Moving pictures of the human microbiome

Abstract

BackgroundUnderstanding the normal temporal variation in the human microbiome is critical to developing treatments for putative microbiome-related afflictions such as obesity, Crohn's disease, inflammatory bowel disease and malnutrition. Sequencing and computational technologies, however, have been a limiting factor in performing dense time series analysis of the human microbiome. Here, we present the largest human microbiota time series analysis to date, covering two individuals at four body sites over 396 timepoints.ResultsWe find that despite stable differences between body sites and individuals, there is pronounced variability in an individual's microbiota across months, weeks and even days. Additionally, only a small fraction of the total taxa found within a single body site appear to be present across all time points, suggesting that no core temporal microbiome exists at high abundance (although some microbes may be present but drop below the detection threshold). Many more taxa appear to be persistent but non-permanent community members.ConclusionsDNA sequencing and computational advances described here provide the ability to go beyond infrequent snapshots of our human-associated microbial ecology to high-resolution assessments of temporal variations over protracted periods, within and between body habitats and individuals. This capacity will allow us to define normal variation and pathologic states, and assess responses to therapeutic interventions.

Correlation detection strategies in microbial data sets vary widely in sensitivity and precision

“…For example, in Caporaso et al, the fluctuations appear sinusoidal (Caporaso et al, 2011). Generally, detected edges varied depending upon at which point in time/how many samples were taken of the fluctuating OTUs ( Figure 5).…”

“…Time-dependent relationships vary based on signal, sampling frequency and time shift Correlations in time-series data are well studied in other fields, but microbiological studies are just beginning to show predictable shifts in microbial communities over time (Caporaso et al, 2011;Gonzalez et al, 2012;Shade et al, 2013). For example, in Caporaso et al, the fluctuations appear sinusoidal (Caporaso et al, 2011).…”

Recurrent Clostridium difficile infection and the microbiome

“…The indigenous intestinal microbiota is a highly dynamic ecosystem that is perturbed by environmental factors [38,43,44]. While the altered ecosystem seems to restore itself to homeostasis after CDI clearance with antibiotics, in the remaining 20 % of CDI cases, the microbiome has likely been altered beyond the point of spontaneous recovery, rendering the host susceptible to recurrent infection (Fig.…”

The role of inflammation in temporal shifts in the inflammatory bowel disease mucosal microbiome

“…While the human gut microbiome has been shown to maintain a certain degree of stability over time, 12 , 13 several factors are associated with disruption of its diversity and species richness. For example, perturbations in the intestinal microbiome follow gastrointestinal infection, antibiotic use and smoking.…”