The Influence of Staphylococcus aureus on Gut Microbial Ecology in an In Vitro Continuous Culture Human Colonic Model System (original) (raw)
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Understanding the interactions between bacteria in the human gut through metabolic modeling
2013
The human gut microbiome plays an influential role in maintaining human health, and it is a potential target for prevention and treatment of disease. Genome-scale metabolic models (GEMs) can provide an increased understanding of the mechanisms behind the effects of diet, the genotype-phenotype relationship and microbial robustness. Here we reconstructed GEMs for three key species, (Bacteroides thetaiotamicron, Eubacterium rectale and Methanobrevibacter smithii) as relevant representatives of three main phyla in the human gut (Bacteroidetes, Firmicutes and Euryarchaeota). We simulated the interactions between these three bacteria in different combinations of gut ecosystems and compared the predictions with the experimental results obtained from colonization of germ free mice. Furthermore, we used our GEMs for analyzing the contribution of each species to the overall metabolism of the gut microbiota based on transcriptome data and demonstrated that these models can be used as a scaffold for understanding bacterial interactions in the gut.
Applied and Environmental Microbiology, 2005
The effects of changes in the gut environment upon the human colonic microbiota are poorly understood. The response of human fecal microbial communities from two donors to alterations in pH (5.5 or 6.5) and peptides (0.6 or 0.1%) was studied here in anaerobic continuous cultures supplied with a mixed carbohydrate source. Final butyrate concentrations were markedly higher at pH 5.5 (0.6% peptide mean, 24.9 mM; 0.1% peptide mean, 13.8 mM) than at pH 6.5 (0.6% peptide mean, 5.3 mM; 0.1% peptide mean, 7.6 mM). At pH 5.5 and 0.6% peptide input, a high butyrate production coincided with decreasing acetate concentrations. The highest propionate concentrations (mean, 20.6 mM) occurred at pH 6.5 and 0.6% peptide input. In parallel, major bacterial groups were monitored by using fluorescence in situ hybridization with a panel of specific 16S rRNA probes. Bacteroides levels increased from ca. 20 to 75% of total eubacteria after a shift from pH 5.5 to 6.5, at 0.6% peptide, coinciding with high ...
British Journal of Nutrition, 2008
Fermentation products, SCFA, particularly butyrate, are considered a sign of 'good' bowel health but the influence of bacterial population composition and diet on inter-individual difference in metabolites and colonic health is poorly understood. Faecal specimens were collected weekly from eight healthy human volunteers over 12 weeks. Dietary intake was self-reported and ten macronutrient factors were analysed at selected weekly periods. Faecal weight, pH and moisture were recorded, and SCFA concentrations were measured in all samples. From each specimen, DNA was prepared and eubacterial 16S rRNA gene PCR performed. Bacterial population profiles were captured by denaturing gradient gel electrophoresis (DGGE) of PCR products, and multivariate statistical analysis was performed. Faecal weight, pH and moisture varied widely within and between individuals. Average total SCFA concentrations over 12 weeks ranged from 36·9 to 144·4 mmol/kg in 48 h specimens and faecal butyrate concentrations ranged from 1·8 to 48·5 mmol/kg. Two individuals with butyrate concentrations below 10 mmol/kg were considered to be 'low butyrate types' and may represent an at-risk population for bowel health. Dietary fat, sugar and carbohydrate showed weak correlation with SCFA (R 20·612, P¼0·015; R 0·607, P¼0·016; R 0·610, P¼0·016, respectively) and butyrate concentrations (R 20·593, P¼ 0·02; R 0·504, P¼0·054; R 0·528, P¼0·043, respectively). Multivariate analysis of DGGE bacterial profiles demonstrated concise and repeated grouping of intra-individual samples, but these were combined with distinct inter-individual differences (analysis of similarities P,0·001, R $ 0·99) The exact relationship of these SCFA values to the overall bacterial profiles and SCFA-producer bacterial groups was not direct nor linear. Short-chain fatty acids: Bacterial population dynamics: Healthy humans * Corresponding author: Dr Alexandra L. McOrist, fax þ 61 8 8303 8899, email sandi.mcorist@csiro.au Abbreviation: DGGE, denaturing gradient gel electrophoresis.
Annals of Microbiology, 2011
Bacteria in the human gut exceed the number of cells in our body by a 100-fold. At the level of the gastrointestinal epithelium, a constant battle is fought for equilibrium between the microbiota and the human body. These interactions play a key role in many aspects of host health, influencing energy harvest from food, colonization by pathogens, and the immune system, to name but a few. Unfortunately, the study of this host-microbiota interaction in vivo is limited by the inaccessibility of the digestive tract. Therefore, in vitro technology that focuses on the simulation of this epithelial environment offers an ideal platform with which to conduct mechanistic research that could shed more light on this environment and help explain in vivo observations. However, the limitation of currently available tools could yield results with limited reliability for an in vivo situation. The aim of this mini-review is to focus on the importance of studying the host-microbiota interaction in the gastrointestinal tract and to evaluate the state of the art of the available in vitro techniques. Finally, we aim to identify those missing factors that, if present, would allow the creation of a model that would constitute a better simulation of biofilm formation, i.e. one more closely resembling the in vivo situation.
FEMS Microbiology Ecology, 2000
Fluorescence in situ hybridization was used to quantitate bacteria growing in a three-stage continuous culture system inoculated with human faeces, operated at two system retention times (60 and 20 h). Twenty-three different 16S rRNA gene oligonucleotide probes of varying specificities were used to detect bacteria. Organisms belonging to genera Bacteroides and Bifidobacterium, together with the Eubacterium rectale/Clostridium coccoides group, the Atopobium, Faecalibacterium prausnitzii and Eubacterium cylindroides groups, as well as the segmented filamentous bacteria, the Roseburia intestinalis group and lactic acid bacteria, were all present in high numbers in the continuous culture system. Other groups and species such as Ruminococci and Enterobacteria also persisted in the model, though not always at levels that allowed reliable quantitation. Some organisms such as Streptococci and Corynebacteria, present in the faecal inoculum, did not colonize the system. Other probes specific for Eubacterium lentum and for members of the genus Desulfovibrio did not detect these organisms at any time. Short chain fatty acid production was always highest in vessel I of the continuous culture system, however, a marked increase in acetate formation and a reduction in butyrate production occurred when system retention time was reduced to 20 h, which correlated with reductions in the numbers of butyrate-producing Roseburia.
Colonization-induced host-gut microbial metabolic interaction
2011
The gut microbiota enhances the host's metabolic capacity for processing nutrients and drugs and modulate the activities of multiple pathways in a variety of organ systems. We have probed the systemic metabolic adaptation to gut colonization for 20 days following exposure of axenic mice (n ؍ 35) to a typical environmental microbial background using high-resolution 1 H nuclear magnetic resonance (NMR) spectroscopy to analyze urine, plasma, liver, kidney, and colon (5 time points) metabolic profiles. Acquisition of the gut microbiota was associated with rapid increase in body weight (4%) over the first 5 days of colonization with parallel changes in multiple pathways in all compartments analyzed. The colonization process stimulated glycogenesis in the liver prior to triggering increases in hepatic triglyceride synthesis. These changes were associated with modifications of hepatic Cyp8b1 expression and the subsequent alteration of bile acid metabolites, including taurocholate and tauromuricholate, which are essential regulators of lipid absorption. Expression and activity of major drug-metabolizing enzymes (Cyp3a11 and Cyp2c29) were also significantly stimulated. Remarkably, statistical modeling of the interactions between hepatic metabolic profiles and microbial composition analyzed by 16S rRNA gene pyrosequencing revealed strong associations of the Coriobacteriaceae family with both the hepatic triglyceride, glucose, and glycogen levels and the metabolism of xenobiotics. These data demonstrate the importance of microbial activity in metabolic phenotype development, indicating that microbiota manipulation is a useful tool for beneficially modulating xenobiotic metabolism and pharmacokinetics in personalized health care. IMPORTANCE Gut bacteria have been associated with various essential biological functions in humans such as energy harvest and regulation of blood pressure. Furthermore, gut microbial colonization occurs after birth in parallel with other critical processes such as immune and cognitive development. Thus, it is essential to understand the bidirectional interaction between the host metabolism and its symbionts. Here, we describe the first evidence of an in vivo association between a family of bacteria and hepatic lipid metabolism. These results provide new insights into the fundamental mechanisms that regulate host-gut microbiota interactions and are thus of wide interest to microbiological, nutrition, metabolic, systems biology, and pharmaceutical research communities. This work will also contribute to developing novel strategies in the alteration of host-gut microbiota relationships which can in turn beneficially modulate the host metabolism.
Foods
Functional symbiotic intestinal microbiota regulates immune defense and the metabolic processing of xenobiotics in the host. The aryl hydrocarbon receptor (AhR) is one of the transcription factors mediating host–microbe interaction. An in vitro static simulation of the human colon was used in this work to analyze the evolution of bacterial populations, the microbial metabolic output, and the potential induction of AhR transcriptional activity in healthy gut ecosystems. Fifteen target taxa were explored by qPCR, and the metabolic content was chromatographically profiled using SPME-GC-MS and UPLC-FLD to quantify short-chain fatty acids (SCFA) and biogenic amines, respectively. Over 72 h of fermentation, the microbiota and most produced metabolites remained stable. Fermentation supernatant induced AhR transcription in two of the three reporter gene cell lines (T47D, HepG2, HT29) evaluated. Mammary and intestinal cells were more sensitive to microbiota metabolic production, which showed...
LWT - Food Science and Technology, 2015
This study presents a computer-controlled dynamic SIMulator of the GastroIntestinal tract, SIMGI, which was designed to simulate the complete processes of digestion and fermentation. The system includes three-stage culture reactors intended to simulate in vitro the microbial conditions of different regions of the human large intestine. The evolution and composition of the microbial community in the ascending (AC), transverse (TC) and descending colon (DC) vessels was evaluated by PCR-DGGE and quantitative PCR. An overall decrease in counts of Bifidobacterium and Prevotella and an increase of Enterobacteriaceae was observed between the inoculation with human faeces and the bacterial community stabilized in the colon vessels. Regarding microbial differentiation, Bacteroides counts were more representative of the AC and TC vessels than the DC compartment. Within the butyrate producer groups, a low occurrence of Clostridium leptum and Ruminoccocus was observed in the AC compartment. The net SCFA production was highest in the AC compartment, whereas the ammonium levels indicated that proteolysis occurred similarly throughout the entire colon compartments. The results observed in the in vitro model SIMGI indicate that it can be used as a tool for studying the effects of diet or food components on modulating the gut microbiota and its metabolic activity.