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An Introduction to Microbiomes

• Video 1 – What is the human microbiome? by The Conversation. Licensed under Creative Commons: By Attribution 3.0 License https://creativecommons.org/licenses/by/3.0/
• Video 2 – Human Science (Part I) – The Gut Brain Axis, Microbiome & the power of Probiotics by Infognostica. Licensed under Creative Commons: By Attribution 3.0 License https://creativecommons.org/licenses/by/3.0/
• Figure 1 – Microbiome Schematic by Berg et al., 2020 adapted by Dylan Parks. Licensed under Creative Commons: By Attribution 4.0 License http://creativecommons.org/licenses/by/4.0/
• Figure 2 – History of Microbiome Research by Berg et al., 2020. Licensed under Creative Commons: By Attribution 4.0 License http://creativecommons.org/licenses/by/4.0/

Analyzing Microbiomes

• Figure 1 – Targeted amplicon and metagenomic sequencing approaches to microbiome analysis by Bharti and Grimm, 2021. Licensed under Creative Commons: By Attribution 4.0 License http://creativecommons.org/licenses/by/4.0/
• Figure 2 – In Vitro Model Schematic by Ventura et al., 2020. Licensed under Creative Commons: By Attribution 4.0 License http://creativecommons.org/licenses/by/4.0/
• Figure 3 – Example microbiome samples and challenge of analysis by Jiang et al., 2019. Licensed under Creative Commons: By Attribution 4.0 License http://creativecommons.org/licenses/by/4.0/
• Video 1 – Life in the Lab: Working with human gut microbiota by yourgenome. Licensed under Creative Commons: By Attribution 3.0 License https://creativecommons.org/licenses/by/3.0/
• Video 2 – New technique explores gut microbiome one microbe at a time by Research Square. Licensed under Creative Commons: By Attribution 3.0 License https://creativecommons.org/licenses/by/3.0/

Human Health and Disease

• Figure 1 – Possible definitions of a healthy microbiome: composition, function, dynamics, and ecology by Lloyd-Price et al., 2016 adapted by Dylan Parks. Licensed under Creative Commons Attribution 4.0 International License http://creativecommons.org/licenses/by/4.0/
• Video 1 – You have the microbiome you deserve by Research Square. Licensed under Creative Commons: By Attribution 3.0 License https://creativecommons.org/licenses/by/3.0/

The Gut Microbiome

• Video 1 – Gut microbiome and individual genetics by Latest Thinking. Licensed under Creative Commons: By Attribution 3.0 License https://creativecommons.org/licenses/by/3.0/
• Video 2 – Diet and gut microbiome interactions in irritable bowel syndrome by Research Square. Licensed under Creative Commons: By Attribution 3.0 License https://creativecommons.org/licenses/by/3.0/
• Video 3 – Microbiome and Obesity – Martin Blaser by National Human Genome Research Institute. Licensed under Creative Commons: By Attribution 3.0 License https://creativecommons.org/licenses/by/3.0/
• Video 4 – Gut microbiome composition after multi-donor fecal microbiota transplantation for obesity by Research Square. Licensed under Creative Commons: By Attribution 3.0 License https://creativecommons.org/licenses/by/3.0/
• Video 5 – Rob Knight: Fecal Transplants? The Disgusting is Par for the Course by World Economic Forum. Licensed under Creative Commons: By Attribution 3.0 License https://creativecommons.org/licenses/by/3.0/

The Oral Microbiome

• Video 1 – GM2: Periodontal Microbiome – Murray Brilliant by National Human Genome Research Institute. Licensed under Creative Commons: By Attribution 3.0 License https://creativecommons.org/licenses/by/3.0/
• Figure 1 – Oral and systemic diseases associated with the oral microbiome by Willis and Gabaldon, 2020, caption adapted by Dylan Parks. Licensed under Creative Commons: By Attribution 4.0 License http://creativecommons.org/licenses/by/4.0/
• Images of body sites and organs in Figure 1 by Servier Medical Art. Licensed under Creative Commons: By Attribution 3.0 License https://creativecommons.org/licenses/by/3.0/
• Figure 2 – Examples of metagenomic studies of associations between the oral microbiome and oral diseases by Willis and Gabaldon, 2020, caption adapted by Dylan Parks. Licensed under Creative Commons: By Attribution 4.0 License http://creativecommons.org/licenses/by/4.0/

The Skin Microbiome

• Video 1 – A mixed community of skin microbiome representatives influences cutaneous processes by Research Square. Licensed under Creative Commons: By Attribution 3.0 License https://creativecommons.org/licenses/by/3.0/
• Video 2 – Eczema, Immunity, and the Skin Microbiome – Heidi Hong by National Human Genome Research Institute. Licensed under Creative Commons: By Attribution 3.0 License https://creativecommons.org/licenses/by/3.0/
• Video 3 – Expansion of known skin microbes could aid skin health research by Research Square. Licensed under Creative Commons: By Attribution 3.0 License https://creativecommons.org/licenses/by/3.0/
• Hot Spot Quiz Image – Skin Microbiome by Jane Ades, NHGRI under Public Domain

The Respiratory Microbiome

• Figure 1 – Ecological Determinants of the Respiratory Microbiome by Dickson and Huffnagle, 2015. Licensed under Creative Commons: Attribution 4.0 International (CC BY 4.0) License https://creativecommons.org/licenses/by/4.0/
• Video 1 – The Lung Microbiome: Challenging Old Paradigms about Microbes by National Human Genome Research Institute. Licensed under Creative Commons: By Attribution 3.0 License https://creativecommons.org/licenses/by/3.0/

The Vaginal Microbiome

• Video 1 – VALENCIA: A nearest centroid classification for vaginal microbial communities by Research Square. Licensed under Creative Commons: By Attribution 3.0 License https://creativecommons.org/licenses/by/3.0/
• Figure 1 – Examples of Gram-stained slides from women with (right, Nugent score = 9) and without (left, Nugent score = 1) BV by Lewis and Gilbert, 2020. Licensed under Creative Commons Attribution 4.0 License https://creativecommons.org/licenses/by/4.0/
• Figure 2 – Schematic illustrating vaginal bacteria with potential to impact the urinary tract by Lewis and Gilbert, 2020. Licensed under Creative Commons Attribution 4.0 License https://creativecommons.org/licenses/by/4.0/
• Video 2 – Beyond bacterial vaginosis: vaginal lactobacilli and HIV risk by Research Square. Licensed under Creative Commons: By Attribution 3.0 License https://creativecommons.org/licenses/by/3.0/
• Video 3 – A temporal model of cervicovaginal microbiota identifies targets to promote reproductive health by Research Square. Licensed under Creative Commons: By Attribution 3.0 License https://creativecommons.org/licenses/by/3.0/

Mental Health and Multi-Microbiome Interactions

• Figure 1 – Inflammatory and microbial influences between the gut and skin for a healthy state by De Pessemier et al., 2021. Licensed under the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
• Video 1 – Remodeling of the maternal gut microbiome during pregnancy is shaped by parity by Research Square. Licensed under Creative Commons: By Attribution 3.0 License https://creativecommons.org/licenses/by/3.0/
• Figure 2 – Gut-brain interactions with mental health by Bear et al., 2021. Licensed under the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
• Figure 3 – Development of the gut-brain over time by Liang et al., 2018. Licensed under the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
• Video 2 – Functional GI Disorders: The role of the gut-brain interaction, microbiome and nutrition by UMMCVideos. Licensed under Creative Commons Attribution license (reuse allowed).
• Figure 4 – Direct and indirect mechanisms of infecting the brain by Olsen and Hicks, 2019 licensed under under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0
• Figure 5 – Chronic wounds and skin-brain axis by Hadian et al., 2020 under Public Domain

Environmental Nutrient Cycling and Human Health

• Video 1 – Elevated atmospheric CO₂ increases phosphorous mineralization and alters the rhizosphere microbiome by Research Square. Licensed under Creative Commons: By Attribution 3.0 License https://creativecommons.org/licenses/by/3.0/
• Hotspot Image – Urban multispecies health by Robinson et al., 2021 licensed under the Creative Commons Attribution License

The Ocean Microbiome and Marine Life

• Figure 1 – Illustration and common names of representative ocean animal life within their approximate depth-defined ecological habitats by Apprill, 2017. Licensed under the terms of the Creative Commons Attribution License (CC BY).
• Figure 2 – Conceptual diagram of a host-microbiome relationship by Apprill, 2017. Licensed under the terms of the Creative Commons Attribution License (CC BY).
• Figure 3 – Photographs of marine animals and their associated microbiomes from select study systems by Apprill, 2017. Licensed under the terms of the Creative Commons Attribution License (CC BY).

Soil Microbiomes

• Video 1 – Understanding Our Soil: The Nitrogen Cycle, Fixers, and Fertilizer by Jimi Sol. Licensed under Creative Commons: By Attribution 3.0 License https://creativecommons.org/licenses/by/3.0/
• Hot Spot Quiz Figure – Plant and Soil Microbiomes by Gopal & Gupta, 2016 licensed under Creative Commons Attribution-Share Alike 4.0

Plant Microbiomes

• Video 1 – Disease-induced changes in plant microbiome assembly and functional adaptation by Research Square licensed under Creative Commons Attribution license (reuse allowed)
• Video 2 – [microbiome] The Plant Microbiome: The plant microbiome in facts (3.1) by iMooX at licenced under Creative Commons Attribution-ShareAlike 4.0 International. (https://creativecommons.org/licenses/…)
• Video 3 – [microbiome] The Plant Microbiome: The apple microbiome (3.2) by iMooX at licenced under Creative Commons Attribution-ShareAlike 4.0 International. (https://creativecommons.org/licenses/…)
• Video 4 – [microbiome] The Plant Microbiome: Managing the plant microbiome (3.3) by iMooX at licenced under Creative Commons Attribution-ShareAlike 4.0 International. (https://creativecommons.org/licenses/…)

Pollution and Bioremediation

• Video 1 – [microbiome] Microbiome and Planetary Health (6.1) by iMooX at licenced under Creative Commons Attribution-ShareAlike 4.0 International. (https://creativecommons.org/licenses/…)
• Video 2 – [microbiome] Microbiome and SDGs (6.2) by iMooX at licenced under Creative Commons Attribution-ShareAlike 4.0 International. (https://creativecommons.org/licenses/…)

Forensic Microbiomes

• Figure 1 – A summary of possible sources of forensically relevant microbiota identified by the literature review by Robinson et al., 2021 licensed under the terms of the Creative Commons Attribution License (CC BY).

Case study #1 – The Farmer’s Flu

Part I – Background and Problem

• Video 1 – Raising temperatures: the immunology of influenza by British Society for Immunology under a Creative Commons Attribution License (reuse allowed)
• Article 1: Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia by Hanada et al., 2018 under CC BY 4.0 license
• Article 2 – Allergic inflammation alters the lung microbiome and hinders synergistic co-infection with H1N1 influenza virus and Streptococcus pneumoniae in C57BL/6 mice by LeMessurier et al., 2019 under CC BY 4.0 license
• Figure 1 – Antigenic Shift of the Flu Virus by NIAID licensed under CC BY 2.0 license

Part II – Approach, Implementation, Reasoning

• Video 1 – Influenza Virus – Viral entry and fusion inhibitor by iCAP Université Claude Bernard Lyon 1 under a Creative Commons Attribution License (reuse allowed)
• Article 1 – The respiratory microbiome and susceptibility to influenza virus infection by Lee et al., 2019 under CC BY 4.0 license
• Article 2 – Secondary Bacterial Infections in Patients With Viral Pneumonia by Manohar et al., 2020 under CC BY 4.0 license
• Article 3 – Patterns in the longitudinal oropharyngeal microbiome evolution related to ventilator-associated pneumonia by Sommerstein et al., 2019 under CC BY 4.0 license

Part III – Discussion

• Article 1 – The distribution of microbiomes and resistomes across farm environments in conventional and organic dairy herds in Pennsylvania by Pitta et al., 2020 under CC BY 4.0
• Article 2 – Antimicrobial use and production system shape the fecal, environmental, and slurry resistomes of pig farms by Mencía-Ares et al., 2020 under CC BY 4.0
• Article 3 – Influence of Pig Farming on the Human Nasal Microbiota: Key Role of Airborne Microbial Communities by Kraemer et al., 2018 under CC BY 4.0
• Video 1 – Fact Check: Agriculture and Antibiotic Resistance by Livestock & Poultry Environ. Learning Community under a Creative Commons Attribution License (reuse allowed)
• Article 4 – Incidence, outcome, and risk factors for recurrence of nosocomial Clostridioides difficile infection in adults: A prospective cohort study by Karaoui et al., 2020 under CC BY-NC-ND 4.0
• Video 2 – Antibiotics and the Digestive Microbiota | Jean Carlet by World Economic Forum under a Creative Commons Attribution License (reuse allowed)

Part IV – Resolution

• Article 1 – Basic Characterization of Natural Transformation in a Highly Transformable Haemophilus parasuis Strain SC1401 by Dai et al., 2019 under CC BY 4.0
• Video 1 – Microbiota and Vaccines – Eric Brown by National Human Genome Research Institute under a Creative Commons Attribution Liscence (reuse allowed)
• Article 2 – The Gut-Lung Axis in Health and Respiratory Diseases: A Place for Inter-Organ and Inter-Kingdom Crosstalks by Enaud et al., 2020 under CC BY 4.0
• Article 3 – Translating Lung Microbiome Profiles into the Next-Generation Diagnostic Gold Standard for Pneumonia: a Clinical Investigator’s Perspective by Kitsios, 2018 under CC BY 4.0

Case study #2 – The Land is Sick

Part I – Background and Problem

• Figure 1 – Coffee exports by country 2019-20 by Dylan Parks. Data source: International Coffee Organization
• Figure 2 – A world map of countries by coffee production, 2019 by Cbahrs licensed under CC BY-SA 4.0
• Article 1 – The Bacterial Microbiome of Meloidogyne-Based Disease Complex in Coffee and Tomato by Lamelas et al., 2020 licensed under the terms of the Creative Commons Attribution License (CC BY).
• Article 2 – A review of three major fungal diseases of Coffea Arabica L. in the rainforests of Ethiopia and progress in breeding for resistance in Kenya by Hindorf and Omondi, 2011 licensed under CC BY-NC-ND 3.0
• Article 3 – Structure and Dynamics of the Gut Bacterial Community Across the Developmental Stages of the Coffee Berry Borer, Hypothenemus hampei by Mejía-Alvarado et al., 2021 licensed under the terms of the Creative Commons Attribution License (CC BY).
• Video 1 – The biggest threats to the coffee industry by Startup to Storefront licensed under a Creative Commons Attribution License (reuse allowed)
• Video 2 – #1 Specialty coffee and the price crisis | Producer Crossover 2019 by Coffee Circle licensed under a Creative Commons Attribution License (reuse allowed)

Part II – Approach, Implementation, Reasoning

• Article 1 – Prokaryotic diversity in the rhizosphere of organic, intensive, and transitional coffee farms in Brazil by Caldwell et al., 2015 licensed under a Creative Commons Attribution-ShareAlike 4.0 International (CC BY-SA 4.0) license.
• Article 2 – A metagenomics approach in the evaluation of the soil microbiome in coffee plantations under organic and conventional production in tropical agroecosystems by Rodriguez et al., 2020 licensed under a Creative Commons Attribution-NonCommercial 4.0 International License.
• Video 1 – #2 Producer Crossover 2019 by Coffee Circle licensed under a Creative Commons Attribution License (reuse allowed)
• Video 2 – How countries farm and make coffee differently by Startup to Storefront licensed under a Creative Commons Attribution License (reuse allowed)

Part III – Discussion

• Figure 1 – Shade grown coffee in Guatamala by John Blake under Public Domain
• Figure 2. Sun-grown coffee plantation in Brazil by Knase caption adapted by Dylan Parks licensed under the Creative CommonsAttribution 3.0 Germany license.
• Video 1 – #3 The future of the price crisis by Coffee Circle licensed under a Creative Commons Attribution License (reuse allowed)
• Video 2 – How coffee destroys the environment by Startup to Storefront licensed under a Creative Commons Attribution License (reuse allowed)
• Article 1 – Root endophytes of coffee (Coffea Arabica): Variation across climatic gradients and relationships with functional traits by Fulthorpe et al., 2020 licensed under Creative Commons Attribution License (CC BY).
• Article 2 – Brazilian Coffee Production and the Future Microbiome and Mycotoxin Profile Considering the Climate Change Scenario by dos Santos et al., 2021 licensed under the terms and conditions of the Creative Commons Attribution (CC BY) license.
• Article 3 – Effects of environmental factors on microbiota of fruits and soil of Coffea arabica in Brazil by Veloso et al., 2020 licensed under the terms and conditions of the Creative Commons Attribution (CC BY) license.

Part IV – Resolution

• Article 1 – Coffee Microbiota and Its Potential Use in Sustainable Crop Management. A Review by Duong et al., 2020 licensed under the terms of the Creative Commons Attribution License (CC BY).
• Article 2 – Soil fungal communities differ between shaded and sun-intensive coffee plantations in El Salvador by Rao et al., 2020 licensed under the Creative Commons CC0 public domain dedication.
• Article 3 – https://www.frontiersin.org/articles/10.3389/fpubh.2018.00235/full by Trinh et al., 2018 licensed under the terms of the Creative Commons Attribution License (CC BY).
• Video 1 – Teaching coffee farmers about the birds and the bees by VOA Learning English licensed under a Creative Commons Attribution License (reuse allowed)