Genomic studies in bifidobacteria often focus only on CAZymes. IMHO, in Gram-positives, transporters are the true gatekeepers of glycan metabolism. We need to prioritize improving their functional annotations and include them in metabolic reconstructions (7/7)

We demonstrated that phylogenetically closely related strains can exhibit substantial differences in HMO utilization, which is driven by subtle variations in HMO transporter genes. Species/subspecies names alone don’t tell the full story; one needs to look at gene content in individual strains(6/7)

Among the new pathways we uncovered was a xyloglucan degradation pathway that was present in rare B. catenulatum subsp. kashiwanohense strains and conserved in B. dentium and B. tsurumiense (5/7)

We validated phenotypic predictions for 30 bifidobacterial strains, achieving 94% accuracy. For example, we confirmed the unique ability of the new B. longum clade to grow on starch and pullulan, and described an unconventional B. adolescentis strain that can use 2’-fucosyllactose (4/7)

Our analysis revealed notable inter- and intra-species variability. Among notable findings was a new Bifidobacterium longum clade harboring pathways for starch, pullulan, and difructose dianhydride metabolism but lacking pathways for LNB/GNB, N-glycan, and human milk oligosaccharide utilization(3/7)

We reconstructed 68 glycan utilization pathways encoded in 3,083 bif genomes by looking at the distribution of 589 curated metabolic functions (transporters, CAZymes, etc). Several years of manual curation greatly improved the quality of functional gene annotations (>90% for transporters!) (2/7)

Among the new pathways we uncovered was a xyloglucan degradation pathway that was present in rare B. catenulatum subsp. kashiwanohense strains and conserved in B. dentium and B. tsurumiense (5/7)

We validated phenotypic predictions for 30 bifidobacterial strains, achieving 94% accuracy. For example, we confirmed the unique ability of the new B. longum clade to grow on starch and pullulan, and described a B. adolescentis strain that can use 2’-fucosyllactose (4/7)

Our analysis revealed notable inter- and intra-species variability. Among notable findings was a new Bifidobacterium longum clade harboring pathways for starch, pullulan, and difructose dianhydride metabolism but lacking pathways for LNB/GNB, N-glycan, and human milk oligosaccharide utilization(3/7)

We reconstructed 68 glycan utilization pathways encoded in 3,083 bif genomes by looking at the distribution of 589 curated metabolic functions (transporters, CAZymes, etc). Several years of manual curation greatly improved the quality of functional gene annotations (>90% for transporters!) (2/7)

Thanks! Also, maybe of interest, I think PSORTb and the new tool DeepLocPro perform better for bifido proteins than signalP
academic.oup.com/bioinformati...

4) The GH136 lacto-N-biosidase from B. longum that you cite does not release LacNAc from Lacto-N-neotetraose (Fig. 4b from Sakurama et al). The B. bifidum GH136 is not identical to the B. longum one, but I haven't seen papers describing activity on LNnT (only LNT)
www.jbc.org/article/S002...

3) Additionally, B. bifidum possesses an ortholog of an ABC transporter that can uptake GNB (GltABC), so it would make sense for the GH101 enzyme to be extracellular, so the released disaccharide is then imported.
www.jbc.org/article/S002...

2) Your predictions about the localization of some other GHs (like GH89 and GH101) also differ from previously published literature. For example, the GH89 was described as a membrane-anchored extracellular enzyme before.
link.springer.com/article/10.1...

Hi, very cool to see this out! I have a couple of comments about the model. 1) I think the GH20 enzyme that removes GlcNAc-6S (BbhII) is extracellular. The released GlcNAc-6S can be cross-fed to Bifidobacterium breve (some strains have a dedicated utilization pathway)
doi.org/10.1080/0916...

3) Additionally, B. bifidum possesses an ortholog of an ABC transporter that can uptake GNB (GltABC), so it would make sense for this GH89 to be extracellular, so the released disaccharide is then imported.
www.jbc.org/article/S002...

Is the original 1924 article publicly available somewhere?