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Journal of Bacteriology, July 2009, p. 4144-4151, Vol. 191, No. 13
0021-9193/09/$08.00+0 doi:10.1128/JB.00155-09
Copyright © 2009, American Society for Microbiology. All Rights Reserved.
Comparison of the Complete Genome Sequences of Bifidobacterium animalis subsp. lactis DSM 10140 and Bl-04 
,
Rodolphe Barrangou,1
Elizabeth P. Briczinski,2,3
Lindsay L. Traeger,1
Joseph R. Loquasto,2
Melissa Richards,1
Philippe Horvath,4
Anne-Claire Coûté-Monvoisin,4
Gregory Leyer,1
Snjezana Rendulic,5,
James L. Steele,3
Jeffery R. Broadbent,6
Taylor Oberg,6
Edward G. Dudley,2
Stephan Schuster,5
Dennis A. Romero,1 and
Robert F. Roberts2*
Danisco USA Inc., 3329 Agriculture Drive, Madison, Wisconsin 53716,1 The Pennsylvania State University, Department of Food Science, University Park, Pennsylvania 16802,2 University of Wisconsin-Madison, Department of Food Science, Madison, Wisconsin 53706,3 Danisco France SAS, BP10, F-86220 Dangé-Saint-Romain, France,4 The Pennsylvania State University, Department of Biochemistry and Molecular Biology, University Park, Pennsylvania 16802,5 Utah State University, Department of Food Science and Nutrition, Logan, Utah 843226
Received 4 February 2009/ Accepted 11 April 2009
Bifidobacteria are important members of the human gut flora, especially in infants. Comparative genomic analysis of two Bifidobacterium animalis subsp. lactis strains revealed evolution by internal deletion of consecutive spacer-repeat units within a novel clustered regularly interspaced short palindromic repeat locus, which represented the largest differential content between the two genomes. Additionally, 47 single nucleotide polymorphisms were identified, consisting primarily of nonsynonymous mutations, indicating positive selection and/or recent divergence. A particular nonsynonymous mutation in a putative glucose transporter was linked to a negative phenotypic effect on the ability of the variant to catabolize glucose, consistent with a modification in the predicted protein transmembrane topology. Comparative genome sequence analysis of three Bifidobacterium species provided a core genome set of 1,117 orthologs complemented by a pan-genome of 2,445 genes. The genome sequences of the intestinal bacterium B. animalis subsp. lactis provide insights into rapid genome evolution and the genetic basis for adaptation to the human gut environment, notably with regard to catabolism of dietary carbohydrates, resistance to bile and acid, and interaction with the intestinal epithelium. The high degree of genome conservation observed between the two strains in terms of size, organization, and sequence is indicative of a genomically monomorphic subspecies and explains the inability to differentiate the strains by standard techniques such as pulsed-field gel electrophoresis.
* Corresponding author. Mailing address: The Pennsylvania State University, Department of Food Science, 428 Food Science Building, University Park, PA 16802. Phone: (814) 863-2959. Fax: (814) 863-6132. E-mail: rfr3{at}psu.edu
Published ahead of print on 17 April 2009.
Supplemental material for this article may be found at http://jb.asm.org/.
Present address: Stanford University, Institute for Stem Cell Biology and Regenerative Medicine, Pacific Grove, CA 93950.
Journal of Bacteriology, July 2009, p. 4144-4151, Vol. 191, No. 13
0021-9193/09/$08.00+0 doi:10.1128/JB.00155-09
Copyright © 2009, American Society for Microbiology. All Rights Reserved.
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