Meeting report of the third annual Tri-Service Microbiome Consortium symposium

The Tri-Service Microbiome Consortium (TSMC) was founded to enhance collaboration, coordination, and communication of microbiome research among U.S. Department of Defense (DoD) organizations and to facilitate resource, material and information sharing among consortium members. The 2019 annual symposium was held 22–24 October 2019 at Wright-Patterson Air Force Base in Dayton, OH. Presentations and discussions centered on microbiome-related topics within five broad thematic areas: 1) human microbiomes; 2) transitioning products into Warfighter solutions; 3) environmental microbiomes; 4) engineering microbiomes; and 5) microbiome simulation and characterization. Collectively, the symposium provided an update on the scope of current DoD microbiome research efforts, highlighted innovative research being done in academia and industry that can be leveraged by the DoD, and fostered collaborative opportunities. This report summarizes the presentations and outcomes of the 3rd annual TSMC symposium.

[1]  John E. Anderson,et al.  Linking vegetation cover and seasonal thaw depths in interior Alaska permafrost terrains using remote sensing , 2019, Remote Sensing of Environment.

[2]  Jennifer Barrila,et al.  Microbiology of the Built Environment in Spacecraft Used for Human Flight , 2018 .

[3]  T. Fukami,et al.  Ectomycorrhizal fungal traits reflect environmental conditions along a coastal California edaphic gradient. , 2014, FEMS microbiology ecology.

[4]  Jennifer Lu,et al.  Improved metagenomic analysis with Kraken 2 , 2019, Genome Biology.

[5]  C. Jung,et al.  Effects of acute exposures of 2,4,6-trinitrotoluene and inorganic lead on the fecal microbiome of the green anole (Anolis carolinensis) , 2018, PloS one.

[6]  Andrew J. Hoisington,et al.  Military-Related Exposures, Social Determinants of Health, and Dysbiosis: The United States-Veteran Microbiome Project (US-VMP) , 2018, Front. Cell. Infect. Microbiol..

[7]  Dagmar H. Leary,et al.  Integrated metagenomic and metaproteomic analyses of marine biofilm communities , 2014, Biofouling.

[8]  P. Sims,et al.  Spatial metagenomic characterization of microbial biogeography in the gut , 2019, Nature Biotechnology.

[9]  M. Betenbaugh,et al.  Environmental stimuli drive a transition from cooperation to competition in synthetic phototrophic communities , 2019, Nature Microbiology.

[10]  T. Fukami,et al.  Mycorrhizal co-invasion and novel interactions depend on neighborhood context. , 2015, Ecology.

[11]  Robert A. Player,et al.  A diet of U.S. military food rations alters gut microbiota composition and does not increase intestinal permeability. , 2019, The Journal of nutritional biochemistry.

[12]  Florian P Breitwieser,et al.  Pavian: interactive analysis of metagenomics data for microbiome studies and pathogen identification , 2019, Bioinform..

[13]  G. Reid,et al.  Probiotics and prebiotics in intestinal health and disease: from biology to the clinic , 2019, Nature Reviews Gastroenterology & Hepatology.

[14]  G. Ballard,et al.  Identification of an avian polyomavirus associated with Adélie penguins (Pygoscelis adeliae). , 2015, The Journal of general virology.

[15]  Laurel A. Doherty,et al.  Acute stressor alters inter-species microbial competition for resistant starch-supplemented medium , 2018, Gut microbes.

[16]  Sean P. Gilmore,et al.  Top-down Enrichment Guides in Formation of Synthetic Microbial Consortia for Biomass Degradation. , 2019, ACS synthetic biology.

[17]  C. Jung,et al.  Effects of chitin and temperature on sub-Arctic soil microbial and fungal communities and biodegradation of hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) and 2,4-dinitrotoluene (DNT) , 2019, Biodegradation.

[18]  Xuefeng “Nick” Peng,et al.  Microbial communities for bioprocessing: lessons learned from nature , 2016 .

[19]  J. Soares,et al.  The current state and future direction of DoD gut microbiome research: a summary of the first DoD gut microbiome informational meeting , 2018, Standards in Genomic Sciences.

[20]  Harris H. Wang,et al.  Scalable and cost-effective ribonuclease-based rRNA depletion for transcriptomics , 2019, bioRxiv.

[21]  S. Montain,et al.  Changes in intestinal microbiota composition and metabolism coincide with increased intestinal permeability in young adults under prolonged physiological stress. , 2017, American journal of physiology. Gastrointestinal and liver physiology.

[22]  Harris H. Wang,et al.  Metagenomic engineering of the mammalian gut microbiome in situ , 2018, Nature Methods.

[23]  J. Karl,et al.  Intestinal in vitro and ex vivo Models to Study Host-Microbiome Interactions and Acute Stressors , 2018, Front. Physiol..

[24]  Kevin V. Solomon,et al.  Early-branching gut fungi possess a large, comprehensive array of biomass-degrading enzymes , 2016, Science.

[25]  R. Dickson The Lung Microbiome and ARDS. It Is Time to Broaden the Model. , 2017, American journal of respiratory and critical care medicine.

[26]  F. Martinez,et al.  The Microbiome and the Respiratory Tract. , 2016, Annual review of physiology.

[27]  Christian Munck,et al.  Recording mobile DNA in the gut microbiota using an Escherichia coli CRISPR-Cas spacer acquisition platform , 2020, Nature Communications.

[28]  Claire E. Berryman,et al.  Associations between the gut microbiota and host responses to high altitude , 2018, American journal of physiology. Gastrointestinal and liver physiology.

[29]  William A. Walters,et al.  Multi-Body-Site Microbiome and Culture Profiling of Military Trainees Suffering from Skin and Soft Tissue Infections at Fort Benning, Georgia , 2016, mSphere.

[30]  Hilde van der Togt,et al.  Publisher's Note , 2003, J. Netw. Comput. Appl..

[31]  D. Karig,et al.  Trait-based analysis of the human skin microbiome , 2019, Microbiome.

[32]  M. Neubert,et al.  Multiple Friends with Benefits: An Optimal Mutualist Management Strategy? , 2016, The American Naturalist.

[33]  P. Wilmes,et al.  A Dietary Fiber-Deprived Gut Microbiota Degrades the Colonic Mucus Barrier and Enhances Pathogen Susceptibility , 2016, Cell.

[34]  Erica M. Hartmann,et al.  Antimicrobial Chemicals Are Associated with Elevated Antibiotic Resistance Genes in the Indoor Dust Microbiome , 2016, Environmental science & technology.

[35]  D. Ainley,et al.  Viruses associated with Antarctic wildlife: From serology based detection to identification of genomes using high throughput sequencing , 2017, Virus Research.

[36]  J. Soares,et al.  Evaluation of Probiotics for Warfighter Health and Performance , 2020, Frontiers in Nutrition.

[37]  C. Lowry,et al.  Growing literature but limited evidence: A systematic review regarding prebiotic and probiotic interventions for those with traumatic brain injury and/or posttraumatic stress disorder , 2017, Brain, Behavior, and Immunity.

[38]  Karsten Zengler,et al.  Modelling approaches for studying the microbiome , 2019, Nature Microbiology.

[39]  R. Malmstrom,et al.  Visualizing in situ translational activity for identifying and sorting slow-growing archaeal−bacterial consortia , 2016, Proceedings of the National Academy of Sciences.

[40]  Akira A Shishido,et al.  Trial Evaluating Ambulatory Therapy of Travelers’ Diarrhea (TrEAT TD) Study: A Randomized Controlled Trial Comparing 3 Single-Dose Antibiotic Regimens With Loperamide , 2017, Clinical infectious diseases : an official publication of the Infectious Diseases Society of America.

[41]  Steven Salzberg,et al.  Bracken: Estimating species abundance in metagenomics data , 2016, bioRxiv.

[42]  J. Gilbert,et al.  Impacts of indoor surface finishes on bacterial viability , 2019, Indoor air.

[43]  Andrew J. Hoisington,et al.  Longitudinal homogenization of the microbiome between both occupants and the built environment in a cohort of United States Air Force Cadets , 2019, Microbiome.

[44]  Daniel N. Baker,et al.  KrakenUniq: confident and fast metagenomics classification using unique k-mer counts , 2018, Genome Biology.

[45]  Sarah M. Strycharz-Glaven,et al.  Microbial Electrochemical Energy Storage and Recovery in a Combined Electrotrophic and Electrogenic Biofilm , 2017 .

[46]  Laurel A. Doherty,et al.  Effects of Psychological, Environmental and Physical Stressors on the Gut Microbiota , 2018, Front. Microbiol..

[47]  T. Douglas,et al.  The role of changing temperature in microbial metabolic processes during permafrost thaw , 2020, PloS one.

[48]  M. Jett,et al.  Altered fecal microbiota composition in all male aggressor‐exposed rodent model simulating features of post‐traumatic stress disorder , 2018, Journal of neuroscience research.

[49]  Erica M. Hartmann,et al.  Pangenomic Approach To Understanding Microbial Adaptations within a Model Built Environment, the International Space Station, Relative to Human Hosts and Soil , 2019, mSystems.

[50]  S. Salzberg,et al.  Centrifuge: rapid and sensitive classification of metagenomic sequences , 2016, bioRxiv.

[51]  Glenn R. Gibson,et al.  The International Scientific Association for Probiotics and Prebiotics ( ISAPP ) consensus statement on the definition and scope of prebiotics , 2018 .

[52]  Brittany L. Lenz,et al.  Temporal shifts in the collective dermatologic microbiome of military trainees , 2019, Clinical, cosmetic and investigational dermatology.

[53]  Alexander G. McFarland,et al.  Antimicrobial Chemicals Associate with Microbial Function and Antibiotic Resistance Indoors , 2018, mSystems.

[54]  Matthew A. Perisin,et al.  Human gut microbe co-cultures have greater potential than monocultures for food waste remediation to commodity chemicals , 2018, Scientific Reports.

[55]  Aarti Gautam,et al.  Department of Defense Microbiome Research: A Summary of the Second Annual DOD Tri-Service Microbiome Consortium Informational Meeting , 2020 .

[56]  D. Merrell,et al.  Correlation between Nasal Microbiome Composition and Remote Purulent Skin and Soft Tissue Infections , 2014, Infection and Immunity.

[57]  Jason W. Soares,et al.  The Current and Future State of Department of Defense (DoD) Microbiome Research: a Summary of the Inaugural DoD Tri-Service Microbiome Consortium Informational Meeting , 2018, mSystems.

[58]  Justin C. Biffinger,et al.  Carbon Catabolite Repression and Impranil Polyurethane Degradation in Pseudomonas protegens Strain Pf-5 , 2016, Applied and Environmental Microbiology.