neWs & analysis

genome watch milk and two oligosaccharides Alan Walker

This month’s Genome Watch reviews the genes involved in HMO catabolism in the three recent papers that describe B. longum subsp. infantis genome were not bifidobacterial genomes. present in B. animalis subsp. lactis, indicat- ing that there are niche-specific adaptations Bifidobacteria comprise a phylogenetically between these two groups. Genome analysis distinct group of approximately 30 species did, however, indicate the presence of a range of Gram-positive, anaerobic rods belonging of other factors that are important for coloni- to the Actinobacteria phylum and are com- zation and persistence in the gastro intestinal mon inhabitants of the gastrointestinal tract tract, such as the ability to degrade a range of of humans and other mammals. Infants milk galactosides and plant-derived oligosac- are born sterile but bacterial colonization charides, and a bile salt hydrolase that medi- of the gut occurs rapidly after birth. In ates tolerance to bile. Insight into the probiotic breast-fed infants, bifidobacteria frequently function of B. animalis subsp. lactis was pro- predominate in the gastrointestinal tract vided by the identification of the fos gene and consequently might have a role in the cluster. This cluster is involved in processing development and maturation of the healthy fructo oligosaccharides, which are common gut. After weaning, however, the popula- prebiotics and known bifidogenic factors. tion of bifidobacteria declines, and these There are now several complete and species are less abundant members of the ongoing bifidobacterial genome sequencing gut microbiota in adults. Bifidobacterium Nature Reviews | Microbiology projects. The results promise to increase our species have therefore gained attention as mechanism for HMO utilization in this sub- understanding of the co-evolution between potential probiotics, with several postulated species. From a human evolutionary point mammalian hosts and their commensal therapeutic benefits. of view, supplying milk oligo saccharides that inhabitants, niche adaptation by gut micro- Sela et al.1 recently reported the com- have no nutritional value for the infant would organisms and the genetic basis for coloniza- plete genome sequence of Bifidobacterium seem to be an inefficient use of the mother’s tion and persistence in the human gut, which longum subsp. infantis, a subspecies that com- resources. The authors postulate that instead, could prove useful for the development of new monly inhabits the infant gastro intestinal these oligosaccharides might be involved in probiotics. tract. B. longum subsp. infantis has the larg- the selective enrichment of commensal species Alan Walker is at the Sanger Institute, Wellcome Trust est bifidobacterial genome reported to date, such as B. longum subsp. infantis. Genome Campus, Hinxton, Cambridge, CB10 1SA, UK. comprising a 2.83 Mb chromosome that Genome sequences from three strains of e-mail: [email protected] is estimated to contain 2,423 protein cod- Bifidobacterium animalis subsp. lactis have 2,3 1. Sela, D. A. et al. The genome sequence of Bifidobacterium ing sequences. Genomic analysis revealed also recently been reported . B. animalis longum subsp. infantis reveals adaptations for milk intriguing insights into the intimate connec- subsp. lactis naturally inhabits the gastro- utilization within the infant microbiome. Proc. Natl Acad. Sci. USA 105, 18964–18969 (2008). tion between this bacterium and its infant intestinal tract but is also the most com- 2. Kim, J. F. et al. Genome sequence of the probiotic host. The genome contains complete path- mon Bifidobacterium species to be used as a bacterium Bifidobacterium animalis subsp. lactis AD011. J. Bacteriol. 191, 678–679 (2009). ways for the synthesis of the vitamins ribo- probiotic in North America and Europe. At 3. Barrangou, R. et al. Comparison of the complete genome flavin, thiamine and folate, which could around 1.9 Mb in size, these three genomes sequences of Bifidobacterium animalis subsp. lactis DSM 10140 and BI-04. J. Bacteriol. 17 Apr 2009 benefit the infant. In addition, a novel 43 kb are smaller than those found in other bifido- (doi:10.1128/JB.00155–09). cluster of genes dedicated to the import and bacteria. However, a comparison of these use of human milk oligosaccharides (HMOs) strains with previously sequenced genomes of DataBaSeS Entrez Genome Project: that infants cannot digest was identified. B. longum subsp. longum and Bifidobacterium http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=genomeprj Sequence analysis confirmed the presence of adolescentis indicated that a reasonable pro- Bifidobacterium adolescentis | Bifidobacterium animalis subsp. lactis | Bifidobacterium longum subsp. infantis this cluster in other B. longum subsp. infantis portion of genes are conserved among all All links Are Active in the online pdf strains, suggesting that there is a conserved bifidobacteria. Notably, however, many of

NATurE rEvIEwS | Microbiology vOluME 7 | july 2009 | 483 © 2009 Macmillan Publishers Limited. All rights reserved