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

6 Citations (Scopus)

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
Pages (from-to)1-10
Number of pages10
JournalFEMS Microbiology Letters
Volume362
Issue number3
Early online date22 Dec 2014
DOIs
Publication statusPublished - Feb 2015

Fingerprint

Ruminococcus
Microbiota
Rumen
Metagenomics
Cellulosomes
Carbohydrates
vpr Genes
Bacteria
Herbivory
Glycoside Hydrolases
Genes
Sequence Analysis
Enzymes
Population

Keywords

  • family 48 glycoside hydrolase (Cel48A)
  • carbohydrate-binding modules
  • CBM37
  • metagenomics

Cite this

Grinberg, I. R., Yin, G., Borovok, I., Miller, M. E. B., Yeoman, C. J., Dassa, B., ... Lamed, R. (2015). Functional phylotyping approach for assessing intraspecific diversity of Ruminococcus albus within the rumen microbiome. FEMS Microbiology Letters, 362(3), 1-10. https://doi.org/10.1093/femsle/fnu047

Functional phylotyping approach for assessing intraspecific diversity of Ruminococcus albus within the rumen microbiome. / Grinberg, Inna Rozman; Yin, Guohua; Borovok, Ilya; Miller, Margret E Berg; Yeoman, Carl J; Dassa, Bareket; Yu, Zhongtang; Mizrahi, Itzhak; Flint, Harry J; Bayer, Edward A; White, Bryan A; Lamed, Raphael.

In: FEMS Microbiology Letters, Vol. 362, No. 3, 02.2015, p. 1-10.

Research output: Contribution to journalArticle

Grinberg, IR, Yin, G, Borovok, I, Miller, MEB, Yeoman, CJ, Dassa, B, Yu, Z, Mizrahi, I, Flint, HJ, Bayer, EA, White, BA & Lamed, R 2015, 'Functional phylotyping approach for assessing intraspecific diversity of Ruminococcus albus within the rumen microbiome', FEMS Microbiology Letters, vol. 362, no. 3, pp. 1-10. https://doi.org/10.1093/femsle/fnu047
Grinberg, Inna Rozman ; Yin, Guohua ; Borovok, Ilya ; Miller, Margret E Berg ; Yeoman, Carl J ; Dassa, Bareket ; Yu, Zhongtang ; Mizrahi, Itzhak ; Flint, Harry J ; Bayer, Edward A ; White, Bryan A ; Lamed, Raphael. / Functional phylotyping approach for assessing intraspecific diversity of Ruminococcus albus within the rumen microbiome. In: FEMS Microbiology Letters. 2015 ; Vol. 362, No. 3. pp. 1-10.
@article{f9df31b3be014ef99e5413d89c6d271b,
title = "Functional phylotyping approach for assessing intraspecific diversity of Ruminococcus albus within the rumen microbiome",
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.",
keywords = "family 48 glycoside hydrolase (Cel48A), carbohydrate-binding modules, CBM37, metagenomics",
author = "Grinberg, {Inna Rozman} and Guohua Yin and Ilya Borovok and Miller, {Margret E Berg} and Yeoman, {Carl J} and Bareket Dassa and Zhongtang Yu and Itzhak Mizrahi and Flint, {Harry J} and Bayer, {Edward A} and White, {Bryan A} and Raphael Lamed",
note = "{\circledC} FEMS 2014. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com. Acknowledgments The authors are grateful to Dr Mark Morrison (University of Queensland) for critical reading of the manuscript. They also appreciate the kind gift of R. albus strain 20 genomic DNA from Dr Pascale Mosoni (INRA, Saint-Gen{\`e}s-Champanelle, France).",
year = "2015",
month = "2",
doi = "10.1093/femsle/fnu047",
language = "English",
volume = "362",
pages = "1--10",
journal = "FEMS Microbiology Letters",
issn = "0378-1097",
publisher = "Oxford University Press",
number = "3",

}

TY - JOUR

T1 - Functional phylotyping approach for assessing intraspecific diversity of Ruminococcus albus within the rumen microbiome

AU - Grinberg, Inna Rozman

AU - Yin, Guohua

AU - Borovok, Ilya

AU - Miller, Margret E Berg

AU - Yeoman, Carl J

AU - Dassa, Bareket

AU - Yu, Zhongtang

AU - Mizrahi, Itzhak

AU - Flint, Harry J

AU - Bayer, Edward A

AU - White, Bryan A

AU - Lamed, Raphael

N1 - © FEMS 2014. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com. Acknowledgments The authors are grateful to Dr Mark Morrison (University of Queensland) for critical reading of the manuscript. They also appreciate the kind gift of R. albus strain 20 genomic DNA from Dr Pascale Mosoni (INRA, Saint-Genès-Champanelle, France).

PY - 2015/2

Y1 - 2015/2

N2 - 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.

AB - 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.

KW - family 48 glycoside hydrolase (Cel48A)

KW - carbohydrate-binding modules

KW - CBM37

KW - metagenomics

U2 - 10.1093/femsle/fnu047

DO - 10.1093/femsle/fnu047

M3 - Article

VL - 362

SP - 1

EP - 10

JO - FEMS Microbiology Letters

JF - FEMS Microbiology Letters

SN - 0378-1097

IS - 3

ER -