The genome sequence of Bifidobacterium longum reflects its adaptation to the human gastrointestinal tract

Abstract

Bifidobacteria are Gram-positive prokaryotes that naturally colonize the human gastrointestinal tract (GIT) and vagina. Although not numerically dominant in the complex intestinal microflora, they are considered as key commensals that promote a healthy GIT. We determined the 2.26-Mb genome sequence of an infant-derived strain of Bifidobacterium longum, and identified 1,730 possible coding sequences organized in a 60%-GC circular chromosome. Bioinformatic analysis revealed several physiological traits that could partially explain the successful adaptation of this bacteria to the colon. An unexpectedly large number of the predicted proteins appeared to be specialized for catabolism of a variety of oligosaccharides, some possibly released by rare or novel glycosyl hydrolases acting on ''nondigestible'' plant polymers or host-derived glycoproteins and glycoconjugates. This ability to scavenge from a large variety of nutrients likely contributes to the competitiveness and persistence of bifidobacteria in the colon. Many genes for oligosaccharide metabolism were found in self-regulated modules that appear to have arisen in part from gene duplication or horizontal acquisition. Complete pathways for all amino acids, nucleotides, and some key vitamins were identified; however, routes for Asp and Cys were atypical. More importantly, genome analysis provided insights into the reciprocal interactions of bifidobacteria with their hosts. We identified polypeptides that showed homology to most major proteins needed for production of glycoprotein-binding fimbriae, structures that could possibly be important for adhesion and persistence in the GIT. We also found a eukaryotic-type serine protease inhibitor (serpin) possibly involved in the reported immunomodulatory activity of bifidobacteria.

Cloning and characterization of a bile salt hydrolase (bsh) from Bifidobacterium adolescentis

“…A protein sequence comparison showed that this sequence was homologous to the N-terminal amino acid sequences of the BSH enzymes from many enteric bacteria, with the highest identity to that of the B. longum BSH enzyme (42,48). Only one difference between the amino acids, Thr 13 of B. longum BSH and Met 13 from B. bifidum BSH, was found.…”

“…The importance of the SH group in the N-terminal cysteine was confirmed by the fact that replacing Cys with other (42,48). The predicted ORF of 951 bp displayed 83% DNA sequence identity and 95% deduced amino acid sequence similarity to BSH from B. longum NCC 2705 (42). Such a discrepancy is due to different codon usage, mostly at the third position.…”

“…The absence of a Met residue at the N-terminal end could be explained by the fact that the Cys-1 residue becomes a catalytic center after removal of the initiation formyl methionine by an autoproteolytic process, which is one of the common features of the Ntn hydrolase superfamily (34). The importance of the SH group in the N-terminal cysteine was confirmed by the fact that replacing Cys with other (42,48). The predicted ORF of 951 bp displayed 83% DNA sequence identity and 95% deduced amino acid sequence similarity to BSH from B. longum NCC 2705 (42).…”

The cell-envelope proteome of Bifidobacterium longum in an in vitro bile environment

“…The number of surface-associated proteins in B. longum was predicted through a bioinformatic analysis using dedicated software (Table 1), taking into account the genome annotation of B. longum NCC 2705 (Schell et al, 2002). The results of the different location predictions were combined by grouping the proteins into classes according to signal peptides for export features (145 proteins), at least one hypothetical transmembrane segment (361 proteins), proteins anchored covalently to the peptidoglycan (LPXTG sorting signal; 13 proteins) or to the membrane (lipoprotein motifs; 25 proteins), and proteins which are noncovalently bound to the surface (8 proteins).…”

Short-term modifications in the distal gut microbiota of weaning mice induced by a high-fat diet

“…HF/carbohydratefree diet). Analysis of the genome sequence of Bifidobacterium longum reveals that bifidobacteria possess long-chain fatty acyl-coenzyme A synthetases that may play a role in fatty acid utilization (Schell et al, 2002). Thus the potential ability of Bifidobacterium spp.…”