Journal
INFECTION AND IMMUNITY
Volume 77, Issue 10, Pages 4668-4678Publisher
AMER SOC MICROBIOLOGY
DOI: 10.1128/IAI.00493-09
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Funding
- Penn Genome Frontiers Institute
- Pennsylvania Department of Health. Research
- National Institutes of Health (NIH) [AI61570, AI074878, T32 AI060516]
- Burroughs Wellcome Fund
- Crohns and Colitis Foundation of America's William and Shelby Model Family Foundation Research Award
- University of Pennsylvania (University Research Foundation Award, Veterinary Center for Infectious Diseases Pilot
- National Institute of Diabetes and Digestive Kidney Diseases [DK50306.]
- NIH [S10RR024525]
- Department of Health
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We investigated the spatial and temporal response of the murine gut microbiome to infection with Citrobacter rodentium, an attaching-and-effacing bacterium that provokes innate and adaptive immune responses, resulting in transient bacterial colitis. Previous studies have suggested that C. rodentium-induced inflammation is associated with an increased abundance of Enterobacteriaceae. We report here a deeper analysis of this model using DNA bar coding and 454 pyrosequencing to characterize 101,894 partial 16S rRNA gene sequences from 85 microbial samples from tissue-adhered and luminal bacteria of the cecum, proximal colon, and distal colon, which allowed us to identify previously unappreciated spatial and kinetic changes in multiple bacterial lineages. The deep sequencing data revealed that C. rodentium was most abundantly associated with the cecal mucosa at day 9 postinfection and then diminished in abundance, providing the first reported use of deep sequencing to track a pathogen in vivo through the course of infection. Notable changes were associated with both the mucosally adhered and luminal microbiota at both day 9 and day 14 postinfection. Alterations in abundance were seen for Proteobacteria, Deferribacteres, Clostridia, and others; however, changes in Enterobacteriaceae could be accounted for by the presence of C. rodentium itself, which is a member of this family. The Lactobacillus group decreased in abundance during infection, which may be important for pathogenesis because members of this lineage modulate the composition of the gut microbiota and are used as probiotics. Thus, deep sequencing provides previously inaccessible information on how Citrobacter infection and clearance reshapes the gut microbial community in space and time.
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