Functional phylotyping approach for assessing intraspecific diversity of Ruminococcus albus within the rumen microbiome

Inna Rozman Grinberg, Guohua Yin, Ilya Borovok, Margret E. Berg Miller, Carl J. Yeoman, Bareket Dassa, Zhongtang Yu, Itzhak Mizrahi, Harry J. Flint, Edward A. Bayer, Bryan A. White, Raphael Lamed

Research output: Contribution to journalArticle

Abstract

Ruminococcus albus, a cellulolytic bacterium, is a critical member of the rumen community. Ruminococcus albus lacks a classical cellulosome complex, but it possesses a unique family 37 carbohydrate-binding module (CBM37), which is integrated into a variety of carbohydrate-active enzymes. We developed a potential molecular tool for functional phylotyping of the R. albus population in the rumen, based on a variable region in the cel48A gene. cel48A encodes a single copy of the CBM37-associated family 48 glycoside hydrolase in all known strains of this bacterium. A segment of the cel48A gene was amplified from rumen metagenomic samples of four bovines, and its abundance and diversity were evaluated. Analysis of the obtained sequences revealed the co-existence of multiple functional phylotypes of cel48A in all four animals. These included sequences identical or similar to those of R. albus isolates (reference strains), as well as several novel sequences. The dominant cel48A type varied among animals. This method can be used for detection of intraspecific diversity of R. albus in metagenomic samples. Together with scaC, a previously reported gene marker for R. flavefaciens, we present a set of two species-specific markers for phylotyping of Ruminococci in the herbivore rumen.

Original languageEnglish (US)
Article numberfnu047
JournalFEMS microbiology letters
Volume362
Issue number3
DOIs
StatePublished - 2015

Keywords

  • CBM37
  • Carbohydrate-binding modules
  • Family 48 glycoside hydrolase (Cel48A)
  • Metagenomics

ASJC Scopus subject areas

  • Microbiology
  • Molecular Biology
  • Genetics

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    Grinberg, I. R., Yin, G., Borovok, I., Berg Miller, M. E., Yeoman, C. J., Dassa, B., Yu, Z., Mizrahi, I., Flint, H. J., Bayer, E. A., White, B. A., & Lamed, R. (2015). Functional phylotyping approach for assessing intraspecific diversity of Ruminococcus albus within the rumen microbiome. FEMS microbiology letters, 362(3), [fnu047]. https://doi.org/10.1093/femsle/fnu047