Abstract
The community of the diverse microorganisms residing in the gastrointestinal tract, known as the gut microbiota, is exceedingly being studied for its impact on health and disease. This community plays a major role in nutrient metabolism, maintenance of the intestinal epithelial barrier but also in local and systemic immunomodulation. A dysbiosis of the gut microbiota, characterized by an unbalanced microbial ecology, often leads to a loss of essential functions that may be associated with proinflammatory conditions. Specifically, some key microbes that are depleted in dysbiotic ecosystems, called keystone species, carry unique functions that are essential for the balance of the microbiota. In this review, we discuss current understanding of reported keystone species and their proposed functions in health. We also elaborate on current and future bioinformatics tools needed to identify missing functions in the gut carried by keystone species. We propose that the identification of such keystone species functions is a major step for the understanding of microbiome dynamics in disease and toward the development of microbiome-based therapeutics.
Highlights
Animals are superorganisms composed of eukaryotic and prokaryotic cells in a similar proportion along an even larger number of viruses (Sender et al, 2016)
Among the multitude of metabolic activities harbored by human gut microbiomes, we focus on the roles of short chain fatty acids (SCFA), tryptophan- and cholesterolderived metabolites, and their crosstalk with host factors, e.g., histone modifying enzymes, G proteins-coupled receptors, aryl hydrocarbon receptor (AhR), indoleamine 2,3-dioxygenase 1 (IDO1) and tryptophan hydroxylase 1 (TpH1) in barrier maintenance, immune regulation, and the gut-brain axis
This study revealed that high mean degree, high closeness centrality, high transitivity and low betweenness centrality can predict the keystone nature of species with 85% accuracy (Berry and Widder, 2014)
Summary
Animals are superorganisms composed of eukaryotic and prokaryotic cells in a similar proportion along an even larger number of viruses (Sender et al, 2016). Even if the Firmicutes phylum regroups a large number of potentially beneficial bacteria, this ratio has progressively been established as a hallmark of the obese dysbiotic gut microbiome (Crovesy et al, 2020). Another feature of obesity-associated dysbiosis is a reduced microbiome diversity, as illustrated by the high proportion of fecal samples from obese individuals that fall within the “low gene count” category (Le Chatelier et al, 2013). Several chronic diseases have been associated with reduced gut microbiome diversity, such as Crohn’s disease (Manichanh et al, 2006), hypertension (Li et al, 2017) and non-alcoholic steatohepatitis (NASH) (Astbury et al, 2020)
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