Metagenomics-based, strain-level analysis of Escherichia coli from a time-series of microbiome samples from a Crohn's disease patient

Xin Fang, Jonathan M. Monk, Sergey Nurk, Margarita Akseshina, Qiyun Zhu, Christopher Gemmell, Connor Gianetto-Hill, Nelly Leung, Richard Szubin, Jon Sanders, Paul L. Beck, Weizhong Li, William J. Sandborn, Scott D. Gray-Owen, Rob Knight, Emma Allen-Vercoe, Bernhard O. Palsson, Larry Smarr

Research output: Contribution to journalArticlepeer-review

31 Scopus citations


Dysbiosis of the gut microbiome, including elevated abundance of putative leading bacterial triggers such as E. coli in inflammatory bowel disease (IBD) patients, is of great interest. To date, most E. coli studies in IBD patients are focused on clinical isolates, overlooking their relative abundances and turnover over time. Metagenomics-based studies, on the other hand, are less focused on strain-level investigations. Here, using recently developed bioinformatic tools, we analyzed the abundance and properties of specific E. coli strains in a Crohns disease (CD) patient longitudinally, while also considering the composition of the entire community over time. In this report, we conducted a pilot study on metagenomic-based, strain-level analysis of a time-series of E. coli strains in a left-sided CD patient, who exhibited sustained levels of E. coli greater than 100X healthy controls. We: (1) mapped out the composition of the gut microbiome over time, particularly the presence of E. coli strains, and found that the abundance and dominance of specific E. coli strains in the community varied over time; (2) performed strain-level de novo assemblies of seven dominant E. coli strains, and illustrated disparity between these strains in both phylogenetic origin and genomic content; (3) observed that strain ST1 (recovered during peak inflammation) is highly similar to known pathogenic AIEC strains NC101 and LF82 in both virulence factors and metabolic functions, while other strains (ST2-ST7) that were collected during more stable states displayed diverse characteristics; (4) isolated, sequenced, experimentally characterized ST1, and confirmed the accuracy of the de novo assembly; and (5) assessed growth capability of ST1 with a newly reconstructed genome-scale metabolic model of the strain, and showed its potential to use substrates found abundantly in the human gut to outcompete other microbes. In conclusion, inflammation status (assessed by the blood C-reactive protein and stool calprotectin) is likely correlated with the abundance of a subgroup of E. coli strains with specific traits. Therefore, strain-level time-series analysis of dominant E. coli strains in a CD patient is highly informative, and motivates a study of a larger cohort of IBD patients.

Original languageEnglish (US)
Article number2559
JournalFrontiers in Microbiology
StatePublished - Mar 29 2018
Externally publishedYes


  • De novo assembly
  • Escherichia coli
  • Gut microbiome
  • Inflammatory bowel disease
  • Metagenomics

ASJC Scopus subject areas

  • Microbiology
  • Microbiology (medical)


Dive into the research topics of 'Metagenomics-based, strain-level analysis of Escherichia coli from a time-series of microbiome samples from a Crohn's disease patient'. Together they form a unique fingerprint.

Cite this