fong, S. S., Sheth, N. U., Jean, S., Lee, V., Bokhari, Y. A., Lara, A. M., … Buck, G. A. (2019). The vaginal microbiome and preterm birth. Nature Medicine, 25(6), 1012–1021.
  33. Foxman B. (2014). Urinary tract infection syndromes: occurrence, recurrence, bacteriology, risk factors, and disease burden. Infectious disease clinics of North America28(1), 1–13.
  34. France, M. T., Ma, B., Gajer, P., Brown, S., Humphrys, M. S., Holm, J. B., Waetjen, L. E., Brotman, R. M., & Ravel, J. (2020). VALENCIA: a nearest centroid classification method for vaginal microbial communities based on composition. Microbiome, 8(1), 166.
  35. Gajer, P., Brotman, R. M., Bai, G., Sakamoto, J., Schütte, U. M., Zhong, X., Koenig, S. S., Fu, L., Ma, Z. S., Zhou, X., Abdo, Z., Forney, L. J., & Ravel, J. (2012). Temporal dynamics of the human vaginal microbiota. Science translational medicine4(132), 132ra52.
  36. Goldacre, M. J., Watt, B., Loudon, N., Milne, L. J., Loudon, J. D., & Vessey, M. P. (1979). Vaginal microbial flora in normal young women. British Medical Journal, 1(6176), 1450.
  37. Greenbaum, S., Greenbaum, G., Moran-Gilad, J., & Weintraub, A. Y. (2019). Ecological dynamics of the vaginal microbiome in relation to health and disease. American Journal of Obstetrics and Gynecology, 220(4), 324–335.
  38. Gupta, P., Singh, M. P., & Goyal, K. (2020). Diversity of Vaginal Microbiome in Pregnancy: Deciphering the Obscurity. Frontiers in Public Health, 8, 326.
  39. Gupta, S., Kakkar, V., & Bhushan, I. (2019). Crosstalk between Vaginal Microbiome and Female Health: A review. Microbial Pathogenesis, 136, 103696.
  40. Happel, A. U., Varsani, A., Balle, C., Passmore, J. A., & Jaspan, H. (2020). The Vaginal Virome-Balancing Female Genital Tract Bacteriome, Mucosal Immunity, and Sexual and Reproductive Health Outcomes?. Viruses12(8), 832.
  41. Hemmerling, A., Harrison, W., Schroeder, A., Park, J., Korn, A., Shiboski, S., Foster-Rosales, A., & Cohen, C. R. (2010). Phase 2a Study Assessing Colonization Efficiency, Safety, and Acceptability of Lactobacillus crispatus CTV-05 in Women With Bacterial Vaginosis. Sexually Transmitted Diseases, 37(12).,.3.aspx
  42. Hillebrand, L., Harmanli, O. H., Whiteman, V., & Khandelwal, M. (2002). Urinary tract infections in pregnant women with bacterial vaginosis. American journal of obstetrics and gynecology186(5), 916–917.
  43. Hooton, T. M. (2012). Uncomplicated Urinary Tract Infection. New England Journal of Medicine, 366(11), 1028–1037.
  44. Hyman, R. W., Fukushima, M., Jiang, H., Fung, E., Rand, L., Johnson, B., Vo, K. C., Caughey, A. B., Hilton, J. F., Davis, R. W., & Giudice, L. C. (2014). Diversity of the Vaginal Microbiome Correlates With Preterm Birth. Reproductive Sciences, 21(1), 32–40.
  45. Jang, S. J., Lee, K., Kwon, B., You, H. J., & Ko, G. (2019). Vaginal lactobacilli inhibit growth and hyphae formation of Candida albicans. Scientific Reports, 9(1), 8121.
  46. Kim, J.-M., & Park, Y. J. (2017). Probiotics in the Prevention and Treatment of Postmenopausal Vaginal Infections: Review Article. Jmm, 23(3), 139–145.
  47. Kolter, J., & Henneke, P. (2017). Codevelopment of Microbiota and Innate Immunity and the Risk for Group B Streptococcal Disease. Frontiers in Immunology, 8, 1497.
  48. Lagenaur, L. A., Hemmerling, A., Chiu, C., Miller, S., Lee, P. P., Cohen, C. R., & Parks, T. P. (2021). Connecting the Dots: Translating the Vaginal Microbiome Into a Drug. The Journal of Infectious Diseases, 223(Supplement_3), S296–S306.
  49. Lai, S. K., Hida, K., Shukair, S., Wang, Y. Y., Figueiredo, A., Cone, R., Hope, T. J., & Hanes, J. (2009). Human immunodeficiency virus type 1 is trapped by acidic but not by neutralized human cervicovaginal mucus. Journal of virology83(21), 11196–11200.
  50. Lee, J. B. L., & Neild, G. H. (2007). Urinary tract infection. Medicine, 35(8), 423–428.
  51. Lewis, A. L., & Gilbert, N. M. (2020). Roles of the vagina and the vaginal microbiota in urinary tract infection: evidence from clinical correlations and experimental models. GMS Infectious Diseases, 8, Doc02–Doc02.
  52. Liebenberg, L. J. P., Masson, L., Arnold, K. B., Mckinnon, L. R., Werner, L., Proctor, E., Archary, D., Mansoor, L. E., Lauffenburger, D. A., Abdool Karim, Q., Abdool Karim, S. S., & Passmore, J.-A. S. (2017). Genital-Systemic Chemokine Gradients and the Risk of HIV Acquisition in Women. Journal of Acquired Immune Deficiency Syndromes (1999), 74(3), 318–325.
  53. Ma, B., Forney, L. J., & Ravel, J. (2012). Vaginal Microbiome: Rethinking Health and Disease. Annual Review of Microbiology, 66(1), 371–389.
  54. Mancabelli, L., Tarracchini, C., Milani, C., Lugli, G. A., Fontana, F., Turroni, F., van Sinderen, D., & Ventura, M. (2021). Vaginotypes of the human vaginal microbiome. Environmental Microbiology, 23(3), 1780–1792.
  55. Margolis, E., & Fredricks, D. N. (2015). Chapter 83 – Bacterial Vaginosis-Associated Bacteria. In Y.-W. Tang, M. Sussman, D. Liu, I. Poxton, & J. Schwartzman (Eds.), Molecular Medical Microbiology (Second Edition) (pp. 1487–1496). Academic Press.
  56. Marrazzo, J. M., Fiedler, T. L., Srinivasan, S., Thomas, K. K., Liu, C., Ko, D., Xie, H., Saracino, M., & Fredricks, D. N. (2012). Extravaginal Reservoirs of Vaginal Bacteria as Risk Factors for Incident Bacterial Vaginosis. The Journal of Infectious Diseases, 205(10), 1580–1588.
  57. Martin, D. H., & Marrazzo, J. M. (2016). The Vaginal Microbiome: Current Understanding and Future Directions. The Journal of Infectious Diseases, 214(suppl_1), S36–S41.
  58. Martin, H. L., Richardson, B. A., Nyange, P. M., Lavreys, L., Hillier, S. L., Chohan, B., Mandaliya, K., Ndinya-Achola, J. O., Bwayo, J., & Kreiss, J. (1999). Vaginal lactobacilli, microbial flora, and risk of human immunodeficiency virus type 1 and sexually transmitted disease acquisition. The Journal of infectious diseases180(6), 1863–1868.
  59. Miller, C. J., & Shattock, R. J. (2003). Target cells in vaginal HIV transmission. Microbes and Infection, 5(1), 59–67.
  60. Mitchell, H. (2004). Vaginal discharge—causes, diagnosis, and treatment. BMJ, 328(7451), 1306.
  61. Molenaar, M. C., Singer, M., & Ouburg, S. (2018). The two-sided role of the vaginal microbiome in Chlamydia trachomatis and Mycoplasma genitalium pathogenesis. Journal of reproductive immunology130, 11–17.
  62. Murphy, K., & Mitchell, C. M. (2016). The Interplay of Host Immunity, Environment and the Risk of Bacterial Vaginosis and Associated Reproductive Health Outcomes. The Journal of Infectious Diseases, 214(suppl_1), S29–S35.
  63. Neggers, Y. H., Nansel, T. R., Andrews, W. W., Schwebke, J. R., Yu, K., Goldenberg, R. L., & Klebanoff, M. A. (2007). Dietary Intake of Selected Nutrients Affects Bacterial Vaginosis in Women. The Journal of Nutrition, 137(9), 2128–2133.
  64. Nicolle, L. E., Harding, G. K., Preiksaitis, J., & Ronald, A. R. (1982). The association of urinary tract infection with sexual intercourse. The Journal of infectious diseases146(5), 579–583.
  65. Nugent, R. P., Krohn, M. A., & Hillier, S. L. (1991). Reliability of diagnosing bacterial vaginosis is improved by a standardized method of gram stain interpretation. Journal of Clinical Microbiology, 29(2), 297–301.
  66. Oduyebo, O. O., Anorlu, R. I., & Ogunsola, F. T. (2009). The effects of antimicrobial therapy on bacterial vaginosis in non-pregnant women. The Cochrane database of systematic reviews, (3), CD006055.
  67. Oerlemans, E. F. M., Bellen, G., Claes, I., Henkens, T., Allonsius, C. N., Wittouck, S., van den Broek, M. F. L., Wuyts, S., Kiekens, F., Donders, G. G. G., & Lebeer, S. (2020). Impact of a lactobacilli-containing gel on vulvovaginal candidosis and the vaginal microbiome. Scientific Reports, 10(1), 7976.
  68. Onderdonk, A. B., Delaney, M. L., & Fichorova, R. N. (2016). The Human Microbiome during Bacterial Vaginosis. Clinical Microbiology Reviews, 29(2), 223–238.
  69. Peipert, J. F., Lapane, K. L., Allsworth, J. E., Redding, C. A., Blume, J. D., & Stein, M. D. (2008). Bacterial vaginosis, race, and sexually transmitted infections: does race modify the association?. Sexually transmitted diseases35(4), 363–367.
  70. Peters, B. M., Yano, J., Noverr, M. C., & Fidel Jr, P. L. (2014). Candida Vaginitis: When Opportunism Knocks, the Host Responds. PLOS Pathogens, 10(4), e1003965-.
  71. Petrova, M. I., Imholz, N. C. E., Verhoeven, T. L. A., Balzarini, J., van Damme, E. J. M., Schols, D., Vanderleyden, J., & Lebeer, S. (2016). Lectin-Like Molecules of Lactobacillus rhamnosus GG Inhibit Pathogenic Escherichia coli and Salmonella Biofilm Formation. PLOS ONE, 11(8), e0161337-.
  72. Phares, C. R., Lynfield, R., Farley, M. M., Mohle-Boetani, J., Harrison, L. H., Petit, S., Craig, A. S., Schaffner, W., Zansky, S. M., Gershman, K., Stefonek, K. R., Albanese, B. A., Zell, E. R., Schuchat, A., & Schrag, S. J. (2008). Epidemiology of Invasive Group B Streptococcal Disease in the United States, 1999-2005. JAMA, 299(17), 2056–2065.
  73. Pino, A., Bartolo, E., Caggia, C., Cianci, A., & Randazzo, C. L. (2019). Detection of vaginal lactobacilli as probiotic candidates. Scientific Reports, 9(1), 3355.
  74. Prais, D., Straussberg, R., Avitzur, Y., Nussinovitch, M., Harel, L., & Amir, J. (2003). Bacterial susceptibility to oral antibiotics in community acquired urinary tract infection. Archives of Disease in Childhood, 88(3), 215.
  75. Prince, A. L., Chu, D. M., Seferovic, M. D., Antony, K. M., Ma, J., & Aagaard, K. M. (2015). The Perinatal Microbiome and Pregnancy: Moving Beyond the Vaginal Microbiome. Cold Spring Harbor Perspectives in Medicine, 5(6).
  76. Quin, C., Vollman, D. M., Ghosh, S., Haskey, N., Estaki, M., Pither, J., Barnett, J. A., Jay, M. N., Birnie, B. W., & Gibson, D. L. (2020). Fish oil supplementation reduces maternal defensive inflammation and predicts a gut bacteriome with reduced immune priming capacity in infants. The ISME Journal, 14(8), 2090–2104.
  77. Rautava, S., Luoto, R., Salminen, S., & Isolauri, E. (2012). Microbial contact during pregnancy, intestinal colonization and human disease. Nature Reviews Gastroenterology & Hepatology, 9(10), 565–576.
  78. Ravel, J., Gajer, P., Abdo, Z., Schneider, G. M., Koenig, S. S. K., McCulle, S. L., Karlebach, S., Gorle, R., Russell, J., Tacket, C. O., Brotman, R. M., Davis, C. C., Ault, K., Peralta, L., & Forney, L. J. (2011). Vaginal microbiome of reproductive-age women. Proceedings of the National Academy of Sciences, 108(Supplement 1), 4680.
  79. Raz, R., & Stamm, W. E. (1993). A controlled trial of intravaginal estriol in postmenopausal women with recurrent urinary tract infections. The New England journal of medicine329(11), 753–756.
  80. Schwebke, J. R. (2000). Asymptomatic bacterial vaginosis: Response to therapy. American Journal of Obstetrics and Gynecology, 183(6), 1434–1439.
  81. Sewankambo, N., Gray, R. H., Wawer, M. J., Paxton, L., McNaim, D., Wabwire-Mangen, F., Serwadda, D., Li, C., Kiwanuka, N., Hillier, S. L., Rabe, L., Gaydos, C. A., Quinn, T. C., & Konde-Lule, J. (1997). HIV-1 infection associated with abnormal vaginal flora morphology and bacterial vaginosis. Lancet (London, England)350(9077), 546–550.
  82. Sheerin, N. S. (2011). Urinary tract infection. Medicine, 39(7), 384–389.
  83. Siqueira, J. D., Curty, G., Xutao, D., Hofer, C. B., Machado, E. S., Seuánez, H. N., Soares, M. A., Delwart, & E., Soares, E. A. (2019). Composite Analysis of the Virome and Bacteriome of HIV/HPV Co-Infected Women Reveals Proxies for Immunodeficiency. Viruses, 11(5):422.
  84. Stapleton A. E. (2016). The Vaginal Microbiota and Urinary Tract Infection. Microbiology spectrum4(6), 10.1128/microbiolspec.UTI-0025-2016.
  85. Stapleton, A. E., Au-Yeung, M., Hooton, T. M., Fredricks, D. N., Roberts, P. L., Czaja, C. A., Yarova-Yarovaya, Y., Fiedler, T., Cox, M., & Stamm, W. E. (2011). Randomized, placebo-controlled phase 2 trial of a Lactobacillus crispatus probiotic given intravaginally for prevention of recurrent urinary tract infection. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America52(10), 1212–1217.
  86. Sumati, A. H., & Saritha, N. K. (2009). Association of urinary tract infection in women with bacterial vaginosis. Journal of global infectious diseases1(2), 151–152.
  87. Swidsinski, A., Mendling, W., Loening-Baucke, V., Swidsinski, S., Dörffel, Y., Scholze, J., Lochs, H., & Verstraelen, H. (2008). An adherent Gardnerella vaginalis biofilm persists on the vaginal epithelium after standard therapy with oral metronidazole. American Journal of Obstetrics and Gynecology, 198(1), 97.e1-97.e6.
  88. Ta, L. D. H., Chan, J. C. Y., Yap, G. C., Purbojati, R. W., Drautz-Moses, D. I., Koh, Y. M., Tay, C. J. X., Huang, C.-H., Kioh, D. Y. Q., Woon, J. Y., Tham, E. H., Loo, E. X. L., Shek, L. P. C., Karnani, N., Goh, A., van Bever, H. P. S., Teoh, O. H., Chan, Y. H., Lay, C., … Lee, B. W. (2020). A compromised developmental trajectory of the infant gut microbiome and metabolome in atopic eczema. Gut Microbes, 12(1), 1801964.
  89. Tachedjian, G., Aldunate, M., Bradshaw, C. S., & Cone, R. A. (2017). The role of lactic acid production by probiotic Lactobacillus species in vaginal health. Research in Microbiology, 168(9), 782–792.
  90. Taha, T. E., Hoover, D. R., Dallabetta, G. A., Kumwenda, N. I., Mtimavalye, L. A. R., Yang, L.-P., Liomba, G. N., Broadhead, R. L., Chiphangwi, J. D., & Miotti, P. G. (1998). Bacterial vaginosis and disturbances of vaginal flora: association with increased acquisition of HIV. AIDS, 12(13).
  91. Tan, C. W., & Chlebicki, M. P. (2016). Urinary tract infections in adults. Singapore Medical Journal, 57(9), 485–490.
  92. Tazi, A., Plainvert, C., Anselem, O., Ballon, M., Marcou, V., Seco, A., el Alaoui, F., Joubrel, C., el Helali, N., Falloukh, E., Frigo, A., Raymond, J., Trieu-Cuot, P., Branger, C., le Monnier, A., Azria, E., Ancel, P.-Y., Jarreau, P. H., Mandelbrot, L., … Poyart, C. (2019). Risk Factors for Infant Colonization by Hypervirulent CC17 Group B Streptococcus: Toward the Understanding of Late-onset Disease. Clinical Infectious Diseases, 69(10), 1740–1748.
  93. Torcia, M. G. (2019). Interplay among Vaginal Microbiome, Immune Response and Sexually Transmitted Viral Infections. International Journal of Molecular Sciences, 20(2):266.
  94. van de Wijgert, J., & Verwijs, M. C. (2020). Lactobacilli-containing vaginal probiotics to cure or prevent bacterial or fungal vaginal dysbiosis: a systematic review and recommendations for future trial designs. BJOG: An International Journal of Obstetrics & Gynaecology, 127(2), 287–299.
  95. Verstraelen, H., Verhelst, R., Vaneechoutte, M., & Temmerman, M. (2010). The epidemiology of bacterial vaginosis in relation to sexual behaviour. BMC Infectious Diseases, 10(1), 81.
  96. Wiesenfeld, H. C., Hillier, S. L., Krohn, M. A., Landers, D. v, & Sweet, R. L. (2003). Bacterial Vaginosis Is a Strong Predictor of Neisseria gonorrhoeae and Chlamydia trachomatis Infection. Clinical Infectious Diseases, 36(5), 663–668.
  97. Wylie, K. M., Wylie, T. N., Cahill, A. G., Macones, G. A., Tuuli, M. G., & Stout, M. J. (2018). The vaginal eukaryotic DNA virome and preterm birth. American Journal of Obstetrics and Gynecology, 219(2), 189.e1-189.e12.
  98. Xu, J., Bian, G., Zheng, M., Lu, G., Chan, W.-Y., Li, W., Yang, K., Chen, Z.-J., & Du, Y. (2020). Fertility factors affect the vaginal microbiome in women of reproductive age. American Journal of Reproductive Immunology, 83(4), e13220.
  99. Zabor, E. C., Klebanoff, M., Yu, K., Zhang, J., Nansel, T., Andrews, W., Schwebke, J., & Jeffcoat, M. (2010). Association between periodontal disease, bacterial vaginosis, and sexual risk behaviours. Journal of Clinical Periodontology, 37(10), 888–893.
  100. Zaleznik, D. F., Rench, M. A., Hillier, S., Krohn, M. A., Platt, R., Lee, M.-L. T., Flores, A. E., Ferrieri, P., & Baker, C. J. (2000). Invasive Disease Due to Group B Streptococcus in Pregnant Women and Neonates from Diverse Population Groups. Clinical Infectious Diseases, 30(2), 276–281.
  101. Zapata, H. J., & Quagliarello, V. J. (2015). The Microbiota and Microbiome in Aging: Potential Implications in Health and Age-Related Diseases. Journal of the American Geriatrics Society, 63(4), 776–781.
  102. Zozaya, M., Ferris, M. J., Siren, J. D., Lillis, R., Myers, L., Nsuami, M. J., Eren, A. M., Brown, J., Taylor, C. M., & Martin, D. H. (2016). Bacterial communities in penile skin, male urethra, and vaginas of heterosexual couples with and without bacterial vaginosis. Microbiome, 4(1), 16.

Mental Health and Multi-Microbiome Interactions

  1. Acharya, C., Sahingur, S. E., & Bajaj, J. S. (2017). Microbiota, cirrhosis, and the emerging oral-gut-liver axis. JCI Insight, 2(19), e94416.
  2. Allali, I., Bakri, Y., Amzazi, S., & Ghazal, H. (2021). Gut-Lung Axis in COVID-19. Interdisciplinary Perspectives on Infectious Diseases, 2021, 6655380.
  3. Alonso, R., Pisa, D., Fernández-Fernández, A. M., & Carrasco, L. (2018). Infection of Fungi and Bacteria in Brain Tissue From Elderly Persons and Patients With Alzheimer’s Disease. Frontiers in Aging Neuroscience, 10.
  4. Bäsler, K., Galliano, M.-F., Bergmann, S., Rohde, H., Wladykowski, E., Vidal-y-Sy, S., Guiraud, B., Houdek, P., Schüring, G., Volksdorf, T., Caruana, A., Bessou-Touya, S., Schneider, S. W., Duplan, H., & Brandner, J. M. (2017). Biphasic influence of Staphylococcus aureus on human epidermal tight junctions. Annals of the New York Academy of Sciences, 1405(1), 53–70.
  5. Bear T, Dalziel J, Coad J, Roy N, Butts C, & Gopal P. (2021). The Microbiome-Gut-Brain Axis and Resilience to Developing Anxiety or Depression under Stress. Microorganisms, 9(4):723.
  6. Beri, K. (2018). Skin microbiome & host immunity: applications in regenerative cosmetics & transdermal drug delivery. Future Science OA, 4(6), FSO302.
  7. Boix-Amorós, A., Collado, M. C., & Mira, A. (2016). Relationship between Milk Microbiota, Bacterial Load, Macronutrients, and Human Cells during Lactation. Frontiers in microbiology7, 492.
  8. Borre, Y. E., O’Keeffe, G. W., Clarke, G., Stanton, C., Dinan, T. G., & Cryan, J. F. (2014). Microbiota and neurodevelopmental windows: implications for brain disorders. Trends in Molecular Medicine, 20(9), 509–518.
  9. Branton, W. G., Ellestad, K. K., Maingat, F., Wheatley, B. M., Rud, E., Warren, R. L., Holt, R. A., Surette, M. G., & Power, C. (2013). Brain Microbial Populations in HIV/AIDS: α-Proteobacteria Predominate Independent of Host Immune Status. PLOS ONE, 8(1), e54673-.
  10. Bruce-Keller, A. J., Salbaum, J. M., & Berthoud, H.-R. (2018). Harnessing Gut Microbes for Mental Health: Getting From Here to There. Biological Psychiatry, 83(3), 214–223.
  11. Bui, U. T., Finlayson, K., & Edwards, H. (2018). Risk factors for infection in patients with chronic leg ulcers: A survival analysis. International Journal of Clinical Practice, 72(12), e13263.
  12. Carlson, A. L., Xia, K., Azcarate-Peril, M. A., Goldman, B. D., Ahn, M., Styner, M. A., Thompson, A. L., Geng, X., Gilmore, J. H., & Knickmeyer, R. C. (2018). Infant Gut Microbiome Associated With Cognitive Development. Biological Psychiatry, 83(2), 148–159.
  13. Civardi, E., Garofoli, F., Tzialla, C., Paolillo, P., Bollani, L., & Stronati, M. (2013). Microorganisms in human milk: lights and shadows. The journal of maternal-fetal & neonatal medicine : the official journal of the European Association of Perinatal Medicine, the Federation of Asia and Oceania Perinatal Societies, the International Society of Perinatal Obstetricians26 Suppl 2, 30–34.
  14. Cowan, C. S. M., Hoban, A. E., Ventura-Silva, A. P., Dinan, T. G., Clarke, G., & Cryan, J. F. (2018). Gutsy Moves: The Amygdala as a Critical Node in Microbiota to Brain Signaling. BioEssays, 40(1), 1700172.
  15. Cryan, J. F., & Dinan, T. G. (2012). Mind-altering microorganisms: the impact of the gut microbiota on brain and behaviour. Nature Reviews Neuroscience, 13(10), 701–712.
  16. Cryan, J. F., O’Riordan, K. J., Cowan, C. S. M., Sandhu, K. v, Bastiaanssen, T. F. S., Boehme, M., Codagnone, M. G., Cussotto, S., Fulling, C., Golubeva, A. v, Guzzetta, K. E., Jaggar, M., Long-Smith, C. M., Lyte, J. M., Martin, J. A., Molinero-Perez, A., Moloney, G., Morelli, E., Morillas, E., … Dinan, T. G. (2019). The Microbiota-Gut-Brain Axis. Physiological Reviews, 99(4), 1877–2013.
  17. Dash, S., Clarke, G., Berk, M., & Jacka, F. N. (2015). The gut microbiome and diet in psychiatry: focus on depression. Current Opinion in Psychiatry, 28(1).
  18. De Pessemier B, Grine L, Debaere M, Maes A, Paetzold B, Callewaert C. (2021). Gut–Skin Axis: Current Knowledge of the Interrelationship between Microbial Dysbiosis and Skin Conditions. Microorganisms, 9(2):353.
  19. Desbonnet, L., Clarke, G., Shanahan, F., Dinan, T. G., & Cryan, J. F. (2014). Microbiota is essential for social development in the mouse. Molecular Psychiatry, 19(2), 146–148.
  20. Diaz Heijtz, R. (2016). Fetal, neonatal, and infant microbiome: Perturbations and subsequent effects on brain development and behavior. Seminars in Fetal and Neonatal Medicine, 21(6), 410–417.
  21. Dinan, T. G., & Cryan, J. F. (2017). Gut instincts: microbiota as a key regulator of brain development, ageing and neurodegeneration. The Journal of Physiology, 595(2), 489–503.
  22. Dinan, T. G., Stanton, C., & Cryan, J. F. (2013). Psychobiotics: A Novel Class of Psychotropic. Biological Psychiatry, 74(10), 720–726.
  23. Dominy, S. S., Casey, L., Florian, E., Malgorzata, B., Agata, M., Andrei, K., Mai, N., Ursula, H., Debasish, R., Christina, G., J, H. L., Shirin, A.-K., Samer, K., Alexander, L., I, R. M., Barbara, P., Piotr, M., Annelie, H., Karina, A., … Jan, P. (2022). Porphyromonas gingivalis in Alzheimer’s disease brains: Evidence for disease causation and treatment with small-molecule inhibitors. Science Advances, 5(1), eaau3333.
  24. Drago, L., Zuccotti, G. V., Romanò, C. L., Goswami, K., Villafañe, J. H., Mattina, R., & Parvizi, J. (2019). Oral–Gut Microbiota and Arthritis: Is There an Evidence-Based Axis? Journal of Clinical Medicine, 8(10):1753.
  25. du Teil Espina, M., Gabarrini, G., Harmsen, H. J. M., Westra, J., van Winkelhoff, A. J., & van Dijl, J. M. (2019). Talk to your gut: the oral-gut microbiome axis and its immunomodulatory role in the etiology of rheumatoid arthritis. FEMS Microbiology Reviews, 43(1), 1–18.
  26. Enaud, R., Prevel, R., Ciarlo, E., Beaufils, F., Wieërs, G., Guery, B., & Delhaes, L. (2020). The Gut-Lung Axis in Health and Respiratory Diseases: A Place for Inter-Organ and Inter-Kingdom Crosstalks. Frontiers in Cellular and Infection Microbiology, 10.
  27. Frati F, Salvatori C, Incorvaia C, Bellucci A, Di Cara G, Marcucci F, & Esposito S. (2019). The Role of the Microbiome in Asthma: The Gut–Lung Axis. International Journal of Molecular Sciences, 20(1):123.
  28. Gareau, M. G. (2016). Chapter Eleven – Cognitive Function and the Microbiome. In J. F. Cryan & G. Clarke (Eds.), International Review of Neurobiology (Vol. 131, pp. 227–246). Academic Press.
  29. Green, J., Jester, R., McKinley, R., & Pooler, A. (2014). The impact of chronic venous leg ulcers: a systematic review. Journal of Wound Care, 23(12), 601–612.
  30. Gupta, M. A., Jarosz, P., & Gupta, A. K. (2017). Posttraumatic stress disorder (PTSD) and the dermatology patient. Clinics in Dermatology, 35(3), 260–266.
  31. Gur, T. L., Worly, B. L., & Bailey, M. T. (2015). Stress and the Commensal Microbiota: Importance in Parturition and Infant Neurodevelopment. Frontiers in Psychiatry, 6.
  32. Hassan, Z., Mustafa, S., Rahim, R. A., & Isa, N. M. (2016). Anti-breast cancer effects of live, heat-killed and cytoplasmic fractions of Enterococcus faecalis and Staphylococcus hominis isolated from human breast milk. In vitro cellular & developmental biology. Animal52(3), 337–348.
  33. He, Z., Cui, B.-T., Zhang, T., Li, P., Long, C.-Y., Ji, G.-Z., & Zhang, F.-M. (2017). Fecal microbiota transplantation cured epilepsy in a case with Crohn’s disease: The first report. World Journal of Gastroenterology, 23(19), 3565–3568.
  34. Heikkilä, M. P., & Saris, P. E. (2003). Inhibition of Staphylococcus aureus by the commensal bacteria of human milk. Journal of applied microbiology95(3), 471–478.
  35. Heneka, M. T., Kummer, M. P., & Latz, E. (2014). Innate immune activation in neurodegenerative disease. Nature Reviews Immunology, 14(7), 463–477.
  36. Hoban, A. E., Stilling, R. M., Moloney, G., Shanahan, F., Dinan, T. G., Clarke, G., & Cryan, J. F. (2018). The microbiome regulates amygdala-dependent fear recall. Molecular Psychiatry, 23(5), 1134–1144.
  37. Ilievski, V., Zuchowska, P. K., Green, S. J., Toth, P. T., Ragozzino, M. E., Le, K., Aljewari, H. W., O’Brien-Simpson, N. M., Reynolds, E. C., & Watanabe, K. (2018). Chronic oral application of a periodontal pathogen results in brain inflammation, neurodegeneration and amyloid beta production in wild type mice. PLOS ONE, 13(10), e0204941-.
  38. Jung, C.-R., Lin, Y.-T., & Hwang, B.-F. (2015). Ozone, Particulate Matter, and Newly Diagnosed Alzheimer’s Disease: A Population-Based Cohort Study in Taiwan. Journal of Alzheimer’s Disease, 44, 573–584.
  39. Kang, D.-W., Adams, J. B., Gregory, A. C., Borody, T., Chittick, L., Fasano, A., Khoruts, A., Geis, E., Maldonado, J., McDonough-Means, S., Pollard, E. L., Roux, S., Sadowsky, M. J., Lipson, K. S., Sullivan, M. B., Caporaso, J. G., & Krajmalnik-Brown, R. (2017). Microbiota Transfer Therapy alters gut ecosystem and improves gastrointestinal and autism symptoms: an open-label study. Microbiome, 5(1), 10.
  40. Kelly, J., Kennedy, P., Cryan, J., Dinan, T., Clarke, G., & Hyland, N. (2015). Breaking Down the Barriers: The Gut Microbiome, Intestinal Permeability and Stress-related Psychiatric Disorders. Frontiers in Cellular Neuroscience, 9.
  41. Kesika, P., Suganthy, N., Sivamaruthi, B. S., & Chaiyasut, C. (2021). Role of gut-brain axis, gut microbial composition, and probiotic intervention in Alzheimer’s disease. Life Sciences, 264, 118627.
  42. Kirrane, E. F., Bowman, C., Davis, J. A., Hoppin, J. A., Blair, A., Chen, H., Patel, M. M., Sandler, D. P., Tanner, C. M., Vinikoor-Imler, L., Ward, M. H., Luben, T. J., & Kamel, F. (2015). Associations of Ozone and PM2.5 Concentrations With Parkinson’s Disease Among Participants in the Agricultural Health Study. Journal of Occupational and Environmental Medicine, 57(5), 509–517.
  43. Kundu, P., Blacher, E., Elinav, E., & Pettersson, S. (2017). Our Gut Microbiome: The Evolving Inner Self. Cell, 171(7), 1481–1493.
  44. Lara-Villoslada, F., Olivares, M., Sierra, S., Rodríguez, J. M., Boza, J., & Xaus, J. (2007). Beneficial effects of probiotic bacteria isolated from breast milk. The British journal of nutrition98 Suppl 1, S96–S100.
  45. Leclercq, S., Cani, P. D., Neyrinck, A. M., Stärkel, P., Jamar, F., Mikolajczak, M., Delzenne, N. M., & de Timary, P. (2012). Role of intestinal permeability and inflammation in the biological and behavioral control of alcohol-dependent subjects. Brain, Behavior, and Immunity, 26(6), 911–918.
  46. Li, M., van Esch, B. C. A. M., Wagenaar, G. T. M., Garssen, J., Folkerts, G., & Henricks, P. A. J. (2018). Pro- and anti-inflammatory effects of short chain fatty acids on immune and endothelial cells. European Journal of Pharmacology, 831, 52–59.
  47. Liang S, Wu X, Hu X, Wang T, & Jin F. (2018b). Recognizing Depression from the Microbiota–Gut–Brain Axis. International Journal of Molecular Sciences, 19(6):1592.
  48. Liang, S., Wang, T., Hu, X., Luo, J., Li, W., Wu, X., Duan, Y., & Jin, F. (2015). Administration of Lactobacillus helveticus NS8 improves behavioral, cognitive, and biochemical aberrations caused by chronic restraint stress. Neuroscience, 310, 561–577.
  49. Liang, S., Wu, X., & Jin, F. (2018). Gut-Brain Psychology: Rethinking Psychology From the Microbiota–Gut–Brain Axis. Frontiers in Integrative Neuroscience, 12.
  50. Limon, J. J., Tang, J., Li, D., Wolf, A. J., Michelsen, K. S., Funari, V., Gargus, M., Nguyen, C., Sharma, P., Maymi, V. I., Iliev, I. D., Skalski, J. H., Brown, J., Landers, C., Borneman, J., Braun, J., Targan, S. R., McGovern, D. P. B., & Underhill, D. M. (2019). Malassezia Is Associated with Crohn’s Disease and Exacerbates Colitis in Mouse Models. Cell Host & Microbe, 25(3), 377-388.e6.
  51. Link, C. D. (2021). Is There a Brain Microbiome? Neuroscience Insights, 16, 26331055211018708–26331055211018708.
  52. Luczynski, P., McVey Neufeld, K.-A., Oriach, C. S., Clarke, G., Dinan, T. G., & Cryan, J. F. (2016). Growing up in a Bubble: Using Germ-Free Animals to Assess the Influence of the Gut Microbiota on Brain and Behavior. International Journal of Neuropsychopharmacology, 19(8), pyw020.
  53. Ma, Q., Xing, C., Long, W., Wang, H. Y., Liu, Q., & Wang, R.-F. (2019). Impact of microbiota on central nervous system and neurological diseases: the gut-brain axis. Journal of Neuroinflammation, 16(1), 53.
  54. Maitre Y, Micheneau P, Delpierre A, Mahalli R, Guerin M, Amador G, Denis F. (2020). Did the Brain and Oral Microbiota Talk to Each Other? A Review of the Literature. Journal of Clinical Medicine, 9(12):3876.
  55. Manderino L, Carroll I, Azcarate-Peril MA, Rochette A, Heinberg L, Peat C, Steffen K, Mitchell J, Gunstad J. Preliminary Evidence for an Association Between the Composition of the Gut Microbiome and Cognitive Function in Neurologically Healthy Older Adults. J Int Neuropsychol Soc. 2017 Sep;23(8):700-705. doi: 10.1017/S1355617717000492. Epub 2017 Jun 23. PMID: 28641593; PMCID: PMC6111127.
  56. Mika, A., Day, H. E. W., Martinez, A., Rumian, N. L., Greenwood, B. N., Chichlowski, M., Berg, B. M., & Fleshner, M. (2017). Early life diets with prebiotics and bioactive milk fractions attenuate the impact of stress on learned helplessness behaviours and alter gene expression within neural circuits important for stress resistance. European Journal of Neuroscience, 45(3), 342–357.
  57. Mika, A., Day, H. E. W., Martinez, A., Rumian, N. L., Greenwood, B. N., Chichlowski, M., Berg, B. M., & Fleshner, M. (2017). Early life diets with prebiotics and bioactive milk fractions attenuate the impact of stress on learned helplessness behaviours and alter gene expression within neural circuits important for stress resistance. European Journal of Neuroscience, 45(3), 342–357.
  58. Mousavi, S. E., Delgado-Saborit, J. M., Adivi, A., Pauwels, S., & Godderis, L. (2021). Air pollution and endocrine disruptors induce human microbiome imbalances: A systematic review of recent evidence and possible biological mechanisms. Science of The Total Environment, 151654.
  59. Mumaw, C. L., Levesque, S., McGraw, C., Robertson, S., Lucas, S., Stafflinger, J. E., Campen, M. J., Hall, P., Norenberg, J. P., Anderson, T., Lund, A. K., McDonald, J. D., Ottens, A. K., & Block, M. L. (2016). Microglial priming through the lung—brain axis: the role of air pollution-induced circulating factors. The FASEB Journal, 30(5), 1880–1891.
  60. Mussap, M., Noto, A., & Fanos, V. (2016). Metabolomics of autism spectrum disorders: early insights regarding mammalian-microbial cometabolites. Expert Review of Molecular Diagnostics, 16(8), 869–881.
  61. Narengaowa, Kong, W., Lan, F., Awan, U. F., Qing, H., & Ni, J. (2021). The Oral-Gut-Brain AXIS: The Influence of Microbes in Alzheimer’s Disease. Frontiers in Cellular Neuroscience, 15.
  62. Nishida, A. H., & Ochman, H. (2018). Rates of gut microbiome divergence in mammals. Molecular Ecology, 27(8), 1884–1897.
  63. Nyangahu, D. D., & Jaspan, H. B. (2019). Influence of maternal microbiota during pregnancy on infant immunity. Clinical & Experimental Immunology, 198(1), 47–56.
  64. O’Mahony, S. M., Clarke, G., Dinan, T. G., & Cryan, J. F. (2017). Early-life adversity and brain development: Is the microbiome a missing piece of the puzzle? Neuroscience, 342, 37–54.
  65. O’Neill, C. A., Monteleone, G., McLaughlin, J. T., & Paus, R. (2016). The gut-skin axis in health and disease: A paradigm with therapeutic implications. BioEssays, 38(11), 1167–1176.
  66. Ojo-Okunola, A., Claassen-Weitz, S., Mwaikono, K. S., Gardner-Lubbe, S., Stein, D. J., Zar, H. J., Nicol, M. P., & du Toit, E. (2019) Influence of Socio-Economic and Psychosocial Profiles on the Human Breast Milk Bacteriome of South African Women. Nutrients, 11(6):1390.
  67. Ojo-Okunola, A., Nicol, M., & Du Toit, E. (2018). Human Breast Milk Bacteriome in Health and Disease. Nutrients, 10(11):1643.
  68. Olivares, M., Díaz-Ropero, M. P., Martín, R., Rodríguez, J. M., & Xaus, J. (2006). Antimicrobial potential of four Lactobacillus strains isolated from breast milk. Journal of applied microbiology101(1), 72–79.
  69. Olsen, I. (2008). Update on bacteraemia related to dental procedures. Transfusion and Apheresis Science, 39(2), 173–178.
  70. Olsen, I., & Hicks, S. D. (2020). Oral microbiota and autism spectrum disorder (ASD). Journal of Oral Microbiology, 12(1), 1702806.
  71. Olsen, I., & Singhrao, S. K. (2015). Can oral infection be a risk factor for Alzheimer’s disease? Journal of Oral Microbiology, 7(1), 29143.
  72. Park S-Y, Hwang B-O, Lim M, Ok S-H, Lee S-K, Chun K-S, Park K-K, Hu Y, Chung W-Y, Song N-Y. (2021). Oral–Gut Microbiome Axis in Gastrointestinal Disease and Cancer. Cancers, 13(9):2124.
  73. Pedras, S., Carvalho, R., & Pereira, M. G. (2016). Predictors of quality of life in patients with diabetic foot ulcer: The role of anxiety, depression, and functionality. Journal of Health Psychology, 23(11), 1488–1498.
  74. Penders, J., Thijs, C., van den Brandt, P. A., Kummeling, I., Snijders, B., Stelma, F., Adams, H., van Ree, R., & Stobberingh, E. E. (2007). Gut microbiota composition and development of atopic manifestations in infancy: the KOALA Birth Cohort Study. Gut, 56(5), 661.
  75. Pirbaglou, M., Katz, J., de Souza, R. J., Stearns, J. C., Motamed, M., & Ritvo, P. (2016). Probiotic supplementation can positively affect anxiety and depressive symptoms: a systematic review of randomized controlled trials. Nutrition Research, 36(9), 889–898.
  76. Potgieter, M., Bester, J., Kell, D. B., & Pretorius, E. (2015). The dormant blood microbiome in chronic, inflammatory diseases. FEMS Microbiology Reviews, 39(4), 567–591.
  77. Power, M. C., Weisskopf, M. G., Alexeeff, S. E., Coull, B. A., Spiro, A., & Swartz, J. (2011). Traffic-Related Air Pollution and Cognitive Function in a Cohort of Older Men. Environmental Health Perspectives, 119(5), 682–687.
  78. Ranjan, R., Abhinay, A., & Mishra, M. (2018). Can oral microbial infections be a risk factor for neurodegeneration? A review of the literature. Neurol India, 66:344-51
  79. Renner R, Erfurt-Berge C. (2017). Depression and quality of life in patients with chronic wounds: ways to measure their influence and their effect on daily life. Chronic Wound Care Management and Research, 4:143-151
  80. Roberts, A. L., Kristen, L., Hart, J. E., Francine, L., Just, A. C., Bobb, J. F., Koenen, K. C., Alberto, A., & Weisskopf, M. G. (2013). Perinatal Air Pollutant Exposures and Autism Spectrum Disorder in the Children of Nurses’ Health Study II Participants. Environmental Health Perspectives, 121(8), 978–984.
  81. Rook, G. A. W., & Lowry, C. A. (2008). The hygiene hypothesis and psychiatric disorders. Trends in Immunology, 29(4), 150–158.
  82. Roy, S., Elgharably, H., Sinha, M., Ganesh, K., Chaney, S., Mann, E., Miller, C., Khanna, S., Bergdall, V. K., Powell, H. M., Cook, C. H., Gordillo, G. M., Wozniak, D. J., & Sen, C. K. (2014). Mixed-species biofilm compromises wound healing by disrupting epidermal barrier function. The Journal of Pathology, 233(4), 331–343.
  83. Salem, I., Ramser, A., Isham, N., & Ghannoum, M. A. (2018). The Gut Microbiome as a Major Regulator of the Gut-Skin Axis. Frontiers in Microbiology, 9.
  84. Salliss, M. E., Farland, L. v, Mahnert, N. D., & Herbst-Kralovetz, M. M. (2022). The role of gut and genital microbiota and the estrobolome in endometriosis, infertility and chronic pelvic pain. Human Reproduction Update, 28(1), 92–131.
  85. Sampson, T. R., & Mazmanian, S. K. (2015). Control of Brain Development, Function, and Behavior by the Microbiome. Cell Host & Microbe, 17(5), 565–576.
  86. Sencio, V., Barthelemy, A., Tavares, L. P., Machado, M. G., Soulard, D., Cuinat, C., Queiroz-Junior, C. M., Noordine, M.-L., Salomé-Desnoulez, S., Deryuter, L., Foligné, B., Wahl, C., Frisch, B., Vieira, A. T., Paget, C., Milligan, G., Ulven, T., Wolowczuk, I., Faveeuw, C., … Trottein, F. (2020). Gut Dysbiosis during Influenza Contributes to Pulmonary Pneumococcal Superinfection through Altered Short-Chain Fatty Acid Production. Cell Reports, 30(9), 2934-2947.e6.
  87. Sharon, G., Sampson, T. R., Geschwind, D. H., & Mazmanian, S. K. (2016). The Central Nervous System and the Gut Microbiome. Cell, 167(4), 915–932.
  88. Sinha, S., Lin, G., & Ferenczi, K. (2021). The skin microbiome and the gut-skin axis. Clinics in Dermatology, 39(5), 829–839.
  89. Slyepchenko, A., Maes, M., Jacka, F. N., Köhler, C. A., Barichello, T., McIntyre, R. S., Berk, M., Grande, I., Foster, J. A., Vieta, E., & Carvalho, A. F. (2017). Gut Microbiota, Bacterial Translocation, and Interactions with Diet: Pathophysiological Links between Major Depressive Disorder and Non-Communicable Medical Comorbidities. Psychotherapy and Psychosomatics, 86(1), 31–46.
  90. Slykerman, R. F., Thompson, J., Waldie, K. E., Murphy, R., Wall, C., & Mitchell, E. A. (2017). Antibiotics in the first year of life and subsequent neurocognitive outcomes. Acta Paediatrica, 106(1), 87–94.
  91. Smythies, L. E., & Smythies, J. R. (2014). Microbiota, the immune system, black moods and the brain—melancholia updated. Frontiers in Human Neuroscience, 8.
  92. Strachan, D. P. (1989). Hay fever, hygiene, and household size. BMJ (Clinical Research Ed.), 299(6710), 1259–1260.
  93. Stumpf, R. M., Wilson, B. A., Rivera, A., Yildirim, S., Yeoman, C. J., Polk, J. D., White, B. A., & Leigh, S. R. (2013). The primate vaginal microbiome: Comparative context and implications for human health and disease. American Journal of Physical Anthropology, 152(S57), 119–134.
  94. Taghinezhad-S, S., Keyvani, H., Bermúdez-Humarán, L. G., Donders, G. G. G., Fu, X., & Mohseni, A. H. (2021). Twenty years of research on HPV vaccines based on genetically modified lactic acid bacteria: an overview on the gut-vagina axis. Cellular and Molecular Life Sciences, 78(4), 1191–1206.
  95. Vaughan, A., Frazer, Z. A., Hansbro, P. M., & Yang, I. A. (2019). COPD and the gut-lung axis: the therapeutic potential of fibre. Journal of Thoracic Disease, 11(Suppl 17), S2173–S2180.
  96. Volk, H. E., Lurmann, F., Penfold, B., Hertz-Picciotto, I., & McConnell, R. (2013). Traffic-Related Air Pollution, Particulate Matter, and Autism. JAMA Psychiatry, 70(1), 71–77.
  97. Vuong, H. E., Yano, J. M., Fung, T. C., & Hsiao, E. Y. (2017). The Microbiome and Host Behavior. Annual Review of Neuroscience, 40(1), 21–49.
  98. Walker, R. W., Clemente, J. C., Peter, I., & Loos, R. J. F. (2017). The prenatal gut microbiome: are we colonized with bacteria in utero? Pediatric Obesity, 12(S1), 3–17.
  99. Walker, W. A., & Iyengar, R. S. (2015). Breast milk, microbiota, and intestinal immune homeostasis. Pediatric research77(1-2), 220–228.
  100. Wang, H., Liang, S., Wang, M., Gao, J., Sun, C., Wang, J., Xia, W., Wu, S., Sumner, S. J., Zhang, F., Sun, C., & Wu, L. (2016). Potential serum biomarkers from a metabolomics study of autism. Journal of Psychiatry & Neuroscience : JPN, 41(1), 27–37.
  101. Wang, T., Sha, L., Li, Y., Zhu, L., Wang, Z., Li, K., Lu, H., Bao, T., Guo, L., Zhang, X., & Wang, H. (2020). Dietary α-Linolenic Acid-Rich Flaxseed Oil Exerts Beneficial Effects on Polycystic Ovary Syndrome Through Sex Steroid Hormones—Microbiota—Inflammation Axis in Rats. Frontiers in Endocrinology, 11.
  102. Wang, W., Lv, S., Zhou, Y., Fu, J., Li, C., & Liu, P. (2011). Tumor necrosis factor-α affects blood–brain barrier permeability in acetaminophen-induced acute liver failure. European Journal of Gastroenterology & Hepatology, 23(7).
  103. Watson, R. L., de Koff, E. M., & Bogaert, D. (2019). Characterising the respiratory microbiome. European Respiratory Journal, 53(2), 1801711.
  104. Wellenius, G. A., Boyle, L. D., Coull, B. A., Milberg, W. P., Gryparis, A., Schwartz, J., Mittleman, M. A., & Lipsitz, L. A. (2012). Residential Proximity to Nearest Major Roadway and Cognitive Function in Community-Dwelling Seniors: Results from the MOBILIZE Boston Study. Journal of the American Geriatrics Society, 60(11), 2075–2080.
  105. Whiteside, S. A., McGinniss, J. E., & Collman, R. G. (2021). The lung microbiome: progress and promise. The Journal of Clinical Investigation, 131(15).
  106. Yang, Y., Tian, J., & Yang, B. (2018). Targeting gut microbiome: A novel and potential therapy for autism. Life Sciences, 194, 111–119.
  107. Zhan, X., Stamova, B., Jin, L.-W., DeCarli, C., Phinney, B., & Sharp, F. R. (2016). Gram-negative bacterial molecules associate with Alzheimer disease pathology. Neurology, 87(22), 2324.
  108. Zhang, J., Sadowska, G. B., Chen, X., Park, S. Y., Kim, J.-E., Bodge, C. A., Cummings, E., Lim, Y.-P., Makeyev, O., Besio, W. G., Gaitanis, J., Banks, W. A., & Stonestreet, B. S. (2015). Anti-IL-6 neutralizing antibody modulates blood-brain barrier function in the ovine fetus. The FASEB Journal, 29(5), 1739–1753.

Environmental Nutrient Cycling and Human Health

  1. Acinas, S. G., Sánchez, P., Salazar, G., Cornejo-Castillo, F. M., Sebastián, M., Logares, R., Sunagawa, S., Hingamp, P., Ogata, H., Lima-Mendez, G., Roux, S., González, J. M., Arrieta, J. M., Alam, I. S., Kamau, A., Bowler, C., Raes, J., Pesant, S., Bork, P., … Gasol, J. M. (2019). Metabolic Architecture of the Deep Ocean Microbiome.
  2. Albright, M. B. N., Johansen, R., Thompson, J., Lopez, D., Gallegos-Graves, L. v, Kroeger, M. E., Runde, A., Mueller, R. C., Washburne, A., Munsky, B., Yoshida, T., & Dunbar, J. (2020). Soil Bacterial and Fungal Richness Forecast Patterns of Early Pine Litter Decomposition. Frontiers in Microbiology, 11.
  3. Amado, A. M., & Roland, F. (2017). Editorial: Microbial Role in the Carbon Cycle in Tropical Inland Aquatic Ecosystems. Frontiers in Microbiology, 8.
  4. Ávila, M. P., Oliveira-Junior, E. S., Reis, M. P., Hester, E. R., Diamantino, C., Veraart, A. J., Lamers, L. P. M., Kosten, S., & Nascimento, A. M. A. (2019). The Water Hyacinth Microbiome: Link Between Carbon Turnover and Nutrient Cycling. Microbial Ecology, 78(3), 575–588.
  5. Feng, J., Wang, C., Lei, J., Yang, Y., Yan, Q., Zhou, X., Tao, X., Ning, D., Yuan, M. M., Qin, Y., Shi, Z. J., Guo, X., He, Z., van Nostrand, J. D., Wu, L., Bracho-Garillo, R. G., Penton, C. R., Cole, J. R., Konstantinidis, K. T., … Zhou, J. (2020). Warming-induced permafrost thaw exacerbates tundra soil carbon decomposition mediated by microbial community. Microbiome, 8(1), 3.
  6. Hamilton, T. L., Peters, J. W., Skidmore, M. L., & Boyd, E. S. (2013). Molecular evidence for an active endogenous microbiome beneath glacial ice. The ISME Journal, 7(7), 1402–1412.
  7. Hough, M., McClure, A., Bolduc, B., Dorrepaal, E., Saleska, S., Klepac-Ceraj, V., & Rich, V. (2020). Biotic and Environmental Drivers of Plant Microbiomes Across a Permafrost Thaw Gradient. Frontiers in Microbiology, 11.
  8. März, C., Butler, P. G., Carter, G. D. O., & Verhagen, I. T. E. (2021). Editorial: The Marine Carbon Cycle: From Ancient Storage to Future Challenges. Frontiers in Earth Science, 9.
  9. Moran, M. A. (2015). The global ocean microbiome. Science, 350(6266), aac8455.
  10. Naylor, D., Sadler, N., Bhattacharjee, A., Graham, E. B., Anderton, C. R., McClure, R., Lipton, M., Hofmockel, K. S., & Jansson, J. K. (2020). Soil Microbiomes Under Climate Change and Implications for Carbon Cycling. Annual Review of Environment and Resources, 45(1), 29–59.
  11. Ochoa-Hueso, R. (2017). Global Change and the Soil Microbiome: A Human-Health Perspective. Frontiers in Ecology and Evolution, 5.
  12. Paoli, L., Ruscheweyh, H.-J., Forneris, C. C., Kautsar, S., Clayssen, Q., Salazar, G., Milanese, A., Gehrig, D., Larralde, M., Carroll, L. M., Sánchez, P., Zayed, A. A., Cronin, D. R., Acinas, S. G., Bork, P., Bowler, C., Delmont, T. O., Sullivan, M. B., Wincker, P., … Sunagawa, S. (2021). Uncharted biosynthetic potential of the ocean microbiome. BioRxiv, 2021.03.24.436479.
  13. Ray, A. E., Zhang, E., Terauds, A., Ji, M., Kong, W., & Ferrari, B. C. (2020). Soil Microbiomes With the Genetic Capacity for Atmospheric Chemosynthesis Are Widespread Across the Poles and Are Associated With Moisture, Carbon, and Nitrogen Limitation. Frontiers in Microbiology, 11.
  14. Robinson, J.; Watkins, H.; Man, I.; Liddicoat, C.; Cameron, R.; Parker, B.; Cruz, M.; Meagher, L. Microbiome-Inspired Green Infrastructure (MIGI): A Bioscience Roadmap for Urban Ecosystem Health. Preprints 2021, 2021040560 (doi: 10.20944/preprints202104.0560.v1).
  15. Trevathan-Tackett, S. M., Kepfer-Rojas, S., Engelen, A. H., York, P. H., Ola, A., Li, J., Kelleway, J. J., Jinks, K. I., Jackson, E. L., Adame, M. F., Pendall, E., Lovelock, C. E., Connolly, R. M., Watson, A., Visby, I., Trethowan, A., Taylor, B., Roberts, T. N. B., Petch, J., … Macreadie, P. I. (2021). Ecosystem type drives tea litter decomposition and associated prokaryotic microbiome communities in freshwater and coastal wetlands at a continental scale. Science of The Total Environment, 782, 146819.
  16. Tripathi, B. M., Kim1, H. M., Jung, J. Y., Nam, S., Ju, H. T., Kim, M., & Lee, Y. K. (2019). Distinct Taxonomic and Functional Profiles of the Microbiome Associated With Different Soil Horizons of a Moist Tussock Tundra in Alaska. Frontiers in Microbiology, 10.
  17. Vigneron, A., Lovejoy, C., Cruaud, P., Kalenitchenko, D., Culley, A., & Vincent, W. F. (2019). Contrasting Winter Versus Summer Microbial Communities and Metabolic Functions in a Permafrost Thaw Lake. Frontiers in Microbiology, 10.

The Ocean Microbiome and Marine Life

  1. Apprill, A. (2017). Marine Animal Microbiomes: Toward Understanding Host–Microbiome Interactions in a Changing Ocean. Frontiers in Marine Science, 4.
  2. Doney, S. C., Ruckelshaus, M., Emmett Duffy, J., Barry, J. P., Chan, F., English, C. A., Galindo, H. M., Grebmeier, J. M., Hollowed, A. B., Knowlton, N., Polovina, J., Rabalais, N. N., Sydeman, W. J., & Talley, L. D. (2011). Climate Change Impacts on Marine Ecosystems. Annual Review of Marine Science, 4(1), 11–37.
  3. Moran, M. A. (2015). The global ocean microbiome. Science, 350(6266), aac8455.
  4. Stévenne, C., Micha, M., Plumier, J.-C., & Roberty, S. (2021). Corals and Sponges Under the Light of the Holobiont Concept: How Microbiomes Underpin Our Understanding of Marine Ecosystems. Frontiers in Marine Science, 8.
  5. Sunagawa, S., Pedro, C. L., Samuel, C., Roat, K. J., Karine, L., Guillem, S., Bardya, D., Georg, Z., R, M. D., Adriana, A., M, C.-C. F., I, C. P., Corinne, C., Francesco, d’Ovidio, Stefan, E., Isabel, F., M, G. J., Lionel, G., Falk, H., … Didier, V. (2015). Structure and function of the global ocean microbiome. Science, 348(6237), 1261359.

Soil Microbiomes

  1. Gopal, M., & Gupta, A. (2016). Microbiome Selection Could Spur Next-Generation Plant Breeding Strategies. Frontiers in microbiology7, 1971.
  2. Omotayo, O. P., & Babalola, O. O. (2021). Resident rhizosphere microbiome’s ecological dynamics and conservation: Towards achieving the envisioned Sustainable Development Goals, a review. International Soil and Water Conservation Research, 9(1), 127–142.
  3. Ray, P., Lakshmanan, V., Labbé, J. L., & Craven, K. D. (2020). Microbe to Microbiome: A Paradigm Shift in the Application of Microorganisms for Sustainable Agriculture. Frontiers in Microbiology, 11.
  4. Tosi, M., Mitter, E. K., Gaiero, J., & Dunfield, K. (2020). It takes three to tango: the importance of microbes, host plant, and soil management to elucidate manipulation strategies for the plant microbiome. Canadian Journal of Microbiology, 66(7), 413–433.

Plant Microbiomes

  1. Dastogeer, K. M. G., Tumpa, F. H., Sultana, A., Akter, M. A., & Chakraborty, A. (2020). Plant microbiome–an account of the factors that shape community composition and diversity. Current Plant Biology, 23, 100161.

Pollution and Bioremediation

  1. Jaiswal, S., & Shukla, P. (2020). Alternative Strategies for Microbial Remediation of Pollutants via Synthetic Biology. Frontiers in Microbiology, 11.

Forensic Microbiomes

  1. Robinson, J. M., Pasternak, Z., Mason, C. E., & Elhaik, E. (2021). Forensic Applications of Microbiomics: A Review. Frontiers in Microbiology, 11.


Icon for the Creative Commons Attribution 4.0 International License

Microbiomes: Health and the Environment Copyright © 2022 by Dylan Parks is licensed under a Creative Commons Attribution 4.0 International License, except where otherwise noted.

Share This Book