Poster Session 2022

Presenter Name	Poster Title
Lama Abdel-Rahman	Searching for a consensus among inflammatory bowel disease studies: a systematic meta-analysisAbdel-Rahman, LI and Morgan, XC
Varun Aggarwala	Stable and specific engraftment of donor strains post fecal microbiota transplant explains remission in patients with Ulcerative ColitisVarun Aggarwala, Ilaria Mogno, Zhihua Li, Jean-Frederic Colombel, Sudarshan Paramsothy, Nadeem Kakoush, and Jeremiah Faith*
Sena Bae	Discovery of new bioactive microbial metabolites in inflammatory bowel diseaseSena Bae, Amrisha Bhosle, Eunyoung Chun, Grace Cao, Yancong Zhang, Julian Avila-Pacheco, Jessica K. Langa, Kathryn G. Rosinski, Clary Clish, Ramnik Xavier, Hera Vlamakis , Eric A. Franzosa , Curtis Huttenhower and Wendy Garrett
Nitin Bayal	Pathogenomic studies on dysbiosis in skin microbiome of leprosy patients undergoing drug regimen treatment from IndiaNitin Bayal, National Centre for Cell Science, Pune, India
Amrisha Bhosle	Identifying Novel Bioactive Metabolites in Inflammatory Bowel DiseaseAmrisha Bhosle, Sena Bae, Yancong Zhang, Eunyoung Chun, Julian Avila-Pacheco, Ludwig Geistlinger, Jonathan Glickman, Monia Michaud, Levi Waldron, Clary Clish, Ramnik J. Xavier, Hera Vlamakis, Eric A. Franzosa, Wendy S. Garrett, Curtis Huttenhower
Dana Binyamin	The effect of the gut microbiome of adult and aging mice on metabolic characteristicsDana Binyamin, Nir Werbner, Meital Nuriel-Ohayon, Atara Uzan, Hadar Mor, Atallah Abbas, Oren Ziv, Roee Guttman, Omry Koren
Tobyn Branck	Quantifying the effects of diet and the microbiomeTobyn Branck, Jason Lloyd-Price, Kelsey N. Thompson, George Weingart, Long H. Nguyen2, Raaj S. Metha, Dong D. Wang, Wenjie Ma2, Yan Yan, Meghan I. Short, Cesar Arze, Galeb Abu-Ali, Himel Mallick, Gholamali Rahnavard, Amit D. Joshi, Kerry L. Ivey, Jacques Izard, Wendy S. Garrett, Eric B. Rimm, Andrew T. Chan, Curtis Huttenhower
Yiyun Cao	Human commensal bacteria produce novel genotoxic metabolites and exacerbate colorectal cancerY Cao, J Oh, M Xue, AL Martin, D Song,JM Crawford, SB Herzon, NW Palm
Karthikeyani Chellappa	Host-derived nicotinamide in circulation feed gut microbiomeKarthikeyani Chellappa, Melanie R. McReynolds, Wenyun Lu, Xianfeng Zeng, Mikhail Makarov, Faisal Hayat, Sarmistha Mukherjee, Yashaswini R. Bhat, Siddharth R. Lingala, Rafaella T. Shima, Hélène C. Descamps, Timothy Cox, Lixin Ji, Connor Jankowski, Qingwei Chu, Shawn M. Davidson, Christoph A. Thaiss, Marie E. Migaud, Joshua D. Rabinowtiz and Joseph A. Baur
Marina Chen	Characterizing bacterial and fungal communities in childcare environments: a study overviewMarina Chen, Lea Wang, Kelsey N. Thompson, Jeremy E. Wilkinson, Yan Yan, John D. Spengler, Curtis Huttenhower
Georgia Doing	Gene expression and essentiality in model skin microbesGeorgia Doing and Julia Oh
Pedro Jesús Fernández Juliá	Syntropic interactions between different members of the human gut microbiota in the β-glucan metabolism of the fusarium venenatumPedro Jesús Fernández Juliá, Jose Luis Muñoz Muñoz
Eric Franzosa	Statistical approaches for differential expression analysis in metatranscriptomicsYancong Zhang, Kelsey N. Thompson, Curtis Huttenhower, and Eric A. Franzosa
Miguel A. Garcia-Salcido	Gut microbiome diversity and biochemical traits associated with metabolic diseases in urban and semi-urban adults in Mexico City, 2021Miguel A. Garcia-Salcido, Eira E. Huerta-Avila, Angélica Martínez-Hernández, Francisco M. Barajas-Olmos, Humberto García-Ortiz, Lorena Orozco
Andrew Ghazi	Statistical analysis of microbial strains with anpanAndrew R. Ghazi, Yan Yan, Eric A. Franzosa, Curtis Huttenhower
Maryam Hamidi	Maternal Stress During Pregnancy and the Neonatal Gut MicrobiomeSandra J. Weiss, Maryam Hamidi
Eira E Huerta-Avila	Polygenic risk: gut microbiome and genetic risk on preprandial and postprandial metabolic in apparently healthy individualsEira E. Huerta-Avila, Angélica Martínez-Hernández, Fabiola Escalante-Araiza,Francisco M. Barajas-Olmos, Humberto García-Ortiz, Raul A. Bastarrachea, Lorena Orozco
Jordan Jensen	Evaluating Assembly- and Reference-Based Methods for Virome Analysis with and without EnrichmentJordan Jensen, Lea Wang, Moreno Zolfo, Nicola Segata, Eric A. Franzosa, Curtis Huttenhower
Shanlin Ke	The Long-term Association of Post-Traumatic Stress Disorder with Dietary Pattern and Gut Microbiome in a Cohort of WomenShanlin Ke, Xu-Wen Wang, Andrew D. Ratanatharathorn, Tianyi Huang, Andrea Roberts，Francine Grodstein, Laura D. Kubzansky, Karestan C. Koenen, Yang-Yu Liu
Wei Li	Human gut bacteria produce Treg-modulating bile acid metaboliteWei Li, Saiyu Hang, Yuan Fang, Sena Bae, Yancong Zhang, Minghao Zhang, Gang Wang, Megan D. McCurry, Munhyung Bae, Donggi Paik, Eric A. Franzosa, Fraydoon Rastinejad, Curtis Huttenhower, Lina Yao, A. Sloan Devlin, Jun R. Huh
Jason P. Lynch	Engineered E. coli for the targeted deposition of therapeutic payloads to sites of diseaseJason P. Lynch, Coral González-Prieto, Analise Z. Reeves, Urmila Powale, Neha Godbole, Jacqueline M. Tremblay, Florian I. Schmidt, Hidde L. Ploegh, Jonathan N. Glickman, John M. Leong, Charles B. Shoemaker, Wendy S. Garrett, Cammie F. Lesser
Chaoran Ma	Association of Bowel Movement Frequency with Cognitive Function in Women and MenChaoran Ma, Kristine K. Dennis, Raaj Mehta, Changzheng Yuan, Jae Hee Kang, Francine Grodstein, Alberto Ascherio, Walter C. Willett, Andrew T. Chan, Curtis Huttenhower, Meir J. Stampfer, Dong D. Wang
Raaj S. Mehta	Gut Microbial Metabolism of 5-ASA Diminishes Its Clinical Efficacy in Inflammatory Bowel DiseaseRaaj S. Mehta, Jared R. Mayers, Yancong Zhang, Nathaniel R. Glasser, Amrisha Bhosle, Long H. Nguyen, Wenjie Ma, Sena Bae, Tobyn Branck, Ashwin N. Ananthakrishnan, Eric A. Franzosa, Emily P. Balskus, Andrew T. Chan, Curtis Huttenhower
Morgan Martin	Vaginal Lactobacilli-mediated Anti-Inflammatory Effects on Host Immune ResponseMorgan Martin, Cecilia Webber, Ki Hyun Kim, Sunghee Bang, Jon Clardy and Smita Gopinath
Matthew S Miyasaka	Linking individual microbial and metabolite biomarkers of Colorectal Cancer using computational models of gut microbiota metabolismMatthew S. Miyasaka and Ali R. Zomorrodi
Maria Montibeller	Effects of whey protein supplementation on gut microbiota in colitis mouse modelMontibeller Maria Jara, Ferrocino Ilario, Rodrigues Cardoso Daniel, Cardoso Umbelino Cavallini Daniela
Xochitl Morgan	The Harvard T.H. Chan School of Public Health Microbiome Analysis CoreXochitl C. Morgan, Lauren J. McIver, Thomas Kuntz, Curtis Huttenhower
Paul Nelson	Changes in taxonomic and metabolic composition among NAFLD patientsPaul Nelson, Hanseul Kim, Kelsey N. Thompson, Long H. Nguyen, Curtis Huttenhower
Natalia Palacios	The Gut Microbiome in Parkinson’s Disease in the Nurses’ Health Study and Health Professionals Follow-up StudyNatalia Palacios, Jeremy Wilkinson, Kjetil Bjornevik, Michael Schwarzschild, Lauren McIver, Alberto Ascherio, Curtis Huttenhower
Marie Ryan	Inflammation as Acne Vulgaris (AV): 15-day exclusion diet examined with concurrent changes in the gut microbiomeMarie Ryan, Laurent Ferradini, Ammala Philavanh
Meghan Short	Sample size calculation for differential abundance tests in microbiome epidemiologyMeghan I. Short, Emma Schwager, Siyuan Ma, Paulo Manrique, Lauren McIver, Jeremy E. Wilkinson, Eric A. Franzosa, Curtis Huttenhower
Magnus Stefansson	The Microbiome Collection Core at the Harvard T.H. Chan School of Public Health (HCMCC) Xochitl Morgan, Magnus Stefansson, Curtis Huttenhower
Jarrod Smith	A symbiont’s sensing of host mucin regulates its biogeography and inflammatory potential in the intestineT. Jarrod Smith, Deepika Sundarraman, Raghuveer Parthasarathy, Karen Guillemin
Aayushi Uberoi	Commensal microbes can regulate skin barrier through the control of Tryptophan-Aryl Hydrocarbon Receptor cascadeAayushi Uberoi, Casey Bartow-McKenney, Qi Zheng, Laurice Flowers, Amy Campbell, Simon Knight, Debra Crumrine, Carrie H. Sutter, Peter Elias, Clementina Mesaros, Thomas R. Sutter, Elizabeth A. Grice
Ya Lea Wang	Evaluating isolation methods for human gut viral communitiesYa Wang, Jordan Jensen, Eric Franzosa, Seth Rakoff-Nahoum, Curtis Huttenhower
Yiqing Wang	Diet and the gut microbial interactions in irritable bowel syndrome subtypesYiqing Wang, Wenjie Ma, Raaj Mheta, Long H. Nguyen, Mingyang Song, David A. Drew, Francesco Asnicar, Curtis Huttenhower, Nicola Segata, Jonathan Wolf, Tim Spector, Sarah Berry, Kyle D. Staller, Andrew T. Chan.
Yan Yan	Identifying strain-specific functional genes in colorectal cancerYan Yan, Kelsey N. Thompson, Andrew Ghazi, Andrew M. Thomas, Long H. Nguyen, Paolo Manghi, Lauren J. Mciver, Emma Accorsi, Eric A. Franzosa Nicola Segata,  Andrew T. Chan, Wendy S. Garrett, Curtis Huttenhower
Jianan Zhang	Pharmacological inhibition of gut microbial β-glucuronidase enzymes blocks DSS-induced colon inflammationJianan Zhang, Shan Sun, Ermin Zhao, Anthony Fodor, Eric A. Decker, Guodong Zhang, Matthew R. Redinbo
Yancong Zhang	Predicting functions of uncharacterized gene products from microbial communitiesYancong Zhang, Xueying (Sonia) Huang, Amrisha Bhosle, Sena Bae, Andy Krueger, Wendy S. Garrett, Eric A. Franzosa, Curtis Huttenhower
Samuel Zimmerman	Quantifying shared and unique gene content across 17 microbial ecosystemsSamuel Zimmerman, Braden T Tierney, Chirag J Patel, Aleksandar D Kostic

Searching for a consensus among inflammatory bowel disease studies: a systematic meta-analysis

Presented by: Lama Abdel-Rahman

Numerous studies have examined the gut microbial ecology of patients with Crohn’s disease and ulcerative colitis, but IBD-associated taxa and ecological effect sizes are not consistent between studies. We have systematically searched PubMed and Google Scholar and performed a meta-analysis of 13 studies to analyse how variables such as sample type (stool, biopsy, and lavage) affect results in IBD gut microbiome studies. Reduced alpha diversity was a consistent feature of both CD and UC, but was more pronounced in CD. Disease contributed significantly variation in beta diversity in most studies, but effect size varied, and the effect of sample type was greater than the effect of disease. Fusobacterium was the genus most consistently associated with CD, but disease-associated genera were mostly inconsistent between studies. Stool studies had lower heterogeneity than biopsy studies, especially for CD. Our results indicate that sample type variation is an important contributor to study variability.

Stable and specific engraftment of donor strains post fecal microbiota transplant explains remission in patients with Ulcerative Colitis

Presented by: Varun Aggarwala

Several placebo-controlled trials have demonstrated that FMT can induce remission in a subset of patients (27-53% response rate) with Ulcerative Colitis (UC). However open questions regarding FMT study design, dosage, choice of donors, strain level dynamics and predictors of response remain unanswered. Here, we comprehensively culture 551 bacterial isolates from 13 donors in the successful FMT FOCUS trial for UC patients, and tracked their engraftment and inter-intra strain dynamics (each patient received FMT from 4-7 donors) in 243 longitudinal metagenomics samples upto 5 years later from 55 recipients. We detect high and stable engraftment (p value < 0.001) of donor strains in patients achieving the primary endpoint of corticosteroid-free clinical remission together with endoscopic remission or response at week 8 compared to those that did not. This reduced at year 5 (coinciding with relapse) and reaches the level (p value < 0.01) seen in patients who had not achieved the endpoint earlier. Patients who only received 40 doses of enema (open phase) did not have lower engraftment or response compared to patients who also received an added initial colonoscopic infusion (blind phase). 40 doses of enema at week 8 did not result in higher engraftment compared to receiving 20 by week 4. High engraftment from individual donors increased the odds for achieving the endpoint (p value < 0.05) and the most effective donor in FOCUS trial was also found to have 100% efficacy (n=4) in another FMT LOTUS trial for UC patients. We provide a list of bacterial strains that are over-enriched and stably engrafted in recipients achieving the endpoint compared to those that did not, and for use in Live Biotherapeutic Products (LBP) as a safer alternative to FMT.

Discovery of new bioactive microbial metabolites in inflammatory bowel disease

Presented by: Sena Bae

Gut microbiota-associated bioactive compounds has been implicated as both disease-causing and –attenuating targets in GI disorder including inflammatory bowel diseases (IBD). However, discovery of new bioactive compounds relevant for IBD treatment has been severely limited, because most metabolite signals that are enriched or depleted in IBD patients’ fecal metabolome are uncharacterized. To address this challenge, we have computationally prioritized the metabolites putrescine from publicly-available IBD fecal metabolomic dataset and validated its biological function in vivo. We have also identified microbially-modified putrescine derivatives and these derivatives may selectively affect host colonic M2 macrophage cell populations in a gut microbiota-dependent manner. These finding suggest that the power of combined computational and experimental approaches for identifying microbially derived metabolites with general immunomodulatory activity and specific relevance for IBD patient care.

Pathogenomic studies on dysbiosis in skin microbiome of leprosy patients undergoing drug regimen treatment from India

Presented by: Nitin Bayal

Background: The morphology and physiological features of various sites on the human skin define the composition of skin microbiome. Several recent studies have also described associations between compositional variations for skin microbiome and progression of dermatological disorders specifically acne, psoriasis, atopic dermatitis and vitiligo. Leprosy is one of the skin related disease linked with social stigma. It is caused by Mycobacterium leprae and Mycobacterium lepromatosis. Dysbiosis of skin microbiome and its effect on outcome of the leprosy requires detailed investigation.

Objectives: This study was conducted to explore the community structure of skin microbial communities in Indian leprosy patients undergoing drug regimen treatment and healthy individuals as controls.

Methods: Institutional ethics clearance and informed consents were considered for the study. Skin swabs from lesional and non-lesional skin sites for 29 leprosy patients and similar sites from 30 healthy individuals were collected in leprosy clinics in accordance with the study design. All the patients were diagnosed for high bacillary load of M.leprae. Microbiome DNA was isolated and sequenced for V1-V3 16S rRNA variable region using Illumina sequencers. All the sequences were de-multiplexed and subjected to Microbiome analysis using QIIME 2 tools to investigate the variability in microbiome between different study groups.

Results: A stark difference was observed between the taxonomic profiles for skin microbiota of leprosy patients and healthy individuals but insignificant results with the samples analyzed for respective leprosy lesional and adjoining non-lesional skin sites.

Discussions: Our analysis shows a decline in firmicutes related OTUs in leprosy patients in comparison to healthy individuals. Alpha diversity accessed using various diversity indices indicates a distinct depletion of Staphylococcus genera in samples from affected sites of leprosy patients. This kind of studies can assist skin microbiome restoration research that corresponds to better disease management and diagnosis.

Identifying Novel Bioactive Metabolites in Inflammatory Bowel Disease

Presented by: Amrisha Bhosle

Microbial community biochemistry is responsible for processing hundreds of thousands of compounds, of which only a few percent are typically identified and even fewer linked to specific functions or phenotypes. This is true even in the relatively well-characterized human gut, in which perturbation of microbial metabolism is an important aspect of the pathophysiology of conditions including the inflammatory bowel diseases (IBD). Improved knowledge of microbial metabolites and their immunomodulatory roles is thus necessary to the understanding of the gut and other ecologies, as well as diagnosis and clinical management of IBD. Here, we systematically analyzed the molecular, ecological, and epidemiological properties of ~82k metabolic features in 546 Integrative Human Microbiome Project (iHMP/HMP2) untargeted fecal metabolomes and prioritized >1,000 metabolic features as potentially bioactive in IBD. This methodology associated 18,699 (~42%) of prevalent but unidentified metabolic features with at least one well-characterized annotated metabolite, thereby ‘de-orphaning’ a significant portion of the fecal metabolome. Prioritized unidentified metabolites were both abundant and significantly perturbed during IBD, and they included known IBD-linked chemical families such as bile acids and short-chain fatty acids, as well as less-explored bilirubin derivatives, polyamines, vitamins, and other microbial products. One of these previously unannotated but highly prioritized compounds, nicotinamide riboside, successfully reduced histological colitis scores in DSS-treated mice. The resulting chemical prioritization and identification strategy, implemented as MACARRoN, is generalizable to untargeted metabolomes from other environments, with the potential to improve microbial community characterization and provide new therapeutic candidates in the human microbiome.

The effect of the gut microbiome of adult and aging mice on metabolic characteristics

Presented by: Dana Binyamin

During aging, there is a physiological decline, an increase of morbidity and mortality and a natural change in the gut microbiome. In this study, we investigated the influence of the gut microbiome on different metabolic parameters in adult and aging mice.
Fecal and blood samples from adult (n=42, 100-300 days) and aging (n=32, 550-750 days) mice were collected. 16S rRNA gene sequence analysis was carried out using Qiime2. Mice weight and body composition were measured by using NMR, and insulin and leptin levels in the blood were measured using the Mouse Adipokine Magnetic Bead Panel kit. We then preformed Fecal Microbiota Transplantation (FMT) from adult and aging mice into young germ-free (GF) mice in order to examine the effect of the gut microbiome of adult and aging mice on weight, body composition and insulin and leptin levels. We also monitored food consumption and RQ 10 days after FMT using Metabolic Cages.
We found that adults and aging mice have different microbiomes. We observed a high Firmicutes/Bacteroidetes ratio in aging mice compared to adult mice in addition to several genera that were significantly different between the groups. In the examined metabolic parameters, we observed significantly higher weight and fat mass and lower lean mass in aging mice along with high insulin and leptin levels in the blood. In the FMT mice, the gut microbiome from aging mice caused several metabolic changes in the young transplanted mice. Fat body mass and insulin levels were higher in the mice who received aging feces than mice receiving adult feces. In addition, they consumed more food and had higher metabolic activity (average RQ) compared to mice receiving adult feces.
We conclude that aging mice have a gut microbiota that is associated with obesity, and they also exhibit metabolic parameters related to obesity. In addition, the gut bacterial population itself is sufficient to induce some of the manifestations of obesity.

Quantifying the effects of diet and the microbiome

Presented by: Tobyn Branck

Host diet affects the structure and function of the gut microbiome, but these effects are far more context-dependent than is generally acknowledged. For instance, dietary changes drastically affect the microbiome in animal models, and in human infants during a shift to solid foods. In contrast, day-to-day dietary variation in healthy adults typically elicit only minor compositional shifts – although differences in pre-existing resident microbes among individuals can result in distinct chemical and metabolic responses to the same dietary intake. This indicates two separate mechanisms of action by which the microbiome interacts with diet: the first as a direct target, the second as a mediator. Here, we quantify these previously undifferentiated effects across different populations, life stages, environments, and dietary metadata. Seven publicly available metagenomic datasets spanning human adult, human infant, non-human primate, and mouse populations were reanalyzed through a standard bioinformatic workflow (total n=2,074 samples). The metagenomic profiles were accompanied by cohort-specific dietary information ranging from general diet types to resolved profiles of dietary components. To measure the effects of diet and the microbiome in these cohorts, we uniformly applied a set of models across studies. We assessed the relationship between overall dietary patterns or individual dietary compounds and microbial profiles, in addition to the specific interactions between dietary compounds and microbes. We found that, in a typical Western diet, the effect of day-to-day diet variation is small but significant, as expected. Instead, diet affects the microbiome indirectly via alterations in microbial transcription (but not, generally, organismal abundances), which in turn can have a mediating effect on host responses to diet. Applying the same models across populations, we also found that when the microbiome has not fully stabilized, as in human infants and laboratory animals, diet changes have a substantially larger effect on the gut community structure. Direct diet-driven variation thus depends largely on the resilience of the microbiome and on the extent of the dietary perturbation, while indirect interactions can be highly chemically and microbiologically specific.

Human commensal bacteria produce novel genotoxic metabolites and exacerbate colorectal cancer

Presented by: Yiyun Cao

Microbiota-derived metabolites that elicit DNA damage can contribute to intestinal tumorigenesis. However, the full spectrum of genotoxic chemicals produced by indigenous gut microbes remains to be defined. We established a pipeline to systematically evaluate the genotoxicity of a large collection of human gut commensals and identified isolates from divergent phylogenies whose small molecule metabolites caused DNA damage. Using comparative metabolomics and bioactivity-guided natural product-discovery techniques, we discovered a previously undescribed family of genotoxic metabolites—termed the indolimines—produced by the colorectal cancer (CRC)-associated species Morganella morganii. The synthesis of indolimines was catalyzed by aspartate aminotransferase with IAld and amino acids as precursors. Finally, we found that indolimine-producing M. morganii exacerbated CRC in gnotobiotic mice. These studies reveal the existence of a previously unexplored universe of genotoxic small molecules from the human microbiome and imply a broader role for microbiota-derived genotoxins in CRC.

Host-derived nicotinamide in circulation feed gut microbiome

Presented by: Karthikeyani Chellappa

Nicotinamide adenine nucleotide (NAD), a redox cofactor and a co-substrate for signaling enzymes, is essential in mammals and microbes. In this study we used heavy isotope labeled tracers to identify the precursors used by gut microbiome for NAD synthesis. We found that precursors available in the diet, amino acids and vitamin B3 (nicotinamide and nicotinic acid), are absorbed in the proximal parts of the digestive tract. Dietary fiber that reaches the colon feed into de novo NAD synthesis, but a large portion of NAD synthesis in gut microbiome remained unaccounted. We made a surprising discovery that the host-derived nicotinamide in circulation enter gut lumen and support NAD synthesis, almost in entirety in small intestinal microbiota and more than 50% to large intestinal microbiota. We show that nicotinic acid produced by microbial deamidation of nicotinamide provide alternate precursor to by-pass salvage synthesis in host tissues. Moreover, the main route from oral nicotinamide riboside, a widely used nutraceutical, to boost host NAD is via conversion into nicotinic acid by the gut microbiome. Together, we establish that vitamin B3 cycles between host and gut microbiome to increase mammalian robustness.

Characterizing bacterial and fungal communities in childcare environments: a study overview

Presented by: Marina Chen

Indoor environments harbor diverse microbes to which occupants are constantly exposed. Exposure to environmental microbes has been shown to have both negative and positive health impacts, particularly relating to children’s immune maturation during early development. Many preschool-aged children spend 7 to 10 hours per day in childcares, almost as much as at home, yet the environmental microbes associated with childcares have yet to be fully elucidated.
The first component of this study is to characterize viable microbial communities in the childcare environments. While high-throughput sequencing provides powerful methods for surveying microbial communities, it remains challenging to differentiate biochemically active (“viable”) microbes that are often outnumbered by their “dead” counterparts in the built environment (BE) due to its unusual chemical makeup. Critically, the functions of a microbial community are defined by these viable microbes, therefore, the distinction of microbial viability is essential for understanding indoor microbial impacts on occupant health. To date, few studies could reliably distinguish viable community members, which hinders the interpretation of health implications. Here, we will use paired metagenomics and metatranscriptomics to characterize viable BE microbial communities, including functional molecular mechanisms responsible for microbial persistence and antimicrobial resistance burden in childcare environments.
The second component of this study is to identify indoor fungal communities with higher resolution using full-length internal transcribed spacer (ITS) amplicon sequencing. The traditional fungal identification marker ITS ranges from 500-1200 base pairs in size, which cannot be sequenced as a single DNA fragment with short-read sequencing. There have been controversies in the selection of ITS1 or ITS2 (both are subregions of the full-length ITS) for sequencing, and using either alone often results in lower taxonomic resolution, higher proportion of unidentified taxa and greater extent of underclustering. This study will utilize the single molecule real-time (SMRT) technology from Pacifici Biosciences to sequence the full-length ITS region. Here will also include substantial full-length ITS reference database curation and evaluation to improve our fungal taxonomic resolution.

Gene expression and essentiality in model skin microbes

Presented by: Georgia Doing

Of the trillions of microbial cells associated with a human body at any given point in time, about half are identifiable at the genus level, a quarter are culturable, and only a handful have been isolated and extensively studied in the laboratory over decades. Analogous to how model organisms, such as mice, have been used to study human biology, “transfers” of the great depth of knowledge accumulated for model microbial species, such as the pathogen Staphylococcus aureus, to related but less-studied microbes such as the commensal and opportunistic pathogen Staphylococcus epidermidis, will greatly facilitate understanding microbial diversity and microbial communities. To date, transfer learning has been successful in the fields of image, video and natural language processing and has been applied in genomics to bridge different mammalian cell types and is starting to be used to connect different species, including plant and insect model and non-model organisms. The genetic diversity and transcriptional plasticity of S. epidermidis is sparsely annotated, and we aim to apply transfer learning to genetic, transcriptomic and functional data to integrate the wealth of S. aureus data collected over previous decades and drive hypothesis generation around S. epidermidis pathogenicity.

Syntropic interactions between different members of the human gut microbiota in the β-glucan metabolism of the fusarium venenatum

Presented by: Pedro Jesús Fernández Juliá

This project is going to explore how human gut Bacteroides spp. and Bifidobacterium spp can use β-glucan from the microfungus Fusarium venenatum, which is used to elaborate mycoprotein of QUORN® products. The study is focused on the search of the metabolic pathways for the β-glucan degradation together with the presumable cross-feeding relations established between different members of the Human Gut Microbiota (HGM) involved in the process.
The human gut microbiota (HGM) contributes to the physiology and health of its host in a variety of ways, maintaining gut homeostasis and modulating the immune system but also allowing the use of a wide range of substrates, specially polysaccharides whose intact structures are not digest by human intestinal enzymes. The health benefits provided by dietary manipulation of the HGM require knowledge of how polysaccharides may shape the gut microbiota community, specially β-glucans which have been described as potential prebiotics. Nevertheless, the mechanisms of action underpinning these health effects related to β-glucans are still unclear, and the its precise impact on the gut microbiota has been subject to debate and revision.
The utilization of a mixed linkage fungal β-glucan as a energy source by gut bacteria species have not been studied so far, and it will clarify the different effects that these polysaccharides may have on the populations of gut bacteria and the health of the host, showing us its potential as a new prebiotic and its power as a realistic alternative for the excessive meat consumption in the current fat-based diet.

Statistical approaches for differential expression analysis in metatranscriptomics

Presented by: Eric Franzosa

Metatranscriptomics (MTX) has become an increasingly practical way to profile the functional activity of microbial communities in situ. However, MTX remains underutilized due to experimental and computational limitations. The latter are complicated by non-independent changes in both RNA transcript levels and their underlying genomic DNA copies (as microbes simultaneously change their overall abundance in the population and regulate individual transcripts), genetic plasticity (as whole loci are frequently gained and lost in microbial lineages), and measurement compositionality and zero-inflation. Here, we present a systematic evaluation of and recommendations for differential expression (DE) analysis in MTX. We designed and assessed six statistical models for DE discovery in MTX that incorporate different combinations of DNA and RNA normalization and assumptions about the underlying changes of gene copies or species abundance within communities. We evaluated these models on multiple simulated and real multi-omic datasets. Models adjusting transcripts relative to their encoding gene copies as a covariate were significantly more accurate in identifying DE from MTX in both simulated and real datasets. Moreover, we show that when paired DNA measurements (metagenomic data, MGX) are not available, models normalizing MTX measurements within-species while also adjusting for total-species RNA balance sensitivity, specificity, and interpretability of DE detection, as does filtering likely technical zeros. The efficiency and accuracy of these models pave the way for more effective MTX-based DE discovery in microbial communities.

Gut microbiome diversity and biochemical traits associated with metabolic diseases in urban and semi-urban adults in Mexico City, 2021

Presented by: Miguel A. Garcia-Salcido

Background: multiple mechanisms linking the diversity and composition of the gut microbiome with metabolic diseases have been described. Some of those mechanisms are: the theory of energy harvesting, the microbiota-gut-brain axis, microbiota-host interactions, metabolites produced by microbiota, changes in the gut epithelium permeability and low-grade chronic inflammation. One of the major determinants of the composition and diversity of gut microbiota is the diet, and it´ s determined by the food environment (physical, economic, socio-cultural and political). Some authors described how industrialized-western-lifestyles have generated urban and semi-urban food environments (characterized by high consumption of saturated fat, animal-origin protein and food additives; with low consumption of fiber and plant-based protein). Replacing traditional food environments.

Aim: to determine the relationship between food environments with the gut microbiome diversity, biochemical and anthropometric measures associated with metabolic diseases in the Mexican population.

Methods: we conducted an observational, descriptive, cross-sectional study, from the gut microbiome analysis of metagenomic data. In a population composed of 42 participants from urban and semi-urban (including amerindians) environments in Mexico City.

Results: our results demonstrate differences in the composition and diversity of the gut microbiome between urban and semi-urban environments. We observed that 68.5% of the participants were women and 31.43% men, with a mean age of 41.8 (±11.3) years. There were no statistically significant differences for age (p=0.560) or sex (p=0.413) in the analized groups. Concerning the most consumed meals and products, semi-urban participants showed higher daily consumption frequencies of ultra-processed cereals (p=0.023), soft drinks (p<0.0001) and corn-based traditional meals (p=0.018); than urban participants. In the structural metagenomic analysis, for the urban group, we observed that the most abundant phylum was Bacteroidetes, followed by Firmicutes, Proteobacterias and Actinobacterias. In contrast, for the semi-urban group; the most abundant phylum was Firmicutes, followed by Bacteroidetes, Proteobacterias and Actinobacterias. We observed statistically significant differences in relative abundances of Bacteroidetes (p<0.0001), Firmicutes (p=0.0003), Actinobacteria (p<0.0001) and Euryarchaeota (p=0.002); between the groups. The principal coordinates analysis showed two clusters, grouping according to the food environment origin. Also, we identified four participants located in the transition zone of the clusters. Regarding the alpha diversity, the P50 value for Shannon Index was 2.81 (RIC 3.01-2.55) for urban group and 2.71 (3.05-2.22) for semi-urban group (p=0.734). P. copri, A. putredinis and F. parusnitzii species showed higher relative abundances for semi-urban, compared with urban group.

Conclusions: the composition and diversity of the gut microbiome of people from urban food environments are different, with respect to those from semi-urban food environments. There are differences in beta diversity between these two communities. However, there aren’t statistically significant differences in alpha diversity indices between food environments or between biochemical or anthropometric alterations. It is necessary to conduct studies with larger sample sizes to observe differences in these indices and to be able to make inferences at the species and strain levels.

Statistical analysis of microbial strains with anpan

Presented by: Andrew Ghazi

Microbial strain variation can strongly influence the impact of microbes on host health, though methods for quantitatively understanding these important differences have been lacking. Strain data have several features that make traditional statistical methods challenging to use, including high dimensionality, person-specific strain carriage, and complex phylogenetic relatedness. We present anpan, an R package that consolidates methods for strain statistics. Combining modern hierarchical modeling strategies with novel adaptive filtering methods specifically designed to interrogate microbial strain profiles, anpan facilitates the identification of strain-specific genetic elements associated with host health outcomes. Additionally, we use regularized phylogenetic generalized linear mixed models to characterize the effect of strain-level community structure. We validate our methods by simulation, as well as application to a dataset of 1262 colorectal cancer patients, showing that we achieve more accurate effect size estimation and a lower false positive rate compared to current methodologies. The open source repository with help documentation and a tutorial vignette are available at https://github.com/biobakery/anpan.

Maternal Stress During Pregnancy and the Neonatal Gut Microbiome

Presented by: Maryam Hamidi

Purpose: Preliminary research suggests that prenatal stress may alter programming of the fetal microbiome. The purpose of this study was to determine relationships of pregnancy stress to diversity and composition of the neonate’s gut microbiome.

Design: This cross-sectional analysis is part of a longitudinal, cohort study.

Methods: Fifty-one women and their future newborns were recruited during the third trimester of pregnancy. Women completed demographics and Cohen’s Perceived Stress Scale at recruitment. A stool sample was collected from the neonate at one month of age. Data on potential confounds (e.g. gestational age) were extracted from the medical record to control for their effects. 16s rRNA gene sequencing and DESeq were used to identify diversity and abundance of species and test for differential expression of various taxa. We employed multiple linear regression to examine the aims.

Results: Greater pregnancy stress was associated with greater diversity of the neonate’s gut microbiome (β = .30, p=.025). However, the abundance of certain species appeared perturbed in neonate’s exposed to greater stress in utero. For instance, they had a significantly lower abundance of potentially beneficial bacteria such as Lactobacillus, Lactococcus, and Bifidobacterium.

Conclusions: A more complex, multi-species gut microbiome may lead to less stability and greater susceptibility to functional perturbations during development. Lower levels of beneficial bacteria can lead to less ability to ward off pathogenic organisms, and related infections or intestinal disorders.

Relevance: Research could eventually yield microbial markers and microbial gene pathways that are bio-signatures of risk and inform targets for probiotic therapies.

Key words: microbiome, maternal stress, neonate, pregnancy

Polygenic risk: gut microbiome and genetic risk on preprandial and postprandial metabolic in apparently healthy individuals

Presented by: Eira E Huerta-Avila

Background: The prevalence of the different metabolic syndrome phenotypes (MetSP) such as hypertriglyceridemia, hyperglycemia, hypoalphalipoproteinemia, central obesity and arterial hypertension are increasing and they are risk factors for other comorbidities such as type 2 diabetes and cardiovascular diseases. It has been documented that, even prior to the appearance of MetSP, an altered postprandial metabolism may occur. As if that were not enough, a large number of genetic variants associated with the risk of developing MetSP have been identified. Moreover, it has recently been documented that the gut microbiota (GM) represents an environmental risk factor for the development of these entities. Hence, that it is necessary to implement methodologies that allow genetic and environmental factors to be combined to establish the risk of developing these entities even before the appearance of symptoms. A widely used methodology is the polygenic risk score (PRS) that allows identifying people at risk by combining the environmental and genetic part. Therefore, the aim of this work was to determine if there is a correlation between the composition of the GM, the pre and postprandial metabolic state of the individual and the PRS to develop MetSP.

Methods: A cross-sectional and observational study was carried out with 33 apparently healthy individuals. Blood samples were taken for biochemical analysis (pre and postprandial metabolism), and stool samples. Genotyping and sequencing (metagenomic) were performed. We used previously reported genetic variants for the different MetSP and in combination with the GM metagenomic data, the PRS was performed for the different MetSP. A second analysis consisted of stratifying individuals without preprandial alterations to assess PRS and GM data in their postprandial metabolism.  

Results: In the 33 individuals, the mean age of the population was 39.7±13.4 years and more than 70% were female. The prevalence of metabolic syndrome was 42.4% while the prevalence of type 2 diabetes was 3.1%. The average of the studied population presented an overweight nutritional status according to BMI (29.7±5.1 kg/m2) and a high percentage of body fat (39.7±8.9%). Ancestry analysis showed that the population has an average Amerindian ancestry of 79.1%, followed by 18.0% European and 2.9% African. The construction of the different PRS by the FSM showed a power of discrimination between individuals with and without the different components of metabolic syndrome above 0.75. In other words, most PRS have the ability to detect 75% of cases or more of each condition. The metagenomic analysis showed that the dominant phyla were Bacteroidetes, Firmicutes, Proteobacteria and Actinobacteria. Regarding a species level, the most abundant were Prevotella copri, Faecalibacterium prausnitzii and Eubacterium rectale. The relative abundance of Prevotella copri and Parabacteroides merdae was directly proportional to glucose levels, and Eubacterium rectale to blood HbA1c concentration (p<0.05). Other microorganisms had a significant correlation (p<0.05), with postprandial data and even with the different PRS, such as Methanobrevibacter smithii that negatively correlated with the PRS of hypertriglyceridemia. Finally, the alpha diversity (such as the Shannon and Simpson index) in the different MetSP did not show significant correlations and when the analysis was performed only in those who did not have preprandial glucose and triglyceride alterations, we observed higher levels of these indices in people who did not have altered triglyceride curves.

Conclusions: These data suggest that the decrease in gut microbiome diversity could occur in the stages prior to the onset of manifestation MetSP. And that there are species that seem to favor the increase of pre and postprandial metabolites related to cardiovascular risk and polygenic risk for some MetSP. It is necessary to increase the sample size to corroborate these data.

Evaluating Assembly- and Reference-Based Methods for Virome Analysis with and without Enrichment

Presented by: Jordan Jensen

Capturing an accurate representation of the viral members of a microbial community presents significant experimental and computational challenges. Current metagenomic approaches include assembly-based reconstruction and detection of virus-like sequences (which is limited to highly abundant or enriched viruses) or detection by homology (which is limited by the rapid evolutionary rate and great diversity of viruses, and thus their representation in reference databases). Additionally, RNA viruses within microbial communities are both underrepresented and understudied. To address these limitations, we generated synthetic community sequencing data capturing mixtures of viral and bacterial DNA and RNA, and used these synthetic sample sets along with shotgun metagenomes, metatranscriptomes, and virus-like particle (VLP)-enriched viromes from the IBDMDB cohort of the Integrative Human Microbiome Project to systematically evaluate a series of assembly- and reference-based approaches to viral profiling. Using the synthetic and real samples, we evaluated nucleotide and translated mapping to gold-standard reference sets (RefSeq) and novel Metagenome-Assembled Genome viral databases (vMAG). Assembly of metagenomic reads accessed only a small fraction of likely viral sequences, although those observed by assembly were highly accurate. Conversely, reference-based methods were accurate for detection (although not generally quantification) of viruses represented in all three data types, particularly using translated protein mapping; however, RNA viral references in particular remain extremely sparse. Mapping to well-characterized reference sets such as RefSeq maintained high specificity across a wide range of bacterial contamination, but failed to capture highly novel viral content. vMAG reference sets varied in mapping rates of viral reads, but were able to expand mapping of simulated novel microbial sequences. This work is ongoing, including integration of machine learning approaches to fill gaps remaining after reference-based mapping. Ultimately, we expect this study to provide a set of single, unified best practices for virome profiling from diverse microbial community sequencing assays.

The Long-term Association of Post-Traumatic Stress Disorder with Dietary Pattern and Gut Microbiome in a Cohort of Women

Presented by: Shanlin Ke

Post-Traumatic Stress Disorder (PTSD) is a psychiatric condition that may occur in people who have experienced or witnessed traumatic or horrifying events. PTSD has been linked to increased risk of various chronic diseases and eating disorders. The gut microbiome plays a critical role in modulating the immune, metabolic, psychological and cognitive activities of the host. Understanding PTSD’s long-term associations on dietary pattern and gut microbiome may improve the physical and mental health of people with PTSD, but remains unexplored. Here we analyzed information on trauma exposure and PTSD symptoms with microbiome data and dietary information collected about 5 years later, in 191 individuals enrolled in the Mind-Body Study (MBS). We found that inter-individual differences in gut microbiome appear to be stable over time intervals as long as six months, and thus a limited number of measurements may be adequate to reliably investigate associations with long-term health. Notably, we demonstrated that PTSD has a long-term inverse association with host dietary habits, especially a healthy Mediterranean-style dietary pattern. Moreover, three (i.e., Bacteroides ovatus, Roseburia inulinivorans, and Dorea longicatena) and four (i.e., Eubacterium siraeum, Bacteroides massiliensis, Ruminococcus gnavus, and Oscillibacter unclassified) differentially abundant species were identified in No-trauma vs. Trauma-no-PTSD and Trauma-no-PTSD vs. PTSD comparisons, respectively. Overall, these findings suggest that PTSD is associated with long-term changes in dietary pattern and gut microbiome, highlighting the critical importance of incorporating the human gut microbiome and diet in our understanding of PTSD and their association with physical health.
Keywords: Posttraumatic stress disorder, gut microbiome, Mediterranean diet

Human gut bacteria produce Treg-modulating bile acid metabolite

Presented by: Wei Li

Primary bile acids discharged into the gut lumen are subject to biotransformation by commensal bacteria and converted into secondary metabolites. These bile acids and bile acid metabolites are signaling molecules that regulate immune homeostasis, including the differentiation of CD4+ T cells into distinct T cell subsets. Previously, we have shown that the bile acid metabolite isoallolithocholic acid (isoalloLCA) enhances the differentiation of anti-inflammatory regulatory T cells (Treg cells). Here, we identify gut bacteria that synthesize isoalloLCA from 3-oxolithocholic acid and uncover a gene cluster responsible for the conversion in members of the abundant human gut bacterial phylum Bacteroidetes. Moreover, the levels of isoalloLCA and its biosynthetic genes are significantly reduced in patients with inflammatory bowel diseases, suggesting that isoalloLCA and its bacterial producers may play a critical role in maintaining immune homeostasis in humans. Our results reveal new ways in which commensal bacteria regulate immune tolerance in the gut, laying the groundwork for potential new therapeutic avenues to control IBD.

Engineered E. coli for the targeted deposition of therapeutic payloads to sites of disease

Presented by: Jason P. Lynch

New drug platforms are needed which enable the directed delivery of therapeutics to sites of disease to maximize efficacy and limit off-target effects. Here, we report the development of PROT3EcT, commensal Escherichia coli engineered for the direct secretion of proteins into their surroundings. PROT3EcT is composed of four modular components: an E. coli chassis, a modified bacterial protein secretion system, a regulatable transcriptional activator, and a secretable therapeutic payload. We demonstrate that PROT3EcT can secrete fully functional payloads, including single-domain antibodies nanobodies (Nb), into the extracellular space. Nb-secreting PROT3EcT stably colonizes and maintains a functional secretion system within the intestines of mice. A single prophylactic dose of PROT3EcT that secretes a tumor necrosis factor-alpha (TNFα) neutralizing Nb, but not PROT3EcT alone, is sufficient to ablate TNF levels and prevent the development of injury and inflammation in a chemically-induced model of inflammatory bowel disease. This work lays the foundation for the development of PROT3EcT as a therapeutic platform for the treatment of at least gastrointestinal-based diseases.

Association of Bowel Movement Frequency with Cognitive Function in Women and Men

Presented by: Chaoran Ma

Background: Abnormal gastrointestinal motility and perturbations in the gut microbiome may contribute to cognitive impairment and dementia. We examined the associations of bowel movement (BM) frequency with objective and subjective cognitive function in 139,978 women and men from Nurses’ Health Study (NHS), Nurses’ Health Study II (NHSII) and Health Professionals Follow-Up Study (HPFS), and explored the mediating role of the gut microbiome in a subsample.

Methods: Participants in all three cohorts reported their BM frequency in 2012/2013 and subsequently (2014-2017) self-reported subjective cognitive dysfunction. In NHSII, 14,586 participants completed the CogState neuropsychological battery for objective cognitive assessment annually 2014-2018. We profiled the gut microbiome using shotgun metagenomics in fecal samples collected from a subpopulation of 515 women and men.

Results: The average age was 76 years in NHS, 61 in NHSII, and 75 in HPFS at the first cognitive assessment. After adjustment for potential confounders, BM frequency was associated with global objective cognitive function and its subdomain,learning and working memory, in an inverse U-shape dose-response manner (both P quadratic=0.02). Compared to those with daily BM, participants in the highest (>twice/day) and lowest categories (every 3+ days) of BM frequency had 0.03 and 0.06 standard units (equivalent to 1-2 additional years of age) lower in global cognition, respectively. We found similar inverse U-shape dose-response associations of BM frequency with overall subjective cognitive function and its subdomains (all P quadratic <0.001).  Compared to daily BM, the odds ratios (95% CI) of cognitive decline were 1.18 (1.08, 1.30) for every 3+ days, 1.08 (1.01, 1.15) for every 2 days, and 1.10 (1.05, 1.15) for ≥ twice/day (P quadratic <0.001). The association between BM frequency and cognition was consistent across subgroups defined by age, laxative use, antibiotic use, hypertension, hypercholesterolemia, diabetes, smoking status, weight status, and APOE4 genotype. BM frequency and subjective cognition were each significantly associated with the overall variation of the gut microbiome (P <0.001 for BM frequency; P = 0.02 for cognition) and specific microbial species. Methanogenic bacteria, e.g., Methanobrevibacter smithii, were enriched in participants with less frequent bowel movements. Pro-inflammatory bacteria, e.g., Ruminococcus gnavus, were enriched at one of the extreme ends of BM frequency. Many microbial features, e.g., increased Veillonella parvula, were associated with both more frequent BM and worse cognition. Our mediation analysis suggested that the gut microbial taxonomy explained 81% of the association between BM frequency and cognition.

Conclusions: Abnormal bowel movement frequency was associated with worse cognitive function. The association may be mediated through differences in gut microbiome composition.

Gut Microbial Metabolism of 5-ASA Diminishes Its Clinical Efficacy in Inflammatory Bowel Disease

Presented by: Raaj S. Mehta

For decades, the variable clinical efficacy of the widely used inflammatory bowel disease (IBD) drug, 5-aminosalicylic acid (5-ASA), has been attributed in part to its acetylation and inactivation by gut microbes. Identification of the responsible microbes and enzyme(s), however, has proved elusive. To uncover the source of this metabolism, we created an integrated workflow combining metagenomics, metatranscriptomics, and metabolomics data from a longitudinal cohort of patients with IBD and controls. This identified 12 previously uncharacterized microbial acetyltransferases belonging to two protein superfamilies, the thiolases and acyl-CoA N-acyltransferases. In vitro characterization of a representative from the highly conserved thiolase family confirmed the ability of these enzymes to acetylate 5-ASA. A subsequent cross-sectional case-control analysis within the discovery cohort then confirmed that this and other microbial thiolases were associated with an increased risk of treatment failure among 5-ASA users. Together, these data address a long-standing challenge in IBD management, outline a workflow for the discovery of previously uncharacterized gut microbial activities, and advance the possibility of microbiome-based personalized medicine.
One-Sentence Summary: Gut microbial enzymes inactivate a commonly used drug in inflammatory bowel disease, 5-ASA, and, in turn, are associated with treatment failure.

Vaginal Lactobacilli-mediated Anti-Inflammatory Effects on Host Immune Response

Presented by: Morgan Martin

Vaginal bacterial communities of people across the world are dominated by a few lactobacilli species. Loss of lactobacilli dominance is linked to increased vaginal inflammation with higher levels of pro-inflammatory cytokines.  Our work aims to understand how the presence of dominant Lactobacilli species may modulate host immune response to reduce inflammation. We used a human monocyte-derived macrophage reporter cell line, THP1, to screen cell-free supernatants from vaginal lactobacilli for immunomodulatory effects on type I Interferon and NFkB activation and downstream signaling. Addition of cell-free supernatant from vaginal but not intestinal lactobacilli strains suppressed activation of multiple Toll-Like Receptors including TLR2, 3 and 4.  Prior activation of cells with TLR agonists induced Interferon and NFkB activation which was suppressed upon addition of cell-free supernatant from vaginal but not intestinal lactobacilli species. Our results suggest that vaginal lactobacilli secrete compounds that suppress inflammatory signaling in human macrophages. With our collaborators, we have screened for and identified active fractions from the supernatant of Lactobacillus crispatus strain MV1A. This work aims to help elucidate the bacterial metabolite(s) responsible for suppression of host TLR signaling pathways. The findings of this study will help increase our understanding of how the lactobacilli-dominated vaginal microbial communities influence host immunity to reduce inflammation.

Linking individual microbial and metabolite biomarkers of Colorectal Cancer using computational models of gut microbiota metabolism

Presented by: Matthew S Miyasaka

Colorectal cancer (CRC) is the second most deadly cancer in the world, affecting almost 150,000 Americans each year and leading to over 50,000 deaths. Numerous microbial species and the metabolites they produce in the gut have been associated with the development and spread of CRC. However, it remains unknown to what extent the gut microbes, individually or collectively, contribute to the gut metabolome and affect CRC carcinogenesis. To better understand the functional role of individual microbial species in CRC carcinogenesis, we used a bottom-up systems biology approach based on GEnome-scale Models (GEMs) of metabolism to functionally profile the gut microbiota at species and molecular level resolution in CRC. To this end, we used publicly available fecal metagenomic data from 30 subjects with CRC and 30 non- CRC controls to construct GEMs of the gut microbiota metabolism at species-level resolution (spanning 113 microbial species). By computationally simulating these models, we could infer the metabolic activity of each microbial species in the gut, which allowed us to trace back individual microbial species producing specific secreted metabolites. This analysis identified 338 metabolites with differential production levels by the gut microbiota as well as over 400 linkages between specific microbial species and metabolites that were significantly different between CRC subjects and non-CRC controls (Wilcoxon, adjusted p < 0.01). Several of these identified metabolites and species have been previously implicated in CRC, examples of which include chicory inulin, deoxycytidine, and acetate that are produced by Faecallibacterium prausnitzi, Eubacterium eligens, and Bacteroides vulgatus, respectively, amongst other species, according to our models. Overall, our study provides a roadmap for mechanistically linking microbial and metabolite biomarkers of CRC.

Effects of whey protein supplementation on gut microbiota in colitis mouse model

Presented by: Maria Montibeller

The Ulcerative Colitis (UC) is characterized by chronic relapsing intestinal inflammation. Considering the impact of UC on the quality of life, dietary interventions have been proposed to reduce the associated symptoms. Supplementation with bioactive peptides like whey protein (WP) may reduce symptoms of UC by modulation of gut microbiota and immune system due the production of mucins and metabolites. In this way, the short-wave ultraviolet (UV-C) procedures have been used to improve the digestibility and release of bioactive peptides during WP digestion. In the present study induced UC mice were fed a standard diet plus WP with or without UV-C treatment. We induced UC in mice by a treatment with dextran sulfate sodium (DSS). Male C57BL/6J mice (n = 10 per group) were divided in: H group – healthy mice; C group – DSS mice that did not receive WP; W group – DSS mice fed with WP without UV-C treatment and WU group – DSS mice fed with WP functionalized by UV-C treatment. WP administration started seven days before colitis induction and continued through the seven days of DSS induction. The severity of colitis was daily determined by disease activity index (DAI) and the fecal microbiota was analyzed in the days 0, 7, 12 and 14. In all DSS-induced mice, a reduction in the alpha-diversity was observed across the experimental time. Moreover, all groups display a similar Shannon index through the experiment (p > 0.05). Microbiota composition was affected by the treatment. A decrease in Lachnospiraceae both in W and WU groups (p < 0.05) was observed. However, at study end (day 14) a restore in Lachnospiraceae was observed (p > 0.05). Finally, Oscillospiraceae (associated with H group) and Turicibacter (W group), increased during the experiment. The animals in the WU group showed a reduction in the characteristic symptoms of colitis (diarrhea, weight loss, and presence of blood in the feces), without differing from the H group on day 11 of the protocol (p<0.05). The results indicate that the different WP production could result in a restoration in beneficial taxa and slower symptom progression in colitis mouse model. Although future studies are needed to confirm these beneficial effects. This study was financed in part by the Coordenação de Aperfeiçoamento de Pessoal de Nível Superior – Brasil (CAPES) – Finance Code 001. Processo FAPESP: 2017/01189-0.

The Harvard T.H. Chan School of Public Health Microbiome Analysis Core

Presented by: Xochitl Morgan

The Microbiome Analysis Core at the Harvard T.H. Chan School of Public Health was established in response to the rapidly emerging field of microbiome research and its potential to affect studies across the biomedical sciences. The Core’s goal is to aid researchers with microbiome study design and interpretation, reducing the gap between primary data and translatable biology. The Microbiome Analysis Core provides end-to-end support for microbial community and human microbiome research, from experimental design through data generation, bioinformatics, and statistics. This includes general consulting, power calculations, and selection of data generation options, as well as analysis of data from amplicon (16S/18S/ITS), shotgun metagenomic sequencing, metatranscriptomics, metabolomics, and other molecular assays. The Microbiome Analysis Core has extensive experience with microbiome profiles in diverse populations, including taxonomic and functional profiles from large cohorts, qualitative ecology, multi’omics and meta-analysis, and microbial systems and human epidemiological analysis. By integrating microbial community profiles with host clinical and environmental information, we enable researchers to interpret molecular activities of the microbiota and assess its impact on human health.

Changes in taxonomic and metabolic composition among NAFLD patients

Presented by: Paul Nelson

Non-alcoholic fatty liver disease (NAFLD), which is strongly associated with obesity and type 2 diabetes, affects up to 25% of the adult population in the US. Human and mouse studies1, 2 have suggested gut microbiome as a causal factor in the pathogenesis of NAFLD. To investigate the role of the gut microbiome in NAFLD, we examined metagenomics and metabolomics from 211 subjects with NAFLD and 457 healthy controls from the Nurses’ Health Study II. We found that NAFLD explains a significant, but relatively small (>1%), amount of the taxonomic and metabolic variability in the microbiome. Despite this relatively weak signal, we identified several metabolites and species associated with the disease phenotype. Specifically, we highlight the role of the microbially produced bile acid, isoallolithocholic acid (isoalloLCA) in NAFLD. Our results link together previous research on microbial manipulation of Treg and Th17 immune cells3, and the role of the immune system in NAFLD4. All together this study represents the largest multi-omics study to date of the microbiome in NAFLD.

The Gut Microbiome in Parkinson’s Disease in the Nurses’ Health Study and Health Professionals Follow-up Study

Presented by: Natalia Palacios

Funding Sources for study: This study was funded by NIH (R01NS097723; PI: Palacios).

Objective:  Prior studies on the gut microbiome in Parkinson’s disease (PD) have yielded conflicting results, and few studies have focused on prodromal (premotor) PD or used metagenomic profiling.  We conducted a nested case-control study within two large epidemiological cohorts to examine the role of the gut microbiome in PD.

Methods: We profiled the fecal metagenomes of 420 participants in the Nurses’ Health Study and the Health Professionals Follow-up Study with recent onset PD (N = 75), with features of prodromal PD (N = 101), controls with constipation (N = 113), and healthy controls (N = 131) to identify microbial taxonomic and functional features associated with PD and PPS.  We conducted omnibus and feature-wise analyses to identify bacterial species and pathways associated with prodromal and recently onset PD.

Results: We observed depletion of several strict anaerobes associated with production of anti-inflammatory short-chain fatty acids among participants with PD or features of prodromal PD.  A microbiome-based classifier had moderate power (AUC = 0.76 for species and 0.74 for pathways) to discriminate between recently onset PD cases and controls.  These taxonomic shifts corresponded with functional shifts indicative of alternative in carbohydrate degradation.  Similar, but less marked, changes were observed in people with PPS, in both microbial features and functions.

Interpretation: In this study nested within two large cohorts with rich covariate data and rigorous PD identification, we observed that PD and PPS were associated with similar changes in the gut microbiome. These findings suggest that changes in the microbiome could represent novel biomarkers for the earliest phases of PD.

Inflammation as Acne Vulgaris (AV): 15-day exclusion diet examined with concurrent changes in the gut microbiome

Presented by: Marie Ryan

AV is the world’s most common inflammatory skin disease, and has been associated with a range of agents such as C.acnes, androgens, genetics, dairy products, stress, or sugary foods such as chocolate1. A pilot study spanning 15 days was completed in 2019-2020 in Vientiane, Laos2 to test if limiting the consumption of three simple sugar groups found in everyday foods could regulate inflammation occurring in AV and correlated with changes in the gut microbiome over the same period. An adult Lao AV cohort was advantageous as Lao people consume little to no dairy, wheat products, or highly processed foods that have often been cited as contributing to the development of AV.
Design and method: The study was a non-randomized, prospective observational dietary cohort of 27 healthy adult AV cases (25F/2M). A catered diet low in target sugars was supplied for 15 days, where glycemic load and dairy products were not restricted. IGA scores (IGA 1-5) were agreed (baseline and endpoint) by two dermatologists. Self-reported adherence was >90%. Fecal samples from 27 AV cases were taken at baseline and endpoint as well as samples from 4 non-AV healthy adults as controls, for DNA analysis (Shallow Shotgun Metagenomic Sequencing (SSMS) Diversigen Laboratories MN USA) Intestinal parasite exams were completed at pre-inclusion, baseline and endpoint, with treatment as appropriate.

Results at endpoint Day 15: Any IGA improvement was observed for 19/27 (70.3%) with at least a 2-point IGA improvement for 6 of them (22.2%) representing a clinically meaningful outcome (asspecified by the US-FDA). No change in IGA score was observed for 6 participants (22.2%) and worsening for 2 (7.4%). Positive parasite exams were found for 5/27 at baseline (18.5%), 5 at endpoint (18.5%) with 2 both at baseline and endpoint. Weight loss (-1-4 kg) was reported for 20/27 cases (74.1%) All participants reported bathroom frequency/ease improvement. Observed/reported excess consumption and resultant AV lesions (<2 hours) has meant analysis of the gut microbiome is focused on bacterial species/strains located in the proximal end of the small intestine.

Conclusions: Our dietary cohort results suggest that limiting target simple sugar groups (<40grams total/day) impacted positively on AV and improved bathroom frequency and ease in our cohort. Preliminary analysis for 26 subjects (1 sample excluded) suggest nine bacterial strains may be of interest in helping establish the etiology of AV.
Keywords: acne vulgaris, microbiome, simple sugar groups, malabsorption, inflammation
1 https://ada.com/conditions/acne-vulgaris/#causes
2 Ethics Approval No.075/NECHR Lao National Ethics Committee for Health Research

Sample size calculation for differential abundance tests in microbiome epidemiology

Presented by: Meghan Short

Tests of feature differential abundance are a cornerstone of microbiome analysis, and a wide variety of such tests is available. Reliable methods for power and sample size estimation for such tests, however, are lacking. Traditional parametric or rank-based sample size formulae do not account for the unique challenges posed by microbial feature data, including an abundance of biological and technical zero values, compositionality, and the potential for associations of clinical or environmental variables with feature abundance and/or prevalence. To benchmark existing power formulae, we use a rich simulation framework previously implemented in SparseDOSSA2 to fit zero-inflated log-linear models to microbial read counts and generate realistic synthetic feature tables. By simulating many feature tables with the same underlying distributions, we estimate power for various scenarios. We identified strong relationships between power and feature prevalence, which is unaccounted for in standard formulae for parametric tests. Use of an “effective” sample size accounting for feature prevalence improved power calculation accuracy (i.e., similarity to simulated power) in these cases. We plan to streamline best approaches in a new software, Sample Sizes for Microbiome Research (SSMoRe), which we will validate using resampling techniques in previously published data from 16S and metagenomic studies.

A symbiont’s sensing of host mucin regulates its biogeography and inflammatory potential in the intestine

Presented by: Jarrod Smith

Intestinal mucus is thought to promote host health by functioning as a passive barrier that
distances potentially inflammatory symbiotic microbiota from the gut epithelium. Here we report
new evidence that beneficial microbes sense and respond to intestinal mucus by self-limiting
their intestinal distribution and inflammatory capacity, thus actively promoting host health. Our
work couples experimental microbial evolution with live imaging of bacterial dynamics and
transgenic reporters of host inflammation across the entire intestine to probe the distribution,
physiology, and inflammatory potential of a beneficial bacterium Aeromonas (Aer01) in its
native host, the larval zebrafish. Aer01 typically forms large aggregates in a distinct intestinal
region. Phenotypic and subsequent genomic analysis of evolved Aer01 that do not respond to
mucin in culture identified a putative mucin-sensing two-component system and surface associated mucin-binding adhesin that are crucial for driving Aer01 aggregation and localization in the host intestinal environment. Disruptions in either pathway dramatically transformed Aer01 intestinal distribution and aggregative clustering, stimulating the host innate immune system and leading to increased intestinal inflammation. We also found Aer01 mucin-sensing disruptions altered the community composition in defined 2- and 5- member communities. Together, our work highlights the important but largely unexplored role of microbial mucin sensory pathways in promoting host health and contributing to community composition.

The Microbiome Collection Core at the Harvard T.H. Chan School of Public Health (HCMCC)

Presented by: Magnus Stefansson

The Microbiome Collection Core at the Harvard T.H. Chan School of Public Health (HCMCC) was established in response to a strong demand among the research community for validated microbiome sample collection kit configurations and easy usability for in-home sampling. Under the umbrella of the Harvard Chan Microbiome in Public Health Center (HCMPH), HCMCC aims to support population-scale microbiome sample collection and expand our understanding of the microbiome to improve population health. The HCMCC has developed a multi carrier-compatible home stool and oral sample collection kit that permits cost-effective multi’omic microbiome studies, leveraging the intellectual and infrastructure foundation laid by the HMP2 (the 2nd phase of the NIH Human Microbiome Project) and the MLSC (Massachusetts Life Sciences Center)-funded MICRO-N (MICRObiome Among Nurses) collection. By providing this customizable microbiome collection kit, we enable researchers to perform multiple different molecular assays and tailor collection plan to study-specific needs.

Commensal microbes can regulate skin barrier through the control of Tryptophan-Aryl Hydrocarbon Receptor cascade

Presented by: Aayushi Uberoi

Commensal microbes are critical in maintaining skin homeostasis. However, their mechanisms of crosstalk with host epithelia during barrier disruption and repair are not defined. Our goal is to understand mechanisms by which skin microbiome regulate skin barrier. Using germ free (GF) mice, we have recently demonstrated that microbiota is necessary and sufficient for proper differentiation and repair of the epidermal barrier (Uberoi et al., Cell Host & Microbe, 2021). By comparing epithelial transcriptomes of GF mice to specific pathogen free (SPF) mice we found that microbiota regulate genes involved in epithelial development and differentiation. GF mice were impaired in barrier repair compared to SPF mice following tape-stripping, as measured by transepidermal water loss. We identified the aryl hydrocarbon receptor (AHR) pathway as downregulated in GF epidermis. As AHR is a regulator of epidermal differentiation, we hypothesized that skin microbiota promotes barrier repair by activating AHR. Activating AHR in GF mouse skin through a topical AHR-activator, rescued impaired barrier repair function of GF skin. We found that colonization with a defined consortium of human skin commensals curated from healthy human skin restored barrier competence in AHR-dependent manner in homeostasis as well as in models of atopic dermatitis. Tryptophan (Trp) metabolites are potent AHR ligands and cornified skin envelope is a rich source of substrates for Trp metabolism by microbes. We constructed Trp metabolic enzyme profiles and mined them against healthy human skin metagenomes and microbe genomes within the defined consortium. We found motif enrichment for enzymes that metabolize Trp to indole and its derivatives, e.g., indole-3-acetaldehyde, indole propionic acid. We tested 14 indole-derived metabolites and found that several metabolites can improve skin barrier in vitro in primary keratinocytes and in models of reconstructed human epidermis. We reveal a fundamental mechanism whereby the microbiota regulates skin barrier formation and repair through Trp metabolism, with far-reaching implications for the numerous skin disorders characterized by epidermal barrier dysfunction.

Evaluating isolation methods for human gut viral communities

Presented by: Ya Lea Wang

Characterization of gut viral communities is of great importance: there are enormous viruses living in human gut – equaling or exceeding the number of human cells, whereas the majority of this population remain uncharacterized. Molecular and computational methods have both been utilized in previous studies to isolate and quantify the viral portion of microbial communities.
These have ranged from experimental approaches that isolate virus-like particles (VLPs), to the analysis platforms profiling the compositions and functions of viral communities. However, these studies mostly focused on analyzing the resulting viral communities without systematic evaluations of the isolation strategy. Particularly, it often remains unclear whether the selected protocol could efficiently remove bacterial-originated nucleic acids while leaving the viral potion unaffected.
Here, we present our work in optimizing and validating a workflow for the isolation of virus-like particles from gut microbial communities with thorough evaluation of different experimental parameters known to potentially affect viral extraction, including storage buffer, filtration combinations, methods for nucleic acid concentration after filtration, and various enzymatic treatments. Different combinations of the above parameters were first evaluated in stool samples spiked with simple synthetic viral communities comprising an sRNA phage (MS2) and a dsDNA phage (T4), to find out a combination with the highest purification efficiency as well as the minimum impact on the spiked viruses. The optimized protocol was then applied in more complicated mock viral communities consisting of more complexed viruses representing several common viral families in the gut (i.e. T4, T1, P1, PhiX174 and MS2). Stool samples were spiked with these mock communities, to see if the VLP isolation protocol caused any differential bias to different families of viruses. Results showing that the optimized VLP isolation protocol efficiently reduces the signals from bacterial communities (16S rRNA genes) from ~105 copies/ml to undetectable in mock communities. By comparison, minimal variations were observed in virus copies between whole communities vs. VLP concentrated communities. When applied in stool samples spiked with synthetic viral communities, the protocol depleted bacterial signals by approximately 100 fold. P1, T1 and T4 phages were depleted in VLP concentrated communities, while PhiX174 and MS2 phages were slightly enriched. This differentiation is likely introduced by the detection method (i.e. qPCR) rather than the protocol itself, given that the quantification of viruses varied greatly across different measurements.
We are currently continuing this work to further validate this VLP isolation protocol using shotgun metagenomic and metatranscriptomic sequencing in spiked stool samples (as above) and in stool samples collected from preemie babies, as well as to develop optimized computational approaches for the taxonomic and functional profiling of gut viral communities. These can circumvent some of the current limitations of the VLP isolation protocol, providing a complementary view of viral communities, and directly observing functional activities involved in the gut-virome-bacteriome interaction.

Diet and the gut microbial interactions in irritable bowel syndrome subtypes

Presented by: Yiqing Wang

Background: Irritable bowel syndrome (IBS) is a common functional gastrointestinal disorder, yet the role of diet and gut microbial communities in the pathophysiology of IBS is not fully understood. Thus, we investigated the interplay between dietary risk factors and specific taxonomic and functional groups in IBS subtypes.

Methods: We drew data from the Personalized Responses to Dietary Composition Trial (PREDICT) 1 study, a single-arm, single-blind intervention study of 969 UK adults aged 18-65 years using standardized meals to predict individual metabolic response to foods. Participants were classified into non-IBS and IBS subtypes (IBS-C, constipation; IBS-D, diarrhea; IBS-M, mixed) according to Rome III criteria. Habitual diet was assessed using a food frequency questionnaire and gut microbiome by metagenomic sequencing of stool samples.

Results: Participants with IBS (172, 18%) were predominantly female, younger, and attained higher levels of education than those without IBS (Figure 1A). Participants with IBS-D (49, 5%) more frequently consumed healthy plant-based foods compared to other participants, as well as higher levels of animal-based foods but lower levels of lactose than those without IBS (Figure 1B). Gut microbiome composition differed slightly by IBS subtype, as reflected by nominally lower microbial diversity in IBS-D (Figure 2 A-B). Using linear regression adjusted for a wide range of host factors, we identified several taxa and functional pathways associated with specific IBS subtypes, including slight increases in typically pro-inflammatory taxa during IBS-C (e.g. Ruminococcus gnavus, Escherichia coli) and loss of typical gut strict anaerobes during IBS-D (e.g Faecalibacterium prausnitzii), explaining the overall lower diversity. Although limited by the available population size, these taxa showed intriguing evidence of interaction with dietary risk factors in association with IBS subtypes (Figure 2C). For example, while the predicted probability for IBS-D based on a multivariable-adjusted binomial model was lower at higher levels of Faecalibacterium prausnitzii when fiber intake was low, this association was reversed as fiber intake increased. Although outperformed by other host factors, as expected for the notoriously multifactorial etiology of IBS, gut microbial taxa and functional pathways were significant independent machine learning predictors for distinguishing participants with IBS-D from those with IBS-C or no IBS (Figure 2D).

Conclusions: We identified variations in gut microbial composition, function, and diet-microbiota interactions specific to IBS subtypes. Our findings may provide insights into microbiome-aware dietary interventions for IBS treatment. Further longitudinal studies are needed to confirm our results.

Identifying strain-specific functional genes in colorectal cancer

Presented by: Yan Yan

Changes in the gut microbiota have been associated with colorectal cancer (CRC), but neither the causal mechanisms nor the underlying microbial strains and molecular products needed to understand mechanistic connections have been elucidated. To identify these, we extended a previous meta-analysis to include stool metagenomic profiles of 600 CRC patients, 143 with precancerous adenomas, and 662 healthy controls from nine recently published CRC microbiome studies. We developed a method called MMUPHin to jointly normalise these datasets and identify specific microbial species and strains significantly correlated with the presence and/or severity of CRC neoplasia. Our approach uncovered novel CRC biomarkers, including several strains typical of the oral cavity, as well as enrichment in encoded metabolic pathways underlying the production of butyrate, lysine, acetate, and several tumor-promoting metabolites, such as ammonia and polyamines. These metabolic capabilities were carried predominantly by prevalent species of Bacteroides, Alistipes, or facultative anaerobes Escherichia and Klebsiella. Interestingly, we identified instances where the gene carriage was significantly different among strains of the same species in CRC patients compared to control individuals, indicating strain-specific functional distinctions in the CRC microbiome that would be invisible in taxonomically-focused analyses. We also found a group of genes unique to subsets of E. coli pan-genome associated with CRC phenotypes, comprising encoded pathways for lysine degradation, adhesion, and flagellar motility. We are currently testing whether these strain associations are phylogenetically enriched. Our work thus uncovers specific microbial strains, gene products, and pathways with potential bioactivity in CRC, providing new leads for future mechanistic studies that will advance our understanding of the microbiome’s role in CRC initiation and development.

Pharmacological inhibition of gut microbial β-glucuronidase enzymes blocks DSS-induced colon inflammation

Presented by: Jianan Zhang

Colon inflammation and colitis-induced colon tumorigenesis show a gradually increasing incidence with patient age. Due to the complicated genetic and environmental factors involved, however, there are currently no targeted therapeutic approaches available to reduce colon inflammation. Furthermore, the molecular mechanisms involved in how gut microbiota influence colon inflammation are poorly understood. Here we report that microbial β-glucuronidase (GUS) enzymes act as a therapeutic target to reduce colon inflammation in mice. We find that pharmacological inhibition of microbial GUS enzyme using UNC 10201652 abolishes dextran sodium sulfate (DSS)-induced colon inflammation in a dose-dependent manner. Inhibitor-treated mice show increased the colon length, decreased infiltration of immune cells (CD45+ cells, CD45+F4/80+ cells and CD45+ Gr1+ cells), decreased the inflammatory gene expression (Tnf- α, Il-6, Il-17, Il-23 and Tlr-4), and increased tight junction gene expression (Muc3 and Occludin) in colon. Furthermore, 16S rRNA sequencing reveals that inhibition of GUS altered the alpha diversity and the dysbiotic composition of gut microbiota caused by DSS, with changes in the abundance of Actinobacteria, Proteobacteria, Bacteroidetes and Firmicutes taxa. Overall, these results support the conclusion that microbial GUS enzymes could be a potential therapeutic target for the prevention and/or treatment of colon inflammation.

ACKNOWLEDGEMENT
Funded by NIH grants GM135218 and GM137286 (MRR).
Funded by interdisciplinary faculty research award from the University of Massachusetts
Amherst, USDA NIFA 2019-67017-29248 and 2020-67017-30844, and USDA/ Hatch MAS00556
(G.Z.)

Predicting functions of uncharacterized gene products from microbial communities

Presented by: Yancong Zhang

Microbial communities are rich reservoirs for molecular functions that influence environmental and host-associated chemistry, with numerous roles in ecosystem maintenance, health, and disease. However, our knowledge of these molecular mechanisms is limited, due to the massive range of microbial genetic material in comparison to the limited throughput available for experimental characterization. Here, we used a novel method to systematically predict functional capacity of uncharacterized proteins in the human microbiome by assessing high-dimensionality  community-wide data. We predicted potential functions for the large proportion of uncharacterized protein families (~70% of total) in 1,595 metagenomes and 800 metatranscriptomes from the Integrative Human Microbiome Project (HMP2). Using only MTX-based information, our approach achieved an average AUC for Gene Ontology (GO) biological process term prediction of approximately 0.7. By aggregating predictions from other types of information, the AUC was further improved to about 0.88. Further evaluations showed that our method is capable of recapitulating comparable, realistic prediction profiles from communities when compared against state-of-art single-organism tools. These results demonstrate the effectiveness of MTX-based evidence, which represents community-specific information independent of sequence similarity and can be used for predicting functions for novel microbial community proteins  (i.e. those which lack significant homologs to sequences in characterized microbial isolates). Our method is generalizable to any types of microbial communities, providing a new approach to predict microbial protein functions. We implemented it as an open-source tool, FUGAsseM (Uncharacterized Gene products by Assessing high-dimensional community data in Microbiome), along with documentation available at http://huttenhower.sph.harvard.edu/fugassem. This study expands our understanding of the capability of uncharacterized proteins in the human microbiome and establishes a key community-based methodology to unravel function for uncharacterized microbial proteins in communities.

Quantifying shared and unique gene content across 17 microbial ecosystems

Presented by: Samuel Zimmerman

Measuring microbial diversity is traditionally based on microbe taxonomy. Here, in contrast, we aimed to quantify heterogeneity in microbial gene content across 14,183 metagenomic samples spanning 17 ecologies including — 6 human-associated, 7 non-human-host-associated, and 4 in other non-human host environments. In total, we identified 117,629,181 non-redundant genes. The vast majority of genes (66%) occurred in only one sample (i.e. “singletons”). By contrast, we found 1,864 sequences present in every metagenome, but not necessarily every bacterial genome. Additionally, we report datasets of other ecology-associated genes (e.g. abundant in only gut ecosystems) and simultaneously demonstrated that prior microbiome gene catalogs are both incomplete and inaccurately cluster microbial genetic life (e.g. at gene-sequence identifies that are too restrictive). We provide our results and the sets of environmentally-differentiating genes described above at http://www.microbial-genes.bio