2020 – Poster Session

Presenter Name	Poster Title
Emma Accorsi	Determinants of Staphylococcus aureus carriage in the developing infant nasal microbiomeEmma K. Accorsi, Eric A. Franzosa, Tiffany Hsu, Regina Joice Cordy, Ayala Maayan-Metzger, Hanaa Jaber, Aylana Reiss-Mandel, Casey DuLong, Marc Lipsitch, Gili Regev-Yochay, Curtis Huttenhower
Nicole Altomare	Changes in intestinal gene expression in antibiotic-treated NOD miceNicole Altomare, Xue-Song Zhang, Martin J. Blaser
Aline Alves de Santana	Effect of the Moro and Pera orange juice intake on gut microbiota composition in obese individualsSantana A.A,  Santos K.G,  Kovacs C, Magnoni C.D., Thomatielli-Santos R.V, Hassimotto N.M.A, Lajolo F
Sena Bae	Discovery of new bioactive microbial metabolites in inflammatory bowel diseaseSena Bae, Amrisha Bhosle, Eunyoung Chun, Yancong Zhang, Julian Avila-Pacheco, Jessica K. Lang, Kathryn G. Rosinski, Clary Clish, Ramnik Xavier, Hera Vlamakis, Eric A. Franzosa, Curtis Huttenhower, Wendy Garrett
Amrisha Bhosle	Prioritization and annotation of novel bioactive small molecules from the microbiomeAmrisha Bhosle, Sena Bae, Yancong Zhang, Eunyoung Chun, Julian Avila-Pacheco, Clary Clish, Ramnik Xavier, Hera Vlamakis, Eric A. Franzosa, Wendy S.Garrett, Curtis Huttenhower
Caitlin Brennan	Modulation of the intestinal immune cell compartment by Fusobacterium nucleatum in mice with a minimal complexity microbiotaCaitlin A. Brennan, Sydney L. Lavoie, Jessica K. Lang, Kathryn G. Rosinski, Slater L. Clay, Wendy S. Garrett
Tobyn Branck	Diet-linked dynamics of metagenomes and metatranscriptomesTobyn A. Branck, Jason Lloyd-Price, Long H. Nguyen, Dong D. Wong, Mingyang Song, Yin Cao, Wenjie Ma, David Drew, Raaj S. Metha, Cesar Arze, Galeb Abu-Ali, Himel Mallick, Gholamali Rahnavard, Yan Yan, Amit D. Joshi, Kerry Ivey, Jacques Izard, Wendy S. Garrett, Eric Rimm, Andrew T. Chan, Curtis Huttenhower
Eunyoung Chun	SCFA-sensing receptor Ffar2 regulates group 3 innate lymphoid cells and gut immunityEunyoung Chun, Sydney Lavoie, Diogo Fonseca-Pereira, Sena Bae, Monia Michaud, Graeme L. Fraser, Jonathan N. Glickman, Brian T. Layden, Wendy S. Garrett
Eric Franzosa	The landscape of novel lateral gene transfer events in the human microbiomeEric A. Franzosa, Tiffany Y. Hsu, Dennis Wong, Chengwei Luo, Robert G. Beiko, Morgan Langille, Curtis Huttenhower
Jennifer Lee	The Anti-Diabetic Effects of Palmitic Acid Hydroxy Stearic Acid (PAHSA) Lipids are Transmissible by Fecal Microbiota Transplantation (FMT) in MiceJennifer Lee, Kerry Wellenstein, Barbara B. Kahn
Chengchen (Cherry) Li	The Microbiome Collection Core at the Harvard T.H. Chan School of Public HealthChengchen Li, Jeremy E. Wilkinson, Curtis Huttenhower
Wodan Ling	Microbiome differential abundance analysis by zero-inflated quantile rank-score based testWodan Ling, Michael C. Wu
Siyuan Ma	A Hierarchical Model for Microbial Community StructureSiyuan Ma, Boyu Ren, Eric A. Franzosa, Lucas Janson, Curtis Huttenhower
Wenjie Ma	Dietary fiber intake, gut microbiome, and chronic systemic inflammationWenjie Ma, Long H. Nguyen, Mingyang Song, Daniel D. Wang, Eric Franzosa, Yin Cao, Amit Joshi, David A. Drew, Raaj Mehta, Kerry Ivey, Jacques Izard, Wendy Garrett, Eric B. Rimm, Curtis Huttenhower, Andrew T. Chan
Camila Guazzelli Marques	Effects of endurance exercise on mood state and serotonin levels after thirty days of probiotic supplementation: a pilot studyMarques CG, Tavares-Silva, Tonelli L., Lemos VA, Caris AV, Santos SA, Ravacci GR, Thometieli-Santos RV
Edgar Tavares-Silva	Effects of 30 days Probiotic Supplementation on Monocytes function after a Marathon Race. A randomized, double-blind-placebo studyEdgar Tavares-Silva, Geovana S F Leite, Helena A P Batatinha, Ayane S Resende, Antônio H Lancha Junior, José C R Neto3, Ronaldo V Thomatieli-Santos
Kelsey Thompson	Inflammatory arthritis and the gut microbiomeKelsey N Thompson, Kevin S Bonham, Nicholas E Ilott, Lilian H Lam, Paula Colmenero, Andrew Filer, Sam J Bullers, Matthew A Jackson, India Brough, Chelsea M Regan, Stephen P Young, Arthur G Pratt, Paul Bowness, Dan R Littman, Karim Raza, Fiona Powrie, Curtis Huttenhower
Aaron Walsh	Distinct Actions of the Fermented Beverage Kefir on Host Behaviour, Immunity and Microbiome Gut-Brain Modules in the MouseAaron M. Walsh, Marcel van de Wouw, Fiona Crispie, Lucas van Leuven, Joshua M. Lyte, Marcus Boehme, Gerard Clarke, Timothy G. Dinan, John F. Cryan, Paul D. Cotter
Lea Wang	Characterizing microbial community viability using propidium monoazideLea Wang, Yan Yan, Kelsey N. Thompson, Sena Bae, Jiaxian Shen, Hera Vlamakis, Erica M. Hartman, Curtis Huttenhower
Jeremy Wilkinson	The Harvard T.H. Chan School of Public Health Microbiome Analysis Core: Advancing Microbiome ResearchJeremy E. Wilkinson, Lauren J. McIver, Kelsey N. Thompson, Chengchen Li, Curtis Huttenhower
Yan Yan	Identifying strain-specific functional genes with colorectal cancerYan Yan, Andrew M. Thomas, Eric A. Franzosa, Long H. Nguyen, Tobyn Branck, Nicola Segata, Andrew T. Chan, Wendy S. Garrett, Curtis Huttenhower
Yue (Sandra) Yin	Antibiotic-Induced Perturbations of the Gut Microbiota Alter IlealMicroRNA Expression Profiles in Non-Obese Diabetic MiceYue Sandra Yin, Xue-Song Zhang, Martin J. Blaser
Yue (Sandra) Yin	Deletion of Serum Amyloid A Increases Weight Gain in MiceYue Sandra Yin, Martin J. Blaser
Meifan Zhang	The role of the microbiota in neutralizing trypsin activity in a mouse model of Type 1 diabetesMeifan Zhang, Xue-song Zhang ,Yue (Sandra) Yin, Martin J. Blaser
Yancong Zhang	Identifying Novel Bioactive Microbial Gene Products in Inflammatory Bowel DiseaseYancong Zhang, Eric A. Franzosa, Sena Bae, Lauren Mclver, Gholamali Rahnavard, Cesar Arze, Damian R. Plichita, Ayshwarya Subramanian, Wendy S. Garrett, Andy Krueger, Hera Vlamakis, Ramnik J. Xavier, Curtis Huttenhower

Determinants of Staphylococcus aureus carriage in the developing infant nasal microbiome

Presented by: Emma Accorsi

Staphylococcus aureus is a leading cause of healthcare- and community-associated infections and can be difficult to treat due to antimicrobial resistance. About 30% of individuals carry S. aureus asymptomatically in their nares, a risk factor for later infection, and interactions with other species in the nasal microbiome likely modulate its carriage. It is thus important to identify ecological or functional genetic elements within the maternal or infant nasal microbiomes that influence S. aureus acquisition and retention in early life. We recruited 36 mother-infant pairs and profiled a subset of monthly longitudinal nasal samples from the first year after birth (n=284) using shotgun metagenomic sequencing. The infant nasal microbiome was highly variable, particularly within the first 1-2 months. It was weakly influenced by maternal nasal microbiome composition, but primarily shaped by developmental and external factors (e.g. daycare). Infants displayed distinctive patterns of S. aureus carriage, positively associated with Acinetobacter species, Streptococcus parasanguinis, Streptococcus salivarius, and Veillonella species and inversely associated with maternal Dolosigranulum pigrum. Furthermore, we identified a gene family, likely acting as a taxonomic marker for an unclassified species, that was significantly anticorrelated with S. aureus in infants and mothers. In gene-content based strain profiling, infant S. aureus strains were more similar to maternal strains. This improved understanding of S. aureus colonization is an important first step toward development of novel, ecological therapies for controlling S. aureus carriage.

Changes in intestinal gene expression in antibiotic-treated NOD mice

Presented by: Nicole Altomare

Nicole Altomare, BS, Xue-Song Zhang, PhD, and Martin J. Blaser, MD
Robert Wood Johnson Medical School, Piscataway, NJ; Center for Advanced Biology and Medicine, Piscataway, NJ

Objective: We sought to understand how intestinal gene expression is affected following antibiotic treatment in non-obese diabetic (NOD) mice and to correlate this to the timing of Type 1 diabetes (T1D) onset.

Methods: Samples were obtained from control mice, NOD mice treated with PAT (one course of the macrolide antibiotic tylosin), and from NOD mice treated with PAT given a gavage of their mother’s cecal microbiome. Ileal and colonic samples were obtained at day of life 23 and 42. RNA was extracted, converted to cDNA, and expression was analyzed using RT-qPCR. A total protein assay and ELISA were performed to examine levels of expression of genes involved in host defenses antimicrobial peptides (REG3-γ), G protein-coupled trypsin receptor (F2RL1) and a tight junction molecule (zonulin).

Results:  For REG3-γ, there was a significant decrease in ileal expression between the control and the treatment groups and between the restoration and treatment groups at day 23. The difference between the control and treatment group remained significant at day 42. No significance was found in the colon samples. For F2RL1, no significance was found in the ileal samples. The colon showed a significant decrease between the control and (PAT) treatment group at day 23, which remained at day 42. For zonulin, there were no significant changes in expression within either the ileal or colonic samples.

Conclusions: We conclude that antibiotic exposure and restoration impacted ileal expression of REG3-γ and colonic expression of F2RL1, perhaps because of greater trypsin activity in the intestine, as shown in other studies. These changes may play a role in the earlier onset of T1D in the antibiotic-treated NOD mice. Zonulin expression was not affected by the antibiotic course, providing evidence that the observed dysbiosis did not affect the tight junctions.

Effect of the Moro and Pera orange juice intake on gut microbiota composition in obese individuals

Presented by: Aline Alves de Santana

Background:
Citrus juices contain greater quantities of bioactive compounds as flavones, flavonols, anthocyanins, and flavanones. The blood oranges are a pigmented sweet orange and the most common types of blood orange are varieties Moro, Tarocco, and Sanguinello. In recent years, there was an increase of interest in blood orange varieties because of their higher content of anthocyanins compared with non-pigmented variants (Pera, Navel, Valencia, and Ovale). Many studies have been described blood orange juice, especially variety Moro with antioxidant, antimutagenic, and anti-obesity properties. These are all bioactive compounds in juice and it is health benefits may be mediated by the synergic effects of its compounds. In the last years, the effect of these bioactive compounds, especially anthocyanins has been described in some studies indicating that the consumption of foods high in anthocyanins promotes the growth of certain types of beneficial bacteria and inhibits pathogenic bacteria. It has been demonstrated that obese individuals have a disrupted gut microbiota, with less diversity and richness than lean subjects. This altered gut microbiota is related to the metabolic disorders contributing to the development of type 2 diabetes, metabolic syndrome,
cardiovascular diseases, and certain cancers. Thus, the consumption of food rich in bioactive compounds can confer positive health benefits in obese individuals by modulation on gut microbiota composition.

Objective:
The objective of this study was to evaluate the effect of orange juice intake and the order of treatment in the modulation of gut microbiota of obese individuals with insulin resistance.

Methods:
A crossover clinical trial was conducted with 22 adults between 40 and 60 years old classified as obese according to BMI and insulin resistance by HOMA-IR. The volunteers were divided into two study groups where Group A was composed of 15 people and Group B was composed of 7. In the beginning of the the study group A consumed pera orange juice (POJ) and group B started with the moro orange juice (MOJ), for 15 days they consumed 400ml per day. In a second 40-day intervention (crossover), study-group subjects were switched to the opposite drinking order. The microbiome was analyzed based on new generation sequencing techniques of 16S rRNA genes. For data analysis, volunteers were categorized according to the order of treatment (who started with MOJ and those with POJ). This categorization was made considering the hypothesis that intake of anthocyanins before or after ingesting flavanones could have different effects and it could interfere with the composition of intestinal microbiota.

Statistical analysis:
Data are expressed as means ± SEM. The data were analyzed using a Mann- Whitney t-test for comparison between two groups. A value of P < 0.05 was considered statistically significant.

Results:
There was a significant difference between groups A and B. This difference can be explained by the phenolic compounds found in both juice types associated with synergistic effects that are dependents on the order of the treatment. Group B showed a higher abundance relative of
Ruminoccocaceae, Lachnospiraceae, and Erysipelotrichaceae, however, these were not classified when compared to group A. This suggests that phenolic compounds found on MOJ could directly stimulate the growth of a specific bacteria. The Ruminoccocaceae and Lachnospiraceae families have been linked to the production of short-chain fat acid, an important energy source for colonic epithelial. In addition, the Lachnospiraceae family has been associated with improved insulin resistance, lipid metabolism, reduction of body weight, and antioxidant effects. Erysipelotrichaceae, as well as Lachnospiraceae family, were associated with inflammation reduction and improved insulin sensitivity in mice.

Conclusions:
In conclusion, our results suggest that MOJ followed by POJ intake may improve the dysbiosis associated with obesity through the stimulus of bacterial growth – especially the bacteria that (a) metabolize bioactive compounds and (b) enhance the synthesis of beneficial metabolic
products protecting gut homeostasis.

Discovery of new bioactive microbial metabolites in inflammatory bowel disease

Presented by: Sena Bae

The gut microbiota and associated bioactive compounds have been implicated as causal and as protective factors in gastrointestinal disorders, including the inflammatory bowel diseases (IBD). Both host immune interactions with gut microbes and microbial small molecule products are likely responsible for these bioactivities. Several gut microbial metabolites, e.g. short-chain fatty acids and a subset of omega-3 fatty acids depleted in GI inflammation, have demonstrated therapeutic potential in IBD by attenuating gut inflammation. However, discovery of new bioactive compounds from the gut microbiome relevant to IBD or inflammation is challenging due to the vast numbers of uncharacterized metabolites produced by the microbiome. To address this challenge, we investigated two IBD cohorts with integrated metagenomic and metabolomic profiles of the gut microbiome: PRISM, the Prospective Registry in IBD Study at MGH, and the Integrative Human Microbiome Project (HMP2). Putrescine and a potentially novel family of metabolites microbially derived from it were among the ~10,000 metabolites differentially abundant (PRISM n=8,792 and HMP2 n=9,444) during gut inflammation, of which only ~100 were characterized (PRISM n=157 and HMP2 n=99). We validated the dependence of these putrescine derivatives on the gut microbiome and their bioactivity in vivo by treating germ-free, gnotobiotic and conventional mice with dietary putrescine, which induced changes in immune system activity in a microbial community-dependent manner. This included that putrescine selectively affects host colonic and ileum M2 macrophage cell populations only in conventional mice. These results underscore the power of combined computational and experimental approaches for identifying microbially derived metabolites with general immunomodulatory activity and specific relevance for IBD patient care.

Prioritization and annotation of novel bioactive small molecules from the microbiome

Presented by: Amrisha Bhosle

Microbial communities, and the human gut microbiome, in particular, are a rich source of novel bioactive small molecule metabolites. Tens of thousands of metabolites have been assayed from stool, many in association with millions of microbial enzymes, but as yet with minimal biochemical characterization or knowledge of their therapeutic potential. This is especially true for microbially-derived or -associated small molecule immunomodulators in conditions such as the inflammatory bowel diseases (IBD), in which gut microbial alterations have been implicated in induction of or protection from inflammation. Here, we have developed and validated a new approach for identifying and prioritizing potentially bioactive novel metabolites from the gut microbiome, which we initially applied to ~82k compounds spanning 546 metabolomes from 106 IBD patients and controls in the Integrative Human Microbiome Project (HMP2). We assigned putative biochemical annotations and prioritization of potential bioactivity was done by integrating epidemiological properties (e.g. IBD pathogenesis) with ecological ones (e.g. covariation and prevalence) Top-ranked features were enriched for bile acid derivatives and short-chain fatty acid precursors, among other classes of chemical compounds that have been previously implicated in IBD-related dysbiosis, as well as modestly explored classes such as medium-chain fatty acids, putrescine metabolites and B vitamins. These results point to new potentially microbially-derived and -associated compounds for immunomodulation in inflammatory conditions. The general method can be applied to integrate knowledge of standard compounds from any microbial community metabolomics with phenotypic or environmental indicators of bioactivity. We provide an open source implementation as MACARRoN (Metabolome Analysis and Combined Annotation Ranks for pRediction of Novel bioactives). The metabolites prioritized in this study of IBD expand our understanding of interactions between the microbiota and host during gut inflammation and offer new candidate small molecules with therapeutic potential.

Modulation of the intestinal immune cell compartment by Fusobacterium nucleatum in mice with a minimal complexity microbiota

Presented by: Caitlin Brennan

Colorectal cancer (CRC) is a multifaceted disease, influenced by host genetic and environmental factors. Growing evidence suggests that specific members of the microbiota mediate CRC development, growth and spread. One such microbe is Fusobacterium nucleatum, a normal constituent of the human oral cavity, that has been largely studied for its role in shaping dental biofilms. Fusobacterium spp., while rare in the gut microbiota of healthy individuals, are enriched in human colorectal adenomas and adenocarcinomas, compared to normal colonic tissues, and specifically associated with certain epidemiological subtypes of colorectal cancer. Further experimental evidence has suggested that F. nucleatum can potentiate tumorigenesis in mouse models, influence immune-mediated killing of tumor cells, and promote resistance to chemotherapy drugs. Taken together, this research supports that a greater understanding of the biology underlying F. nucleatum in the gastrointestinal tract—both before and during tumorigenesis—may provide insights into improving CRC diagnosis and treatment. To that end, we seek to understand how F. nucleatum modulates the intestinal immune cell environment. In previous works, F. nucleatum has been shown to influence myeloid cell and T cell frequency in murine and human tumors, respectively. However, we do not yet understand how this oncomicrobe may shape different immune cell populations prior to tumorigenesis, potentially influencing the conversion of healthy intestinal tissue into a pro-tumorigenic microenvironment. As F. nucleatum is a bacterium evolved to live in the oral cavity, we are leveraging gnotobiotic mouse models—in which F. nucleatum can become a stable member of the intestinal microbiota—along with bacterial genetics and immunological approaches to disentangle the interactions at play among F. nucleatum, the colonic epithelium, and the immune system.

Diet-linked dynamics of metagenomes and metatranscriptomes

Presented by: Tobyn Branck

The microbiome is crucial for host processes such as metabolism and is modulated by host diet. The specific interactions between microbial enzymes and dietary compounds are not yet known. To understand these mechanisms, we assess the relationship between dietary compounds and metabolic pathways that are carried and transcribed by individual species. Here, we report on the gut microbiome of 307 participants from the Health Professionals Follow-Up Study, a prospective cohort designed to relate nutrition to health outcomes. The gut metagenome of each participant was surveyed at four timepoints with short (1-3 days) and long (6 month) time intervals. Metatranscriptomes were also generated for 96 participants. These data were complemented with seven-day dietary recalls and long-term dietary histories from food frequency questionnaires. Taxonomic profiling and metabolic reconstruction were performed using MetaPhlAn2 and HUMAaN2, respectively. We integrated the profiled taxonomy and metabolic pathways with dietary compounds using a multivariate linear model
(MaAsLin2). We revealed a &quot;core&quot; set of pathways encoded by many species, and a variably transcribed set that consists of specialized pathways. Dietary fiber was associated with metagenomic pathways such as nucleotide and amino acid biosynthesis, in addition to the carbohydrate fermenter, Collinsella aerofacians. A Gaussian process model is applied to assess the longitudinal relationship between microbiome features and dietary variables. Our findings could help us understand the direct mechanism by which bioavailability impacts microbial metabolism.

SCFA-sensing receptor Ffar2 regulates group 3 innate lymphoid cells and gut immunity

Presented by: Eunyoung Chun

Gut microbial metabolites such as short-chain fatty acids (SCFAs) are increasingly recognized for shaping gut homeostasis and intestinal immunity. These metabolites directly activate a subset of G-protein-coupled receptors (GPCRs), termed the metabolite-sensing GPCRs. Engagement of GPCRs by microbial metabolites influences mucosal homeostasis and epithelial barrier integrity that are driven by interactions between mucosal immune cells, epithelial cell subsets, and the microbiota. Group 3 innate lymphoid cells (ILC3s) are critical innate sentinels that orchestrate mucosal homeostasis and host defense. ILC3s are highly enriched in the gut and sense a multitude of environmental signals derived from microbiota, diet, or host nervous and circadian systems. Diet-derived or host-derived signal that regulates ILC3s have been identified, yet, how microbial metabolites affect ILC3 expansion and function remain unknown.
In this study, we show that colonic ILC3s sense SCFAs via a metabolite-sensing GPCR, Ffar2 (GPR43). Ffar2 agonism by acetate and propionate selectively promotes ILC3 proliferation and IL-22 production which is essential for intestinal barrier immunity. Indeed, Ffar2-deficient ILC3s dampen the epithelial barrier through decreased antimicrobial peptide and mucin production and consequently, increase susceptibility to colonic inflammation and enteric bacterial infection. Mechanistically, Ffar2 regulates ILC3-derived IL-22 production through activation of AKT and STAT3 or partially ERK and STAT3 signal pathways.

Collectively, our findings shed light on how diet and microbiota control gut homeostasis and mucosal immunity via regulating ILC3 biology and open up the new therapeutic possibilities of metabolite-sensing receptors for the treatment of intestinal diseases such as inflammatory bowel diseases.

The landscape of novel lateral gene transfer events in the human microbiome

Presented by: Eric Franzosa

Lateral gene transfer (LGT) is an important mechanism for genome diversification in microbial communities, including the human microbiome. While previous efforts have cataloged LGT in human-associated microbial isolate genomes, directly identifying novel (and potentially recent) LGT events in human microbiomes is an open challenge. To address this, we developed a computational method (WAAFLE) to identify novel LGT events from assembled metagenomes. We applied WAAFLE to ~2K diverse human metagenomes, identifying ~100K high confidence, novel LGT events. These events were enriched for mobile element, restriction-modification, and transport functions, and their frequency was influenced by biogeography, phylogenetic relatedness, and the ecological abundance of donor taxa. These trends manifested as LGT networks in which abundant hub taxa donate unequally with their close phylogenetic neighbors. Our findings suggest that LGT is an active process in the human microbiome.

The Anti-Diabetic Effects of Palmitic Acid Hydroxy Stearic Acid (PAHSA) Lipids are Transmissible by Fecal Microbiota Transplantation (FMT) in Mice

Presented by: Jennifer Lee

Title: The Anti-Diabetic Effects of Palmitic Acid Hydroxy Stearic Acid (PAHSA) Lipids are Transmissible by Fecal Microbiota Transplantation (FMT) in Mice
Authors: Jennifer Lee, Kerry Wellenstein, Barbara B. Kahn
Affiliations: Division of Endocrinology, Diabetes and Metabolism, Beth Israel Deaconess Medical Center, Boston MA 02215.

Objective: A newer class of lipids called PAHSAs have anti-diabetic effects in high-fat diet (HFD)-fed mice and circulating PAHSA levels strongly associated with insulin sensitivity in humans. Whether the gut microbiome contributes to the beneficial effects of PAHSAs on improving glucose homeostasis is unknown. We aimed to determine whether the insulin- sensitizing properties of PAHSAs are transmissible by fecal microbiota transplantation (FMT) in mice.

Methods: Fecal pellets collected from male mice treated with insulin-sensitizing PAHSAs or vehicle (50% PEG400, 0.5% Tween80 in water) for 21 days were used for FMT into recipient germ-free (GF) HFD-fed male mice. Donor feces from PAHSA or vehicle-treated mice were Dounce homogenized and resuspended in 100µL PBS under anaerobic conditions. Recipient GF-HFD mice were conventionalized with two doses of donor feces at days 0 and 35 by oral gavage. Body weight and in vivo glucose homeostasis were assessed in GF-HFD conventionalized mice.

Results: GF-HFD mice conventionalized with PAHSA donor feces gained less weight and were more glucose tolerant and insulin sensitive than GF-HFD mice conventionalized with vehicle donor feces. In addition, GF-HFD-PAHSA mice have reduced glycemia following a 5-hour food removal compared to control mice. Improved glucose tolerance was independent of effects on insulin secretion, suggesting that microbiota in feces from PAHSA-treated mice improves insulin sensitivity possibly by promoting leaness.16S rRNA sequencing and metagenomics analyses of cecal samples from the same PAHSA-treated donor mice identify 26 fatty acids (out of 600 metabolites) and several microbial species and their metabolic pathways that correlated highly with PAHSA-mediated insulin sensitivity.

Conclusion: PAHSAs have beneficial effects on the gut microbiome and these insulin sensitizing effects can be conferred by FMT to improve glucose homeostasis in recipient HFD-fed mice. Identifying PAHSA-mediated microbes and their metabolites that improve host metabolism represent novel therapeutic strategies to treat diet-induced obesity and insulin resistance.

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

Presented by: Chengchen (Cherry) Li

The Microbiome Collection Core at the Harvard T.H. Chan School of Public Health (HCMCC) was established in response to 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 Center for the Microbiome in Public Health, HCMCC aims to support population-scale microbiome sample collection and expand our understanding of the microbiome to improve population health. Leveraging the intellectual and infrastructure foundation laid by the HMP2 (the 2nd phase of Human Microbiome Project) and the MLSC (Massachusetts Life Sciences Center) funded MICRO-N (MICRObiome Among Nurses) collection, the HCMCC has developed a multi carrier-compatible home stool and oral sample collection kit with several different room temperature storage that is compatible with multiple different molecular assays including any combination of amplicon (16S), metagenomic, metatranscriptomic, and metabolomics sequencing. The kit further includes a culture- compatible sample using anaerobic media that yields live microbes for culture or gnotobiotic, as well as user-friendly instructions and standardized questionnaires to capture recent medications, diet, and oral and gastrointestinal health status. By providing support in ordering this customizable microbiome collection kit and post-collection assistance in sample handling, sequencing, and storage, HCMCC enables researchers to tailor the kit configuration and collection plan to study-specific needs, and conduct cost-effective multi’omic microbiome studies.

Microbiome differential abundance analysis by zero-inflated quantile rank-score based test

Presented by: Wodan Ling

Studying the role of microorganisms in the development of diseases such as obesity in human populations is at an all-time high. The very objective of statistical analysis on microbial data is to identify differentially abundant taxa among certain clinical conditions, to guide follow-up pathway analysis. However, the microbiome differential abundance analysis (MDA) is challenging. First, microbiome data needs to be normalized because of differences in read depths. There are many different resampling or scaling normalization methods, and the performance of existing MDA approaches are highly dependent on the normalization choices, which impedes the comparison among various studies. The introduction of a robust method to the normalization is then of interest. Second, microbiome data is complex, usually zero-inflated, dispersed and high-dimensional. It is hopeless to determine a one-size-fit-all parametric method for all taxa; also, these mean-based methods are insufficient to detect the heterogeneous association between the clinical condition and microbial abundance. Quantile regression is a powerful alternative to deal with heterogeneity, as it does not require likelihood specification, and one can use it to examine various locations of the abundance distribution. In this paper, we propose to use a quantile rank-score based test (ZIQRank) under a two-part quantile regression model to analyze the microbiome data processed by any normalization method. The tool consists of a valid test in logistic regression for the zero-inflation, and a series of rank-score based tests on multiple quantiles of the positive part with adjustment for zero-inflation. We applied ZIQRank to study the association between gut microbiota and high blood pressure, confirmed that it increases the power with well-controlled Type I error and is robust to the normalization method. It identified most of the taxa detected by the existing MDA methods and complemented them with finding additional taxa on which hypertension has heterogeneous effects.

A Hierarchical Model for Microbial Community Structure

Presented by: Siyuan Ma

View Abstract

We present a hierarchical model of microbial community count observations, suitable for simulation of such data at population scale. Our model has specialized components targeting characteristics unique to microbiome data, including sparsity, joint effects of biological and sequencing variation, and ecological feature dependencies, and is capable of simulating mock microbial counts that recapitulate the population structures in training template communities. We hope that these methods and findings will be of broad applicability in human microbial epidemiology, and will inform future population study designs and analysis practices.

Dietary fiber intake, gut microbiome, and chronic systemic inflamation

Presented by: Wenjie Ma

Background: Higher intake of dietary fiber is associated with decreased risk of chronic inflammatory diseases. Dietary fiber may abrogate chronic systemic inflammation induced by factors including dysbiotic gut communities. Data regarding the detailed influences of long-term and recent intake of differing fiber sources in human populations are lacking.

Methods: We collected longitudinal stool samples from 307 healthy men in the Health Professionals Follow-up Study (up to 4 stools over 6 months, in 2012-2013) totaling 913 metagenomes and 341 metatranscriptomes with concurrent measurement of the circulating inflammatory biomarker, high- sensitivity C-reactive protein (CRP). We captured recent dietary fiber intake using a 7-day dietary record at the time of stool collection and long-term intake using validated semi-quantitative food frequency questionnaires (FFQs) every 4 years since 1986. Dietary fiber captured by FFQ was further subclassified into their food sources (fruit, cereal, and vegetable). We used transformed generalized linear mixed models via MaAsLin2 to examine the relationship between dietary fiber and microbial features with adjustment for covariates.

Results: Both recent and long-term higher dietary fiber intake were associated with shifts in Clostridiales, including increases of Eubacterium eligens, Faecalibacterium prausnitzii, and genus Roseburia, but also decreases in Clostridium, Lachnospiraceae, and Ruminococcus. Greater fiber intake was also associated with greater relative abundances of Haemophilus parainfluenzae and Bacteroides species, including B. cellulosilyticus. In addition to taxonomic composition, dietary fiber intake was associated with a large number of functional genomic features. Microbial influences were varying according to fiber sources, with predominant effects deriving from pectin and fruit fiber. For instance, abundances of E. eligens and F. prausnitzii as well as their functions in the degradation of polysaccharides as represented by polysaccharide lyase family 9 were enriched in participants with greater dietary fiber and pectin intake. Higher CRP was associated with enrichment of Bacteroides uniformis and Barnesiella intestinihominis and depletion of Lachnospiraceae_bacterium_3_1_46faa, E. eligens, and Bifidobacterium bifidum. The association between recent fiber intake and plasma levels of CRP was significantly modified by gut microbial composition and specifically presence/absence of Prevotella copri (P-interaction=0.01). A stronger inverse association was observed among participants who did not have P. copri.

Conclusions: Our findings offer evidence supporting a fiber-gut microbiome interaction relevant to human chronic systemic inflammation. The differential effects of fiber according to its food source may inform personalized approaches to gut microbial modulation.

Effects of endurance exercise on mood state and serotonin levels after thirty days of probiotic supplementation: a pilot study

Presented by: Camila Guazzelli Marques

The gut-brain axis relationship has been investigated in several studies in the area of health and, more recently, also in physical exercise. Changes in serotonin levels appear to be due to changes in the intestinal microbiota. Serotonin modulates brain activity and the neuropsychological processes involved in mood. In addition to its functions in the central nervous system, serotonin is also active in the gastrointestinal tract, helping in the digestive process. Likewise, the intestinal microbiota is of great importance in its concentrations, and 95% of serotonin production is carried out in the intestine. Some studies question whether these modulations can collaborate with psychobiological aspects and, perhaps, affect athletic performance. Purpose: Evaluate the effect of marathon running on mood aspects and plasma serotonin levels after probiotic supplementation in athletes. Methods: Fourteen athletes were supplemented for thirty days before the marathon. The athletes were randomized in a double-blind study model into two followed groups: placebo group (n=7; 2.0 g/day of corn starch) and probiotic group (n=7; 2.0 g/day of Lactobacillus Acidophilus, Lactobacillus Casei, Lactobacillus Lactis, Bifidobacterium Lactis and Bifidobacterium Bifidum totaling 109 CFU by strain). Blood samples were collected at baseline (before supplementation), pre-exercise (24h before the marathon race), post-exercise (immediately after), and 1h after. Additionally, pre-exercise and post-exercise, the volunteers answered the BRUMS questionnaire. To verify differences between group and time, the ANOVA two-way with Tukey Post-hoc was performed being considered p <0.05. Results: After the marathon, in both placebo and probiotic groups, fatigue and mental confusion increased, as well as vigor reduced (without significant difference between the groups; p>0.05). However, these changes were not dependent on plasma serotonin concentrations, and at different times evaluated, and between groups, no significant differences in serotonin concentrations were found. Conclusion: The supplementation of this combination of probiotic bacteria for 30 days was not effective in mitigating the mood changes generated by the marathon and did not change the plasma levels of serotonin throughout the experiment. Further studies are needed to understand the possible effects of supplementation with probiotics on strenuous exercise, such as the marathon.

Effects of 30 days Probiotic Supplementation on Monocytes function after a Marathon Race. A randomized, double-blind-placebo study.

Presented by: Edgar Tavares-Silva

Background: The gut-brain axis relationship has been investigated in several studies in the area of health and, more recently, also in physical exercise. Changes in serotonin levels appear to be due to changes in the intestinal microbiota. Serotonin modulates brain activity and the neuropsychological processes involved in mood. In addition to its functions in the central nervous system, serotonin is also active in the gastrointestinal tract, helping in the digestive process. Likewise, the intestinal microbiota is of great importance in its concentrations, and 95% of serotonin production is carried out in the intestine. Some studies question whether these modulations can collaborate with psychobiological aspects and, perhaps, affect athletic performance.

Purpose: Evaluate the effect of marathon running on mood aspects and plasma serotonin levels after probiotic supplementation in athletes. Methods: Fourteen athletes were supplemented for thirty days before the marathon. The athletes were randomized in a double-blind study model into two followed groups: placebo group (n=7; 2.0 g/day of corn starch) and probiotic group (n=7; 2.0 g/day of Lactobacillus Acidophilus, Lactobacillus Casei, Lactobacillus Lactis, Bifidobacterium Lactis and Bifidobacterium Bifidum totaling 109 CFU by strain). Blood samples were collected at baseline (before supplementation), pre-exercise (24h before the marathon race), post-exercise (immediately after), and 1h after. Additionally, pre-exercise and post- exercise, the volunteers answered the BRUMS questionnaire. To verify differences between group and time, the ANOVA two-way with Tukey Post-hoc was performed being considered p <0.05. Results: After the marathon, in both placebo and probiotic groups, fatigue and mental confusion increased, as well as vigor reduced (without significant difference between the groups; p>0.05). However, these changes were not dependent on plasma serotonin concentrations, and at different times evaluated, and between groups, no significant differences in serotonin concentrations were found.

Conclusion: The supplementation of this combination of probiotic bacteria for 30 days was not effective in mitigating the mood changes generated by the marathon and did not change the plasma levels of serotonin throughout the experiment. Further studies are needed to understand the possible effects of supplementation with probiotics on strenuous exercises, such as the marathon.

Inflammatory arthritis and the gut microbiome

Presented by: Kelsey Thompson

Nearly 54 million adults in the U.S. are afflicted with various forms of arthritis. Rheumatic conditions are among the many chronic inflammatory diseases in which the microbiome has been implicated, but comprehensive, large-scale multi-omic evaluations conducted in patient cohorts with careful disease and environmental phenotyping are lacking. To characterize the community structure and metabolic processes driving gut microbiome involvement in arthritis, we investigated stool shotgun metagenomes from 273 adults diagnosed with rheumatoid arthritis, ankylosing spondylitis, psoriatic arthritis, and other forms of arthritis, as well as 100 control individuals. We found that ~2% of gut taxonomic variability was explained by patient diagnosis, similar in magnitude to inflammatory bowel disease (IBD), which has been the focus of the considerably greater investigation. Similar findings were identified for gut microbial functional profiles, suggesting a tight coupling between perturbed microbial community structure and the metabolic functions they encode among patients with established arthropathy. After adjusting for age, gender, ethnicity, and other relevant clinical characteristics that may confound the relationship between arthropathy and the microbiome, we identified significant increases in several taxa characteristic of the oral cavity among patients with high rather than low circulating C-reactive protein, an established biomarker for systemic inflammation, including several species from Streptococcus and Ruminococcus genera. We are currently testing for strain-specific carriage of genetic elements implicated in the gut microbiome during arthritis subsets, as well as the ability of microbial elements to discriminate disease or predict response to treatment. Untargeted metabolomic profiles have also been generated for a subset of samples in order to link potentially causal microbial changes to mediating small molecules. Taken together, our efforts represent the first comprehensive investigation of gut microbial communities in a well-defined clinical cohort of individuals with inflammatory and non-inflammatory arthropathies.

Funding source: Versus Arthritis

Distinct Actions of the Fermented Beverage Kefir on Host Behaviour, Immunity and Microbiome Gut-Brain Modules in the Mouse

Presented by: Aaron Walsh

Mounting evidence suggests a role for the gut microbiota in modulating brain physiology and behavior through bi-directional communication along the gut-brain axis. As such, the gut microbiota represents a potential therapeutic target for influencing centrally-mediated events and host behavior. It is thus notable that the fermented foods, such as the milk beverage kefir, have recently been shown to modulate the composition of the gut microbiota in mice. It is unclear whether foods such as kefirs, which include both microbial fermentation products and live probiotic microbes, have differential effects on microbiota-gut-brain axis and whether they can modulate host behaviour per se. To address this, two distinct kefirs (Fr1 and UK4) or unfermented milk control were administered to mice that underwent a battery of tests to characterise their behavioural phenotype. In addition, shotgun metagenomic sequencing of ileal, cecal and faecal matter was performed, as was faecal metabolome analysis. Fr1 ameliorated the stress-induced decrease in serotonergic signalling in the colon and reward-seeking behaviour in the saccharin preference test. On the other hand, UK4 decreased repetitive behaviour and ameliorated stress-induced deficits in reward-seeking behaviour. Furthermore, UK4 increased fear-dependent contextual memory, yet decreased milk gavage-induced improvements long-term spatial learning. In the peripheral immune system, UK4 increased the prevalence of Treg cells and interleukin 10 levels, whereas Fr1 ameliorated the milk gavage stress-induced elevation in neutrophil levels and CXCL1 levels. Analysis of the gut microbiota revealed that both kefirs significantly changed the composition and functional capacity of the host microbiota, where specific bacterial species were changed in a kefir-dependent manner. Furthermore, both kefirs increased the capacity of the gut microbiota to produce GABA, which was linked to an increased prevalence in Lactobacillus reuteri. Altogether, these data show that probiotic fermentation products such as kefir can signal through the microbiota-gut-immune-brain axis and modulate host behaviour. In addition, different products may direct the microbiota toward distinct immunological and behavioural modulatory effects. These results indicate that kefir can positively modulate specific aspects of the microbiota gut-brain axis and support the broadening of the definition of psychobiotic to include fermented foods.

Characterizing microbial community viability using propidium monoazide

Presented by: Lea Wang

Modern humans spend most of their life time in built environments (BE). Characterization of BE microbiomes is of great importance given the associations between microbial exposure and occupant health in indoor settings. Although many studies have explored the taxonomic composition of BE microbiomes using DNA sequencing, this method on its own suffers from an inability to discern viability. Non-viable microorganisms are likely of much greater prevalence and abundance in BEs than in natural settings due to the specific chemical characteristics of those environments. Previous studies have used propidium monoazide (PMA) in the pre-treatment of samples, coupled with downstream molecular profiling (e.g. qPCR or DNA sequencing), to characterize the viable fraction of a microbial community. While these studies have met with some success, most have focused entirely on interpretation of the resulting “viable” microbial community profiles without a systematic evaluation of the accuracy of this measurement.

Here, we present our work to rigorously benchmark “PMA-seq” (PMA treatment followed by 16S rRNA amplicon sequencing) as a screen for microbial viability in both synthetic and environmental microbial communities, ranging from simple in vitro co-culture to full-complexity BE communities. Our first validation focused on synthetic mixtures of living and heat-killed Escherichia coli and Streptococcus sanguinis in known proportions. PMA-seq was able to successfully reconstruct the communities of viable/heat-killed E. coli and S. sanguinis. We next evaluated the effects of biomass and sample diversity on PMA-seq by testing communities of variable biomass (computer screens and mice, soil, and saliva) and spiked them with known concentrations of viable and heat-killed E. coli. Against a background of realistically complex communities, viability was no longer accurately assessed by PMA-seq, with its performance largely affected by initial biomass and compositional diversity. Finally, we applied this technique to environmental swabs from the Boston subway system to identify and quantify living bacteria in that BE. Several taxa were significantly different after PMA treatment including Haemophilus genera, but not all samples respond consistently to PMA treatment. Overall, we revealed that PMA treatment was effective for qPCR or 16S readouts of pure cultures or very simple synthetic communities, but such usage may be premature and poorly quantify viable microbes in realistically complex community samples.

This study provides a comprehensive evaluation of the performance of PMA-treatment to test viability of microbes in BE communities. In the future, we plan to expand our work to the validation of other methodologies to distinguish between viable and non-viable microbes, such as RNA-based amplicon sequencing or metatranscriptomic sequencing. We expect characterization of viable microbes to further elucidate the interplay between microbes and their ecosystems/hosts, potentially unveiling new interactions between BE microbes and human health.

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

Presented by: Jeremy Wilkinson

The Microbiome Analysis Core at the Harvard T.H. School of Public Health 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, selection of data generation options, and 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, quantitative 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.

Identifying strain-specific functional genes with colorectal cancer

Presented by: Yan Yan

Colorectal cancer (CRC) most often occurs sporadically (as compared to genetic forms of the disease) and is one of the leading causes of cancer-related death worldwide. Environmental factors contribute substantially to CRC risk and development, particularly the intestinal microbiota. Recent meta-analyses of gut microbial profiles in CRC have identified multiple taxa (including Fusobacterium) reproducibly associated with late-stage cancers across populations. However, neither the causal mechanisms nor corresponding microbial strains and small molecule products have been pinpointed for CRC, particularly among subsets of non-Fusobacterium clades newly associated with the disease. We leveraged stool metagenomic profiles from 352 CRC patients, 143 with pre-cancerous adenomas, and 312 healthy controls from seven recent CRC microbiome studies in combination with our integrated metagenomic and metatranscriptomic data from the Integrative Human Microbiome Project, Nurses’ Health Study, and Health Professionals Follow-Up Study. Within CRC-associated species, we assessed strain specific gene carriage and sub- species phylogenetic enrichments via gene- and variant-based culture-independent profiling. The former identified gene families carried significantly more or less frequently by individual strains during disease, and the latter called out subclades with significant phylogenetic associations with carcinogenesis. In some cases, these genes and nucleotide variants also corresponded with transcriptional changes. This study adds further evidence to the hypothesis that strain-level genomic variation in gut microbes may be a major driver in the initiation or development of colorectal cancer.

Antibiotic-Induced Perturbations of the Gut Microbiota Alter Ileal MicroRNA Expression Profiles in Non-Obese Diabetic Mice

Presented by: Yue (Sandra) Yin

Background: Disruptions to the intestinal microbiota in early life increase the risk for autoimmune diseases, such as type 1 diabetes (T1D). A single course of antibiotic treatment (1PAT) from 5-10 days of life accelerated T1D development in male non-obese diabetic (NOD) mice, inducing substantial changes in gut microbial composition and ileal gene expression. MicroRNAs (miRNAs) are important post-transcriptional regulators of gene expression, and recent findings suggest an association of particular miRNAs with T1D pathogenesis. Here we investigated the role of ileal miRNAs in microbiota-mediated regulation of host protein-encoding genes.

Methods: We treated NOD mice of 5-10 days of age with 1PAT only or with no antibiotics (Control), and a group of 1PAT-mice were given cecal microbiota from healthy donors, as a restorative (Restore). Ileal mRNA and miRNA gene expression were evaluated by RNA-Seq and NanoString, respectively, with further quantitation using RT- qPCR. We then employed a computational approach to predict the interactions between differentially expressed mRNAs and miRNAs.

Results: Receiving cecal microbiota transfer rescued the antibiotic-induced acceleration of T1D in NOD mice. Unsupervised hierarchical clustering of mRNA and miRNA expression showed restorative effects of the cecal microbiota transfer at a global level. Among 599 miRNAs measured, 68 had significantly differential expression between treatment groups, including six major miRNAs that responded to both antibiotic exposure and microbiota restoration. These six miRNAs were predicted to target 432 significantly differential mRNAs, many related to host defenses and inflammation. Particular miRNAs also were identified to regulate critical antimicrobial genes via multiple signaling
pathways.

Conclusion: These findings provide evidence that perturbations of the gut microbiota alter ileal miRNA expression profiles which further impact mRNA gene expression. Signaling from both the 1PAT-perturbed and the cecally transplanted restored microbiota involve specific miRNA expression differences to affect ileal mRNA expression. Further investigations of the identified miRNAs and their targeted mRNA genes will deepen insights into the role of miRNAs in mediating microbiota-host interactions and T1D development.

Deletion of Serum Amyloid A Increases Weight Gain in Mice

Presented by: Yue (Sandra) Yin

Background: The serum amyloid A (SAA) proteins are acute-phase reactants that mediates inflammation and metabolism. Here we investigated potential mechanistic links between the intestinal microbiota and SAA using two murine models.

Methods: In germ-free (GF) and conventional (CONV) mice, we assessed ileal and colonic SAA over time by RT-qPCR. Then we examined microbiota perturbation and microbiota-mediated phenotypic changes in the presence (WT) or absence of SAA (KO mice). WT and KO mice were either reared separately or co-housed post-weaning. Mice were switched from normal chow to high-fat diet at 8 weeks of life. Body weight was monitored weekly, and ileal gene expression was examined by RT-qPCR.

Results: GF and CONV mice expressed differential microbiota-dependent regulation of SAA isoforms in the ileum and colon. In the presence of microbes, ileal SAA expression significantly increased over time, with greater expression of SAA1, SAA2, and SAA3 than in GF mice at day 42. In the colon, this age-related induction and subsequent enhanced expression of SAA1 and SAA2 was observed in GF mice instead. SAA knockout led to significantly higher post-weaning body weight gain than in WT mice. By week 11, KO mice gained 21% more weight than WT mice. Cohousing diminished the weight difference between WT and KO mice. SAA KO mice showed significantly higher expression of ileal SOCS1, a gene associated with obesity and metabolic syndrome.

Conclusion: Our results suggest that SAA expression is highly sensitive to microbial composition in the ileum and colon. The increased body weight in SAA KO mice may be mediated through altered gut microbiota and impaired host metabolism, which requires further investigation.

The role of the microbiota in neutralizing trypsin activity in a mouse model of Type 1 diabetes

Presented by: Meifan Zhang

The gastrointestinal tract contains high levels of proteases, one of the most abundant of which is trypsin, which is synthesized and secreted by pancreatic acinar cells. In addition to its primary function in digestion, proteolytic activity is also believed to play a role in mucus consistency and mucosal antigen processing. Accumulated evidence indicates that dysregulated proteolysis plays a pivotal role in the pathophysiology of several disorders centered on the colon. In our recent studies to investigate the effects of early-life gut microbiota on T1D onset in the non obese diabetic (NOD) mouse model, we observed that the perturbed early life gut microbiota may dysregulate mucosal physiology through mucin genes muc2 and muc4. Therefore, in this study, we aimed to evaluate intestinal trypsin activities in cecal contents in germ-free and conventional C57BL/6 mice, as well as in the single pulsed antibiotic (1PAT)-exposed NOD mice. Using an enzymatic approach, as expected, we found significantly higher trypsin activity in the cecum of germ-free compared with conventional mice. We also found that mice with antibiotic-perturbed microbiota had increased fecal trypsin levels at the end of the antibiotic treatment; however, the differences became reduced over time. By tracking the occurrence and development of T1D, we observed that the fecal trypsin levels in mice that developed T1D were higher than the mice that did not develop T1D. These results suggest that gut microbiota perturbation may dysregulate trypsin activity in the gut, which may have downstream effects on intestinal proteins, affecting T1D pathogenesis.

Identifying Novel Bioactive Microbial Gene Products in Inflammatory Bowel Disease

Presented by: Yancong Zhang

The gut microbiome and associated bioactive compounds are often disrupted in gastrointestinal conditions such as the inflammatory bowel diseases (IBD). Even in well-characterized environments (e.g. the human gastrointestinal tract), more than one-third of microbial proteins are uncharacterized. We prioritized potentially bioactive proteins from the human gut microbiome during IBD, beginning with a catalog of 1.6M protein families assembled from 1,595 metagenomes in the Integrative Human Microbiome Project (HMP2). ~70% of these proteins were uncharacterized, including those with strong homology to known functionally uncharacterized proteins (24%), new proteins with weak homology (33%), and completely novel proteins without homology (12%). We assigned putative annotations to uncharacterized proteins using a combination of guilt-by-association, taxonomic binning, secondary structure analysis, and host phenotype analysis, ultimately leaving only 30,529 families (3%) still functionally and taxonomically uncharacterized. &gt;340,000 protein families were specifically prioritized as potentially bioactive with respect to gut inflammation by integrating evidence from host disease phenotypes, ecological properties. Strikingly, ~23% of them were novel proteins, 36% of which expanded the pangenomes of common gut taxa and 90% of the remainder were assigned at least one putative biochemical annotation. Our analysis methods are generalizable to other microbial communities and human disease, and we provide an open source implementation as MetaWIBELE. The prioritized results suggest thousands of new candidate microbial proteins likely to interact with host immunity in IBD and gut inflammation, offering a rational and targeted compendium of potential therapeutic compounds.