ArticlePublisher preview available

Growth effects of N-acylethanolamines on gut bacteria reflect altered bacterial abundances in inflammatory bowel disease

March 2020
Nature Microbiology 5(5):1-12

Authors:

Broad Institute of MIT and Harvard

Inflammatory bowel diseases (IBD) are associated with alterations in gut microbial abundances and lumenal metabolite concentrations, but the effects of specific metabolites on the gut microbiota in health and disease remain largely unknown. Here, we analysed the influences of metabolites that are differentially abundant in IBD on the growth and physiology of gut bacteria that are also differentially abundant in IBD. We found that N-acylethanolamines (NAEs), a class of endogenously produced signalling lipids elevated in the stool of IBD patients and a T-cell transfer model of colitis, stimulated growth of species over-represented in IBD and inhibited that of species depleted in IBD in vitro. Using metagenomic sequencing, we recapitulated the effects of NAEs in complex microbial communities ex vivo, with Proteobacteria blooming and Bacteroidetes declining in the presence of NAEs. Metatranscriptomic analysis of the same communities identified components of the respiratory chain as important for the metabolism of NAEs, and this was verified using a mutant deficient for respiratory complex I. In this study, we identified NAEs as a class of metabolites that are elevated in IBD and have the potential to shift gut microbiota towards an IBD-like composition. Inflammatory bowel diseases (IBD) are associated with increased faecal N-acylethanolamines (NAEs), which are primarily host-produced signalling lipids, in patients and a mouse model of colitis. These metabolites can enhance the growth of bacterial species enriched in IBD faecal samples and are associated with the expression of respiratory chain genes necessary for microbial metabolism of NAEs.

Validation of metabolite screen results in dose assays Growth curves are shown for three strains using seven metabolites in multiple concentrations. Growth was monitored over time in a volume of 40 µL per well in 384-well plates. The final concentration of DMSO per treated and control well was 0.25%. Growth curves representative of three independent tests are shown and error bars in controls represent the standard deviation of the mean of six technical replicates.

…

Changes in transcriptional activity (KEGG orthologies) in complex microbial communities in response to NAE treatment Log2 relative expression is shown for bacterial families contributing to a selection of KEGG orthologies in samples from chemostats A and B treated with DMSO control, individual NAEs, a combination of all four NAEs (denoted as NAE-mix), or oleic acid (OA). Family-level relative expression values were computed at the species level, averaged over replicates, and then averaged within-family while weighting by species abundance. Unknown (“x”) values represent cases where a function’s DNA and/or RNA abundance were zero for a given stratification (resulting in non-finite log2 relative expression). Col_sort refers to the measure (treatment, time or chemostat) used to order the metadata columns.

…

Correlation between absolute and relative NAE abundances in stool from PRISM subjects NAEs detected in stool from PRISM Crohn’s disease (CD) patients (n=21) in absolute abundances (ng mg⁻¹) are plotted against their respective relative abundances⁸. Pearson correlation coefficients (r) are shown. Progenesis QI (nonlinear DYNAMICS) was used for the extraction of non-targeted LC-MS features and TraceFinder (Thermo Fisher Scientific) was used for the manual peak extraction of known metabolites on basis of their mass to charge ratio (m/z) and retention times determined using authentic standards.

…

Growth effects of NAEs on intestinal bacteria elevated in IBD Palmitoylethanolamide (PEA), linoleoyl ethanolamide (LEA), oleoyl ethanolamide (OEA) and arachidonoyl ethanolamide (AEA) were added to growing cells (in the range of 10⁶ to 10⁸ CFU mL⁻¹) in three concentrations (0 µM, 50 µM and 100 µM), and growth was monitored in an absorbance reader in the anaerobic chamber over time. Controls contained 0.4% DMSO. Growth curves representative of two independent experiments are shown and error bars represent the standard deviation of the mean of three technical replicates. Source data

…

Transcriptional responses of Bacteroides fragilis to linoleoyl ethanolamide (LEA) and arachidonoyl ethanolamine (AEA) a, Differential gene expression between three independent exponential cultures treated for 10 minutes with a sub-inhibitory concentration (25 µM) of LEA or AEA and controls (0.04% DMSO). Differential expression was determined with edgeR, and gene functions were defined using InterPro (EMBL), the NCBI Conserved Domain Database (CDD) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. Selected significantly differentially expressed genes (|log2 fold-change (treated/control)|>0.5, FDR<0.05; Benjamini-Hochberg FDR values were derived from p-values calculated using the likelihood-ratio test) are shown in color. b, Genomic environment of the differentially expressed genes using colors that correspond with (a). Genes in white were not significantly differentially expressed. Coordinate maps refer to the genome of strain B. fragilis ATCC 25285. Gene products that have been experimentally shown to be associated with the outer membrane by LC-MS/MS analysis are in bold (Wilson, M. M., Anderson, D. E. & Bernstein, H. D. Analysis of the outer membrane proteome and secretome of Bacteroides fragilis reveals a multiplicity of secretion mechanisms. PLoS ONE10, e0117732 (2015)).

…

Figures - available from: Nature Microbiology

This content is subject to copyright. Terms and conditions apply.

A preview of this full-text is provided by Springer Nature.

Learn more

Content available from Nature Microbiology

This content is subject to copyright. Terms and conditions apply.

Articles

https://doi.org/10.1038/s41564-019-0655-7

1Broad Institute of MIT and Harvard, Cambridge, MA, USA. 2Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA.

3Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research Inc., Cambridge, MA, USA. 4Departments of Medicine, Microbiology

and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA. 5Center for Microbiome Informatics and Therapeutics, Massachusetts

Institute of Technology, Cambridge, MA, USA. 6Department of Molecular Biology, Massachusetts General Hospital and Harvard Medical School, Boston,

MA, USA. 7Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.

8These authors contributed equally: Eric A. Franzosa, Jason Bishai. *e-mail: hera@broadinstitute.org; xavier@molbio.mgh.harvard.edu

Inflammatory bowel diseases (IBD), including ulcerative colitis

(UC) and Crohn’s disease (CD), are conditions of chronic gas-

trointestinal inflammation resulting from genetic predisposition

and perturbed interactions between gut microorganisms and host

immunity1,2. Many studies focus on microbial taxonomic and func-

tional changes during IBD3–5; however, the gut metabolome (com-

prising diet-, host- and microorganism-derived metabolites) is an

equally important contributor to intestinal health6–8.

Certain gut bacteria metabolize dietary fibre into short-chain

fatty acids such as butyrate that nourish colonocytes, promote

regulatory T-cell expansion and have immunosuppressive func-

tions9,10. Butyrate concentration and butyrate-producing bacte-

ria are depleted in the IBD gut11,12. Other bacteria (for example,

Lactobacillus spp., Bacteroides spp. and Clostridium sporogenes) con-

vert tryptophan into indole derivatives that promote healthy intes-

tinal barrier function and immune tolerance13. Indole producers are

also depleted in IBD8,12. Urease activity, predominantly contributed

by Proteobacteria, shifts the microbiome towards the imbalanced

state seen in IBD and worsens disease in a murine colitis model14.

Host-derived metabolites likewise affect microbiota composition:

bile acids, enriched in the IBD gut8, promote growth of bile acid-

metabolizing bacteria and inhibit growth of bile-sensitive bacteria15.

Inferring covariations between metabolites and bacteria that

are differentially abundant in IBD can functionally implicate gut

metabolites and microorganisms in intestinal health7,16. Two recent

studies combined microbial metagenomics and untargeted mass

spectrometry of metabolites to identify associations between stool

bacterial species and metabolites8,12. The first was a cross-sectional

study of UC, CD and non-IBD subjects within the Prospective

Registry in IBD Study at MGH (PRISM) cohort, and the sec-

ond was the longitudinal integrative Human Microbiome Project

(iHMP). Both concluded that microbial taxonomic changes associ-

ated with IBD, such as blooms of facultative anaerobes including

Proteobacteria4,5, are accompanied by significant shifts in metabo-

lite composition.

Here, we investigated the effects of intestinal metabolites that are

differentially abundant in IBD on the growth of gut bacteria that are

also differentially abundant in IBD, finding that metabolites includ-

ing amines and fatty acids strongly affect bacterial growth. Linoleoyl

ethanolamide (LEA), an NAE, impacted growth in ways that reflect

altered bacterial abundances in the IBD microbiome. We show that

LEA and three structurally related NAEs—palmitoylethanolamide

(PEA), oleoyl ethanolamide (OEA) and arachidonoyl ethanolamide

(AEA)—are enriched in stool from IBD patients and a T-cell trans-

fer model of colitis. These NAEs share common receptors and are

part of the endocannabinoid system, although only AEA is con-

sidered a true endocannabinoid as it binds the cannabinoid recep-

tors CB1 and CB217. We treated monocultures of bacteria that shift

Growth effects of N-acylethanolamines on gut

bacteria reflect altered bacterial abundances in

inflammatory bowel disease

Nadine Fornelos1, Eric A. Franzosa 1,2,8, Jason Bishai 1,8, John W. Annand3, Akihiko Oka 4,

Jason Lloyd-Price 1,2, Timothy D. Arthur1, Ashley Garner1, Julian Avila-Pacheco1, Henry J. Haiser3,

Andrew C. Tolonen1, Jeffrey A. Porter3, Clary B. Clish 1, R. Balfour Sartor4, Curtis Huttenhower 1,2,

Hera Vlamakis 1* and Ramnik J. Xavier 1,5,6,7*

Inflammatory bowel diseases (IBD) are associated with alterations in gut microbial abundances and lumenal metabolite

concentrations, but the effects of specific metabolites on the gut microbiota in health and disease remain largely unknown.

Here, we analysed the influences of metabolites that are differentially abundant in IBD on the growth and physiology of gut

bacteria that are also differentially abundant in IBD. We found that N-acylethanolamines (NAEs), a class of endogenously

produced signalling lipids elevated in the stool of IBD patients and a T-cell transfer model of colitis, stimulated growth of

species over-represented in IBD and inhibited that of species depleted in IBD invitro. Using metagenomic sequencing, we

recapitulated the effects of NAEs in complex microbial communities ex vivo, with Proteobacteria blooming and Bacteroidetes

declining in the presence of NAEs. Metatranscriptomic analysis of the same communities identified components of the respira-

tory chain as important for the metabolism of NAEs, and this was verified using a mutant deficient for respiratory complex I.

In this study, we identified NAEs as a class of metabolites that are elevated in IBD and have the potential to shift gut microbiota

towards an IBD-like composition.

NATURE MICROBIOLOGY | VOL 5 | MARCH 2020 | 486–497 | www.nature.com/naturemicrobiology

486

Content courtesy of Springer Nature, terms of use apply. Rights reserved

Citation: International Journal of Molecular Sciences Healing from Within: How Gut Microbiota Predicts IBD Treatment Success-A Systematic Review

Article

Full-text available

Aug 2024
INT J MOL SCI

Recent research indicates that the microbiome has a significant impact on the progression of inflammatory bowel disease (IBD) and that creating therapies that change its composition could positively impact the outcomes of IBD treatment. This review summarizes the results of extensive studies that examined IBD patients undergoing several therapies, including anti-TNF medication, vedolizumab, ustekinumab, probiotics, and fecal microbiota transplantation (FMT), and the alterations in their gut microbiota's composition and function. The objective was to investigate the variety and effectiveness of microbial species in order to discover new biomarkers or therapeutic targets that could improve the outcome of treatment for these patients. This research aimed to offer useful insights into personalized medicine techniques for managing IBD. Beneficial bacteria such as Faecalibacterium prausnitzii and Roseburia have been consistently linked to favorable clinical outcomes, whereas pathogenic bacteria such as Escherichia coli and Clostridioides difficile are associated with worsening disease conditions. Although many studies have examined the role of gut microbiota in IBD, there is still a need for more targeted research on the connection between specific microbial communities and treatment outcomes. This study sought to address this gap by exploring the intricate relationship between the gut microbiota composition and the effectiveness of IBD medications.

Gut microbiota metabolically mediate intestinal helminth infection in zebrafish

Article

Full-text available

Aug 2024

Intestinal helminth parasite (IHP) infection induces alterations in the composition of microbial communities across vertebrates, although how gut microbiota may facilitate or hinder parasite infection remains poorly defined. In this work, we utilized a zebrafish model to investigate the relationship between gut microbiota, gut metabolites, and IHP infection. We found that extreme disparity in zebrafish parasite infection burden is linked to the composition of the gut microbiome and that changes in the gut microbiome are associated with variation in a class of endogenously produced signaling compounds, N-acylethanolamines, that are known to be involved in parasite infection. Using a statistical mediation analysis, we uncovered a set of gut microbes whose relative abundance explains the association between gut metabolites and infection outcomes. Experimental investigation of one of the compounds in this analysis reveals salicylaldehyde, which is putatively produced by the gut microbe Pelomonas, as a potent anthelmintic with activity against Pseudocapillaria tomentosa egg hatching, both in vitro and in vivo. Collectively, our findings underscore the importance of the gut microbiome as a mediating agent in parasitic infection and highlight specific gut metabolites as tools for the advancement of novel therapeutic interventions against IHP infection. IMPORTANCE Intestinal helminth parasites (IHPs) impact human health globally and interfere with animal health and agricultural productivity. While anthelmintics are critical to controlling parasite infections, their efficacy is increasingly compromised by drug resistance. Recent investigations suggest the gut microbiome might mediate helminth infection dynamics. So, identifying how gut microbes interact with parasites could yield new therapeutic targets for infection prevention and management. We conducted a study using a zebrafish model of parasitic infection to identify routes by which gut microbes might impact helminth infection outcomes. Our research linked the gut microbiome to both parasite infection and to metabolites in the gut to understand how microbes could alter parasite infection. We identified a metabolite in the gut, salicylaldehyde, that is putatively produced by a gut microbe and that inhibits parasitic egg growth. Our results also point to a class of compounds, N-acyl-ethanolamines, which are affected by changes in the gut microbiome and are linked to parasite infection. Collectively, our results indicate the gut microbiome may be a source of novel anthelmintics that can be harnessed to control IHPs.

Mouse adaptation of human inflammatory bowel diseases microbiota enhances colonization efficiency and alters microbiome aggressiveness depending on the recipient colonic inflammatory environment

Article

Full-text available

Aug 2024

Background Understanding the cause vs consequence relationship of gut inflammation and microbial dysbiosis in inflammatory bowel diseases (IBD) requires a reproducible mouse model of human-microbiota-driven experimental colitis. Results Our study demonstrated that human fecal microbiota transplant (FMT) transfer efficiency is an underappreciated source of experimental variability in human microbiota-associated (HMA) mice. Pooled human IBD patient fecal microbiota engrafted germ-free (GF) mice with low amplicon sequence variant (ASV)-level transfer efficiency, resulting in high recipient-to-recipient variation of microbiota composition and colitis severity in HMA Il-10−/− mice. In contrast, mouse-to-mouse transfer of mouse-adapted human IBD patient microbiota transferred with high efficiency and low compositional variability resulting in highly consistent and reproducible colitis phenotypes in recipient Il-10−/− mice. Engraftment of human-to-mouse FMT stochastically varied with individual transplantation events more than mouse-adapted FMT. Human-to-mouse FMT caused a population bottleneck with reassembly of microbiota composition that was host inflammatory environment specific. Mouse-adaptation in the inflamed Il-10−/− host reassembled a more aggressive microbiota that induced more severe colitis in serial transplant to Il-10−/− mice than the distinct microbiota reassembled in non-inflamed WT hosts. Conclusions Our findings support a model of IBD pathogenesis in which host inflammation promotes aggressive resident bacteria, which further drives a feed-forward process of dysbiosis exacerbated by gut inflammation. This model implies that effective management of IBD requires treating both the dysregulated host immune response and aggressive inflammation-driven microbiota. We propose that our mouse-adapted human microbiota model is an optimized, reproducible, and rigorous system to study human microbiome-driven disease phenotypes, which may be generalized to mouse models of other human microbiota-modulated diseases, including metabolic syndrome/obesity, diabetes, autoimmune diseases, and cancer. 9-8iLEe2BorBmu_z2q_8UWVideo Abstract

Effect of the catabolic control protein A of Lactiplantibacillus plantarum AR113 on its colonization in vivo

Article

Full-text available

Apr 2024

Lactiplantibacillus plantarum is selective for carbohydrate utilization, which is primarily regulated by the catabolic control protein A (ccpA). To investigate the impact of carbohydrate metabolism on the in vivo colonization of L. plantarum AR113, we constructed a ccpA knockout strain (AR113ΔccpA). In vitro assays showed that AR113ΔccpA had a 0.34 decrease in maximum biomass, and a 2.63 h increase in hysteresis time compared to AR113. In a single administration, there was no significant difference in the number of AR113 and AR113ΔccpA in the mucus layers, and the number of AR113 was approximately 34‐times higher than AR113ΔccpA at 48 h in the intestinal lumen. Notably, the knockout of the ccpA gene did not affect the colonization time of AR113 in the intestine during continuous administration. Therefore, the present work demonstrated that the ccpA did not play a crucial role in the in vivo colonization time of AR113 and provided valuable insights into the role of carbohydrate metabolism in bacterial colonization time in vivo.

Plasma endocannabinoidome and fecal microbiota interplay in people with HIV and subclinical coronary artery disease: Results from the Canadian HIV and Aging Cohort Study

Article

Full-text available

Jul 2024

Chronic HIV infection is associated with accelerated coronary artery disease (CAD) due to chronic inflammation. The expanded endocannabinoid system (eCBome) and gut microbiota modulate each other and are key regulators of cardiovascular functions and inflammation. We herein investigated the interplay between plasma eCBome mediators and gut microbiota in people with HIV (PWH) and/or subclinical CAD versus HIV-uninfected individuals. CAD was determined by coronary computed tomography (CT) angiography performed on all participants. Plasma eCBome mediator and fecal microbiota composition were assessed by tandem mass spectrometry and 16S rDNA sequencing, respectively. HIV infection was associated with perturbed plasma eCBome mediators characterized by an inverse relationship between anandamide and N-acyl-ethanolamines (NAEs) versus 2-AG and 2-monoacylglycerols (MAGs). Plasma triglyceride levels were positively associated with MAGs. Several fecal bacterial taxa were altered in HIV−CAD+ versus controls and correlated with plasma eCBome mediators. CAD-associated taxonomic alterations in fecal bacterial taxa were not found in PWH.

The Human Fecal Endocannabinoidome Mediator Profile Is Mainly Defined by the Fecal Microbiota and Diet

Article

Aug 2024
J CLIN ENDOCR METAB

Background The endocannabinoid system and its extension, the endocannabinoidome (eCBome), are involved in numerous biological processes, notably energy homeostasis, across virtually all tissues. While the circulating eCBome mediator profile is associated with dietary intakes and metabolic status, an important knowledge gap resides in the identification of the precise determinants of these mediators in the gut lumen. We aimed at establishing the profile of eCBome mediators in human feces and investigating their association with circulating eCBome mediators, dietary intakes, metabolic status and gut microbiota composition. Methods N-acyl-ethanolamines (NAEs) and 2-monoacyl-glycerols (2-MAGs) were profiled by LC-MS/MS in plasma and feces of a cross-sectional cohort (n = 195) and a short term dietary intervention trials (n = 21) with comprehensive dietary intakes and gut microbiota measures. Results Six NAEs and seven 2-MAGs were identified in fecal samples, but some, especially omega-3 derived mediators, were undetectable in the majority of samples. Fecal NAEs, and to a lower extent 2-MAGs, were positively albeit weakly correlated with the circulating levels of eCBome mediators. Fecal 2-AG, PEA and DHEA levels were positively associated with visceral adiposity and with some parameters of the metabolic profile. Dietary intakes of foods rich in fibers were associated with lower fecal levels of several eCBome mediators, while intakes of unsaturated fatty acids were associated with fecal 2-OG and 2-LG. Interestingly, gut microbiota diversity and composition were a strong correlate of the fecal eCBome profile. Conclusion The fecal eCBome profile is associated with gut microbiota composition and dietary intakes, more than with the circulating profile. These results strengthen the hypothesis of an interrelation between the gut microbiome and eCBome signaling involved in the regulation of numerous host biological processes.

Integration of Gut Mycobiota and Oxidative Stress to Decipher the Roles of C-Type Lectin Receptors in Inflammatory Bowel Diseases

Article

Aug 2024
IMMUNOL INVEST

Background: Ulcerative colitis (UC) and Crohn's disease (CD) are two subtypes of inflammatory bowel disease (IBD) with rapidly increased incidence worldwide. Although multiple factors contribute to the occurrence and progression of IBD, the role of intestinal fungal species (gut mycobiota) in regulating the severity of these conditions has been increasingly recognized. C-type lectin receptors (CLRs) on hematopoietic cells, including Dectin-1, Dectin-2, Dectin-3, Mincle and DC-SIGN, are a group of pattern recognition receptors (PRRs) that primarily recognize fungi and mediate defense responses, such as oxidative stress. Recent studies have demonstrated the indispensable role of CLRs in protecting the colon from intestinal inflammation and mucosal damage. Methods and results: This review provides a comprehensive overview of the role of CLRs in the pathogenesis of IBD. Given the significant impact of mycobiota and oxidative stress in IBD, this review also discusses recent advancements in understanding how these factors exacerbate or ameliorate IBD. Furthermore, the latest developments in CLR-guided IBD therapy are examined to highlight the modulation of CLRs in fungal recognition and oxidative burst during the IBD process. Conclusion: This review emphasizes the importance of CLRs in IBD, offering new perspectives on the etiology and therapeutic approaches for this disease.

A combination of metabolomics and microbiome analyses reveal the modulation of lipid metabolism effect of Nannochloropsis gaditana polysaccharides on alcohol-induced dyslipidemia in mice

Article

Aug 2024

The role of intestinal microbiota and metabolites in intestinal inflammation

Article

Jul 2024
MICROBIOL RES

Bifidobacterium breve Modulates Lactic Acid to Curtail Escherichia coli Expansion and Alleviate Inflammatory Bowel Disease

Article

Jun 2024

Microbiota maintain colonic homeostasis by activating TLR2/MyD88/PI3K signaling in IL-10-producing regulatory B cells

Article

Full-text available

Jun 2019
J CLIN INVEST

Resident microbiota activate regulatory cells that modulate intestinal inflammation and promote and maintain intestinal homeostasis. IL-10 is a key mediator of immune regulatory function. Our studies described the functional importance and mechanisms by which gut microbiota and specific microbial components influenced the development of intestinal IL-10-producing B cells. We used fecal transplant to germ-free (GF) Il10+/EGFP reporter and Il10-/- mice to demonstrate that microbiota from specific pathogen-free mice primarily stimulated IL-10-producing colon-specific B cells and T regulatory-1 cells in ex-GF mice. IL-10 in turn down-regulated microbiota-activated mucosal inflammatory cytokines. TLR2/9 ligands and enteric bacterial lysates preferentially induced IL-10 production and regulatory capacity of intestinal B cells. Analysis of Il10+/EGFP mice crossed with additional gene-deficient strains and B cell co-transfer studies demonstrated that microbiota-induced IL-10-producing intestinal B cells ameliorated chronic T cell-mediated colitis in a TLR2, MyD88 and PI3K-dependent fashion. In vitro studies implicated PI3Kp110δ and AKT downstream signaling. These studies demonstrated that resident enteric bacteria activated intestinal IL-10-producing B cells through TLR2, MyD88 and PI3K pathways. These B cells reduced colonic T cell activation and maintained mucosal homeostasis in response to intestinal microbiota.

Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases

Article

Full-text available

May 2019
NATURE

Inflammatory bowel diseases, which include Crohn’s disease and ulcerative colitis, affect several million individuals worldwide. Crohn’s disease and ulcerative colitis are complex diseases that are heterogeneous at the clinical, immunological, molecular, genetic, and microbial levels. Individual contributing factors have been the focus of extensive research. As part of the Integrative Human Microbiome Project (HMP2 or iHMP), we followed 132 subjects for one year each to generate integrated longitudinal molecular profiles of host and microbial activity during disease (up to 24 time points each; in total 2,965 stool, biopsy, and blood specimens). Here we present the results, which provide a comprehensive view of functional dysbiosis in the gut microbiome during inflammatory bowel disease activity. We demonstrate a characteristic increase in facultative anaerobes at the expense of obligate anaerobes, as well as molecular disruptions in microbial transcription (for example, among clostridia), metabolite pools (acylcarnitines, bile acids, and short-chain fatty acids), and levels of antibodies in host serum. Periods of disease activity were also marked by increases in temporal variability, with characteristic taxonomic, functional, and biochemical shifts. Finally, integrative analysis identified microbial, biochemical, and host factors central to this dysregulation. The study’s infrastructure resources, results, and data, which are available through the Inflammatory Bowel Disease Multi’omics Database (http://ibdmdb.org), provide the most comprehensive description to date of host and microbial activities in inflammatory bowel diseases. The Inflammatory Bowel Disease Multi’omics Database includes longitudinal data encompassing a multitude of analyses of stool, blood and biopsies of more than 100 individuals, and provides a comprehensive description of host and microbial activities in inflammatory bowel diseases.

Gut Microbiome Structure and Metabolic Activity in Inflammatory Bowel Disease

Article

Full-text available

Feb 2019

The inflammatory bowel diseases (IBDs), which include Crohn’s disease (CD) and ulcerative colitis (UC), are multifactorial chronic conditions of the gastrointestinal tract. While IBD has been associated with dramatic changes in the gut microbiota, changes in the gut metabolome—the molecular interface between host and microbiota—are less well understood. To address this gap, we performed untargeted metabolomic and shotgun metagenomic profiling of cross-sectional stool samples from discovery (n = 155) and validation (n = 65) cohorts of CD, UC and non-IBD control patients. Metabolomic and metagenomic profiles were broadly correlated with faecal calprotectin levels (a measure of gut inflammation). Across >8,000 measured metabolite features, we identified chemicals and chemical classes that were differentially abundant in IBD, including enrichments for sphingolipids and bile acids, and depletions for triacylglycerols and tetrapyrroles. While > 50% of differentially abundant metabolite features were uncharacterized, many could be assigned putative roles through metabolomic ‘guilt by association’ (covariation with known metabolites). Differentially abundant species and functions from the metagenomic profiles reflected adaptation to oxidative stress in the IBD gut, and were individually consistent with previous findings. Integrating these data, however, we identified 122 robust associations between differentially abundant species and well-characterized differentially abundant metabolites, indicating possible mechanistic relationships that are perturbed in IBD. Finally, we found that metabolome- and metagenome-based classifiers of IBD status were highly accurate and, like the vast majority of individual trends, generalized well to the independent validation cohort. Our findings thus provide an improved understanding of perturbations of the microbiome–metabolome interface in IBD, including identification of many potential diagnostic and therapeutic targets.

Species-level functional profiling of metagenomes and metatranscriptomes

Article

Full-text available

Nov 2018
Br J Pharmacol

Functional profiles of microbial communities are typically generated using comprehensive metagenomic or metatranscriptomic sequence read searches, which are time-consuming, prone to spurious mapping, and often limited to community-level quantification. We developed HUMAnN2, a tiered search strategy that enables fast, accurate, and species-resolved functional profiling of host-associated and environmental communities. HUMAnN2 identifies a community’s known species, aligns reads to their pangenomes, performs translated search on unclassified reads, and finally quantifies gene families and pathways. Relative to pure translated search, HUMAnN2 is faster and produces more accurate gene family profiles. We applied HUMAnN2 to study clinal variation in marine metabolism, ecological contribution patterns among human microbiome pathways, variation in species’ genomic versus transcriptional contributions, and strain profiling. Further, we introduce ‘contributional diversity’ to explain patterns of ecological assembly across different microbial community types.

Oleoylethanolamide treatment affects gut microbiota composition and the expression of intestinal cytokines in Peyer’s patches of mice

Article

Full-text available

Oct 2018

Abstract The lipid sensor oleoylethanolamide (OEA), an endogenous high-affinity agonist of peroxisome proliferator-activated receptor-α (PPAR-α) secreted in the proximal intestine, is endowed with several distinctive homeostatic properties, such as control of appetite, anti-inflammatory activity, stimulation of lipolysis and fatty acid oxidation. When administered exogenously, OEA has beneficial effects in several cognitive paradigms; therefore, in all respects, OEA can be considered a hormone of the gut-brain axis. Here we report an unexplored modulatory effect of OEA on the intestinal microbiota and on immune response. Our study shows for the first time that sub-chronic OEA administration to mice fed a normal chow pellet diet, changes the faecal microbiota profile, shifting the Firmicutes:Bacteroidetes ratio in favour of Bacteroidetes (in particular Bacteroides genus) and decreasing Firmicutes (Lactobacillus), and reduces intestinal cytokines expression by immune cells isolated from Peyer’s patches. Our results suggest that sub-chronic OEA treatment modulates gut microbiota composition towards a “lean-like phenotype”, and polarises gut-specific immune responses mimicking the effect of a diet low in fat and high in polysaccharides content.

Ethanolamine Utilization in Bacteria

Article

Full-text available

Feb 2018

Ethanolamine (EA) is a valuable source of carbon and/or nitrogen for bacteria capable of its catabolism. Because it is derived from the membrane phospholipid phosphatidylethanolamine, it is particularly prevalent in the gastrointestinal tract, which is membrane rich due to turnover of the intestinal epithelium and the resident microbiota. Intriguingly, many gut pathogens carry the eut (ethanolamine utilization) genes. EA utilization has been studied for about 50 years, with most of the early work occurring in just a couple of species of Enterobacteriaceae . Once the metabolic pathways and enzymes were characterized by biochemical approaches, genetic screens were used to map the various activities to the eut genes. With the rise of genomics, the diversity of bacteria containing the eut genes and surprising differences in eut gene content were recognized. Some species contain nearly 20 genes and encode many accessory proteins, while others contain only the core catabolic enzyme. Moreover, the eut genes are regulated by very different mechanisms, depending on the organism and the eut regulator encoded. In the last several years, exciting progress has been made in elucidating the complex regulatory mechanisms that govern eut gene expression. Furthermore, a new appreciation for how EA contributes to infection and colonization in the host is emerging. In addition to providing an overview of EA-related biology, this minireview will give special attention to these recent advances.

BioBakery: A meta'omic analysis environment

Article

Full-text available

Nov 2017
BIOINFORMATICS

bioBakery is a meta'omic analysis environment and collection of individual software tools with the capacity to process raw shotgun sequencing data into actionable microbial community feature profiles, summary reports, and publication-ready figures. It includes a collection of pre-configured analysis modules also joined into workflows for reproducibility. Availability: bioBakery (http://huttenhower.sph.harvard.edu/biobakery) is publicly available for local installation as individual modules and as a virtual machine image. Each individual module has been developed to perform a particular task (e.g. quantitative taxonomic profiling or statistical analysis), and they are provided with source code, tutorials, demonstration data, and validation results; the bioBakery virtual image includes the entire suite of modules and their dependencies pre-installed. Images are available for both Amazon EC2 and Google Compute Engine. All software is open source under the MIT license. bioBakery is actively maintained with a support group at biobakery-users@googlegroups.com and new tools being added upon their release. Contact: chuttenh@hsph.harvard.edu. Supplementary information: Supplementary data are available at Bioinformatics online.

Therapeutic Opportunities in Inflammatory Bowel Disease: Mechanistic Dissection of Host-Microbiome Relationships

Article

Aug 2019
CELL

The current understanding of inflammatory bowel disease (IBD) pathogenesis implicates a complex interaction between host genetics, host immunity, microbiome, and environmental exposures. Mechanisms gleaned from genetics and molecular pathogenesis offer clues to the critical triggers of mucosal inflammation and guide the development of therapeutic interventions. A complex network of interactions between host genetic factors, microbes, and microbial metabolites governs intestinal homeostasis, making classification and mechanistic dissection of involved pathways challenging. In this Review, we discuss these challenges, areas of active translation, and opportunities for development of next-generation therapies.

Microbial genes and pathways in inflammatory bowel disease

Article

Jun 2019
NAT REV MICROBIOL

Perturbations in the intestinal microbiome are implicated in inflammatory bowel disease (IBD). Studies of treatment-naive patients have identified microbial taxa associated with disease course and treatment efficacy. To gain a mechanistic understanding of how the microbiome affects gastrointestinal health, we need to move from census to function. Bacteria, including those that adhere to epithelial cells as well as several Clostridium species, can alter differentiation of T helper 17 cells and regulatory T cells. Similarly, microbial products such as short-chain fatty acids and sphingolipids also influence immune responses. Metagenomics and culturomics have identified strains of Ruminococcus gnavus and adherent invasive Escherichia coli that are linked to IBD and gut inflammation. Integrated analysis of multiomics data, including metagenomics, metatranscriptomics and metabolomics, with measurements of host response and culturomics, have great potential in understanding the role of the microbiome in IBD. In this Review, we highlight current knowledge of gut microbial factors linked to IBD pathogenesis and discuss how multiomics data from large-scale population studies in health and disease have been used to identify specific microbial strains, transcriptional changes and metabolic alterations associated with IBD. Perturbations in the intestinal microbiome are implicated in inflammatory bowel disease (IBD). In this Review, Xavier and colleagues highlight current knowledge of gut microbial factors linked to IBD pathogenesis and discuss how multiomics data from large-scale population studies in health and disease have been used to identify specific microbial strains, transcriptional changes and metabolic alterations associated with IBD.

Cross sectional evaluation of the gut-microbiome metabolome axis in an Italian cohort of IBD patients.

Article