Genomic insights into bifidobacteria

Abstract

Since the discovery in 1899 of bifidobacteria as numerically dominant microbes in the feces of breast-fed infants, there have been numerous studies addressing their role in modulating gut microflora as well as their other potential health benefits. Because of this, they are frequently incorporated into foods as probiotic cultures. An understanding of their full interactions with intestinal microbes and the host is needed to scientifically validate any health benefits they may afford. Recently, the genome sequences of nine strains representing four species of Bifidobacterium became available. A comparative genome analysis of these genomes reveals a likely efficient capacity to adapt to their habitats, with B. longum subsp. infantis exhibiting more genomic potential to utilize human milk oligosaccharides, consistent with its habitat in the infant gut. Conversely, B. longum subsp. longum exhibits a higher genomic potential for utilization of plant-derived complex carbohydrates and polyols, consistent with its habitat in an adult gut. An intriguing observation is the loss of much of this genome potential when strains are adapted to pure culture environments, as highlighted by the genomes of B. animalis subsp. lactis strains, which exhibit the least potential for a gut habitat and are believed to have evolved from the B. animalis species during adaptation to dairy fermentation environments.

FIG. 1.

Phylogenetic analysis of replication proteins expressed by bifidobacterial plasmids. The replication proteins encoded by bifidobacterial plasmids and other homologous replication proteins were compared by ClustalW multiple alignments (313). A phylogenetic tree was generated by the neighbor-joining method, using P distance values (307). The numbers associated with the branches represent the bootstrap values. Bifidobacterial plasmid replicons are indicated in bold. Roman numerals indicate the five different classes of replication proteins expressed from bifidobacterial plasmids.

FIG. 2.

Phylogenetic analysis of the 16S rRNA genes of the nine sequenced bifidobacteria, illustrating their separation into three distinct groups. The 16S rRNA gene sequences from complete or draft bifidobacterial genomes were compared by ClustalW multiple sequence alignments as described in the legend to Fig. 1. The completely sequenced bifidobacteria are indicated in bold.

FIG. 3.

Alignments of the complete genome sequences of the B. longum group and the B. animalis subsp. lactis group. Red lines indicate the relative locations of elements that are oriented in the same direction. Blue lines indicate elements orientated in opposite directions.

FIG. 4.

Overview of predicted carbohydrate uptake and metabolism systems in bifidobacteria. The F6PPK pathway, partial TCA cycle, and UDP-glucose/galactose system (UDP-Gal/Glc) are indicated with different background colors (light yellow for F6PPK, light purple for the partial TCA cycle, and sky blue for the UDP-Glc/Gal system). Blue, ABC transport systems; green, PTS; gray, MFS family; dark purple, major intrinsic protein (MIP) family; orange, GPH cation symporter family. Genes encoding predicted metabolic enzymes from B. longum subsp. longum DJO10A are indicated.

FIG. 5.

Predicted amino acid biosynthesis pathways in bifidobacteria. The biosynthesis of amino acids in bifidobacteria utilizes the intermediate products of the F6PPK pathway. Genes predicted to be involved in amino acid biosynthesis in B. longum subsp. longum DJO10A and the EC numbers of their predicted proteins are indicated in purple. Solid arrows indicate single-step reactions, and dotted arrows indicate multistep reactions.

FIG. 6.

Comparison of predicted EPS gene clusters in bifidobacterial genomes. The EPS biosynthetic gene cluster in Lactobacillus rhamnosus ATCC 9595 was obtained from the work of Peant et al. (228). All genes were categorized according to their potential functions, as follows: A, chain-length determination; B, Wzx flippase for EPS synthesis; C, glycosyltransferase; D, glucose transferase; E, rhamnosyltransferase; F, polysaccharide polymerase/oligosaccharide repeat unit polymerase; G, polysaccharide pyruvyl transferase; H, dTDP-glucose pyrophosphorylase; I, dTDP-4-dehydrorhamnose-3,5-epimerase; J, dTDP-d-glucose-4,6-dehydratase; K, dTDP-4-keto-l-rhamnose reductase; I/K, fused protein of I and K; and L, priming glycosyltransferase/galactosyltransferase/UDP-galactose phosphotransferase. Genes with red numbers are bifidobacterium-specific genes predicted to be involved in EPS biosynthesis, as follows: 1, extracellular exopolygalacturonase; 2, UDP-glucose/GDP-mannose dehydrogenase; 3, UDP-N-acetylglucosamine/glucuronate/galacturonate-4-epimerase; 4, β-1,4-galactosyltransferase enhancer; and 5, UDP-galactopyranose mutase. Gray arrows indicate genes involved in dTDP-rhamnose precursor biosynthesis. Sky blue arrows indicate hypothetical genes. The red boxes indicate IS mobile elements. MIC, mobile integrase cassette consisting of three contiguous integrase genes (green) sandwiched by two IS3 mobile elements (161). The genome locations of the gene clusters are indicated in kilobases.

FIG. 7.

Comparison of the lantibiotic operon in B. longum subsp. longum DJO10A with partial operons in B. longum subsp. infantis ATCC 15697 and B. angulatum DSM 20098. Red arrows indicate IS elements, and white arrows indicate the component genes for lantibiotic production, modification, secretion, and immunity. Amino acid sequence identities with B. longum subsp. longum DJO10A are indicated. The asterisk indicates that the lower overall identity is due to an internal gene deletion, with the common gene regions sharing almost 100% identity. Genes: lanR2, response regulator gene; lanK, histidine kinase gene; lanA, lantibiotic prepeptide gene; lanR1, response regulator gene; lanD, prepeptide modification enzyme gene; lanM, lantibiotic modifying enzyme gene; lanI, lantibiotic immunity protein gene; lanT, lantibiotic transporter/protease fusion protein gene. The gene numbers of the gene analogs in B. angulatum DSM 20098 and B. longum subsp. infantis are indicated.

FIG. 8.

Phylogenetic analysis of DnaJ proteins in Proteobacteria, Firmicutes, Archaea, and Eukarya compared with the two DnaJ proteins encoded by the nine complete bifidobacterial genomes (in bold).