Alex Arzamasov

The lac operon in uropathogenic Escherichia coli enhances intracellular growth by enabling host glycan utilization https://www.biorxiv.org/content/10.64898/2025.12.03.691977v1

Glycoside hydrolase–mediated glucomannan catabolism in Segatella copri, a target of microbiota-directed foods for malnourished children | PNAS Evidence is emerging that perturbed postnatal gut microbiota development is causally related to childhood undernutrition. Clinical trials in undern...

Glycoside hydrolase–mediated glucomannan catabolism in Segatella copri, a target of microbiota-directed foods for malnourished children
www.pnas.org/doi/10.1073/...

Active learning guides automated discovery of DNA delivery via electroporation for non-model microbes Delivery of recombinant DNA is foundational for understanding and engineering a target organism. Electroporation can be applied to any cell type, yet identification of a working protocol for new organ...

Have a look if you are interested in how the team at @cultivarium.bsky.social is finding electroporation protocols for new microbes: both screening lots of conditions on a custom built electroporator concurrently, and cyclical iteration using bayesian optimization

www.biorxiv.org/content/10.1...

Overall, given that FOS are often included in infant formulas and used widely as prebiotics, it’s important to understand the mechanisms by which microbes utilize these oligosaccharides of different chain lengths

Integrative genomic reconstruction reveals heterogeneity in carbohydrate utilization across human gut bifidobacteria - Nature Microbiology A comprehensive genomic analysis reveals species- and strain-level heterogeneity in carbohydrate utilization potential across bifidobacteria of human origin.

We observed a similar pattern in Bifidobacterium: only strains carrying a specific ABC transporter could metabolize long-chain FOS, while utilization of short-chain FOS was broadly conserved
www.nature.com/articles/s41...

Very cool print demonstrating how variation in at TonB-dependent transporter repertoires shapes the ability of Bacteroides and Phocaeicola species to utilize fructooligosaccharides (FOS) of different chain lengths

Some cool data on bifidobacteria and their relatives in honeybees!

Evolution of gut microbiota across honeybee species revealed by comparative metagenomics Nature Communications - Here, the authors perform metagenomic analysis of honeybee gut microbes, uncovering many previously unidentified species and host specific differences in composition and...

Happy to announce that our comparative metagenomic analysis of the gut microbiota of five honeybee species - spearheaded by @aiswarya.bsky.social - is finally published in a peer-reviewed journal! rdcu.be/eKMCs @fbm-unil.bsky.social @dmf-unil.bsky.social 🧵👇

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)

It’s been a bit over 2 months since the main results of my PhD work on reconstructing carbohydrate utilization pathways in human bifidobacteria were finally published; so I guess it’s a good time to update the previous thread (1/7) www.nature.com/articles/s41...

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)

Excited to share our @cp-cellhostmicrobe.bsky.social led by Magda showing how Bif has co-evolved with different animal hosts 🐒🐭🐷🐦

Key takeaways:
🔹 Host ancestry + diet shape Bif evolution
🔹 Mammals enriched for carb-busting enzymes
🔹 Untapped diversity in non-human hosts = new probiotic potential

Our study developing a skin metatranscriptomics protocol is now out in @natbiotech.nature.com!

We finally have the ability to study microbial activity on skin and identify key functional genes playing a role in diseases.

Amazing team of Chia Minghao and Amanda Ng 👏

nature.com/articles/s41...

Uptake of fucosylated type I human milk oligosaccharide blocks by Bifidobacterium longum subsp. infantis | mBio The assembly of the gut microbiota in early life is critical to the health trajectory of human hosts. Breast feeding selects for a Bifidobacterium-rich community, adapted to efficiently utilize human ...

Very nice paper that deciphers the transport mechanisms of fucosylated lacto-N-biose in Bifidobacterium longum subsp. infantis
journals.asm.org/doi/full/10....

High-throughput single-cell isolation of Bifidobacterium strains from the gut microbiome https://www.biorxiv.org/content/10.1101/2025.07.23.666462v1

Predicting the subcellular location of prokaryotic proteins with DeepLocPro AbstractMotivation. Protein subcellular location prediction is a widely explored task in bioinformatics because of its importance in proteomics research. W

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

Lacto-N-biosidase Encoded by a Novel Gene of Bifidobacterium longum Subspecies longum Shows Unique Substrate Specificity and Requires a Designated Chaperone for Its Active Expression * Infant gut-associated bifidobacteria possess species-specific enzymatic sets to assimilate human milk oligosaccharides, and lacto-N-biosidase (LNBase) is a key enzyme that degrades lacto-N-tetraose (G...

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...

Structural and Thermodynamic Analyses of Solute-binding Protein from Bifidobacterium longum Specific for Core 1 Disaccharide and Lacto-N-biose I * Recently, a gene cluster involving a phosphorylase specific for lacto-N-biose I (LNB; Galβ1–3GlcNAc) and galacto-N-biose (GNB; Galβ1–3GalNAc) has been found in Bifidobacterium longum. We showed that t...

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...

α-N-Acetylglucosaminidase from Bifidobacterium bifidum specifically hydrolyzes α-linked N-acetylglucosamine at nonreducing terminus of O-glycan on gastric mucin - Applied Microbiology and Biotechnolog... α-Linked N-acetylglucosamine is one of the major glyco-epitopes in O-glycan of gastroduodenal mucin. Here, we identified glycoside hydrolase (GH) family 89 α-N-acetylglucosaminidase, termed AgnB, from...

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...

Identification and characterization of a sulfoglycosidase from Bifidobacterium bifidum implicated in mucin glycan utilization Abstract. Human gut symbiont bifidobacteria possess carbohydrate-degrading enzymes that act on the O-linked glycans of intestinal mucins to utilize those c

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...

Structural and Thermodynamic Analyses of Solute-binding Protein from Bifidobacterium longum Specific for Core 1 Disaccharide and Lacto-N-biose I * Recently, a gene cluster involving a phosphorylase specific for lacto-N-biose I (LNB; Galβ1–3GlcNAc) and galacto-N-biose (GNB; Galβ1–3GalNAc) has been found in Bifidobacterium longum. We showed that t...

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...

PNGaseA-mediated N-glycan stripping from peptides by infant-derived Bifidobacterium bifidum N-glycans are highly common sources of nutrition for human colonic-dwelling bacteria. These microbes have evolved a several methods to remove N-glycans from proteins; herein we describe the biochemica...

New Pre-print! “PNGaseA-mediated N-glycan stripping from peptides by infant-derived Bifidobacterium bifidum”. This is the first manuscript from the Bifidobacterium and breast milk project🍼🤱👶in collaboration with van Sinderen and Lovering groups
www.biorxiv.org/content/10.1...