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

/pdf/introduction-to-the-human-gut-microbiota-4ihlfrbotw.pdf

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

Several alternative proteins have emerged that may improve the environmental footprint of our food system. Evaluations into the impact of these protein sources on gastrointestinal health is limited. A study was performed to determine whether aqueous extracts from dietary protein sources, both traditional and alternative, had a differential impact on a leaky gut cell culture model. Aqueous extracts of soybean meal, fish meal, Cyberlindnera jadinii, Saccharomyces sp., Bio-Mos, Chlorella pyrenoidosa, Methylobacterium extorquens, Escherichia coli, and Hermetia illucens were administered onto a Caco-2/THP-1 co-culture and the transepithelial electrical resistance (TEER) and IL-1β, IL-6, IL-8, IL-10, TNF-α, CXCL10, and MCP-1 concentrations, and NF-κB activity were determined. Principal components analysis and K means clustering were performed. Three clusters were identified: one for soybean meal, one for bacterial meals, and one for the remaining sources. The bacterial meal cluster exhibited pro-inflammatory properties, i.e., correlated with TNF-α, IL-1β, IL-8, and NF-κB. The soybean meal cluster exhibited both pro- and anti-inflammatory properties, whereas the third cluster containing the remaining proteins exhibited anti-inflammatory properties (correlated with TEER and IL-10). These results suggest that aqueous extracts from yeast proteins contribute more positively, and bacterial proteins contribute the least positively, towards intestinal health in a leaky gut model.

/pdf/the-response-of-a-leaky-gut-cell-culture-model-caco-2-thp-1-lqw8ubg0.pdf

The Response of a Leaky Gut Cell Culture Model (Caco-2/THP-1 Co-Culture) to Administration of Alternative Protein Sources

The gut microbiota plays a pivotal role in health and disease. The use of probiotics as microbiota-targeted therapies is a promising strategy to improve host health. However, dynamic molecular mechanisms are often not elucidated, especially when targeting the small intestinal microbiota. Here, we show that supplementation of a probiotic formula (Ecologic®825) to the adult human small intestinal ileostoma microbiota counteracts the growth of Enterococcaceae and Enterobacteriaceae and reduces ethanol production, leading to major changes in nutrient utilization and resistance to perturbations. The observed alterations coincided with an initial increase in lactate production and decrease in pH by the probiotics, followed by a sharp increase in the levels of butyrate and propionate. Additionally, increased production of multiple N-acyl amino acids was detected in the stoma samples supplemented with the probiotic formula. Overall, this study shows how network theory can be used to improve the current or identify novel microbiota-targeted therapies. The outcome may help further understand the reported effects of these probiotic formula on the host.

Probiotics supplementation to adult human small intestinal stoma microbiota causes dynamic increase in the community resistance to perturbations and nutrient utilization

Pieter Van den Abbeele

Papers

The Response of a Leaky Gut Cell Culture Model (Caco-2/THP-1 Co-Culture) to Administration of Alternative Protein Sources

Probiotics supplementation to adult human small intestinal stoma microbiota causes dynamic increase in the community resistance to perturbations and nutrient utilization

The adherent and invasive Escherichia coli is repressed from mucus by arabinoxylans, inulin and Lactobacillus reuteri in a novel in vitro gut model

Specific butyrate-producing Clostridium cluster XIVa species colonize the mucosal environment of a novel in vitro gut model

The host selects mucosal and luminal teams of co-evolved, submissive gut microbiota