Evaluation of an optimal preparation of human standardized fecal inocula for in vitro fermentation studies

This study investigated the optimal preservation approach to prepare human feces as inoculum for in vitro fermentations as an alternative to the use of fresh feces. The four treatments studied were: Treatment 1) fresh feces resuspended in dialysate solution + glycerol; Treatment 2) fresh feces resuspended in dialysate solution + glycerol and...

To pool or not to pool? Impact of the use of individual and pooled fecal samples for in vitro fermentation studies

This study investigated the stability and the activity of the microbiota from a single and a pool of donors in the TNO in vitro model of the colon (TIM-2 system). Our findings demonstrate the suitability of the preparation of a pool of fecal sample to be used for fermentation experiments. Chemicals/CAS: isobutyric acid, 5711-69-3, 79-31-2;...

Dynamics of the microbiota in response to host infection

Longitudinal studies of the microbiota are important for discovering changes in microbial communities that affect the host. The complexity of these ecosystems requires rigorous integrated experimental and computational methods to identify temporal signatures that promote physiologic or pathophysiologic responses in vivo. Employing a murine model...

In vitro characterization of the impact of different substrates on metabolite production, energy extraction and composition of gut microbiota from lean and obese subjects

The aim of this study was to investigate the effect of galacto-oligosaccharides, lactulose, apple fiber and sugar beet pectin on the composition and activity of human colonic microbiota of lean and obese healthy subjects using an in vitro model of the proximal colon: TIM-2. Substrate fermentation was assessed by measuring the production of short...

Early respiratory microbiota composition determines bacterial succession patterns and respiratory health in children

Rationale: Many bacterial pathogens causing respiratory infections in children are common residents of the respiratory tract. Insight into bacterial colonization patterns and microbiota stability at a young age might elucidate healthy or susceptible conditions for development of respiratory disease. Objectives: To study bacterial succession of...

The impact of breastfeeding on nasopharyngeal microbial communities in infants

Rationale: Breastfeeding elicits significant protection against respiratory tract infections in infancy. Modulation of respiratory microbiota might be part of the natural mechanisms of protection against respiratory diseases induced by breastfeeding. Objectives: To study the association between breastfeeding and nasopharyngeal microbial...

Deep sequencing analyses of low density microbial communities: Working at the boundary of accurate microbiota detection

Introduction: Accurate analyses of microbiota composition of low-density communities (103-104 bacteria/sample) can be challenging. Background DNA from chemicals and consumables, extraction biases as well as differences in PCR efficiency can significantly interfere with microbiota assessment. This study was aiming to establish protocols for...

Mixed-species genomic microarray analysis of fecal samples reveals differential transcriptional responses of bifidobacteria in breast- And formula-fed infants

Although their exact function remains enigmatic, bifidobacteria are among the first colonizers of the newborn infant gut and further develop into abundant communities, notably in response to diet. Therefore, the transcriptional responses of bifidobacteria in rapidly processed fecal samples from young infants that were fed either breast milk or a...

Performance and population analysis of a non-sterile trickle bed reactor inoculated with caldicellulosiruptor saccharolyticus, a thermophilic hydrogen producer

Non-axenic operation of a 400 L trickle bed reactor inoculated with the thermophile Caldicellulosiruptor saccharolyticus, yielded 2.8 molH 2mol hexose converted. The reactor was fed with a complex medium with sucrose as the main substrate, continuously flushed with nitrogen gas, and operated at 73°C. The volumetric productivity was 22 mmolH2(L...

Physiological and phylogenetic characterization of a stable benzene-degrading, chlorate-reducing microbial community

A stable anoxic enrichment culture was obtained that degraded benzene with chlorate as an electron acceptor. The benzene degradation rate was 1.65 mM benzene per day, which is similar to reported aerobic benzene degradation rates but 20-1650 times higher than reported for anaerobic benzene degradation. Denaturing gradient gel electrophoresis of...

About the order in aerobic heterotrophic microbial communities from hydrocarbon-contaminated sites

The organizational structure of communities of aerobic heterotrophic bacteria was studied by means of physiological and molecular typing of the members of arbitrary samples of isolates, ASsI. The isolate sample assay (ISA) was applied to three different hydrocarbon-polluted sites: a dry windrow pile for bioremediation of waste oil-contaminated...