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Nature Nov 2017The human gut microbiota produces dozens of metabolites that accumulate in the bloodstream, where they can have systemic effects on the host. Although these small...
The human gut microbiota produces dozens of metabolites that accumulate in the bloodstream, where they can have systemic effects on the host. Although these small molecules commonly reach concentrations similar to those achieved by pharmaceutical agents, remarkably little is known about the microbial metabolic pathways that produce them. Here we use a combination of genetics and metabolic profiling to characterize a pathway from the gut symbiont Clostridium sporogenes that generates aromatic amino acid metabolites. Our results reveal that this pathway produces twelve compounds, nine of which are known to accumulate in host serum. All three aromatic amino acids (tryptophan, phenylalanine and tyrosine) serve as substrates for the pathway, and it involves branching and alternative reductases for specific intermediates. By genetically manipulating C. sporogenes, we modulate serum levels of these metabolites in gnotobiotic mice, and show that in turn this affects intestinal permeability and systemic immunity. This work has the potential to provide the basis of a systematic effort to engineer the molecular output of the gut bacterial community.
Topics: Amino Acids, Aromatic; Animals; Blood Chemical Analysis; Closterium; Gastrointestinal Microbiome; Germ-Free Life; Humans; Immunity; Indoles; Intestinal Mucosa; Male; Metabolic Networks and Pathways; Metabolome; Metabolomics; Mice; Multigene Family; Permeability; Phenylalanine; Serum; Tryptophan; Tyrosine
PubMed: 29168502
DOI: 10.1038/nature24661 -
Cell Sep 2020The gut microbiome has been implicated in multiple human chronic gastrointestinal (GI) disorders. Determining its mechanistic role in disease has been difficult due to...
The gut microbiome has been implicated in multiple human chronic gastrointestinal (GI) disorders. Determining its mechanistic role in disease has been difficult due to apparent disconnects between animal and human studies and lack of an integrated multi-omics view of disease-specific physiological changes. We integrated longitudinal multi-omics data from the gut microbiome, metabolome, host epigenome, and transcriptome in the context of irritable bowel syndrome (IBS) host physiology. We identified IBS subtype-specific and symptom-related variation in microbial composition and function. A subset of identified changes in microbial metabolites correspond to host physiological mechanisms that are relevant to IBS. By integrating multiple data layers, we identified purine metabolism as a novel host-microbial metabolic pathway in IBS with translational potential. Our study highlights the importance of longitudinal sampling and integrating complementary multi-omics data to identify functional mechanisms that can serve as therapeutic targets in a comprehensive treatment strategy for chronic GI diseases. VIDEO ABSTRACT.
Topics: Animals; Bile Acids and Salts; Biopsy; Butyrates; Chromatography, Liquid; Cross-Sectional Studies; Epigenomics; Feces; Female; Gastrointestinal Microbiome; Gene Expression Regulation; Host Microbial Interactions; Humans; Hypoxanthine; Irritable Bowel Syndrome; Longitudinal Studies; Male; Metabolome; Mice; Observational Studies as Topic; Prospective Studies; Purines; Software; Tandem Mass Spectrometry; Transcriptome
PubMed: 32916129
DOI: 10.1016/j.cell.2020.08.007 -
Nature Jun 2020The gut microbiota synthesize hundreds of molecules, many of which influence host physiology. Among the most abundant metabolites are the secondary bile acids...
The gut microbiota synthesize hundreds of molecules, many of which influence host physiology. Among the most abundant metabolites are the secondary bile acids deoxycholic acid (DCA) and lithocholic acid (LCA), which accumulate at concentrations of around 500 μM and are known to block the growth of Clostridium difficile, promote hepatocellular carcinoma and modulate host metabolism via the G-protein-coupled receptor TGR5 (ref. ). More broadly, DCA, LCA and their derivatives are major components of the recirculating pool of bile acids; the size and composition of this pool are a target of therapies for primary biliary cholangitis and nonalcoholic steatohepatitis. Nonetheless, despite the clear impact of DCA and LCA on host physiology, an incomplete knowledge of their biosynthetic genes and a lack of genetic tools to enable modification of their native microbial producers limit our ability to modulate secondary bile acid levels in the host. Here we complete the pathway to DCA and LCA by assigning and characterizing enzymes for each of the steps in its reductive arm, revealing a strategy in which the A-B rings of the steroid core are transiently converted into an electron acceptor for two reductive steps carried out by Fe-S flavoenzymes. Using anaerobic in vitro reconstitution, we establish that a set of six enzymes is necessary and sufficient for the eight-step conversion of cholic acid to DCA. We then engineer the pathway into Clostridium sporogenes, conferring production of DCA and LCA on a nonproducing commensal and demonstrating that a microbiome-derived pathway can be expressed and controlled heterologously. These data establish a complete pathway to two central components of the bile acid pool.
Topics: Animals; Bile Acids and Salts; Clostridium; Deoxycholic Acid; Gastrointestinal Microbiome; Hydroxylation; Lithocholic Acid; Male; Metabolic Engineering; Metabolic Networks and Pathways; Mice; Operon; Symbiosis
PubMed: 32555455
DOI: 10.1038/s41586-020-2396-4 -
Cell Host & Microbe Jun 2018Tryptamine, a tryptophan-derived monoamine similar to 5-hydroxytryptamine (5-HT), is produced by gut bacteria and is abundant in human and rodent feces. However, the...
Tryptamine, a tryptophan-derived monoamine similar to 5-hydroxytryptamine (5-HT), is produced by gut bacteria and is abundant in human and rodent feces. However, the physiologic effect of tryptamine in the gastrointestinal (GI) tract remains unknown. Here, we show that the biological effects of tryptamine are mediated through the 5-HT receptor (5-HTR), a G-protein-coupled receptor (GPCR) uniquely expressed in the colonic epithelium. Tryptamine increases both ionic flux across the colonic epithelium and fluid secretion in colonoids from germ-free (GF) and humanized (ex-GF colonized with human stool) mice, consistent with increased intestinal secretion. The secretory effect of tryptamine is dependent on 5-HTR activation and is blocked by 5-HTR antagonist and absent in 5-HTR mice. GF mice colonized by Bacteroides thetaiotaomicron engineered to produce tryptamine exhibit accelerated GI transit. Our study demonstrates an aspect of host physiology under control of a bacterial metabolite that can be exploited as a therapeutic modality. VIDEO ABSTRACT.
Topics: Animals; Bacteroides thetaiotaomicron; Colon; Epithelium; Feces; Gastrointestinal Microbiome; Humans; Intestinal Secretions; Mice; Mice, 129 Strain; Mice, Knockout; Primary Cell Culture; Receptors, Serotonin, 5-HT4; Sex Factors; Specific Pathogen-Free Organisms; Tryptamines
PubMed: 29902441
DOI: 10.1016/j.chom.2018.05.004 -
Annals of Surgery Dec 2023The aim was to determine preoperative gut microbiota metabolites that may be associated with postoperative delirium (POD) development in patients and further study in... (Observational Study)
Observational Study
OBJECTIVE
The aim was to determine preoperative gut microbiota metabolites that may be associated with postoperative delirium (POD) development in patients and further study in rodents.
SUMMARY BACKGROUND DATA
POD occurs in 9% to 50% of older patients undergoing anesthesia/surgery but lacks effective treatments or prevention. High-throughput metabolomics using liquid chromatography with tandem mass spectrometry has accelerated disease-related biomarkers discovery. We performed metabolomic studies in humans to identify potential metabolite biomarkers linked to POD and examined potential mechanisms in rodents.
METHODS
We performed a prospective observational cohort study to examine the metabolomic changes that were associated with the development of POD. Then the gut microbiota-related metabolomic changes were recapitulated by gut microbiota perturbation in rodents. POD was assessed in mice using a battery of behavioral tests including novel objective test, Y-maze test, open-field test, and buried food test. The mechanisms through which gut microbiota-related metabolomic changes influenced POD were examined using chemogenetics.
RESULTS
Indole-3-propionic acid (IPA) is a gut microbiota metabolite that belongs to the indole family. Baseline plasma levels of IPA were significantly inversely correlated with the onset of POD in 103 (17 cases) human individuals. This relationship was validated in preclinical mouse models for POD: reducing IPA levels through gut microbiota perturbation promoted POD-like behavior. More importantly, IPA administration deterred POD-like behavior. Colonization of germ-free mice with mutant Clostridium sporogenes that did not produce IPA-promoted POD-like behavior. Chemogenetic studies revealed that the protective effect of IPA in mice was mediated, in part, by peroxisome proliferator-activated receptor gamma coactivator 1-alpha in hippocampal interneurons.
CONCLUSIONS
Gut microbiota-derived IPA is an important molecule implicated in the pathogenesis of POD, which could potentially be harnessed for POD prevention.
Topics: Humans; Mice; Animals; Gastrointestinal Microbiome; Emergence Delirium; Prospective Studies; Indoles; Biomarkers
PubMed: 37185230
DOI: 10.1097/SLA.0000000000005886 -
Current Neuropharmacology 2023Parkinson's disease (PD) is one of the most common neurodegenerative diseases, characterized by the reduction of dopamine neurons in the substantia nigra. Levodopa, as a... (Review)
Review
Parkinson's disease (PD) is one of the most common neurodegenerative diseases, characterized by the reduction of dopamine neurons in the substantia nigra. Levodopa, as a dopamine supplement, is the gold-standard therapeutic drug for PD. The metabolism of levodopa in the periphery not only decreases its bioavailability but also affects its efficacy. Thus, it is necessary to investigate how levodopa is metabolized. A growing number of studies have shown that intestinal bacteria, such as Enterococcus faecalis, Eggerthella lenta and Clostridium sporogenes, could metabolize levodopa in different ways. In addition, several pathways to reduce levodopa metabolism by gut microbiota were confirmed to improve levodopa efficacy. These pathways include aromatic amino acid decarboxylase (AADC) inhibitors, antibiotics, pH and (S)-α-fluoromethyltyrosine (AFMT). In this review, we have summarized the metabolic process of levodopa by intestinal bacteria and analyzed potential approaches to reduce the metabolism of levodopa by gut microbiota, thus improving the efficacy of levodopa.
Topics: Humans; Levodopa; Antiparkinson Agents; Parkinson Disease; Dopamine; Bacteria
PubMed: 36278467
DOI: 10.2174/1570159X21666221019115716 -
Proceedings of the National Academy of... Mar 2009Although it has long been recognized that the enteric community of bacteria that inhabit the human distal intestinal track broadly impacts human health, the biochemical...
Although it has long been recognized that the enteric community of bacteria that inhabit the human distal intestinal track broadly impacts human health, the biochemical details that underlie these effects remain largely undefined. Here, we report a broad MS-based metabolomics study that demonstrates a surprisingly large effect of the gut "microbiome" on mammalian blood metabolites. Plasma extracts from germ-free mice were compared with samples from conventional (conv) animals by using various MS-based methods. Hundreds of features were detected in only 1 sample set, with the majority of these being unique to the conv animals, whereas approximately 10% of all features observed in both sample sets showed significant changes in their relative signal intensity. Amino acid metabolites were particularly affected. For example, the bacterial-mediated production of bioactive indole-containing metabolites derived from tryptophan such as indoxyl sulfate and the antioxidant indole-3-propionic acid (IPA) was impacted. Production of IPA was shown to be completely dependent on the presence of gut microflora and could be established by colonization with the bacterium Clostridium sporogenes. Multiple organic acids containing phenyl groups were also greatly increased in the presence of gut microbes. A broad, drug-like phase II metabolic response of the host to metabolites generated by the microbiome was observed, suggesting that the gut microflora has a direct impact on the drug metabolism capacity of the host. Together, these results suggest a significant interplay between bacterial and mammalian metabolism.
Topics: Animals; Bacteria; Blood; Gastrointestinal Tract; Host-Pathogen Interactions; Humans; Indoles; Mammals; Mass Spectrometry; Metabolomics; Metagenome; Sulfur
PubMed: 19234110
DOI: 10.1073/pnas.0812874106 -
Foods (Basel, Switzerland) Apr 2022Zearalenone (ZEN) is produced by spp. and is widely found in moldy wheat, corn, and other grains. ZEN has a strong toxicity and causes reproductive and immune disorders...
Zearalenone (ZEN) is produced by spp. and is widely found in moldy wheat, corn, and other grains. ZEN has a strong toxicity and causes reproductive and immune disorders and estrogenic syndrome in animals and humans. Biodegradation has been demonstrated as an efficient way to control the hazardous effect of ZEN. A promising way to apply biodegradation in feed is to introduce anaerobic ZEN-degrading microorganisms, which can function during the digestion process in animal intestines. The aim of this study was to isolate anaerobic ZEN-degrading bacteria from anaerobic environments. A strain named F39 was isolated from animal intestinal contents and had a ZEN-degradation rate of 87.35% in 48 h to form trace amount of α- and β-zearalenol. Based on the morphological and physiological properties and phylogenetic analysis of 16S rRNA and gene sequences, F39 was identified as . The optimum temperature for the growth of F39 was 37 °C, the optimum pH was 7.0, and the most suitable carbon source was beef extract, while the optimal conditions for the degradation of ZEN were as follows: 35 °C, pH 7.0, and GAM medium. ZEN was degraded by F39 with a high efficiency in the concentration range of 1-15 mg/L. The bioactive factors responsible for ZEN degradation were mainly distributed intracellularly. F39 can degrade most of the ZEN present, but a small amount is broken down into two secondary metabolites, α- and β-zearalenol, and the toxicity of the degradation products is reduced. With an efficiency of 49%, F39 can more effectively degrade ZEN in wheat-based feedstuffs than in other feedstuff, and the degradation efficiency was pH related. To the best of our knowledge, this is the first report of F39's ability to maintain the biodegradation potentials.
PubMed: 35563917
DOI: 10.3390/foods11091194 -
Polish Journal of Microbiology Sep 2022Research on the susceptibility of the spores of anaerobic bacteria such as or is vital for assessing the sporicidal activity of disinfectants. The diverse...
Research on the susceptibility of the spores of anaerobic bacteria such as or is vital for assessing the sporicidal activity of disinfectants. The diverse susceptibility of anaerobic bacteria spores may lead to different disinfection parameters being determined by laboratories that prepare spore suspensions to test sporicidal effectiveness. The tests were performed using the suspension method according to PN-EN 13704:2018-09. In order to assess the susceptibility of the spores, the criterion established for the ribotype 027 spores was used in accordance with PN‑EN 17126:2019-01. The susceptibility of the spores to glutardialdehyde corresponded to the susceptibility ranges established for the ribotype 027 spores. The spore suspension was susceptible to low concentrations of peracetic acid (0.01%). A disinfectant containing peracetic acid as the active substance showed high sporicidal activity at a low concentration (1%), a short contact time (15 minutes), and a high organic load (3.0 g/l bovine albumin + 3.0 ml/l sheep erythrocytes), as compared to a disinfectant with glutardialdehyde, which was sporicidal at a higher concentration (2.5%), at a longer contact time (60 minutes) and lower organic conditions (3.0 g/l bovine albumin). There is a need to define the minimum susceptibility criteria for the spores to the reference substances most often found in disinfectants with sporicidal activity. Excessive susceptibility of the spores to reference substances may result in low-performance parameters of disinfection products with sporicidal activity and lead to ineffective disinfection in practice.
Topics: Animals; Clostridioides difficile; Clostridium; Disinfectants; Glutaral; Peracetic Acid; Serum Albumin, Bovine; Sheep; Spores, Bacterial; Suspensions
PubMed: 36185021
DOI: 10.33073/pjm-2022-031 -
Food Microbiology Oct 2022An extensive cardinal parameter growth and growth boundary model for C. sporogenes, as a surrogate for proteolytic C. botulinum, was developed to include the inhibitory...
An extensive cardinal parameter growth and growth boundary model for C. sporogenes, as a surrogate for proteolytic C. botulinum, was developed to include the inhibitory effect of 11 environmental factors. 626 maximum specific growth rates (μ) in broth were generated to determine cardinal parameter values for the growth inhibiting effect of temperature, pH, NaCl/water activity (a), organic acids (acetic, benzoic, citric, lactic, sorbic) and phosphate melting salts (ortho-, di- and tri-phosphates). μ-values for C. sporogenes growing in well-characterized processed cheeses were used for product calibration (n = 10) and for product evaluation of the developed broth-model (n = 29). 112 growth/no-growth responses and including 104 μ-values from the scientific literature for 58 different isolates of proteolytic and toxigenic C. botulinum (Group I) were used for further model evaluation. The developed model had less bias and a higher percentage of correct predictions than available models and was acceptable for processed cheese and good for meat products. The new and extensive model can predict combinations of environmental factors that prevent growth of C. sporogenes and of proteolytic C. botulinum. These predictions are expected to facilitate development or re-formulation of processed cheese and meat products where growth is prevented.
Topics: Cheese; Clostridium; Clostridium botulinum; Food Microbiology
PubMed: 35953193
DOI: 10.1016/j.fm.2022.104060