Boolean analysis reveals systematic interactions among low-abundance species in the human gut microbiome

The analysis of microbiome compositions in the human gut has gained increasing interest due to the broader availability of data and functional databases and substantial progress in data analysis methods, but also due to the high relevance of the microbiome in human health and disease. While most analyses infer interactions among highly abundant species, the large number of low-abundance species has received less attention. Here we present a novel analysis method based on Boolean operations applied to microbial co-occurrence patterns. We calibrate our approach with simulated data based on a dynamical Boolean network model from which we interpret the statistics of attractor states as a theoretical proxy for microbiome composition. We show that for given fractions of synergistic and competitive interactions in the model our Boolean abundance analysis can reliably detect these interactions. Analyzing a novel data set of 822 microbiome compositions of the human gut, we find a large number of highly significant synergistic interactions among these low-abundance species, forming a connected network, and a few isolated competitive interactions

Gut microbiota functions: metabolism of nutrients and other food components

The diverse microbial community that inhabits the human gut has an extensive metabolic repertoire that is distinct from, but complements the activity of mammalian enzymes in the liver and gut mucosa and includes functions essential for host digestion. As such, the gut microbiota is a key factor in shaping the biochemical profile of the diet and, therefore, its impact on host health and disease. The important role that the gut microbiota appears to play in human metabolism and health has stimulated research into the identification of specific microorganisms involved in different processes, and the elucidation of metabolic pathways, particularly those associated with metabolism of dietary components and some host-generated substances. In the first part of the review, we discuss the main gut microorganisms, particularly bacteria, and microbial pathways associated with the metabolism of dietary carbohydrates (to short chain fatty acids and gases), proteins, plant polyphenols, bile acids, and vitamins. The second part of the review focuses on the methodologies, existing and novel, that can be employed to explore gut microbial pathways of metabolism. These include mathematical models, omics techniques, isolated microbes, and enzyme assays

Integrative models for TGF-β\beta signaling and extracellular matrix

International audienceThe extracellular matrix (ECM) is the most important regulator of cell-cell communication within tissues. ECM is a complex structure, made up of a wide variety of molecules including proteins, proteglycans and glycoaminoglycans. It contributes to cell signaling through the action of both its constituents and their proteolytic cleaved fragments called ma-tricryptins [Hynes and Naba, 2012, Ricard-Blum and Vallet, 2019]. In addition , ECM acts as a "reservoir" of growth factors and cytokines and regulates their bioavailability at the cell surface. By controlling cell signaling inputs, ECM plays a key role in regulating cell phenotype (differentiation, proliferation, migration, etc.). In this context, signaling networks associated with the polypeptide transforming growth factor TGF-β are unique since their activation are controlled by ECM and TGF-$β$ is a major regulator of ECM remodeling in return