Metagenomics and 16S pyrosequencing have enabled the study of ecosystem structure and dynamics to great depth and accuracy. Co-occurrence and correlation patterns found in these data sets are increasingly used for the prediction of species interactions in environments ranging from the oceans to the human microbiome. In addition, parallelized co-culture assays and combinatorial labelling experiments allow high-throughput discovery of cooperative and competitive relationships between species. In this Review, we describe how these techniques are opening the way towards global ecosystem network prediction and the development of ecosystem-wide dynamic models.

Microbial interactions: from networks to models

The importance of the gut-brain axis in maintaining homeostasis has long been appreciated. However, the past 15 yr have seen the emergence of the microbiota (the trillions of microorganisms within ...

The Microbiota-Gut-Brain Axis

The human gastrointestinal (GI) tract harbours a complex and dynamic population of microorganisms, the gut microbiota, which exert a marked influence on the host during homeostasis and disease Multiple factors contribute to the establishment of the human gut microbiota during infancy Diet is considered as one of the main drivers in shaping the gut microbiota across the life time Intestinal bacteria play a crucial role in maintaining immune and metabolic homeostasis and protecting against pathogens Altered gut bacterial composition (dysbiosis) has been associated with the pathogenesis of many inflammatory diseases and infections The interpretation of these studies relies on a better understanding of inter-individual variations, heterogeneity of bacterial communities along and across the GI tract, functional redundancy and the need to distinguish cause from effect in states of dysbiosis This review summarises our current understanding of the development and composition of the human GI microbiota, and its impact on gut integrity and host health, underlying the need for mechanistic studies focusing on host–microbe interactions

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Introduction to the human gut microbiota

Fecal microbiome variation in the average, healthy population has remained under-investigated. Here, we analyzed two independent, extensively phenotyped cohorts: the Belgian Flemish Gut Flora Project (FGFP; discovery cohort; N = 1106) and the Dutch LifeLines-DEEP study (LLDeep; replication; N = 1135). Integration with global data sets (N combined = 3948) revealed a 14-genera core microbiota, but the 664 identified genera still underexplore total gut diversity. Sixty-nine clinical and questionnaire-based covariates were found associated to microbiota compositional variation with a 92% replication rate. Stool consistency showed the largest effect size, whereas medication explained largest total variance and interacted with other covariate-microbiota associations. Early-life events such as birth mode were not reflected in adult microbiota composition. Finally, we found that proposed disease marker genera associated to host covariates, urging inclusion of the latter in study design.

Population-level analysis of gut microbiome variation

Bacteria that colonize the mammalian intestine collectively possess a far larger repertoire of degradative enzymes and metabolic capabilities than their hosts. Microbial fermentation of complex non...

https://www.tandfonline.com/doi/pdf/10.4161/gmic.19897

Microbial degradation of complex carbohydrates in the gut

The present invention relates to in vitro adhesion modules that allow growth, stabilization and study of microbial communities that adhere to and colonize host- related surfaces, that mimic transport of chemical compounds across epithelial surfaces and simulate host-microorganism interactions and adaptation. It includes the provision of micromolar amounts of oxygen via the basal side of a mucus layer towards the adhered microorganisms thus establishing the microaerophilic conditions prevailing at the base of a biofϊlm. It can also include cells, simulating the host, in a chamber on the basal side of a functional layer comprising said mucus layer. The adhesion module of the present invention can be placed between the different compartments of the SHIME - the Simulator of the Human Intestinal Microbial Ecosystem. An extension of the SHIME is made where the duodenum, jejunum and ileum are separately mimicked.

Technology and method to study microbial growth and adhesion to host-related surface and the host-microbiota interactions

The present invention is directed to a particular arabinoxylan ("AX") preparation and the finding that this preparation has a beneficial effect on the organization of the intestinal microbial community in the lumen and in particular at the site of the gut mucosa, where it modulates the barrier function of the intestinal surface, primarily by modulating the mucosa-associated microbial community towards a relative increase of health beneficial bacteria, such as bifidobacteria and lactobacilli. It is accordingly a first aspect of the present invention to provide said arabinoxylan preparation characterized in comprising isolated water-soluble arabinoxylans and the use thereof to improve functioning (e.g. barrier function) of the intestinal epithelium. Thus, in a further aspect the present invention provides compositions, both pharmaceutical and nutritional compositions, comprising said arabinoxylan preparations; in particular pharmaceuticals, medical foods, food supplements or food compositions, such as infant formula products, dairy products, bakery products or pastry products. The compositions optionally comprise probiotics such as Bifidobacterium or Lactobacillus.

Arabinoxylans for modulating the barrier function of the intestinal surface

Arabinoxylans are the main fraction of non-starch polysaccharides in many cereal grains. Recent in vitro studies point out that a specific concentrate of long-chain water-extractable arabinoxylans (LC-AX) stimulates specific intestinal microbes (e.g. Bifidobacterium longum) and launches specific fermentation patterns with potential health benefits for the host (e.g. propionate production). Human trials demonstrate that a long-term administration of LC-AX can restore the glucose and insulin responses in patients suffering from diabetes type II. Further, in vivo rodent studies show that LC-AX may also counteract the adverse effect of the Westernized high-fat diet. Overall, LC-AX affects multiple targets, both in the gut and the rest of the body, which may lead to promising applications in the field of diabetes and weight management.

Prebiotic effect and potential health benefit of arabinoxylans

Background: The infant gut microbiota establishes during a critical window of opportunity when metabolic and immune functions are highly susceptible to environmental changes, such as diet. Human milk oligosaccharides (HMOs) for instance are suggested to be beneficial for infant health and gut microbiota. Infant formulas supplemented with the HMOs 2′-fucosyllactose (2′-FL) and lacto-N-neotetraose (LNnT) reduce infant morbidity and medication use and promote beneficial bacteria in the infant gut ecosystem. To further improve infant formula and achieve closer proximity to human milk composition, more complex HMO mixtures could be added. However, we currently lack knowledge about their effects on infants’ gut ecosystems. Method: We assessed the effect of lactose, 2′-FL, 2′-FL + LNnT, and a mixture of six HMOs (HMO6: consisting of 2′-FL, LNnT, difucosyllactose, lacto-N-tetraose, 3′- and 6′-sialyllactose) on infant gut microbiota and intestinal barrier integrity using a combination of in vitro models to mimic the microbial ecosystem (baby M-SHIME®) and the intestinal epithelium (Caco-2/HT29-MTX co-culture). Results: All the tested products had bifidogenic potential and increased SCFA levels; however, only the HMOs’ fermented media protected against inflammatory intestinal barrier disruption. 2′-FL/LNnT and HMO6 promoted the highest diversification of OTUs within the Bifidobactericeae family, whereas beneficial butyrate-producers were specifically enriched by HMO6. Conclusion: These results suggest that increased complexity in HMO mixture composition may benefit the infant gut ecosystem, promoting different bifidobacterial communities and protecting the gut barrier against pro-inflammatory imbalances.

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Pieter Van den Abbeele

Papers

Technology and method to study microbial growth and adhesion to host-related surface and the host-microbiota interactions

Arabinoxylans for modulating the barrier function of the intestinal surface

Prebiotic effect and potential health benefit of arabinoxylans

Human Milk Oligosaccharides and Lactose Differentially Affect Infant Gut Microbiota and Intestinal Barrier In Vitro

The impact of environmental pH on the gut microbiota community structure and short chain fatty acid production.