Background: It is now apparent that the complex microbial communities found on and in the human body vary across individuals. What has largely been missing from previous studies is an understanding of how these communities vary over time within individuals. To the extent to which it has been considered, it is often assumed that temporal variability is negligible for healthy adults. Here we address this gap in understanding by profiling the forehead, gut (fecal), palm, and tongue microbial communities in 85 adults, weekly over 3 months. Results: We found that skin (forehead and palm) varied most in the number of taxa present, whereas gut and tongue communities varied more in the relative abundances of taxa. Within each body habitat, there was a wide range of temporal variability across the study population, with some individuals harboring more variable communities than others. The best predictor of these differences in variability across individuals was microbial diversity; individuals with more diverse gut or tongue communities were more stable in composition than individuals with less diverse communities. Conclusions: Longitudinal sampling of a relatively large number of individuals allowed us to observe high levels of temporal variability in both diversity and community structure in all body habitats studied. These findings suggest that temporal dynamics may need to be considered when attempting to link changes in microbiome structure to changes in health status. Furthermore, our findings show that, not only is the composition of an individual’s microbiome highly personalized, but their degree of temporal variability is also a personalized feature.

There is significant interest in the therapeutic and probiotic potential of the common gut bacteriumAkkermansia muciniphila. However, knowledge of both the genomic and physiological diversity of this bacterial lineage is limited. Using a combination of genomic, molecular biological, and traditional microbiological approaches, we identified at least four species-level phylogroups with differing functional potentials that affect how these bacteria interact with both their human host and other members of the human gut microbiome. Specifically, we identified and isolatedAkkermansiastrains that were able to synthesize vitamin B₁₂. The ability to synthesize this important cofactor broadens the physiological capabilities of human-associatedAkkermansiastrains, fundamentally altering our understanding of how this important bacterial lineage may affect human health.

Significance: Much of Earth’s volcanism occurs in the deep sea, yet little is known about the microbial communities inhabiting such extreme and dynamic systems. Using a multidisciplinary approach to study distinct hydrothermal systems at Brothers submarine arc volcano, we provide insights into how microbial community composition and function reflect subtly different fluid chemistries resulting from subsurface fluid interactions with distinct alteration mineral assemblages. These variations can be traced to the subsurface hydrogeologic history beneath Brothers volcano. Further, we show that these systems represent oases of phylogenetically diverse Archaea and Bacteria. Our findings highlight the importance of geologic legacy in understanding drivers of microbial diversity, assembly, and evolution and may have insights into processes that drove early diversification of life on Earth.

Human milk oligosaccharides (HMOs) are the third most abundant component of breast milk and provide several benefits to developing infants, including the recruitment of beneficial bacteria to the human gut. Akkermansia strains are largely considered beneficial bacteria and have been detected in colostrum, breast milk, and young infants. A. muciniphila Muc ^T belonging to the AmI phylogroup contributes to the HMO deconstruction capacity of the infant. Here, using phylogenomics, we examined the genomic capacities of four Akkermansia phylogroups to deconstruct HMOs.