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Nature Feb 2024Bacteria in the gastrointestinal tract produce amino acid bile acid amidates that can affect host-mediated metabolic processes; however, the bacterial gene(s)...
Bacteria in the gastrointestinal tract produce amino acid bile acid amidates that can affect host-mediated metabolic processes; however, the bacterial gene(s) responsible for their production remain unknown. Herein, we report that bile salt hydrolase (BSH) possesses dual functions in bile acid metabolism. Specifically, we identified a previously unknown role for BSH as an amine N-acyltransferase that conjugates amines to bile acids, thus forming bacterial bile acid amidates (BBAAs). To characterize this amine N-acyltransferase BSH activity, we used pharmacological inhibition of BSH, heterologous expression of bsh and mutants in Escherichia coli and bsh knockout and complementation in Bacteroides fragilis to demonstrate that BSH generates BBAAs. We further show in a human infant cohort that BBAA production is positively correlated with the colonization of bsh-expressing bacteria. Lastly, we report that in cell culture models, BBAAs activate host ligand-activated transcription factors including the pregnane X receptor and the aryl hydrocarbon receptor. These findings enhance our understanding of how gut bacteria, through the promiscuous actions of BSH, have a significant role in regulating the bile acid metabolic network.
Topics: Humans; Acyltransferases; Amidohydrolases; Amines; Bacteroides fragilis; Bile Acids and Salts; Biocatalysis; Cohort Studies; Escherichia coli; Gastrointestinal Microbiome; Ligands; Pregnane X Receptor; Receptors, Aryl Hydrocarbon; Transcription Factors; Infant; Cell Culture Techniques
PubMed: 38326609
DOI: 10.1038/s41586-023-06990-w -
Proceedings of the National Academy of... Jul 2023Extracellular vesicles are produced in all three domains of life, and their biogenesis has common ancient origins in eukaryotes and archaea. Although bacterial vesicles...
Extracellular vesicles are produced in all three domains of life, and their biogenesis has common ancient origins in eukaryotes and archaea. Although bacterial vesicles were discovered several decades ago and multiple roles have been attributed to them, no mechanism has been established for vesicles biogenesis in bacteria. For this reason, there is a significant level of skepticism about the biological relevance of bacterial vesicles. (), a prominent member of the human intestinal microbiota, produces significant amounts of outer membrane vesicles (OMVs) which have been proposed to play key physiological roles. Here, we employed a dual marker system, consisting of outer membrane- and OMV-specific markers fused to fluorescent proteins to visualize OMV biogenesis by time-lapse microscopy. Furthermore, we performed comparative proteomic analyses to show that, in , the OMV cargo is adapted for the optimal utilization of different polysaccharides. We also show that a negatively charged N-terminal motif acts as a signal for protein sorting into OMVs irrespective of the nutrient availability. Our results demonstrate that OMV production is the result of a highly regulated process in .
Topics: Humans; Proteomics; Extracellular Vesicles; Bacteroides thetaiotaomicron; Diet; Polysaccharides; Bacterial Outer Membrane Proteins
PubMed: 37364113
DOI: 10.1073/pnas.2306314120 -
EBioMedicine Jul 2021Birth by caesarean section (CS) is associated with aberrant gut microbiome development and greater disease susceptibility later in life. We investigated whether oral... (Randomized Controlled Trial)
Randomized Controlled Trial
Oral administration of maternal vaginal microbes at birth to restore gut microbiome development in infants born by caesarean section: A pilot randomised placebo-controlled trial.
BACKGROUND
Birth by caesarean section (CS) is associated with aberrant gut microbiome development and greater disease susceptibility later in life. We investigated whether oral administration of maternal vaginal microbiota to infants born by CS could restore their gut microbiome development in a pilot single-blinded, randomised placebo-controlled trial (Australian New Zealand Clinical Trials Registry, ACTRN12618000339257).
METHODS
Pregnant women scheduled for a CS underwent comprehensive antenatal pathogen screening. At birth, healthy neonates were randomised to receive a 3 ml solution of either maternal vaginal microbes (CS-seeded, n = 12) or sterile water (CS-placebo, n = 13). Vaginally-born neonates were used as the reference control (VB, n = 22). Clinical assessments occurred within the first 2 h of birth, and at 1 month and 3 months of age. Infant stool samples and maternal vaginal extracts from CS women underwent shotgun metagenomic sequencing. The primary outcome was gut microbiome composition at 1 month of age. Secondary outcomes included maternal strain engraftment, functional potential of the gut microbiome, anthropometry, body composition, and adverse events.
FINDINGS
Despite the presence of viable microbial cells within transplant solutions, there were no observed differences in gut microbiome composition or functional potential between CS-seeded and CS-placebo infants at 1 month or 3 months of age. Both CS groups displayed the characteristic signature of low Bacteroides abundance, which contributed to a number of biosynthesis pathways being underrepresented when compared with VB microbiomes. Maternal vaginal strain engraftment was rare. Vaginal seeding had no observed effects on anthropometry or body composition. There were no serious adverse events associated with treatment.
INTERPRETATION
Our pilot findings question the value of vaginal seeding given that oral administration of maternal vaginal microbiota did not alter early gut microbiome development in CS-born infants. The limited colonisation of maternal vaginal strains suggest that other maternal sources, such as the perianal area, may play a larger role in seeding the neonatal gut microbiome.
FUNDING
Health Research Council of New Zealand, A Better Start - National Science Challenge.
Topics: Administration, Oral; Adult; Bacteroides; Cesarean Section; Fecal Microbiota Transplantation; Female; Gastrointestinal Microbiome; Humans; Infant, Newborn; Infant, Newborn, Diseases; Male; Vagina
PubMed: 34186487
DOI: 10.1016/j.ebiom.2021.103443 -
Nature Oct 2021Humans have co-evolved with a dense community of microbial symbionts that inhabit the lower intestine. In the colon, secreted mucus creates a barrier that separates...
Humans have co-evolved with a dense community of microbial symbionts that inhabit the lower intestine. In the colon, secreted mucus creates a barrier that separates these microorganisms from the intestinal epithelium. Some gut bacteria are able to utilize mucin glycoproteins, the main mucus component, as a nutrient source. However, it remains unclear which bacterial enzymes initiate degradation of the complex O-glycans found in mucins. In the distal colon, these glycans are heavily sulfated, but specific sulfatases that are active on colonic mucins have not been identified. Here we show that sulfatases are essential to the utilization of distal colonic mucin O-glycans by the human gut symbiont Bacteroides thetaiotaomicron. We characterized the activity of 12 different sulfatases produced by this species, showing that they are collectively active on all known sulfate linkages in O-glycans. Crystal structures of three enzymes provide mechanistic insight into the molecular basis of substrate specificity. Unexpectedly, we found that a single sulfatase is essential for utilization of sulfated O-glycans in vitro and also has a major role in vivo. Our results provide insight into the mechanisms of mucin degradation by a prominent group of gut bacteria, an important process for both normal microbial gut colonization and diseases such as inflammatory bowel disease.
Topics: Acetylgalactosamine; Animals; Bacteroides; Colon; Crystallography, X-Ray; Female; Galactose; Gastrointestinal Microbiome; Humans; Male; Mice; Models, Molecular; Mucins; Substrate Specificity; Sulfatases
PubMed: 34616040
DOI: 10.1038/s41586-021-03967-5 -
Nature Reviews. Microbiology Dec 2021The defining trait of obligate anaerobes is that oxygen blocks their growth, yet the underlying mechanisms are unclear. A popular hypothesis was that these... (Review)
Review
The defining trait of obligate anaerobes is that oxygen blocks their growth, yet the underlying mechanisms are unclear. A popular hypothesis was that these microorganisms failed to evolve defences to protect themselves from reactive oxygen species (ROS) such as superoxide and hydrogen peroxide, and that this failure is what prevents their expansion to oxic habitats. However, studies reveal that anaerobes actually wield most of the same defences that aerobes possess, and many of them have the capacity to tolerate substantial levels of oxygen. Therefore, to understand the structures and real-world dynamics of microbial communities, investigators have examined how anaerobes such as Bacteroides, Desulfovibrio, Pyrococcus and Clostridium spp. struggle and cope with oxygen. The hypoxic environments in which these organisms dwell - including the mammalian gut, sulfur vents and deep sediments - experience episodic oxygenation. In this Review, we explore the molecular mechanisms by which oxygen impairs anaerobes and the degree to which bacteria protect their metabolic pathways from it. The emergent view of anaerobiosis is that optimal strategies of anaerobic metabolism depend upon radical chemistry and low-potential metal centres. Such catalytic sites are intrinsically vulnerable to direct poisoning by molecular oxygen and ROS. Observations suggest that anaerobes have evolved tactics that either minimize the extent to which oxygen disrupts their metabolism or restore function shortly after the stress has dissipated.
Topics: Anaerobiosis; Bacteria, Anaerobic; Bacteroides; Clostridium; Desulfovibrio; Hydrogen Peroxide; Oxygen; Pyrococcus; Reactive Oxygen Species; Superoxides
PubMed: 34183820
DOI: 10.1038/s41579-021-00583-y -
Cell May 2024The gut microbiota has been found to play an important role in the progression of metabolic dysfunction-associated steatohepatitis (MASH), but the mechanisms have not...
The gut microbiota has been found to play an important role in the progression of metabolic dysfunction-associated steatohepatitis (MASH), but the mechanisms have not been established. Here, by developing a click-chemistry-based enrichment strategy, we identified several microbial-derived bile acids, including the previously uncharacterized 3-succinylated cholic acid (3-sucCA), which is negatively correlated with liver damage in patients with liver-tissue-biopsy-proven metabolic dysfunction-associated fatty liver disease (MAFLD). By screening human bacterial isolates, we identified Bacteroides uniformis strains as effective producers of 3-sucCA both in vitro and in vivo. By activity-based protein purification and identification, we identified an enzyme annotated as β-lactamase in B. uniformis responsible for 3-sucCA biosynthesis. Furthermore, we found that 3-sucCA is a lumen-restricted metabolite and alleviates MASH by promoting the growth of Akkermansia muciniphila. Together, our data offer new insights into the gut microbiota-liver axis that may be leveraged to augment the management of MASH.
Topics: Animals; Humans; Male; Mice; Akkermansia; Bacteroides; beta-Lactamases; Bile Acids and Salts; Biosynthetic Pathways; Fatty Liver; Gastrointestinal Microbiome; Liver; Mice, Inbred C57BL; Symbiosis; Verrucomicrobia; Non-alcoholic Fatty Liver Disease
PubMed: 38653239
DOI: 10.1016/j.cell.2024.03.034 -
Gut Microbes Dec 2023Synbiotics are increasingly used by the general population to boost immunity. However, there is limited evidence concerning the immunomodulatory effects of synbiotics in... (Randomized Controlled Trial)
Randomized Controlled Trial
Synbiotics are increasingly used by the general population to boost immunity. However, there is limited evidence concerning the immunomodulatory effects of synbiotics in healthy individuals. Therefore, we conducted a double-blind, randomized, placebo-controlled study in 106 healthy adults. Participants were randomly assigned to receive either synbiotics (containing HN019 1.5 × 10 CFU/d, HN001 7.5 × 10 CFU/d, and fructooligosaccharide 500 mg/d) or placebo for 8 weeks. Immune parameters and gut microbiota composition were measured at baseline, mid, and end of the study. Compared to the placebo group, participants receiving synbiotic supplementation exhibited greater reductions in plasma C-reactive protein ( = 0.088) and interferon-gamma ( = 0.008), along with larger increases in plasma interleukin (IL)-10 ( = 0.008) and stool secretory IgA (sIgA) ( = 0.014). Additionally, synbiotic supplementation led to an enrichment of beneficial bacteria (, , , and ) and several functional pathways related to amino acids and short-chain fatty acids biosynthesis, whereas reduced potential pro-inflammatory compared to baseline. Importantly, alternations in anti-inflammatory markers (IL-10 and sIgA) were significantly correlated with microbial variations triggered by synbiotic supplementation. Stratification of participants into two enterotypes based on pre-treatment -to- (/) ratio revealed a more favorable effect of synbiotic supplements in individuals with a higher / ratio. In conclusion, this study suggested the beneficial effects of synbiotic supplementation on immune parameters, which were correlated with synbiotics-induced microbial changes and modified by microbial enterotypes. These findings provided direct evidence supporting the personalized supplementation of synbiotics for immunomodulation.
Topics: Humans; Adult; Gastrointestinal Microbiome; Synbiotics; Actinobacteria; Amino Acids; Bacteroides
PubMed: 37614109
DOI: 10.1080/19490976.2023.2247025 -
Revista Latino-americana de Enfermagem 2021to analyze scientific evidence regarding the relationship between the type of birth and the microbiota acquired by newborns. (Review)
Review
OBJECTIVE
to analyze scientific evidence regarding the relationship between the type of birth and the microbiota acquired by newborns.
METHOD
this integrative review addresses the role of the type of delivery on newborns' microbial colonization. A search was conducted in the Medical Literature Analysis and Retrieval System Online/PubMed and Virtual Health Library databases using the descriptors provided by Medical Subject Headings (MeSH) and Health Science Descriptors (DeCS).
RESULTS
infants born vaginally presented a greater concentration of Bacteroides, Bifidobacteria, and Lactobacillus in the first days of life and more significant microbial variability in the following weeks. The microbiome of infants born via C-section is similar to the maternal skin and the hospital setting and less diverse, mainly composed of Staphylococcus, Streptococcus, and Clostridium.
CONCLUSION
the maternal vaginal microbiota provides newborns with a greater variety of colonizing microorganisms responsible for boosting and preparing the immune system. Vaginal birth is the ideal birth route, and C-sections should only be performed when there are medical indications.
Topics: Bacteroides; Cesarean Section; Female; Gastrointestinal Microbiome; Humans; Infant; Infant, Newborn; Microbiota; Parturition; Pregnancy
PubMed: 34287544
DOI: 10.1590/1518.8345.4466.3446 -
The Turkish Journal of Gastroenterology... Dec 2019
Topics: Akkermansia; Bacteroides fragilis; Fasting; Gastrointestinal Microbiome; Verrucomicrobia
PubMed: 31854304
DOI: 10.5152/tjg.2019.101219 -
Nature Communications Jul 2022Bacteroides species are prominent members of the human gut microbiota. The prevalence and stability of Bacteroides in humans make them ideal candidates to engineer as...
Bacteroides species are prominent members of the human gut microbiota. The prevalence and stability of Bacteroides in humans make them ideal candidates to engineer as programmable living therapeutics. Here we report a biotic decision-making technology in a community of Bacteroides (consortium transcriptional programming) with genetic circuit compression. Circuit compression requires systematic pairing of engineered transcription factors with cognate regulatable promoters. In turn, we demonstrate the compression workflow by designing, building, and testing all fundamental two-input logic gates dependent on the inputs isopropyl-β-D-1-thiogalactopyranoside and D-ribose. We then deploy complete sets of logical operations in five human donor Bacteroides, with which we demonstrate sequential gain-of-function control in co-culture. Finally, we couple transcriptional programs with CRISPR interference to achieve loss-of-function regulation of endogenous genes-demonstrating complex control over community composition in co-culture. This work provides a powerful toolkit to program gene expression in Bacteroides for the development of bespoke therapeutic bacteria.
Topics: Bacteroides; Clustered Regularly Interspaced Short Palindromic Repeats; Gastrointestinal Microbiome; Humans; Promoter Regions, Genetic; Transcription Factors
PubMed: 35794179
DOI: 10.1038/s41467-022-31614-8