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.
authors: Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Ramat Aviv 69978, Israel.
authors: Inna
authors: I
authors: Rozman Grinberg
authors: Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Ramat Aviv 69978, Israel.
authors: Guohua
authors: G
authors: Yin
authors: Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Ramat Aviv 69978, Israel.
authors: Ilya
authors: I
authors: Borovok
authors: Institute for Genomic Biology, University of Illinois, Urbana, IL 61801, USA.
authors: Margret E
authors: ME
authors: Berg Miller
authors: Department of Animal and Range Sciences, Montana State University, Bozeman, MT 59717, USA.
authors: Carl J
authors: CJ
authors: Yeoman
authors: Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot 7610001, Israel.
authors: Bareket
authors: B
authors: Dassa
authors: The MAPLE Research Initiative, Department of Animal Sciences, The Ohio State University, Columbus, OH 43210, USA.
authors: Zhongtang
authors: Z
authors: Yu
authors: Department of Ruminant Science, Institute of Animal Sciences, Agricultural Research Organization, Bet Dagan 50250, Israel.
authors: Itzhak
authors: I
authors: Mizrahi
authors: Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen AB21 9SB, UK.
authors: Harry J
authors: HJ
authors: Flint
authors: Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot 7610001, Israel.
authors: Edward A
authors: EA
authors: Bayer
authors: Institute for Genomic Biology, University of Illinois, Urbana, IL 61801, USA.
authors: Bryan A
authors: BA
authors: White
authors: Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Ramat Aviv 69978, Israel lamedr@post.tau.ac.il.
authors: Raphael
authors: R
authors: Lamed
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D001426:Bacterial Proteins / Q000737:chemistry / Q000235:genetics; D002417:Cattle; D044602:Cellulases / Q000737:chemistry / Q000235:genetics*; D002482:Cellulose / Q000378:metabolism; D014644:Genetic Variation; D064307:Microbiota; D008969:Molecular Sequence Data; D058889:Molecular Typing; D010802:Phylogeny; D012417:Rumen / Q000382:microbiology*; D045857:Ruminococcus / Q000145:classification* / Q000201:enzymology / Q000235:genetics*; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D013045:Species Specificity
chemical_list: D001426:Bacterial Proteins; D002482:Cellulose; D044602:Cellulases
keywords: CBM37; carbohydrate-binding modules; family 48 glycoside hydrolase (Cel48A); metagenomics