Comparative Genomics Of Bifidobacterium Longum Strains Identifies Genes Relevant For Human And Bovine Milk Oligosaccharides Utilization

Human milk oligosaccharides (HMO) are believed to provide protection against pathogens and prebiotic enrichment of beneficial commensals such as bifidobacteria. Bifidobacterium longum bv. infantis ATCC15697, a microorganism commonly present in the feces of breast-fed infants, preferentially consumes four milk oligosaccharides representing nearly 70% of all HMOs present in milk. Genome analysis of B. infantis ATCC15697 has revealed a number of gene clusters putatively associated with HMO consumption. This suggests that HMOs are a class of bioactive milk molecules capable of enriching the growth of specific bacterial populations in the gut of breastfeeding infants.

The purpose of this study was to use genomic and glycomic tools to investigate how the HMOs consumption patterns among several infant gut isolates of Bifidobacteria correlate with their genomic diversity. Using B. infantis ATCC15697 as a reference strain, comparative genomic hybridization (CGH) analyses was performed on fifteen additional strains having various HMO consumption profiles.

In 2008 I presented at this meeting the preliminary analysis of this work, the data analysis is being finalized and drafted as a manuscript for publication. The bacterial strain analyzed clearly cluster into two groups, the first containing exclusively B. infantis strains achieving high growth on HMO, and the second generally containing non-B. infantis or B. longum strains with moderate or little ability to grow on HMOs. The genomes of all the B. infantis analyzed in this study uniquely contain gene clusters associated with bovine and human milk oligosaccharides consumption and for adaptation for populating the breastfed infant gastrointestinal tract. Conversely, the B. longum group consistently lacks the glycosyl hydrolases, oligosaccharide binding proteins and transporters and all other accessory proteins normally present in B. infantis and likely important for bovine and human milk consumption.

Findings of this study:

· B. infantis shows genomic and physiological adaptation of for optimal growth in milk oligosaccharides, and highlight the importance of this organism for use as a probiotic

· Oligosaccharides from bovine and human milk are likely to elicit very specific prebiotic responses only the genomes of B. infantis strains have the complex metabolic machinery needed to utilize them.

· CGH can reveal detailed, genome-wide probiotic strain diversity information which guide into rational selection of cultures food and dairy applications