Functional metagenomic discovery of bacterial effectors in the human microbiome and isolation of commendamide, a GPCR G2A/132 agonist

Abstract

The trillions of bacteria that make up the human microbiome are believed to encode functions that are important to human health; however, little is known about the specific effectors that commensal bacteria use to interact with the human host. Functional metagenomics provides a systematic means of surveying commensal DNA for genes that encode effector functions. Here, we examine 3,000 Mb of metagenomic DNA cloned from three phenotypically distinct patients for effectors that activate NF-κB, a transcription factor known to play a central role in mediating responses to environmental stimuli. This screen led to the identification of 26 unique commensal bacteria effector genes (Cbegs) that are predicted to encode proteins with diverse catabolic, anabolic, and ligand-binding functions and most frequently interact with either glycans or lipids. Detailed analysis of one effector gene family (Cbeg12) recovered from all three patient libraries found that it encodes for the production of N-acyl-3-hydroxypalmitoyl-glycine (commendamide). This metabolite was also found in culture broth from the commensal bacterium Bacteroides vulgatus, which harbors a gene highly similar to Cbeg12. Commendamide resembles long-chain N-acyl-amides that function as mammalian signaling molecules through activation of G-protein–coupled receptors (GPCRs), which led us to the observation that commendamide activates the GPCR G2A/GPR132. G2A has been implicated in disease models of autoimmunity and atherosclerosis. This study shows the utility of functional metagenomics for identifying potential mechanisms used by commensal bacteria for host interactions and outlines a functional metagenomics-based pipeline for the systematic identification of diverse commensal bacteria effectors that impact host cellular functions.

Microbiome and metabolome data integration provides insight into health and disease

“…However, approaches that can identify novel bio-active microbial metabolites as mediators of microbiome-host or microbe-microbe interactions are increasingly being applied 71 . These include: 1) Bioactivity-guided screening, in which a phenotypic bioassay is performed by testing a collection of microbes, chemical extracts, or cosmid libraries generated from metagenomics DNA against a panel of host pathogens or signaling pathways 72,73 . 2) Candidate molecule workflows, which mine existing (meta)genomics data to identify Biosynthetic Gene Clusters (BGCs) that may produce metabolites of interest because they are prevalent or correlate with disease 49 .…”

“…For instance, commendamide, which activates the G-protein-coupled receptor G2A/GPR132 (G2A has been implicated in disease models of autoimmunity and atherosclerosis), was discovered initially in a screen of 3,000 megabases of metagenomic DNA for effectors that activate NF-κB, a transcription factor that plays a role in mediating responses to environmental stimuli 72 . Lugdunin, a novel antibiotic that prohibits colonization by methicillin-resistant Staphylococcus aureus (MRSA), was discovered by screening for the mechanism by which Staphylococcus lugdunensis , a microbe that occupies the same niche as MRSA, could inhibit the growth of MRSA in vitro 73 .…”

“…Lugdunin, a novel antibiotic that prohibits colonization by methicillin-resistant Staphylococcus aureus (MRSA), was discovered by screening for the mechanism by which Staphylococcus lugdunensis , a microbe that occupies the same niche as MRSA, could inhibit the growth of MRSA in vitro 73 . Bioactivity-guided workflows can also include random mutagenesis of the microbe of interest combined with high-throughput phenotypic screening for loss of function, and imaging mass spectrometry of competing microbes in vitro 72,77,78 .…”

“…One study showed that a dietary fiber associated reduction in allergic lung inflammation was driven by the SCFA propionate, which exerted its health effects through G protein–coupled receptor 41 mediated signaling in bone marrow 72 . Other work demonstrated that risk of cardiovascular disease and atherosclerosis was linked with trimethylamine-N-oxide (TMAO), which is produced by host enzymes from trimethylamine (TMA).…”

Vascular Wall Condition, Gut Microbiota Composition, and Diet in Patients Withoutcardiovascular Diseases

“…«западной диетой» с большим содержанием животных белков и жиров [19,20]. Согласно недавно опубликованному исследованию, пред-ставители Bacteroides имеют гены, работа кото-рых запускает воспалительную реакцию [21]. Кроме того, Bacteroides также содержат ЛПС и являются оппортунистическими патогенами.…”