Culture-independent identification of gut bacteria correlated with the onset of diabetes in a rat model
- 19 February 2009
- journal article
- research article
- Published by Oxford University Press (OUP) in The ISME Journal
- Vol. 3 (5) , 536-548
- https://doi.org/10.1038/ismej.2009.5
Abstract
Bacteria associated with the onset of type 1 diabetes in a rat model system were identified. In two experiments, stool samples were collected at three time points after birth from bio-breeding diabetes-prone (BB-DP) and bio-breeding diabetes-resistant (BB-DR) rats. DNA was isolated from these samples and the 16S rRNA gene was amplified using universal primer sets. In the first experiment, bands specific to BB-DP and BB-DR genotypes were identified by automated ribosomal intergenic spacer analysis at the time of diabetes onset in BB-DP. Lactobacillus and Bacteroides strains were identified in the BB-DR- and BB-DP-specific bands, respectively. Sanger sequencing showed that the BB-DP and BB-DR bacterial communities differed significantly but too few reads were available to identify significant differences at the genus or species levels. A second experiment confirmed these results using higher throughput pyrosequencing and quantitative PCR of 16S rRNA with more rats per genotype. An average of 4541 and 3381 16S rRNA bacterial reads were obtained from each of the 10 BB-DR and 10 BB-DP samples collected at time of diabetes onset. Nine genera were more abundant in BB-DP whereas another nine genera were more abundant in BB-DR. Thirteen and eleven species were more abundant in BB-DP and BB-DR, respectively. An average of 23% and 10% of all reads could be classified at the genus and species levels, respectively. Quantitative PCR verified the higher abundance of Lactobacillus and Bifidobacterium in the BB-DR samples. Whether these changes are caused by diabetes or are involved in the development of the disease is unknown.Keywords
This publication has 62 references indexed in Scilit:
- The “Perfect Storm” for Type 1 DiabetesDiabetes, 2008
- Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplexNature Methods, 2008
- Pyrosequencing enumerates and contrasts soil microbial diversityThe ISME Journal, 2007
- Effect of Oral Administration ofButyrivibrio fibrisolvensMDT-1 on Experimental Enterocolitis in MiceClinical and Vaccine Immunology, 2006
- Comparative genomics of the lactic acid bacteriaProceedings of the National Academy of Sciences, 2006
- Rapid Quantitative Detection of Lactobacillus sakei in Meat and Fermented Sausages by Real-Time PCRApplied and Environmental Microbiology, 2006
- NAST: a multiple sequence alignment server for comparative analysis of 16S rRNA genesNucleic Acids Research, 2006
- An Immunomodulatory Molecule of Symbiotic Bacteria Directs Maturation of the Host Immune SystemCell, 2005
- MUSCLE: multiple sequence alignment with high accuracy and high throughputNucleic Acids Research, 2004
- Gapped BLAST and PSI-BLAST: a new generation of protein database search programsNucleic Acids Research, 1997