An Introduction to Microbiomes

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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. https://doi.org/10.1152/physrev.00018.2018
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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 proteomics, 16(6), 501–511. https://doi.org/10.1080/14789450.2018.1523724
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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 genetics, 10, 995. https://doi.org/10.3389/fgene.2019.00995
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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. https://doi.org/10.1002/bies.201600008
35. Petersen, C., & Round, J. L. (2014). Defining dysbiosis and its influence on host immunity and disease. Cellular microbiology, 16(7), 1024–1033. https://doi.org/10.1111/cmi.12308
36. Pratama, A. A., & van Elsas, J. D. (2018). The ‘Neglected’ Soil Virome – Potential Role and Impact. Trends in Microbiology, 26(8), 649–662. https://doi.org/https://doi.org/10.1016/j.tim.2017.12.004
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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. https://doi.org/10.1146/annurev-ecolsys-110617-062605
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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. https://doi.org/10.1126/sciadv.aaw0759

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. https://doi.org/https://doi.org/10.1016/j.cgh.2018.09.017
2. Bashiardes, S., Zilberman-Schapira, G., & Elinav, E. (2016). Use of Metatranscriptomics in Microbiome Research. Bioinformatics and Biology Insights, 10, BBI.S34610. https://doi.org/10.4137/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. https://doi.org/10.1038/s41579-021-00621-9
4. Bharti, R., & Grimm, D. G. (2021). Current challenges and best-practice protocols for microbiome analysis. Briefings in Bioinformatics, 22(1), 178–193. https://doi.org/10.1093/bib/bbz155
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. https://doi.org/10.1186/gb-2011-12-5-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. https://doi.org/10.1093/nar/gkaa939
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. https://doi.org/10.1038/s41596-019-0264-1
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. https://doi.org/10.1126/science.1177486
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. https://doi.org/10.1038/ismej.2010.177
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. https://doi.org/10.1093/nar/gkx295
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. https://doi.org/10.1126/science.1110591
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-. https://doi.org/10.1371/journal.ppat.1004436
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. https://doi.org/10.1073/pnas.1319284111
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. https://doi.org/10.1186/gb-2012-13-3-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. https://doi.org/10.1016/j.annepidem.2016.03.003
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. https://doi.org/10.1038/s41592-018-0141-9
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-. https://doi.org/10.1371/journal.pone.0017447
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. https://doi.org/10.1016/j.tim.2021.04.011
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. https://www.frontiersin.org/article/10.3389/fgene.2019.00995
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. https://doi.org/https://doi.org/10.1111/1469-0691.12023
21. Lee-Sarwar KA, Lasky-Su J, Kelly RS, Litonjua AA, Weiss ST. Metabolome–Microbiome Crosstalk and Human Disease. Metabolites. 2020; 10(5):181. https://doi.org/10.3390/metabo10050181
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. https://doi.org/10.1093/nar/gkm869
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. https://doi.org/10.1128/mSystems.00031-18
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. https://doi.org/10.1093/nar/gkz1035
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. https://doi.org/10.1016/B978-0-323-48552-4.00014-7
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. https://doi.org/10.1128/mSystems.00053-18
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-. https://doi.org/10.1371/journal.pone.0241503
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. https://doi.org/https://doi.org/10.1016/j.jare.2019.04.002
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. https://doi.org/10.1080/14789450.2019.1609944
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. https://doi.org/10.1086/600885
31. Shakya, M., Lo, C.-C., & Chain, P. S. G. (2019). Advances and Challenges in Metatranscriptomic Analysis. Frontiers in Genetics, 10. https://www.frontiersin.org/article/10.3389/fgene.2019.00904
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. https://doi.org/10.1038/nbt.3597
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. https://doi.org/10.1073/pnas.120368910

Human Health and Disease

1. Dąbrowska, K., & Witkiewicz, W. (2016). Correlations of Host Genetics and Gut Microbiome Composition. Frontiers in Microbiology, 7, 1357. https://www.frontiersin.org/article/10.3389/fmicb.2016.01357
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. https://www.frontiersin.org/article/10.3389/fcimb.2020.00073
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. https://doi.org/10.1097/PSY.0000000000000647
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. https://doi.org/10.1136/gutjnl-2012-303954
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. https://doi.org/https://doi.org/10.1016/j.it.2017.06.003
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. https://doi.org/10.1098/rstb.2019.0811
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. https://doi.org/10.1038/nature25973
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. https://doi.org/10.1186/s12864-015-2131-y
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. https://doi.org/10.1016/j.coi.2019.08.007
10. Tabrett, A., & Horton, M. W. (2020). The influence of host genetics on the microbiome. F1000Research, 9, F1000 Faculty Rev-84. https://doi.org/10.12688/f1000research.20835.1
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. https://doi.org/10.1016/j.jaad.2019.08.078

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). https://doi.org/10.3390/nu11020418
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. https://doi.org/10.1056/NEJMoa021933
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. https://doi.org/10.1177/0009922809360927
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. https://doi.org/10.1016/j.molmed.2016.04.003
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. https://doi.org/10.1186/s13073-016-0303-2
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-. https://doi.org/10.1371/journal.pone.0189768
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. https://doi.org/10.1111/apt.13144
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. https://doi.org/10.2337/db06-1491
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. https://doi.org/10.1016/j.chom.2019.10.009
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. https://doi.org/https://doi.org/10.1002/art.38967
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-. https://doi.org/10.1371/journal.pone.0090731
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. https://doi.org/10.1038/nature12820
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). https://journals.lww.com/co-clinicalnutrition/Fulltext/2011/07000/Intestinal_microbiota_in_inflammation_and_insulin.5.aspx
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. https://doi.org/10.1056/NEJMoa1910437
16. Everard, A., & Cani, P. D. (2013). Diabetes, obesity and gut microbiota. Best Practice & Research Clinical Gastroenterology, 27(1), 73–83. https://doi.org/10.1016/j.bpg.2013.03.007
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. https://www.frontiersin.org/article/10.3389/fmicb.2018.03249
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. https://doi.org/10.1053/j.gastro.2021.02.013
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. https://doi.org/10.1038/s41591-018-0210-8
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. https://doi.org/10.1136/bmj.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. https://doi.org/10.1038/ismej.2010.92
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. https://www.frontiersin.org/article/10.3389/fmicb.2019.01894
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. https://doi.org/10.1038/nmicrobiol.2017.4
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. https://doi.org/10.1038/ng.2478
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. https://doi.org/10.1111/j.1469-0691.2012.03853.x
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. https://doi.org/10.1128/mBio.01250-16
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. https://doi.org/10.1038/s41467-018-05184-7
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. https://doi.org/10.1016/j.clinthera.2015.04.004
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. https://doi.org/10.3390/genes6041347
30. Johnson, K. V.-A. (2020). Gut microbiome composition and diversity are related to human personality traits. Human Microbiome Journal, 15, 100069. https://doi.org/10.1016/j.humic.2019.100069
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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. https://doi.org/10.4014/jmb.1906.06064
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-. https://doi.org/10.1371/journal.pone.0009085
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-. https://doi.org/10.1371/journal.pone.0134849
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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). https://doi.org/10.3390/nu12051474
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. https://doi.org/10.1080/19490976.2020.1810531
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. https://doi.org/https://doi.org/10.1053/j.gastro.2011.11.037
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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. https://doi.org/10.1155/2018/3462092
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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. https://doi.org/10.1128/JCM.43.11.5721-5732.2005
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. https://doi.org/10.1093/ije/dyh375
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 dentistry, 21(2), 109–113.
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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. https://doi.org/10.1093/rheumatology/key215
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. https://doi.org/10.1111/j.2041-1014.2010.00595.x
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. https://doi.org/10.1128/AEM.02763-08
94. Wade, W. G. (2013). The oral microbiome in health and disease. Pharmacological Research, 69(1), 137–143. https://doi.org/10.1016/j.phrs.2012.11.006
95. Wang, L., Ganly, I. (2014). The oral microbiome and oral cancer. Clinics in Laboratory Medicine, 34, 711–719. https://doi.org/10.1016/j.cll.2014.08.004
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. https://doi.org/10.1097/MD.0000000000000292
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. https://doi.org/10.1177/00220345580370052601
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. https://www.frontiersin.org/article/10.3389/fmicb.2014.00568
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. https://doi.org/10.1016/j.celrep.2020.02.097
100. Willis, J. R., & Gabaldón, T. (2020). The Human Oral Microbiome in Health and Disease: From Sequences to Ecosystems. Microorganisms, 8(2). https://doi.org/10.3390/microorganisms8020308
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. https://doi.org/10.1177/0022034518790941
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. https://doi.org/10.1111/j.1601-0825.2011.01851.x
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. https://doi.org/https://doi.org/10.1111/jcpe.12247
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-. https://doi.org/10.1371/journal.pone.0223299

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. https://doi.org/10.1128/JCM.00799-08
2. Belkaid, Y., & Harrison, O. J. (2017). Homeostatic Immunity and the Microbiota. Immunity, 46(4), 562–576. https://doi.org/10.1016/j.immuni.2017.04.008
3. Bierber, T. (2008). Mechanisms of disease: atopic dermatitis. N Engl J Med, 358, 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. https://doi.org/10.5114/ada.2019.82821
5. Byrd, A. L., Belkaid, Y., & Segre, J. A. (2018). The human skin microbiome. Nature Reviews Microbiology, 16(3), 143–155. https://doi.org/10.1038/nrmicro.2017.157
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. https://doi.org/10.1038/jid.2011.168
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. https://doi.org/10.1111/exd.12030
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. https://doi.org/10.1038/jid.2009.243
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. https://doi.org/10.1073/pnas.1002601107
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. https://doi.org/10.1111/exd.13296
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. https://doi.org/10.1007/s00403-011-1189-x
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-. https://doi.org/10.1371/journal.ppat.1004436
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. https://doi.org/10.1038/nature12171
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. https://doi.org/10.1038/jid.2013.21
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. https://doi.org/10.1111/j.1468-3083.2011.04310.x
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. https://doi.org/10.1111/j.1365-2133.1993.tb00261.x
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-. https://doi.org/10.1371/journal.pone.0002719
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 https://doi.org/10.7717/peerj.3543
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. https://doi.org/10.1046/j.1468-3083.2001.00331.x
20. Grice, E. A., & Segre, J. A. (2011). The skin microbiome. Nature Reviews Microbiology, 9(4), 244–253. https://doi.org/10.1038/nrmicro2537
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. https://doi.org/10.1126/science.1171700
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. https://doi.org/10.1038/nature09074
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. https://doi.org/10.1016/j.chom.2019.03.006
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. https://doi.org/10.1016/j.jaci.2016.07.029
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-. https://doi.org/10.1371/journal.pone.0016594
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. https://doi.org/10.1016/j.molmed.2011.01.013
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. http://genome.cshlp.org/content/22/5/850.abstract
28. Kuhbacher, A., Burger-Kentischer, A., & Rupp, S. (2017). Interaction of Candida species with the skin. Microorganisms. 5(2), 32. https://doi.org/10.3390/microorganisms5020032
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. https://doi.org/10.1111/j.1365-2133.2007.08028.x
30. Lacey, N., Kavanagh, K., & Tseng, S. C. G. (2009). Under the lash: Demodex mites in human diseases. The Biochemist, 31(4), 20–24. https://doi.org/10.1042/BIO03104020
31. Lacey, N., Ní Raghallaigh, S., & Powell, F. C. (2011). Demodex mites – commensals, parasites or mutualistic organisms? Dermatology, 222(2), 128-30. doi:http://dx.doi.org/10.1159/000323009
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. https://search.informit.org/doi/10.3316/informit.656354654775105
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. https://doi.org/10.1038/nature14052
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. https://doi.org/10.1126/science.1225152
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. https://doi.org/10.1038/nature12655
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. https://doi.org/10.1016/j.jid.2016.05.127
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. https://doi.org/10.1128/IAI.00958-10
38. Norlind, R. (1955). Significance of infections in origin of psoriasis. Acta Rheumatol Scand, 1, 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. https://doi.org/10.1016/j.cell.2016.04.008
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. http://genome.cshlp.org/content/23/12/2103.abstract
41. Otto, M. (2009). Staphylococcus epidermidis — the “accidental” pathogen. Nature Reviews Microbiology, 7(8), 555–567. https://doi.org/10.1038/nrmicro2182
42. Otto, M. (2012). Molecular basis of Staphylococcus epidermidis infections. Seminars in Immunopathology, 34(2), 201–214. https://doi.org/10.1007/s00281-011-0296-2
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. https://doi.org/10.1038/ni0311-189
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-. https://doi.org/10.1371/journal.pone.0006462
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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. https://doi.org/10.1126/scitranslmed.3003783
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. https://doi.org/10.1164/rccm.201501-0128OC
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. https://doi.org/10.1164/rccm.201407-1240OC
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. https://doi.org/10.1016/j.ebiom.2016.05.031
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-. https://doi.org/10.1371/journal.pone.0032486
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. https://doi.org/10.1513/AnnalsATS.201211-107OC
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. https://doi.org/10.1093/cid/cir463
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. https://doi.org/10.1164/rccm.201204-0693OC
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. https://doi.org/10.1513/AnnalsATS.201402-052PL
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. https://doi.org/10.1038/ismej.2015.99
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. https://doi.org/10.1186/2045-7022-4-14
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-. https://doi.org/10.1371/journal.ppat.1004923
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The Vaginal Microbiome

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Mental Health and Multi-Microbiome Interactions

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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. https://doi.org/10.1016/j.celrep.2020.02.013
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. https://doi.org/10.1016/j.cell.2016.10.027
88. Sinha, S., Lin, G., & Ferenczi, K. (2021). The skin microbiome and the gut-skin axis. Clinics in Dermatology, 39(5), 829–839. https://doi.org/10.1016/j.clindermatol.2021.08.021
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. https://doi.org/10.1159/000448957
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. https://doi.org/10.1111/apa.13613
91. Smythies, L. E., & Smythies, J. R. (2014). Microbiota, the immune system, black moods and the brain—melancholia updated. Frontiers in Human Neuroscience, 8. https://www.frontiersin.org/article/10.3389/fnhum.2014.00720
92. Strachan, D. P. (1989). Hay fever, hygiene, and household size. BMJ (Clinical Research Ed.), 299(6710), 1259–1260. https://doi.org/10.1136/bmj.299.6710.1259
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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. https://doi.org/10.1007/s00018-020-03652-2
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. https://doi.org/10.21037/jtd.2019.10.40
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. https://doi.org/10.1001/jamapsychiatry.2013.266
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. https://doi.org/10.1146/annurev-neuro-072116-031347
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. https://doi.org/10.1111/ijpo.12217
99. Walker, W. A., & Iyengar, R. S. (2015). Breast milk, microbiota, and intestinal immune homeostasis. Pediatric research, 77(1-2), 220–228. https://doi.org/10.1038/pr.2014.160
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. https://doi.org/10.1503/jpn.140009
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. https://www.frontiersin.org/article/10.3389/fendo.2020.00284
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). https://journals.lww.com/eurojgh/Fulltext/2011/07000/Tumor_necrosis_factor___affects_blood_brain.2.aspx
103. Watson, R. L., de Koff, E. M., & Bogaert, D. (2019). Characterising the respiratory microbiome. European Respiratory Journal, 53(2), 1801711. https://doi.org/10.1183/13993003.01711-2018
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. https://doi.org/https://doi.org/10.1111/j.1532-5415.2012.04195.x
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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. http://hdl.handle.net/10754/656339
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. https://www.frontiersin.org/article/10.3389/fmicb.2020.542220
3. Amado, A. M., & Roland, F. (2017). Editorial: Microbial Role in the Carbon Cycle in Tropical Inland Aquatic Ecosystems. Frontiers in Microbiology, 8. https://www.frontiersin.org/article/10.3389/fmicb.2017.00020
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. https://doi.org/10.1007/s00248-019-01331-9
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. https://doi.org/10.1186/s40168-019-0778-3
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. https://doi.org/10.1038/ismej.2013.31
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. https://www.frontiersin.org/article/10.3389/fmicb.2020.00796
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. https://www.frontiersin.org/article/10.3389/feart.2021.748701
9. Moran, M. A. (2015). The global ocean microbiome. Science, 350(6266), aac8455. https://doi.org/10.1126/science.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. https://doi.org/10.1146/annurev-environ-012320-082720
11. Ochoa-Hueso, R. (2017). Global Change and the Soil Microbiome: A Human-Health Perspective. Frontiers in Ecology and Evolution, 5. https://www.frontiersin.org/article/10.3389/fevo.2017.00071
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. https://doi.org/10.1101/2021.03.24.436479
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. https://www.frontiersin.org/article/10.3389/fmicb.2020.01936
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. https://doi.org/10.1016/j.scitotenv.2021.146819
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. https://www.frontiersin.org/article/10.3389/fmicb.2019.01442
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. https://www.frontiersin.org/article/10.3389/fmicb.2019.01656

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. https://www.frontiersin.org/article/10.3389/fmars.2017.00222
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. https://doi.org/10.1146/annurev-marine-041911-111611
3. Moran, M. A. (2015). The global ocean microbiome. Science, 350(6266), aac8455. https://doi.org/10.1126/science.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. https://doi.org/10.3389/fmars.2021.698853
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. https://doi.org/10.1126/science.1261359

Soil Microbiomes

1. Gopal, M., & Gupta, A. (2016). Microbiome Selection Could Spur Next-Generation Plant Breeding Strategies. Frontiers in microbiology, 7, 1971. https://doi.org/10.3389/fmicb.2016.01971
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. https://doi.org/10.1016/j.iswcr.2020.08.002
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. https://www.frontiersin.org/article/10.3389/fmicb.2020.622926
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. https://doi.org/10.1139/cjm-2020-0085

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. https://doi.org/https://doi.org/10.1016/j.cpb.2020.100161

Pollution and Bioremediation

1. Jaiswal, S., & Shukla, P. (2020). Alternative Strategies for Microbial Remediation of Pollutants via Synthetic Biology. Frontiers in Microbiology, 11. https://www.frontiersin.org/article/10.3389/fmicb.2020.00808

Forensic Microbiomes

1. Robinson, J. M., Pasternak, Z., Mason, C. E., & Elhaik, E. (2021). Forensic Applications of Microbiomics: A Review. Frontiers in Microbiology, 11. https://www.frontiersin.org/article/10.3389/fmicb.2020.608101