Biotic interactions and temporal dynamics of the human gastrointestinal microbiota

Abstract

The human gastrointestinal (GI) microbiota is important to human health and imbalances or shifts in the gut microbial community have been linked to many diseases. Most studies of the GI microbiota only capture snapshots of this dynamic community at one or a few time points. Although this is valuable in terms of providing knowledge of community composition and variability between individuals, it does not provide the foundation for going beyond descriptive studies and toward truly predictive ecological models. In order to achieve this goal, we need longitudinal data of appropriate temporal and taxonomic resolution, so that established time series analysis tools for identifying and quantifying putative interactions among community members can be used. Here, we present new analyses of existing data to illustrate the potential usefulness of this approach. We discuss challenges related to sampling and data processing, as well as analytical approaches and considerations for future studies of the GI microbiota and other complex microbial systems.

Quantitative analysis of commensal Escherichia coli populations reveals host‐specific enterotypes at the intra‐species level

“…Altogether, these data indicate that a complex network of interactions may exist within the intestinal microbiota between the various genera and phylogenetic groups of the same species (Trosvik et al. ). This network probably involves the availability of various nutrients coupled to the specific metabolism of bacteria, cross‐feeding and toxic interactions involving phages and/or colicins.…”

Proteobacteria: microbial signature of dysbiosis in gut microbiota

“…Proteobacteria in patients with gastric bypass surgery Studies that monitored the daily variations of human gut microbiota in both a healthy man (followed for 15 months) and a woman (followed for 6 months) reported a relatively low abundance of the phylum Proteobacteria (average of 2.5% for the man and 4.1% for the woman) and a stable composition, despite large, abrupt, and long-lasting changes at the class level within the phylum [11,80]. Although these observations are based on only two individuals, the results are intriguing because they open the possibility that the adult human gut regulates the proportions of enteric Proteobacteria.…”

Diet-Dependent Modular Dynamic Interactions of the Equine Cecal Microbiota

“…A stable hindgut environment is crucial for the health of horses, and imbalances in the gut microbiota and fermentation products may lead to diseases such as colic (13) and laminitis (8, 27, 28). However, dynamic models need to be derived in order to understand the temporal stability of and fluctuations in the microbiota, as previously described for the human gut microbiota (38). We have used models for human infants in order to predict the colonization of the infant gut during the first 4 months of life (36).…”