Publications (235) View all
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Article: A meta-analysis of changes in bacterial and archaeal communities with time.
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ABSTRACT: Ecologists have long studied the temporal dynamics of plant and animal communities with much less attention paid to the temporal dynamics exhibited by microbial communities. As a result, we do not know if overarching temporal trends exist for microbial communities or if changes in microbial communities are generally predictable with time. Using microbial time series assessed via high-throughput sequencing, we conducted a meta-analysis of temporal dynamics in microbial communities, including 76 sites representing air, aquatic, soil, brewery wastewater treatment, human- and plant-associated microbial biomes. We found that temporal variability in both within- and between-community diversity was consistent among microbial communities from similar environments. Community structure changed systematically with time in less than half of the cases, and the highest rates of change were observed within ranges of 1 day to 1 month for all communities examined. Microbial communities exhibited species-time relationships (STRs), which describe the accumulation of new taxa to a community, similar to those observed previously for plant and animal communities, suggesting that STRs are remarkably consistent across a broad range of taxa. These results highlight that a continued integration of microbial ecology into the broader field of ecology will provide new insight into the temporal patterns of microbial and 'macro'-bial communities alike.The ISME Journal advance online publication, 11 April 2013; doi:10.1038/ismej.2013.54.The ISME Journal 04/2013; · 7.38 Impact Factor -
Article: Translating the human microbiome.
Nature Biotechnology 04/2013; 31(4):304-8. · 29.50 Impact Factor -
Article: Biphasic assembly of the murine intestinal microbiota during early development.
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ABSTRACT: The birth canal provides mammals with a primary maternal inoculum, which develops into distinctive body site-specific microbial communities post-natally. We characterized the distal gut microbiota from birth to weaning in mice. One-day-old mice had colonic microbiota that resembled maternal vaginal communities, but at days 3 and 9 of age there was a substantial loss of intestinal bacterial diversity and dominance of Lactobacillus. By weaning (21 days), diverse intestinal bacteria had established, including strict anaerobes. Our results are consistent with vertical transmission of maternal microbiota and demonstrate a nonlinear ecological succession involving an early drop in bacterial diversity and shift in dominance from Streptococcus to Lactobacillus, followed by an increase in diversity of anaerobes, after the introduction of solid food. Mammalian newborns are born highly susceptible to colonization, and lactation may control microbiome assembly during early development.The ISME Journal advance online publication, 28 March 2013; doi:10.1038/ismej.2013.15.The ISME Journal 03/2013; · 7.38 Impact Factor -
Dataset: mbt2 12014 7
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Article: Xenobiotics and the human gut microbiome: metatranscriptomics reveal the active players.
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ABSTRACT: The human gut microbiome plays an important role in the metabolism of xenobiotics. In a recent issue of Cell, Maurice et al. (2013) identify the active members of the gut microbiome and show how gene-expression profiles change within the gut microbial community in response to antibiotics and host-targeted xenobiotics.Cell metabolism 03/2013; 17(3):317-8. · 17.35 Impact Factor
