The genome sequence of Bifidobacterium longum subsp. infantis reveals adaptations for milk utilization within the infant microbiome

doi:10.1073/pnas.0809584105

The genome sequence of Bifidobacterium longum subsp. infantis reveals adaptations for milk utilization within the infant microbiome

^aMicrobiology Graduate Group,
^bRobert Mondavi Institute for Wine and Food Sciences, and
Departments of ^eViticulture and Enology,
^gChemistry, and
^hFood Science and Technology, University of California, Davis, CA 95616;
^cDepartment of Energy, Joint Genome Institute, Walnut Creek, CA 94598; and
^dBioproducts and Biocatalysts Research Unit and
^fFermentation Biotechnology Research Unit, Department of Agriculture-Agricultural Research Service-National Center for Agricultural Utilization Research, Peoria, IL 61604

Communicated by Todd R. Klaenhammer, North Carolina State University, Raleigh, NC, September 25, 2008 (received for review May 20, 2008)

Abstract

Following birth, the breast-fed infant gastrointestinal tract is rapidly colonized by a microbial consortium often dominated by bifidobacteria. Accordingly, the complete genome sequence of Bifidobacterium longum subsp. infantis ATCC15697 reflects a competitive nutrient-utilization strategy targeting milk-borne molecules which lack a nutritive value to the neonate. Several chromosomal loci reflect potential adaptation to the infant host including a 43 kbp cluster encoding catabolic genes, extracellular solute binding proteins and permeases predicted to be active on milk oligosaccharides. An examination of in vivo metabolism has detected the hallmarks of milk oligosaccharide utilization via the central fermentative pathway using metabolomic and proteomic approaches. Finally, conservation of gene clusters in multiple isolates corroborates the genomic mechanism underlying milk utilization for this infant-associated phylotype.

Footnotes

²To whom correspondence should be addressed. E-mail: damills{at}ucdavis.edu
Author contributions: D.A.S., D.S.R., C.B.L., J.B.G., N.P.P., P.M.R., and D.A.M. designed research; D.A.S., J.C., A.A., J.H.K., F.C., T.R.W., and A.L. performed research; D.A.S., J.C., A.A., J.H.K., A.L., N.P.P., P.M.R., and D.A.M. analyzed data; and D.A.S. and D.A.M. wrote the paper.
↵¹Present address: Progentech, Emeryville, CA 95119.
The authors declare no conflict of interest.