Ecophysiological insights into the human intestinal microbiota: from single strains to defined consortia

Abstract

High individuality, large complexity and limited understanding of the mechanisms underlying human intestinal microbiome function remain the major challenges for designing beneficial modulation strategies. Exemplified by the analysis of intestinal bacteria in a thousand Western adults, we discuss key concepts of the human intestinal microbiome landscape, i.e. the compositional and functional 'core', the presence of community types and the existence of alternative stable states. Genomic investigation of core taxa revealed functional redundancy, which is expected to stabilize the ecosystem, as well as taxa with specialized functions that have the potential to shape the microbiome landscape. The contrast between Prevotella-and Bacteroidesdominated systems has been well described. However, less known is the effect of not so abundant bacteria, for example, Dialister spp. that have been proposed to exhibit distinct bistable dynamics. Studies employing time-series analysis have highlighted the dynamical variation in the microbiome landscape with and without the effect of defined perturbations, such as the use of antibiotics or dietary changes. We incorporate ecosystem-level observations of the human intestinal microbiota and its keystone species to suggest avenues for designing microbiome modulation strategies to improve host health.

Mucin and human milk oligosaccharides utilization: a strategy of Akkermansia muciniphila to ensure survival in the human gut

“…On the other hand, B. hydrogenotrophica occupied the lowest trophic guild consuming inorganic substrates. The observations for A. soehngenii and C. catus are in accordance with our previous study of 10-species, where we observed similar functional roles for these two species (Shetty 2019). Thus, MDb-MM could be used to assign realized niches and functional roles of each of the key gut species.…”

“…This can be explained by the significant transcriptional activity for lactate consumption primarily via the lctABCDE pathway (Supplementary FigureS10). A. soehngenii showed high transcriptional activity for utilization of lactate plus acetate which further confirms our previous observation of this being a specialized niche for this organism(Shetty 2019;Shetty et al 2020). C. catus demonstrated activity for lactate consumption but is known only to consume the L-form of lactate, while A. soehngenii can use both the D-and L-forms of…”

“…To understand microbe-microbe interactions within a complex community, it is important to create a community that exhibits ecophysiological properties similar to natural ecosystems. Community level ecological properties such as resistance and resilience to perturbations, presence of competitors for nutrients as well as mutualists that support metabolic co-operation can be designed in a synthetic minimal microbiome (Shetty 2019). Here, we sought to investigate microbe-microbe interactions in a synthetic minimal microbiome that represented the human colon.…”

Biotechnology of health-promoting bacteria

“…as well as the related Anaerostipes spp. and this has recently been studied in detail revealing a new and characteristic pathway involved in this conversion (Shetty, 2019). These specialized butyrate producers may have all potential for the development as next-generation therapeutic bacteria, notably for the treatment of subjects with metabolic syndrome to prevent the development of type 2 diabetes.…”

Ecological and biotechnological aspects of Aplysina-associated microorganisms

“…Simultaneously, the importance of high sampling effort should be highlighted. In natural environments, bacterial communities are dominated by a few species accounting for the majority of biomass, with a large number of rare species that are only present in low abundance (Jousset et al, 2017;Shetty, 2019). Microbial cultivation environments are no exception; the vast majority of diversity of microbial OTUs are represented by only a small number of colonies (Sipkema et al 2011;Lavy et al 2014;Versluis et al 2017, Chapter 4).…”