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

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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.
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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:;
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 IBD35; however, the gut metabolome (com-
prising diet-, host- and microorganism-derived metabolites) is an
equally important contributor to intestinal health68.
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 |
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... For example, N-arachidonoyl ethanolamine (anandamide, AEA) was found to have anti-microbial and anti-biofilm activities against methicillin-sensitive and methicillin-resistant Staphylococcus aureus [10][11][12][13]. Fornelos et al. [14] observed that AEA prevented the growth of Streptococcus salivarius and Enterococcus faecalis when applying 17-35 µg/mL (50-100 µM) AEA. Additionally, the endocannabinoids have been found to have anti-fungal activities [15]. ...
... In recent years, the endocannabinoid anandamide (AEA) has been tested alone and in combination with other anti-microbial agents in relation to the growth of different microbes. In Fornelos et al. [14], among the strains tested, the most susceptible bacteria to AEA included Streptococcus salivarius, Bacteroides fragilis and Enterococcus faecalis. AEA was also found to act on multidrug-resistant bacterium Staphylococcus aureus (MDRSA) [11], suggesting that its mechanism of action is unaffected by drug-resistant mechanisms. ...
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Streptococcus mutans is a cariogenic bacterium in the oral cavity involved in plaque formation and dental caries. The endocannabinoid anandamide (AEA), a naturally occurring bioactive lipid, has been shown to have anti-bacterial and anti-biofilm activities against Staphylococcus aureus. We aimed here to study its effects on S. mutans viability, biofilm formation and extracellular polysaccharide substance (EPS) production. S. mutans were cultivated in the absence or presence of various concentrations of AEA, and the planktonic growth was followed by changes in optical density (OD) and colony-forming units (CFU). The resulting biofilms were examined by MTT metabolic assay, Crystal Violet (CV) staining, spinning disk confocal microscopy (SDCM) and high-resolution scanning electron microscopy (HR-SEM). The EPS production was determined by Congo Red and fluorescent dextran staining. Membrane potential and membrane permeability were determined by diethyloxacarbocyanine iodide (DiOC2(3)) and SYTO 9/propidium iodide (PI) staining, respectively, using flow cytometry. We observed that AEA was bactericidal to S. mutans at 12.5 µg/mL and prevented biofilm formation at the same concentration. AEA reduced the biofilm thickness and biomass with concomitant reduction in total EPS production, although there was a net increase in EPS per bacterium. Preformed biofilms were significantly affected at 50 µg/mL AEA. We further show that AEA increased the membrane permeability and induced membrane hyperpolarization of these bacteria. AEA caused S. mutans to become elongated at the minimum inhibitory concentration (MIC). Gene expression studies showed a significant increase in the cell division gene ftsZ. The concentrations of AEA needed for the anti-bacterial effects were below the cytotoxic concentration for normal Vero epithelial cells. Altogether, our data show that AEA has anti-bacterial and anti-biofilm activities against S. mutans and may have a potential role in preventing biofilms as a therapeutic measure.
... These commensal bacteria utilize host lipids as an energy source and metabolize some lipids to new isoforms to enhance mucosal barrier function. Conversely, gut bacteria have also been associated with detrimental changes to dietary lipids, as demonstrated by studies of the microbiome associated with irritable bowel syndrome (69,70). These studies begin to shed light on the potential circular relationship between dietary lipids, changes in the local host environment, and selection for bacteria that metabolize those same nutrients and benefit from changes to the environment (71). ...
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Periodontitis is a chronic inflammatory disease induced by dysbiotic dental biofilms. Management of periodontitis is primarily anti-bacterial via mechanical removal of bacterial biofilm. The successful resolution requires wound healing and tissue regeneration, which are not always achieved with these traditional methods. The discovery of specialized pro-resolving mediators (SPMs), a class of lipid mediators that induce the resolution of inflammation and promote local tissue homeostasis, creates another option for the treatment of periodontitis and other diseases of chronic inflammation. In this mini-review, we discuss the host-modulatory effects of SPMs on periodontal tissues and changes in the taxonomic composition of the gut and oral microbiome in the presence of SPMs and SPM precursor lipids. Further research into the relationship between host SPM production and microbiome-SPM modification has the potential to unveil new diagnostic markers of inflammation and wound healing. Expanding this field may drive the discovery of microbial-derived bioactive therapeutics to modulate immune responses.
... Molecularly complex regulation of abundance, composition, structure and function of gut microbiota requires exact understanding of the role of a designated molecule, but most of our previous understandings are limited in short-chain fatty acids (SCFAs) 37 , glycans 6 , sugar 38 and other molecules 39,40 . Increasing evidence has revealed the important roles of dietary long-chain unsaturated fatty acids in regulating inflammatory responses 13 . ...
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Magnitude and diversity of gut microbiota and metabolic systems are critical in shaping human health and diseases, but it remains largely unclear how complex metabolites may selectively regulate gut microbiota and determine health and diseases. Here, we show that failures or compromised effects of anti-TNF-α therapy in inflammatory bowel diseases (IBD) patients were correlated with intestinal dysbacteriosis with more pro-inflammatory bacteria, extensive unresolved inflammation, failed mucosal repairment, and aberrant lipid metabolism, particularly lower levels of palmitoleic acid (POA). Dietary POA repaired gut mucosal barriers, reduced inflammatory cell infiltrations and expressions of TNF-α and IL-6, and improved efficacy of anti-TNF-α therapy in both acute and chronic IBD mouse models. Ex vivo treatment with POA in cultured inflamed colon tissues derived from Crohn's disease (CD) patients reduced pro-inflammatory signaling/cytokines and conferred appreciable tissue repairment. Mechanistically, POA significantly upregulated the transcriptional signatures of cell division and biosynthetic process of Akkermansia muciniphila, selectively increased the growth and abundance of Akkermansia muciniphila in gut microbiota, and further reprogrammed the composition and structures of gut microbiota. Oral transfer of such POA-reprogrammed, but not control, gut microbiota induced better protection against colitis in anti-TNF-α mAb-treated recipient mice, and co-administration of POA with Akkermansia muciniphila showed significant synergistic protections against colitis in mice. Collectively, this work not only reveals the critical importance of POA as a polyfunctional molecular force to shape the magnitude and diversity of gut microbiota and therefore promote the intestinal homeostasis, but also implicates a new potential therapeutic strategy against intestinal or abenteric inflammatory diseases.
... The original LC-MS data were processed by software Progenesis QI V2.3 (Nonlinear Dynamics, Newcastle, UK) for baseline filtering, peak identification, integral, retention time correction, peak alignment, and normalization (Fornelos et al., 2020). The main parameters of 5 ppm precursor tolerance, 10 ppm product tolerance, and a 5% production threshold were applied. ...
Bloom-forming algae Phaeocystis globosa is one of the most successful blooming algae in the oceans due to its capacity to sense grazer-associated chemical cues and respond adaptively to these grazer-specific cues with opposing shifts in phenotype. P. globosa produces toxic and deterrent compounds as chemical defenses. However, the origin of the signals and underlying mechanisms that triggered the morphological and chemical defenses remain enigmatic. Rotifer was chosen to establish an herbivore-phytoplankton interaction with P. globosa. The influences of rotifer kairomone and conspecific-grazed cue on morphological and chemical defenses in P. globosa were investigated. As a result, rotifer kairomones elicited morphological defenses and broad-spectrum chemical defenses, whereas algae-grazed cues elicited morphological defenses and consumer-specific chemical defenses. According to multi-omics findings, the difference in hemolytic toxicity caused by different stimuli may be related to the upregulation of lipid metabolism pathways and increased lipid metabolite content, while the inhibition of colonial formation and development of P. globosa may be caused by the downscaled production and secretion of glycosaminoglycans. The study demonstrated that zooplankton consumption cues were recognized by intraspecific prey and elicited consumer-specific chemical defenses, highlighting the chemical ecology of herbivore-phytoplankton interactions in the marine ecosystem.
... High-fat diets induce severe disruptions in colonic microbial communities. Fornelos et al. [59] observed that with the increased ratio of omega-6: omega-3 fatty acid in the diet (such as the HF diet), the symbiotic bacteria that maintain host immunological equilibrium are affected, whereas the growth of pathogenic bacteria favoring inflammatory diseases is favored. Our results showed that incorporating VFPE (0.5%, 1%, and 2%) reduced the abundance of Erysipelotrichales, Chloroplast, Mollicutes, and Mycoplasmatales genus of the group of Firmicutes. ...
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Obesity causes systemic inflammation, hepatic and renal damage, as well as gut microbiota dysbiosis. Alternative vegetable sources rich in polyphenols are known to prevent or delay the progression of metabolic abnormalities during obesity. Vachellia farnesiana (VF) is a potent source of polyphenols with antioxidant and anti-inflammatory activities with potential anti-obesity effects. We performed an in vivo preventive or an interventional experimental study in mice and in vitro experiments with different cell types. In the preventive study, male C57BL/6 mice were fed with a Control diet, a high-fat diet, or a high-fat diet containing either 0.1% methyl gallate, 10% powdered VFP, or 0.5%, 1%, or 2% of a polyphenolic extract (PE) derived from VFP (Vachellia farnesiana pods) for 14 weeks. In the intervention study, two groups of mice were fed for 14 weeks with a high-fat diet and then one switched to a high-fat diet with 10% powdered VFP for ten additional weeks. In the in vitro studies, we evaluated the effect of a VFPE (Vachellia farnesiana polyphenolic extract) on glucose-stimulated insulin secretion in INS-1E cells or of naringenin or methyl gallate on mitochondrial activity in primary hepatocytes and C2C12 myotubes. VFP or a VFPE increased whole-body energy expenditure and mitochondrial activity in skeletal muscle; prevented insulin resistance, hepatic steatosis, and kidney damage; exerted immunomodulatory effects; and reshaped fecal gut microbiota composition in mice fed a high-fat diet. VFPE decreased insulin secretion in INS-1E cells, and its isolated compounds naringenin and methyl gallate increased mitochondrial activity in primary hepatocytes and C2C12 myotubes. In conclusion VFP or a VFPE prevented systemic inflammation, insulin resistance, and hepatic and renal damage in mice fed a high-fat diet associated with increased energy expenditure, improved mitochondrial function, and reduction in insulin secretion.
Most diets and medications enhance host health via microbiota-dependent ways, but it is in the present situation of untargeted regulation. Non-targeted regulation may lead to the ineffectiveness of dietary supplements or drug treatment. Microbiota-directed food, aiming to improve diseases by targeting specific microbes without affecting other bacteria, have been proposed to deal with this problem. However, there is currently no universally applicable method to explore such foods or drugs. In this review, thirty studies on recent efforts in microbiota directed diets and medications are summarized from various databases. The methods used to find new foods and medications are primarily divided into four groups depending on the experimental models: in vivo and in vitro, as well as predictions based on bioinformatics. We also discuss their implementation, interpretation, and respective limitations, and describe the present situation. We further put forward a framework for microbiota-directed foods and medicine according to above methods and other microbiome manipulation, which will spur precision medicine.
Probiotics represent a promising tool to improve metabolic health, including lipid profiles and cholesterol levels. Modulation of the gut microbiome and the endocannabinoidome - two interrelated systems involved in several metabolic processes influenced by probiotics - has been proposed as a potential mechanism of action. This study establishes the impact of probiotics on metabolic health, gut microbiota composition and endocannabinoidome mediators in an animal model of hypercholesterolaemia. Syrian hamsters were fed either a low-fat low-cholesterol or high-fat high-cholesterol (HFHC) diet to induce hypercholesterolaemia and gavaged for 6 weeks with either Lactobacillus acidophilus CL1285, Lactiplantibacillus plantarum CHOL-200 or a combination of the two. Globally, probiotic interventions ameliorated, at least partially, lipid metabolism in HFHC-fed hamsters. The interventions, especially those including L. acidophilus, modified the gut microbiota composition of the small intestine and caecum in ways suggesting reversal of HFHC-induced dysbiosis. Several associations were observed between changes in gut microbiota composition and endocannabinoidome mediators following probiotic interventions and both systems were also associated with improved metabolic health parameters. For instance, potential connexions between the Eubacteriaceae and Deferribacteraceae families, levels of 2‑palmitoylglycerol, 2‑oleoylglycerol, 2‑linoleoylglycerol or 2‑eicosapentaenoylglycerol and improved lipid profiles were found. Altogether, our results suggest a potential crosstalk between gut microbiota and the endocannabinoidome in driving metabolic benefits associated with probiotics, especially those including L. acidophilus, in an animal model of hypercholesterolaemia.
Among the sources of chemical signals regulating food intake, energy metabolism and body weight, few have attracted recently as much attention as the expanded endocannabinoid system, or endocannabinoidome (eCBome), and the gut microbiome, the two systems on which this review article is focussed. Therefore, it is legitimate to expect that these two systems also play a major role in the etiopathology of eating disorders (EDs), in particular of anorexia nervosa, bulimia nervosa and binge-eating disorder. The major mechanisms through which, also via interactions with other endogenous signaling systems, the eCBome, with its several lipid mediators and receptors, and the gut microbiome, via its variety of microbial kingdoms, phyla and species, and armamentarium of metabolites, intervene in these disorders, are described here, based on several published studies in either experimental models or patients. Additionally, in view of the emerging multi-faceted cross-talk mechanisms between these two complex systems, we discuss the possibility that the eCBome-gut microbiome axis is also involved in EDs.
The cannabis derivative marijuana is the most widely used recreational drug in the Western world, that is consumed by an estimated 83 million individuals (~3% of the world population). In recent years, there has been a marked transformation in society regarding the risk perception of cannabis, driven by its legalization and medical use in many states in the USA and worldwide. Compelling research evidence and the FDA cannabis-derived cannabidiol approval for severe childhood epilepsy have confirmed the large therapeutic potential of cannabidiol itself, Δ9-tetrahydrocannabinol (THC) and other plant-derived cannabinoids (phytocannabinoids). Of note, our body has a complex endocannabinoid system (ECS) - made of receptors, metabolic enzymes and transporters - that is also regulated by phytocannabinoids. The first endocannabinoid to be discovered 30 years ago was anandamide (N-arachidonoyl-ethanolamine); since then, distinct elements of ECS have been the target of drug design programs aimed at curing (or at least slowing down) a number of human diseases, both in the central nervous system and at the periphery. Here, a critical review of our knowledge of the goods and bads of ECS as a therapeutic target are presented, in order to define the benefits of ECS-active phytocannabinoids and ECS-oriented synthetic drugs for human health. Significance Statement The endocannabinoid system plays important roles everywhere in our body and is either involved in mediating key processes of central and peripheral diseases or represents a therapeutic target for treatment. Understanding structure, function, and pharmacology of the components of this complex system, and in particular of key receptors (like CB1R and CB2R) and metabolic enzymes (like FAAH and MAGL), will advance our understanding of endocannabinoid signaling and activity at molecular, cellular, and system levels providing new opportunities to treat patients.
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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.
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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 (, 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.
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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.
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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.
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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.
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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.
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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 ( 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 and new tools being added upon their release. Contact: Supplementary information: Supplementary data are available at Bioinformatics online.
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.
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.