Gut Anaerobes Research Articles

Bifidobacterium adolescentis shows potential to strengthen host defence against gastrointestinal infection via inhibition of the opportunistic pathogen Candida albicans and stimulation of human-isolated macrophages killing capacity in vitro

The human gut microbiota enhances the host’s resistance to enteric pathogens via colonisation resistance, a phenomenon that is driven by multiple mechanisms, such as production of antimicrobial metabolites and activation of host immune responses. However, there is limited information on how individual gut bacterial species, particularly many of the dominant anaerobes, might impact the host’s defence. This study investigated the potential of specific human gut isolates to bolster the host’s resistance to infection. First, by antagonising the opportunistic fungal pathogen Candida albicans, and secondly, by modulating the killing capacity of human-isolated macrophages in vitro. Co-culturing C. albicans with faecal microbiota from different healthy individuals revealed varying levels of fungal inhibition. In vitro assays with a panel of representative human gut anaerobes confirmed that culture supernatants from certain bacterial isolates, in particular of Bifidobacterium adolescentis, significantly inhibited C. albicans growth. Mechanistic studies revealed that microbial fermentation acids including acetate and lactate, in combination with the associated decrease in pH, were strong drivers of this inhibitory activity. In the second in vitro assay, human-isolated macrophages were exposed to bacterial supernatants, and subsequently tested for their capacity to eliminate adherent-invasive Escherichia coli. Among the gut anaerobes tested, B. adolescentis was revealed to exert the strongest immunostimulatory and killing effect when compared to the unstimulated macrophages control. B. adolescentis is known to be stimulated by dietary consumption of resistant starch andmay therefore represent an attractive target for the development of probiotic and prebiotic interventions tailored to enhancethe host’s natural defences against infection.

Systematic Culturomics Shows that Half of Chicken Caecal Microbiota Members can be Grown in Vitro Except for Two Lineages of Clostridiales and a Single Lineage of Bacteroidetes.

Epidemiological data show that the composition of gut microbiota influences host health, disease status, and even behaviour. However, to confirm these epidemiological observations in controlled experiments, pure cultures of gut anaerobes must be obtained. Since the culture of gut anaerobes is not a simple task due to the large number of bacterial species colonising the intestinal tract, in this study we inoculated 174 different culture media with caecal content from adult hens, and compared the microbiota composition in the original caecal samples and in bacterial masses growing in vitro by 16S rRNA sequencing. In total, 42% of gut microbiota members could be grown in vitro and since there were some species which were not cultured but for which the culture conditions are known, it is likely that more than half of chicken gut microbiota can be grown in vitro. However, there were two lineages of Clostridiales and a single lineage of Bacteroidetes which were common in chicken caecal microbiota but resistant to culture. Of the most selective culture conditions, nutrient broths supplemented with mono- or di-saccharides, including those present in fruits, positively selected for Lactobacillaceae. The addition of bile salts selected for Veillonellaceae and YCFA (yeast casitone fatty acid agar) enriched for Desulfovibrionaceae. In addition, Erysipelotrichaceae were positively selected by colistin, trimethoprim, streptomycin and nalidixic acid. Culture conditions tested in this study can be used for the selective enrichment of desired bacterial species but also point towards the specific functions of individual gut microbiota members.

A Putative Type V Pilus Contributes to Bacteroides thetaiotaomicron Biofilm Formation Capacity.

Bacteroides thetaiotaomicron is a prominent anaerobic member of the healthy human gut microbiota. While the majority of functional studies on B. thetaiotaomicron addressed its impact on the immune system and the utilization of diet polysaccharides, B. thetaiotaomicron biofilm capacity and its contribution to intestinal colonization are still poorly characterized. We tested the natural adhesion of 34 B. thetaiotaomicron isolates and showed that although biofilm capacity is widespread among B. thetaiotaomicron strains, this phenotype is masked or repressed in the widely used reference strain VPI 5482. Using transposon mutagenesis followed by a biofilm positive-selection procedure, we identified VPI 5482 mutants with increased biofilm capacity corresponding to an alteration in the C-terminal region of BT3147, encoded by the BT3148-BT3147 locus, which displays homology with Mfa-like type V pili found in many Bacteroidetes We show that BT3147 is exposed on the B. thetaiotaomicron surface and that BT3147-dependent adhesion also requires BT3148, suggesting that BT3148 and BT3147 correspond to the anchor and stalk subunits of a new type V pilus involved in B. thetaiotaomicron adhesion. This study therefore introduces B. thetaiotaomicron as a model to study proteinaceous adhesins and biofilm-related phenotypes in this important intestinal symbiont.IMPORTANCE Although the gut anaerobe Bacteroides thetaiotaomicron is a prominent member of the healthy human gut microbiota, little is known about its capacity to adhere to surfaces and form biofilms. Here, we identify that alteration of a surface-exposed protein corresponding to a type of pili found in many Bacteroidetes increases B. thetaiotaomicron biofilm formation. This study lays the ground for establishing this bacterium as a model organism for in vitro and in vivo studies of biofilm-related phenotypes in gut anaerobes.

Characterization of fructooligosaccharide-degrading enzymes in human commensal Bifidobacterium longum and Anaerostipes caccae

Kestose and nystose are short chain fructooligosaccharides (scFOSs) with degrees of polymerization of 3 and 4, respectively. A previous study revealed that these scFOSs have different growth stimulation properties against two human commensals, i.e. Bifidobacterium longum subsp. longum and butyrogenic Anaerostipes caccae. The present study characterized genes involved in FOS metabolism in these organisms. A. caccae possesses a single gene cluster consisting of four genes, including a gene encoding the putative FOS degradation enzyme sucrose-6-phosphate hydrolase (S6PH). B. longum possesses two gene clusters consisting of three genes each, including genes encoding β-fructofuranosidase (CscA) and sucrose phosphorylase (ScrP). In A. caccae, the genes were highly transcribed in cells cultured with sucrose or kestose but poorly in cells cultured with glucose or nystose. Heterologously expressed S6PH degraded sucrose and kestose but not nystose. In B. longum, transcription of the genes was high in cells cultured with sucrose or kestose but was poor or not detected in cells cultured with glucose or nystose. Heterologously expressed CscA degraded sucrose, kestose and nystose, but ScrP degraded only sucrose. These data suggested that the different growth stimulation activities of kestose and nystose are due to different substrate specificities of FOS degradation enzymes in the organisms and/or induction activity of the genes in the two scFOSs. This is the first study characterizing the FOS metabolism at the transcriptional level and substrate-specificity of the degradation enzyme in butyrogenic human gut anaerobes.

Each Additional Day of Antibiotics Is Associated With Lower Gut Anaerobes in Neonatal Intensive Care Unit Patients.

BackgroundDiscontinuation of inappropriate antimicrobial therapy is an important target for stewardship intervention. The drug and duration-dependent effects of antibiotics on the developing neonatal gut microbiota needs to be precisely quantified.MethodsIn this retrospective, cross-sectional study, we performed 16S rRNA sequencing on stool swab samples collected from neonatal intensive care unit patients within 7 days of discontinuation of therapy who received ampicillin and tobramycin (AT), ampicillin and cefotaxime (AC), or ampicillin, tobramycin, and metronidazole (ATM). We compared taxonomic composition within term and preterm infant groups between treatment regimens. We calculated adjusted effect estimates for antibiotic type and duration of therapy on the richness of obligate anaerobes and known butyrate-producers in all infants.ResultsA total of 72 infants were included in the study. Term infants received AT (20/28; 71%) or AC (8/28; 29%) with median durations of 3 and 3.5 days, respectively. Preterm infants received AT (32/44; 73%) or ATM (12/44; 27%) with median durations of 4 and 7 days, respectively. Compositional analyses of 67 stool swab samples demonstrated low diversity and dominance by potential pathogens. Within 1 week of discontinuation of therapy, each additional day of antibiotics was associated with lower richness of obligate anaerobes (adjusted risk ratio [aRR], 0.84; 95% confidence interval [CI], .73–.95) and butyrate-producers (aRR, 0.82; 95% CI, .67–.97).ConclusionsEach additional day of antibiotics was associated with lower richness of anaerobes and butyrate-producers within 1 week after therapy. A longitudinally sampled cohort with preexposure sampling is needed to validate our results.

Chemoproteomic Profiling of Gut Microbiota-Associated Bile Salt Hydrolase Activity.

The metagenome of the gut microbiome encodes tremendous potential for biosynthesizing and transforming small-molecule metabolites through the activities of enzymes expressed by intestinal bacteria. Accordingly, elucidating this metabolic network is critical for understanding how the gut microbiota contributes to health and disease. Bile acids, which are first biosynthesized in the liver, are modified in the gut by enzymes expressed by commensal bacteria into secondary bile acids, which regulate myriad host processes, including lipid metabolism, glucose metabolism, and immune homeostasis. The gateway reaction of secondary bile acid biosynthesis is mediated by bile salt hydrolases (BSHs), bacterial cysteine hydrolases whose action precedes other bile acid modifications within the gut. To assess how changes in bile acid metabolism mediated by certain intestinal microbiota impact gut physiology and pathobiology, methods are needed to directly examine the activities of BSHs because they are master regulators of intestinal bile acid metabolism. Here, we developed chemoproteomic tools to profile changes in gut microbiome-associated BSH activity. We showed that these probes can label active BSHs in model microorganisms, including relevant gut anaerobes, and in mouse gut microbiomes. Using these tools, we identified altered BSH activities in a murine model of inflammatory bowel disease, in this case, colitis induced by dextran sodium sulfate, leading to changes in bile acid metabolism that could impact host metabolism and immunity. Importantly, our findings reveal that alterations in BSH enzymatic activities within the gut microbiome do not correlate with changes in gene abundance as determined by metagenomic sequencing, highlighting the utility of chemoproteomic approaches for interrogating the metabolic activities of the gut microbiota.

Development of an Infection Risk Index for Microbiome Targeted Intervention in Children at High-Risk of Multidrug-Resistant Bloodstream Infections

Background Bloodstream infections (BSI) cause significant morbidity and mortality following pediatric hematopoietic stem cell transplantation (HSCT) and are increasingly from multidrug-resistant pathogens. Most of these BSI pathogens arise from the intestines. Increased evidence demonstrates commensal gut anaerobes maintain host resistance from enteric infection, while loss of commensals increases host susceptibility. Antibiotic use reduces gut anaerobes and allows a compensatory increased pathogen burden that precedes BSI; BSI risk is related to colonization burden. Recent reports suggest fecal microbiota transplantation (FMT) can displace an enteric pathogens and broad-spectrum antibiotic resistance genes during restoration of a healthy microbiome. However, the impact of intestinal microbiota on colonization, transmission, and invasive MDR infections is poorly understood in children undergoing HSCT. Methods Using metagenomic shotgun sequencing (MSS) data of longitudinal stool samples from high-risk children, including 63 undergoing HSCT with 166 samples preceding BSI onset (n = 23), we developed a metagenomic-based infection risk index (IRI) from key microbiome features (scaled Brady-Curtis distance relative to healthy controls and relative anaerobe and pathogen abundance). Traditional cart data analysis was compared to advanced machine learning algorithms that consider microbiome distribution, longitudinal sampling, and feature selection. Results A metagenomic-derived IRI from our cohort identified children having up to an 8-fold increased BSI risk. Evaluation of these key microbiome features as a diagnostic screening test by traditional cart analysis accurately identified patients at-risk for BSI with 91% sensitivity using its negative likelihood ratio. However, its specificity of 51% prohibits targeting interventions to those at greatest risk (Figure 1). Therefore, advanced machine learning algorithms were used for metagenomic-derived BSI prediction. While training results suggest overfitting, its performance promises clinical utility with a sensitivity of 92% and specificity of 84% warranting optimization and validation in HSCT patients (Figure 2). Analysis during heterologous FMT interventions in 5 symptomatic high-risk children (including 1 HSCT patient) revealed a concomitant pathogen-dominated gut microbiome harboring a high burden of broad-spectrum antibiotic resistance genes prior to each FMT. Following FMT, we confirmed restoration of a healthy gut microbiome with abundant anaerobes had a low metagenomic-derived IRI in all cases (Figure 3). Conclusions The application of advanced machine learning to shotgun metagenomic data provides the resolution required for accurate BSI prediction to identify HSCT patients at greatest risk preceding an illness providing new opportunity for early FMT intervention to prevent BSI.

Screening and identification of gut anaerobes (Bacteroidetes) from human diabetic stool samples with and without retinopathy in comparison to control subjects

Studies have reported a reciprocal interaction between metabolic disorders and the human gut microbial composition. However, more information is still needed concerning the gut microbiome related to metabolic disorders such as Diabetes. The aim of the present study was to reveal whether stool samples collected from normal individuals and from diabetic subjects with or without retinopathy differ in their gut microbial composition. Data showed higher Bacteroides ratio in diabetic groups gut composition with no significant difference of bacterial strains in diabetic subjects with or without retinopathy compared to lean (control) individuals gut microbiota. These findings indicated that the gut microbiota is altered in accordance to the presence of metabolic disorders. However, further studies have to be elaborated in terms of gut microbial composition with diabetes.

259. A Retrospective Cross-Sectional Comparison of the Neonatal Gut Microbiota After Antimicrobial Exposure: Implications for Stewardship

BackgroundThe development of the infant gut microbiota influences the maturation of the host immune system and has been implicated in both short- and long-term health outcomes. In a healthy infant, the initial stages of gut microbiota development are characterized by the progressive acquisition and proliferation of anaerobes. In the neonatal intensive care unit (NICU), infants are often exposed to antibiotics which disturb the normal development of the gut microbiota. In this retrospective cross-sectional study, we aimed to the evaluate the effects of three different antibiotic regimens on the gut microbiota of infants in the NICU, focusing on the effect on anaerobe colonization.MethodsFrom November 1, 2014 to April 30, 2015, stool swabs were collected from NICU patients at The Hospital for Sick Children. Infants were included in the study if they received any dose or duration of the following antibiotics: ampicillin and tobramycin (AT), ampicillin and cefotaxime (AC), or ampicillin, tobramycin, and metronidazole (ATM). DNA was extracted from stool swabs and subject to Illumina sequencing of the V4 hypervariable region of the 16S rRNA gene. Infants were stratified by gestational age (term or preterm). The first samples taken within 1 week after antibiotic exposure were analyzed for diversity measures, taxonomic composition, and anaerobe relative abundance.ResultsA total of 64 NICU infants were included in the study, 46 (71.9%) received AT, 7 (10.9%) received AC, and 11 (17.2%) received ATM. Term infants received either AT (19/46; 41.3%) or AC (7/7; 100%), whereas preterm infants received either AT (27/46; 58.7%) or ATM (11/11; 100%). Shannon diversity was not statistically significant between term infants receiving AT and AC or preterm infants receiving AT and ATM. However, the relative abundance of anaerobes was significantly decreased after exposure to ATM in comparison to preterm infants receiving AT (P < 0.005)ConclusionWithin 1 week after ATM therapy, the relative abundance of gut anaerobes in preterm infants were significantly decreased in comparison to preterm infants receiving a course of AT. Therefore, limiting the use of ATM in preterm infants may protect the developing gut microbiota.Disclosures All authors: No reported disclosures.

2299. Oral Microbiome of High-Risk Children: A Cohort Study

BackgroundVulnerable pediatric populations are at high risk of bloodstream infection (BSI) and sepsis, such as patients of the pediatric intensive care unit (PICU) and bone marrow transplant (BMT) wards. Previous research demonstrates that commensal gut anaerobes provide host resistance against colonization and infection with pathogens but data on other body sites is lacking. Characterization of overlap or differences in commensal microbes of the mouth can provide insight on factors that may put these populations at risk for invasive disease.MethodsA cohort study of patients (0–18 years) at a large pediatric quaternary care center from 2017 to 2018 was conducted. Cohort group 1 children were admitted to the PICU; cohort group 2 patients were admitted to the BMT unit. Matching was by age range. Metagenomic sequencing of oral swabs and statistical analysis was performed. A retrospective review of causes of BSI in both groups from 2016 to 2018 was also conducted.ResultsEighteen patients in the PICU group and 21 patients in the BMT group were identified. Common causes of BSI from 2016 to 2018 vary in each cohort (Figure 1). Unlike Enterobacteraciae, which were more common in the BMT cohort, Pseudomonas aeruginosa was a more common cause of BSI among PICU patients. When evaluating the oral microbiomes, the number of reads for Pseudomonas aeruginosa was significantly higher in the PICU group compared with the BMT group (P = 0.0019, Figure 2).ConclusionChildren in the PICU have a statistically significant difference in the frequency of oral colonization with Pseudomonas aeruginosa when compared with BMT patients. Unique characteristics of these populations may impact oral microbiomes of patients and their subsequent epidemiology of BSIs. Future studies should focus on preventive measures to decrease the risk of colonization with pathogenic bacteria. Figure 1.Causes of bloodstream infection in critical care and BMT patients 2016–2018.Figure 2.Boxplot of reads per sample of Pseudomonas aeruginosa from the oral microbiome in PICU and BMT patients.Disclosures All authors: No reported disclosures.

Whole genome sequencing and function prediction of 133 gut anaerobes isolated from chicken caecum in pure cultures

BackgroundIn order to start to understand the function of individual members of gut microbiota, we cultured, sequenced and analysed bacterial anaerobes from chicken caecum.ResultsAltogether 204 isolates from chicken caecum were obtained in pure cultures using Wilkins-Chalgren anaerobe agar and anaerobic growth conditions. Genomes of all the isolates were determined using the NextSeq platform and subjected to bioinformatic analysis. Among 204 sequenced isolates we identified 133 different strains belonging to seven different phyla - Firmicutes, Bacteroidetes, Actinobacteria, Proteobacteria, Verrucomicrobia, Elusimicrobia and Synergistetes. Genome sizes ranged from 1.51 Mb in Elusimicrobium minutum to 6.70 Mb in Bacteroides ovatus. Clustering based on the presence of protein coding genes showed that isolates from phyla Proteobacteria, Verrucomicrobia, Elusimicrobia and Synergistetes did not cluster with the remaining isolates. Firmicutes split into families Lactobacillaceae, Enterococcaceae, Veillonellaceae and order Clostridiales from which the Clostridium perfringens isolates formed a distinct sub-cluster. All Bacteroidetes isolates formed a separate cluster showing similar genetic composition in all isolates but distinct from the rest of the gut anaerobes. The majority of Actinobacteria clustered closely together except for the representatives of genus Gordonibacter showing that the genome of this genus differs from the rest of Actinobacteria sequenced in this study. Representatives of Bacteroidetes commonly encoded proteins (collagenase, hemagglutinin, hemolysin, hyaluronidase, heparinases, chondroitinase, mucin-desulfating sulfatase or glutamate decarboxylase) that may enable them to interact with their host. Aerotolerance was recorded in Akkermansia and Cloacibacillus and was also common among representatives of Bacteroidetes. On the other hand, Elusimicrobium and the majority of Clostridiales were highly sensitive to air exposure despite their potential for spore formation.ConclusionsMajor gut microbiota members utilise different strategies for gut colonisation. High oxygen sensitivity of Firmicutes may explain their commonly reported decrease after oxidative burst during gut inflammation.

Collaborating genomic, transcriptomic and microbiomic alterations lead to canine extreme intestinal polyposis

Extreme intestinal polyposis in pet dogs has not yet been reported in literature. We identified a dog patient who developed numerous intestinal polyps, with the severity resembling human classic familial adenomatous polyposis (FAP), except the jejunum-ileum junction being the most polyp-dense. We investigated this dog, in comparison with 22 other dogs with spontaneous intestinal tumors but no severe polyposis, and with numerous published human cancers. We found, not APC mutation, but three other alteration pathways as likely reasons of this canine extreme polyposis. First, somatic truncation mutation W411X of FBXW7, a component of an E3 ubiquitin ligase, over-activates MYC and cell cycle-promoting network, accelerating crypt cell proliferation. Second, genes of protein trafficking and localization are downregulated, likely associated with germline mutation G406D of STAMBPL1, a K63-deubiquitinase, and MYC network activation. This inhibits epithelial apical-basolateral polarity establishment, preventing crypt cell differentiation. Third, Bacteroides uniformis, a commensal gut anaerobe, thrives and expresses abundantly thioredoxin and nitroreductase. These bacterial products could reduce oxidative stress linked to host germline mutation R51X of CYB5RL, a cytochrome b5 reductase homologue, decreasing cell death. Our work emphasizes the close collaboration of alterations across the genome, transcriptome and microbiome in promoting tumorigenesis.

The ability of human intestinal anaerobes to metabolize different oligosaccharides: Novel means for microbiota modulation?

Prebiotic oligosaccharides are known to have significant impacts on gut microbiota and are thus widely used to program healthy microbiota composition and activity from infants to the elderly. Bifidobacteria and lactobacilli are among the major target microorganisms of oligosaccharides, but the metabolic properties of oligosaccharides in other predominant gut microbes have not been well characterized. In the present study, we demonstrated the metabolic properties of six oligosaccharides in 31 key gut anaerobes. Bifidobacteria readily metabolized fructooligosaccharide (FOSs) with degree of polymerization (DP) 3, i.e. 1-kestose, but several strains used did not actively metabolize FOSs with DP4 and DP5, i.e. nystose and fructosylnystose. Akkermansia muciniphila, a potential new probiotic against obesity, did not show significant growth with any of the oligosaccharides tested. The butyrate producer Anaerostipes caccae grew well on 1-kestose but poorly on FOS mixtures, whereas it contained 1-kestose at 30%. Bacteroides-Parabacteroides group species were separated into two groups based on oligosaccharide metabolic properties. One group metabolized well most of the oligosaccharides tested, but the others metabolized only 1 or 2 selected oligosaccharides. Oligosaccharide profiles after culturing revealed that Bifidobacterium spp. preferentially metabolized shorter oligosaccharides (DP3) in the mixtures, whereas Bacteroides-Parabacteroides spp. did not show oligosaccharide selectivity for metabolism or rather preferred longer oligosaccharides (>DP4). The fermentation profiles indicated specific links between the microbial end-products and specific gut microbes. Available carbohydrates had a significant impact on the accumulation of amino acid-derived bacterial metabolites (i.e. phenol, p-cresol, indole and skatole) and short chain fatty acids. The results assist in predicting the impact of oligosaccharides in human intervention and gut microbiota modulation.

Anaerobic 4-hydroxyproline utilization: Discovery of a new glycyl radical enzyme in the human gut microbiome uncovers a widespread microbial metabolic activity

ABSTRACTThe discovery of enzymes responsible for previously unappreciated microbial metabolic pathways furthers our understanding of host-microbe and microbe-microbe interactions. We recently identified and characterized a new gut microbial glycyl radical enzyme (GRE) responsible for anaerobic metabolism of trans-4-hydroxy-l-proline (Hyp). Hyp dehydratase (HypD) catalyzes the removal of water from Hyp to generate Δ1-pyrroline-5-carboxylate (P5C). This enzyme is encoded in the genomes of a diverse set of gut anaerobes and is prevalent and abundant in healthy human stool metagenomes. Here, we discuss the roles HypD may play in different microbial metabolic pathways as well as the potential implications of this activity for colonization resistance and pathogenesis within the human gut. Finally, we present evidence of anaerobic Hyp metabolism in sediments through enrichment culturing of Hyp-degrading bacteria, highlighting the wide distribution of this pathway in anoxic environments beyond the human gut.

Microbiota dysbiosis in inflammatory bowel diseases: in silico investigation of the oxygen hypothesis

BackgroundInflammatory bowel diseases (IBD), which include ulcerative colitis and Crohn’s disease, cause chronic inflammation of the digestive tract in approximately 1.6 million Americans. A signature of IBD is dysbiosis of the gut microbiota marked by a significant reduction of obligate anaerobes and a sharp increase in facultative anaerobes. Numerous experimental studies have shown that IBD is strongly correlated with a decrease of Faecalibacterium prausnitzii and an increase of Escherichia coli. One hypothesis is that chronic inflammation induces increased oxygen levels in the gut, which in turn causes an imbalance between obligate and facultative anaerobes.ResultsTo computationally investigate the oxygen hypothesis, we developed a multispecies biofilm model based on genome-scale metabolic reconstructions of F. prausnitzii, E. coli and the common gut anaerobe Bacteroides thetaiotaomicron. Application of low bulk oxygen concentrations at the biofilm boundary reproduced experimentally observed behavior characterized by a sharp decrease of F. prausnitzii and a large increase of E. coli, demonstrating that dysbiosis consistent with IBD disease progression could be qualitatively predicted solely based on metabolic differences between the species. A diet with balanced carbohydrate and protein content was predicted to represent a metabolic “sweet spot” that increased the oxygen range over which F. prausnitzii could remain competitive and IBD could be sublimated. Host-microbiota feedback incorporated via a simple linear feedback between the average F. prausnitzii concentration and the bulk oxygen concentration did not substantially change the range of oxygen concentrations where dysbiosis was predicted, but the transition from normal species abundances to severe dysbiosis was much more dramatic and occurred over a much longer timescale. Similar predictions were obtained with sustained antibiotic treatment replacing a sustained oxygen perturbation, demonstrating how IBD might progress over several years with few noticeable effects and then suddenly produce severe disease symptoms.ConclusionsThe multispecies biofilm metabolic model predicted that oxygen concentrations of ∼1 micromolar within the gut could cause microbiota dysbiosis consistent with those observed experimentally for inflammatory bowel diseases. Our model predictions could be tested directly through the development of an appropriate in vitro system of the three species community and testing of microbiota-host interactions in gnotobiotic mice.

Role of Microbiota in Strengthening Ocular Mucosal Barrier Function Through Secretory IgA.

PurposeThe purpose of this study was to evaluate mechanisms controlling secretory IgA (SIgA) production, thereby ensuring maintenance of ocular surface health.MethodsTo determine whether the presence of specific gut commensal species regulates SIgA levels and IgA transcripts in the eye-associated lymphoid tissues (EALT), specific-pathogen-free (SPF) Swiss Webster (SW) mice were treated with antibiotic cocktails, germ-free (GF) SW mice were reconstituted with diverse commensal gut microbiota, or monocolonized with gut-specific commensals. Proteomic profiling and quantitative real-time polymerase chain reaction (qRT-PCR) were used to quantify SIgA and IgA levels. 16S rDNA sequencing was carried out to characterize commensal microbiota.ResultsCommensal presence regulated ocular surface SIgA levels and mRNA IgA transcripts in EALT. Oral antibiotic cocktail intake significantly reduced gut commensal presence, while maintaining ocular surface commensal levels reduced SIgA and IgA transcripts in EALT. Analysis of gut microbial communities revealed that SPF SW mice carried abundant Bacteroides organisms when compared to SPF C57BL6/N mice, with B. acidifaciens being the most prominent species in SPF SW mice. Monocolonization of GF SW mice with B. acidifaciens, a strict gut anaerobe, resulted in significant increase of IgA transcripts in the EALT, implying generation of B-cell memory.ConclusionsThese data illustrated a “gut-eye” axis of immune regulation. Exposure of the host to gut commensal species may serve as a priming signal to generate B-cell repertoires at sites different from the gut, such as EALT, thereby ensuring broad protection.

Engineered Regulatory Systems Modulate Gene Expression of Human Commensals in the Gut

The gut microbiota is implicated in numerous aspects of health and disease, but dissecting these connections is challenging because genetic tools for gut anaerobes are limited. Inducible promoters are particularly valuable tools because these platforms allow real-time analysis of the contribution ofmicrobiome gene products to community assembly, host physiology, and disease. We developed a panelof tunable expression platforms for the prominent genus Bacteroides in which gene expression is controlled by a synthetic inducer. In the absence of inducer, promoter activity is fully repressed; addition of inducer rapidly increases gene expression by fourto five orders of magnitude. Because the inducer is absent in mice and their diets, Bacteroides gene expression inside the gut can be modulated by providing the inducer in drinking water. We use this system to measure the dynamic relationship between commensal sialidase activity and liberation of mucosal sialic acid, a receptor and nutrient for pathogens. VIDEO ABSTRACT.

Gut symbiotic microbes imprint intestinal immune cells with the innate receptor SLAMF4 which contributes to gut immune protection against enteric pathogens

BackgroundInteractions between host immune cells and gut microbiota are crucial for the integrity and function of the intestine. How these interactions regulate immune cell responses in the intestine remains a...

In vitro susceptibility of cultured human methanogens to lovastatin

Lovastatin is a prodrug that is hydrolysed in vivo to β-hydroxy acid lovastatin, which inhibits 3-hydroxy-3-methylglutaryl-coenzyme A (HMG-Co-A) reductase (HMGR), thereby lowering cholesterol in humans. A side effect of lovastatin is inhibition of isoprenoid synthesis and cell membrane formation in methanogenic Archaea, which are members of the human digestive tract microbiota and are emerging pathogens. In this study, the in vitro susceptibility of the human-associated methanogens Methanobrevibacter smithii, Methanobrevibacter oralis, Methanobrevibacter massiliense, Methanobrevibacter arboriphilus and Methanomassiliicoccus luminyensis to lovastatin (1–4 µg/mL) was tested in the presence of five gut anaerobes aiming to metabolise lovastatin into β-hydroxy acid lovastatin as confirmed by ultra-high-performance liquid chromatography. Five days of incubation with lovastatin had no measurable effect on the growth of the five gut anaerobes but significantly reduced CH4 production and methanogen growth as measured by quantitative PCR (P < 0.01). Quantitative PCR analyses indicated that compared with controls, β-hydroxy acid lovastatin significantly increased the expression of the genes mta and mcrA implicated in methanogenesis and significantly decreased the expression of the fno gene implicated in methanogenesis. Expression of the HMGR gene (hmg) implicated in cell wall synthesis was significantly increased by β-hydroxy acid lovastatin (P < 0.01). These results strongly suggest that in the presence of gut anaerobes, lovastatin yields β-hydroxy acid lovastatin, which inhibits methane production and growth of methanogens by affecting their cell membrane biosynthesis. Lovastatin is the first licensed drug to exclusively affect the growth of methanogens whilst protecting the bacterial microbiota.

Bypass graft infection and bacteremia caused by Anaerostipes caccae: First report of human infection caused by a recently described gut anaerobe

We report a case of bypass graft infection and bacteremia caused by Anaerostipes caccae. A review of the literature shows no reported human infection caused by this microorganism to date. The patient was initially treated with vancomycin and piperacillin-tazobactam on admission and with amoxicillin-clavulanate upon discharge. The slow-growing organism was subsequently found to be susceptible to metronidazole and ertapenem.