Title
Dynamics of the microbiota in response to host infection
Author
Belzer, C.
Gerber, G.K.
Roeselers, G.
Delaney, M.
DuBois, A.
Liu, Q.
Belavusava, V.
Yeliseyev, V.
Houseman, A.
Onderdonk, A.
Cavanaugh, C.
Bry, L.
Publication year
2014
Abstract
Longitudinal studies of the microbiota are important for discovering changes in microbial communities that affect the host. The complexity of these ecosystems requires rigorous integrated experimental and computational methods to identify temporal signatures that promote physiologic or pathophysiologic responses in vivo. Employing a murine model of infectious colitis with the pathogen Citrobacter rodentium, we generated a 2-month time-series of 16S rDNA gene profiles, and quantitatively cultured commensals, from multiple intestinal sites in infected and uninfected mice. We developed a computational framework to discover time-varying signatures for individual taxa, and to automatically group signatures to identify microbial sub-communities within the larger gut ecosystem that demonstrate common behaviors. Application of this model to the 16S rDNA dataset revealed dynamic alterations in the microbiota at multiple levels of resolution, from effects on systems-level metrics to changes across anatomic sites for individual taxa and species. These analyses revealed unique, time-dependent microbial signatures associated with host responses at different stages of colitis. Signatures included a Mucispirillum OTU associated with early disruption of the colonic surface mucus layer, prior to the onset of symptomatic colitis, and members of the Clostridiales and Lactobacillales that increased with successful resolution of inflammation, after clearance of the pathogen. Quantitative culture data validated findings for predominant species, further refining and strengthening model predictions. These findings provide new insights into the complex behaviors found within host ecosystems, and define several time-dependent microbial signatures that may be leveraged in studies of other infectious or inflammatory conditions. © 2014 Belzer et al.
Subject
ELSS - Earth, Life and Social Sciences
Life
Healthy Living
Biomedical Innovation
DNA 16S
Animal experiment
Animal model
Bacterial clearance
Bacterium detection
Cecum
Citrobacter rodentium
Colitis
Commensal
Descending colon
Gene sequence
Genus
Ileum
Intestine flora
Lactobacillus johnsonii
Lactobacillus reuteri
Microbial community
Microbial diversity
Nonhuman
Phylogeny
Phylum
Taxonomy
MSB - Microbiology and Systems Biology
To reference this document use:
http://resolver.tudelft.nl/uuid:9e21ef3b-48fb-4656-a0d0-c0f7467f480a
DOI
https://doi.org/10.1371/journal.pone.0095534
TNO identifier
513446
ISSN
1932-6203
Source
PLoS ONE, 9 (9)
Document type
article