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Resolution of Phenotypically Distinct Strains of Enterococcus spp. in a Complex Microbial Community Using cpn60 Universal Target Sequencing

  • Genes and Genomes
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Abstract

Characterization of complex microbial communities is frequently based on the examination of polymerase chain reaction amplified sequences from a single phylogenetic marker, usually the 16S rRNA gene. However, this commonly used target often does not offer robust resolution of species or sub-species and is thus not a sufficiently informative target for understanding microbial population dynamics occurring at the strain level. We have used the cpn60 universal target sequence to characterize Enterococcus isolates from feces of growing pigs and have shown that sub-species groups, not detected using 16S rRNA sequences, can be resolved. Furthermore, groups resolved by cpn60-based phylogenetic analysis have distinct phenotypes. We report changes in the structure and function of Enterococcus communities in pig feces sampled from individual animals at three times, from suckling through to maturity. Enterococcus faecalis was largely replaced by Enterococcus hirae between suckling and 9 weeks of age, and a shift from one sub-species group of E. hirae to another was observed in all animals between 9 and 15 weeks. Conversely, E. faecalis strains remained consistent throughout the study period. Our results demonstrate that cpn60 sequences can be used to detect strain level changes in Enterococcus populations during succession in the fecal microbiota of growing pigs.

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Acknowledgments

The authors gratefully acknowledge John Harding and Crissie Baker for collection of pig fecal samples and Champika Fernando for assistance with statistical analysis. Funding for this work was provided by an NSERC Discovery Grant and a grant from the WCVM Vitamin Fund to JEH. Additional support was provided by NSERC Undergraduate Research Award (AHR) and the University of Saskatchewan (CJV & ARD).

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Authors and Affiliations

  1. Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, 52 Campus Drive, Saskatoon, SK, S7N 5B4, Canada

    Catherine J. Vermette, Amanda H. Russell, Atul R. Desai & Janet E. Hill

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  1. Catherine J. Vermette
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  2. Amanda H. Russell
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  3. Atul R. Desai
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  4. Janet E. Hill
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Corresponding author

Correspondence to Janet E. Hill.

Additional information

This manuscript is dedicated to Dr. Roland Brousseau who passed away too soon in May 2008.

Catherine J. Vermette and Amanda H. Russell contributed equally to this work.

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Supplementary Figure 1

a Carbon source utilization profiles for Enterococcus hirae isolates. Only carbon sources that were utilized by at least one isolate are shown. Assignment to strain group is based on cpn60 phylogenetic analysis (Fig. 2). b Carbon source utilization profiles for Enterococcus faecalis isolates. Only carbon sources that were utilized by at least one isolate are shown. Assignment to strain group is based on cpn60 phylogenetic analysis (Fig. 2) (XLS 160 kb)

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Vermette, C.J., Russell, A.H., Desai, A.R. et al. Resolution of Phenotypically Distinct Strains of Enterococcus spp. in a Complex Microbial Community Using cpn60 Universal Target Sequencing. Microb Ecol 59, 14–24 (2010). https://doi.org/10.1007/s00248-009-9601-1

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