Eating patterns contribute to shaping the gut microbiota in the mucosal simulator of the human intestinal microbial ecosystem.

Eating patterns, i.e. meal frequency and circadian timing of meals, are often modified in weight loss and metabolic healing strategies.

Gut microbiota response to in vitro transit time variation is mediated by microbial growth rates, nutrient use efficiency and adaptation to in vivo transit time.

Background: Transit time is an important modulator of the human gut microbiome. The inability to modify transit time as the sole variable hampers mechanistic in vivo microbiome research. We singled out gut transit time in an unprecedented in vitro approach by subjecting faecal microbial communities from six individuals with either short, medium or long in vivo transit times, to three different colonic transit times of 21, 32 and 63 h in the validated human gut in vitro model, SHIME.

Starch-entrapped microspheres enhance gut microbiome-mediated anti-obesity effects of resistant starch in high-fat diet induced obese C57BL/6J mice.

The prevalence of obesity is growing worldwide and has been extensively linked to gut microbiota dysbiosis. In addition to exercise and physical activity, fiber-rich foods may be a first-line prophylactic to manage obesity. This study investigated in vivo dietary intervention with high-amylose maize starch (HAMS) and starch-entrapped microspheres (MS) to treat high-fat diet induced metabolic disorder and gut microbiome dysbiosis in mice.

Postbiotics and Their Health Modulatory Biomolecules.

Postbiotics are a new category of biotics that have the potential to confer health benefits but, unlike probiotics, do not require living cells to induce health effects and thus are not subject to the food safety requirements that apply to live microorganisms. Postbiotics are defined as a "preparation of inanimate microorganisms and/or their components that confers a health benefit on the host". Postbiotic components include short-chain fatty acids, exopolysaccharides, vitamins, teichoic acids, bacteriocins, enzymes and peptides in a non-purified inactivated cell preparation.

Impaired Mucosal Homeostasis in Short-Term Fiber Deprivation Is Due to Reduced Mucus Production Rather Than Overgrowth of Mucus-Degrading Bacteria.

The gut mucosal environment is key in host health; protecting against pathogens and providing a niche for beneficial bacteria, thereby facilitating a mutualistic balance between host and microbiome. Lack of dietary fiber results in erosion of the mucosal layer, suggested to be a result of increased mucus-degrading gut bacteria. This study aimed to use quantitative analyses to investigate the diet-induced imbalance of mucosal homeostasis.

In vitro triple coculture with gut microbiota from spondyloarthritis patients is characterized by inter-individual differences in inflammatory responses.

Spondyloarthritis is a group of chronic inflammatory diseases that primarily affects axial or peripheral joints and is frequently associated with inflammation at non-articular sites. The disease is multifactorial, involving genetics, immunity and environmental factors, including the gut microbiota. In vivo, microbiome contributions are difficult to assess due to the multifactorial disease complexity.

Oral and Gut Microbial Carbohydrate-Active Enzymes Landscape in Health and Disease.

Inter-individual variability in the microbial gene complement encoding for carbohydrate-active enzymes (CAZymes) can profoundly regulate how the host interacts with diverse carbohydrate sources thereby influencing host health. CAZy-typing, characterizing the microbiota-associated CAZyme-coding genes within a host individual, can be a useful tool to predict carbohydrate pools that the host can metabolize, or identify which CAZyme families are underrepresented requiring supplementation via microbiota transplantation or probiotics. CAZy-typing, moreover, provides a novel framework to search for disease biomarkers.

Versatile human in vitro triple coculture model coincubated with adhered gut microbes reproducibly mimics pro-inflammatory host-microbe interactions in the colon.

The colonic epithelial barrier is vital to preserve gut and host health by maintaining the immune homeostasis between host and microbes. The mechanisms underlying beneficial or harmful host-microbe interactions are poorly understood and impossible to study in vivo given the limited accessibility and ethical constraints. Moreover, existing in vitro models lack the required cellular complexity for the routine, yet profound, analysis of the intricate interplay between different types of host and microbial cells.

Starch Microspheres Entrapped with Chitosan Delay Fecal Fermentation and Regulate Human Gut Microbiota Composition.

A slow dietary fiber fermentation rate is desirable to obtain a steady metabolite release and even distribution throughout the entire colon, ensuring to meet the energy needs in the distal colon. In this study, we prepared starch-entrapped microspheres with a variable chitosan-to-starch ratio by means of electrospraying and investigated the fermentability by human fecal microbiota in an batch system. Starch encapsulation reduced microbial gas production and the concentration of short-chain fatty acids.

Aberrant gut-microbiota-immune-brain axis development in premature neonates with brain damage.

Premature infants are at substantial risk for suffering from perinatal white matter injury. Though the gut microbiota has been implicated in early-life development, a detailed understanding of the gut-microbiota-immune-brain axis in premature neonates is lacking. Here, we profiled the gut microbiota, immunological, and neurophysiological development of 60 extremely premature infants, which received standard hospital care including antibiotics and probiotics.

Ultra-high Pressure Treatment Controls Fecal Fermentation Rate of Insoluble Dietary Fiber from Tratt Pomace and Induces Butyrogenic Shifts in Microbiota Composition.

Dietary fiber has been considered a key element in shaping the beneficial host-microbe symbiosis. In the present study, we identified Tratt fruits as a promising dietary fiber source. The physicochemical properties and fermentability by human fecal microbes of pomace water insoluble dietary fiber (RIDF) obtained from ultrasonic extraction and ultrahigh pressure (90 MPa)-treated RIDF (RIDF-90) were compared to those of Tratt pomace (R).

Multi-targeted properties of the probiotic CNCM I-3856 against enterotoxigenic (ETEC) H10407 pathogenesis across human gut models.

Enterotoxigenic (ETEC) is one of the most common causes of acute traveler's diarrhea. Adhesins and enterotoxins constitute the major ETEC virulence traits. With the dramatic increase in antibiotic resistance, probiotics are considered a wholesome alternative to prevent or treat ETEC infections.

Efficacy and safety of spore-forming probiotics in the treatment of functional dyspepsia: a pilot randomised, double-blind, placebo-controlled trial.

Background: Current treatments for functional dyspepsia have limited efficacy or present safety issues. We aimed to assess spore-forming probiotics in functional dyspepsia as monotherapy or add-on therapy to long-term treatment with proton-pump inhibitors.

Methods: In this single-centre, randomised, double-blind, placebo-controlled pilot trial that took place at University Hospitals Leuven (Leuven, Belgium), adult patients (≥18 years) with functional dyspepsia (as defined by Rome IV criteria, on proton-pump inhibitors or off proton-pump inhibitors) were randomly assigned (1:1) via computer-generated blocked lists, stratified by proton-pump inhibitor status, to receive 8 weeks of treatment with probiotics (Bacillus coagulans MY01 and Bacillus subtilis MY02, 2·5 × 10 colony-forming units per capsule) or placebo consumed twice per day, followed by an open-label extension phase of 8 weeks.

Nutrient load acts as a driver of gut microbiota load, community composition and metabolic functionality in the simulator of the human intestinal microbial ecosystem.

A recently introduced quantitative framework for gut microbiota analysis indicated that microbial load alterations can be linked to various diseases, making it essential to pinpoint its determinants. We identified nutrient load as a main driver of the quantitative microbial community composition and functionality in vitro by stepwise decreasing standardized feed concentrations from 100% to 33%, 20% and 10% in 5-day intervals. While the proportional composition and metabolic profile were mainly determined by the inter-individual variability (35% and 41%), nutrient load accounted for 58%, 23% and 65% of the observed variation in the microbial load, quantitative composition and net daily metabolite production, respectively.

Mucin as a Functional Niche is a More Important Driver of Gut Microbiota Composition and Functionality than Supplementation of .

Research into identification of biomarkers for gut health and ways to modulate the microbiota composition and activity to improve health, has put in the spotlight. As a mucin degrader, colonizes the interesting but not-fully described host-glycan degradation niche., .

Dietary Emulsifiers Alter Composition and Activity of the Human Gut Microbiota , Irrespective of Chemical or Natural Emulsifier Origin.

The use of additives in food products has become an important public health concern. In recent reports, dietary emulsifiers have been shown to affect the gut microbiota, contributing to a pro-inflammatory phenotype and metabolic syndrome. So far, it is not yet known whether similar microbiome shifts are observable for a more diverse set of emulsifier types and to what extent these effects vary with the unique features of an individual's microbiome.

Spatial and temporal modulation of enterotoxigenic E. coli H10407 pathogenesis and interplay with microbiota in human gut models.

Background: Enterotoxigenic Escherichia coli (ETEC) substantially contributes to the burden of diarrheal illnesses in developing countries. With the use of complementary in vitro models of the human digestive environment, TNO gastrointestinal model (TIM-1), and Mucosal Simulator of the Human Intestinal Microbial Ecosystem (M-SHIME), we provided the first detailed report on the spatial-temporal modulation of ETEC H10407 survival, virulence, and its interplay with gut microbiota. These systems integrate the main physicochemical parameters of the human upper digestion (TIM-1) and simulate the ileum vs ascending colon microbial communities and luminal vs mucosal microenvironments, captured from six fecal donors (M-SHIME).

Bio-electrochemical COD removal for energy-efficient, maximum and robust nitrogen recovery from urine through membrane aerated nitrification.

Resource recovery from source-separated urine can shorten nutrient cycles on Earth and is essential in regenerative life support systems for deep-space exploration. In this study, a robust two-stage, energy-efficient, gravity-independent urine treatment system was developed to transform fresh real human urine into a stable nutrient solution. In the first stage, up to 85% of the COD was removed in a microbial electrolysis cell (MEC), converting part of the energy in organic compounds (27-46%) into hydrogen gas and enabling full nitrogen recovery by preventing nitrogen losses through denitrification in the second stage.

Gut microbiota generation of protein-bound uremic toxins and related metabolites is not altered at different stages of chronic kidney disease.

Chronic kidney disease (CKD) is characterized by accumulation of protein-bound uremic toxins such as p-cresyl sulfate, p-cresyl glucuronide, indoxyl sulfate and indole-3-acetic acid, which originate in the gut. Intestinal bacteria metabolize aromatic amino acids into p-cresol and indole, (further conjugated in the colon mucosa and liver) and indole-3-acetic acid. Here we measured fecal, plasma and urine metabolite concentrations; the contribution of gut bacterial generation to plasma protein-bound uremic toxins accumulation; and influx into the gut of circulating protein-bound uremic toxins at different stages of CKD.

Development and validation of the Simulator of the Canine Intestinal Microbial Ecosystem (SCIME)1.

Whereas a wide variety of in vitro models have been developed and validated to assess the effect of specific food ingredients on the human gut microbiome, such models have only been developed and applied to a limited extent for companion animals. Since the use of pre- and probiotics to improve gut health is an emerging research topic in the field of companion animals and as dogs are often used as laboratory animals in developing and testing of pharmaceuticals, the current study aimed to establish an adequate canine in vitro model. This consisted of a four-stage reactor composed of a stomach and small intestinal compartment followed by a proximal and distal colon.

Microbial succession during wheat bran fermentation and colonisation by human faecal microbiota as a result of niche diversification.

The human gut can be viewed as a flow-through system with a short residence time, a high turnover rate and a spatial gradient of physiological conditions. As a consequence, the gut microbiota is exposed to highly fluctuating environmental determinants presented by the host and diet. Here, we assessed the fermentation and colonisation of insoluble wheat bran by faecal microbiota of three individuals at an unprecedented sampling intensity.

Experimental models to study intestinal microbes-mucus interactions in health and disease.

A close symbiotic relationship exists between the intestinal microbiota and its host. A critical component of gut homeostasis is the presence of a mucus layer covering the gastrointestinal tract. Mucus is a viscoelastic gel at the interface between the luminal content and the host tissue that provides a habitat to the gut microbiota and protects the intestinal epithelium.

Isolation of wheat bran-colonizing and metabolizing species from the human fecal microbiota.

Undigestible, insoluble food particles, such as wheat bran, are important dietary constituents that serve as a fermentation substrate for the human gut microbiota. The first step in wheat bran fermentation involves the poorly studied solubilization of fibers from the complex insoluble wheat bran structure. Attachment of bacteria has been suggested to promote the efficient hydrolysis of insoluble substrates, but the mechanisms and drivers of this microbial attachment and colonization, as well as subsequent fermentation remain to be elucidated.

Modification of wheat bran particle size and tissue composition affects colonisation and metabolism by human faecal microbiota.

Dietary modulation can alter the gut microbiota composition and activity, in turn affecting health. Particularly, dietary fibre rich foods, such as wheat bran, are an important nutrient source for the gut microbiota. Several processing methods have been developed to modify the functional, textural and breadmaking properties of wheat bran, which can affect the gut microbiota.

An Acetobacterium strain isolated with metallic iron as electron donor enhances iron corrosion by a similar mechanism as Sporomusa sphaeroides.

Sporomusa sphaeroides related strains are to date the only homoacetogens known to increase metallic iron corrosion. The goal of this work was to isolate additional homoacetogenic bacteria capable of using Fe(0) as electron donor and to explore their extracellular electron transfer mechanism. Enrichments were started from anoxic corrosion products and yielded Acetobacterium as main homoacetogenic genus.