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Antibiotics-induced monodominance of a novel gut bacterial order

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Item Type:Article
Title:Antibiotics-induced monodominance of a novel gut bacterial order
Creators Name:Hildebrand, F. and Moitinho-Silva, L. and Blasche, S. and Jahn, M.T.T. and Gossmann, T.I. and Heuerta Cepas, J. and Hercog, R. and Luetge, M. and Bahram, M. and Pryszlak, A. and Alves, R.J. and Waszak, S.M. and Zhu, A. and Ye, L. and Costea, P.I. and Aalvink, S. and Belzer, C. and Forslund, S.K. and Sunagawa, S. and Hentschel, U. and Merten, C. and Patil, K.R. and Benes, V. and Bork, P.
Abstract:OBJECTIVE: The composition of the healthy human adult gut microbiome is relatively stable over prolonged periods, and representatives of the most highly abundant and prevalent species have been cultured and described. However, microbial abundances can change on perturbations, such as antibiotics intake, enabling the identification and characterisation of otherwise low abundant species. DESIGN: Analysing gut microbial time-series data, we used shotgun metagenomics to create strain level taxonomic and functional profiles. Community dynamics were modelled postintervention with a focus on conditionally rare taxa and previously unknown bacteria. RESULTS: In response to a commonly prescribed cephalosporin (ceftriaxone), we observe a strong compositional shift in one subject, in which a previously unknown species, (U)Borkfalki ceftriaxensis, was identified, blooming to 92% relative abundance. The genome assembly reveals that this species (1) belongs to a so far undescribed order of Firmicutes, (2) is ubiquitously present at low abundances in at least one third of adults, (3) is opportunistically growing, being ecologically similar to typical probiotic species and (4) is stably associated to healthy hosts as determined by single nucleotide variation analysis. It was the first coloniser after the antibiotic intervention that led to a long-lasting microbial community shift and likely permanent loss of nine commensals. CONCLUSION: The bloom of (U)B. ceftriaxensis and a subsequent one of Parabacteroides distasonis demonstrate the existence of monodominance community states in the gut. Our study points to an undiscovered wealth of low abundant but common taxa in the human gut and calls for more highly resolved longitudinal studies, in particular on ecosystem perturbations.
Keywords:Anti-Bacterial Agents, Bacteria, Gastrointestinal Microbiome, Metagenomics, Microbiota
Source:Gut
ISSN:0017-5749
Publisher:BMJ Publishing Group (U.K.)
Volume:68
Number:10
Page Range:1781-1790
Date:9 September 2019
Official Publication:https://doi.org/10.1136/gutjnl-2018-317715
PubMed:View item in PubMed

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