E. coli diversity: low in colorectal cancer
Open Access
- 6 April 2020
- journal article
- research article
- Published by Springer Science and Business Media LLC in BMC Medical Genomics
- Vol. 13 (1), 1-17
- https://doi.org/10.1186/s12920-020-0704-3
Abstract
Background Escherichia coli are mostly commensals but also contain pathogenic lineages. It is largely unclear whether the commensal E. coli as the potential origins of pathogenic lineages may consist of monophyletic or polyphyletic populations, elucidation of which is expected to lead to novel insights into the associations of E. coli diversity with human health and diseases. Methods Using genomic sequencing and pulsed field gel electrophoresis (PFGE) techniques, we analyzed E. coli from the intestinal microbiota of three groups of healthy individuals, including preschool children, university students, and seniors of a longevity village, as well as colorectal cancer (CRC) patients, to probe the commensal E. coli populations for their diversity. Results We delineated the 2280 fresh E. coli isolates from 185 subjects into distinct genome types (genotypes) by PFGE. The genomic diversity of the sampled E. coli populations was so high that a given subject may have multiple genotypes of E. coli, with the general diversity within a host going up from preschool children through university students to seniors. Compared to the healthy subjects, the CRC patients had the lowest diversity level among their E. coli isolates. Notably, E. coli isolates from CRC patients could suppress the growth of E. coli bacteria isolated from healthy controls under nutrient-limited culture conditions. Conclusions The coexistence of multiple E. coli lineages in a host may help create and maintain a microbial environment that is beneficial to the host. As such, the low diversity of E. coli bacteria may be associated with unhealthy microenvironment in the intestine and hence facilitate the pathogenesis of diseases such as CRC.Funding Information
- National Natural Science Foundation of China (NSFC31600001, NSFC30970078, NSFC81971910)
- National Postdoctoral Fellowship of China (2016M600266)
- Heilongjiang Innovation Endowment Award for graduate studies (YJSCX2012-214HLJ)
- National Natural Science Foundation of China (NSFC81030029)
- National Natural Science Foundation of China (NSFC81271786)
- National Natural Science Foundation of China (NSFC81671980)
- National Natural Science Foundation of China (NSFC81871623)
This publication has 99 references indexed in Scilit:
- Defining natural species of bacteria: clear-cut genomic boundaries revealed by a turning point in nucleotide sequence divergenceBMC Genomics, 2013
- A novel non-homologous recombination-mediated mechanism for Escherichia coli unilateral flagellar phase variationNucleic Acids Research, 2012
- Comparative genomics reveal the mechanism of the parallel evolution of O157 and non-O157 enterohemorrhagic Escherichia coliProceedings of the National Academy of Sciences of the United States of America, 2009
- Complete Genome Sequence and Comparative Analysis of the Wild-type Commensal Escherichia coli Strain SE11 Isolated from a Healthy AdultDNA Research, 2008
- Comparative genome analysis of Salmonella Enteritidis PT4 and Salmonella Gallinarum 287/91 provides insights into evolutionary and host adaptation pathwaysGenome Research, 2008
- Identifying bacterial genes and endosymbiont DNA with GlimmerBioinformatics, 2007
- Identification of genes subject to positive selection in uropathogenic strains of Escherichia coli : A comparative genomics approachProceedings of the National Academy of Sciences of the United States of America, 2006
- Pathogenic Escherichia coliNature Reviews Microbiology, 2004
- Improved microbial gene identification with GLIMMERNucleic Acids Research, 1999
- The Complete Genome Sequence of Escherichia coli K-12Science, 1997