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Alex Arzamasov @arzamasovalex.bsky.social · 10d

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)

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Alex Arzamasov @arzamasovalex.bsky.social · 10d

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)

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Alex Arzamasov @arzamasovalex.bsky.social · 10d

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)

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Alex Arzamasov @arzamasovalex.bsky.social · 10d

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)

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Alex Arzamasov @arzamasovalex.bsky.social · 10d

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)

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Alex Arzamasov @arzamasovalex.bsky.social · 10d

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)

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Alex Arzamasov @arzamasovalex.bsky.social · 10d

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...

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Alex Arzamasov @arzamasovalex.bsky.social · 10d

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)

Alex Arzamasov @arzamasovalex.bsky.social · 10d

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)

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Alex Arzamasov @arzamasovalex.bsky.social · 10d

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)

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Alex Arzamasov @arzamasovalex.bsky.social · 10d

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)

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Reposted by Alex Arzamasov

Hall Lab @halllab.bsky.social · 29d

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

Cell Host & Microbe @cp-cellhostmicrobe.bsky.social · 29d

Bifido adaptations across hosts

@halllab.bsky.social survey insects, reptiles, birds & mammals to uncover how Bifidobacterium adapts to hosts. Bifidobacterium & host exhibit strong co-phylogenetic associations, driven by vertical transmission & dietary selection
www.cell.com/cell-host-mi...

Host-specific microbiome and genomic signatures in Bifidobacterium reveal co-evolutionary and functional adaptations across diverse animal hosts

Bifidobacterium are beneficial members of the microbiota across animal hosts. Kujawska et al. demonstrate that bifidobacteria have likely co-evolved more closely with mammals, particularly primates, a...

www.cell.com

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Reposted by Alex Arzamasov

Niranjan Nagarajan @niranjantw.bsky.social · Aug 30

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...

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Alex Arzamasov @arzamasovalex.bsky.social · Jul 26

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

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 ...

journals.asm.org

Reposted by Alex Arzamasov

bioRxiv Microbiology @biorxiv-microbiol.bsky.social · Jul 25

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

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Alex Arzamasov @arzamasovalex.bsky.social · Jul 19

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

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

academic.oup.com

Alex Arzamasov @arzamasovalex.bsky.social · Jul 18

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...

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...

www.jbc.org

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Alex Arzamasov @arzamasovalex.bsky.social · Jul 18

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...

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...

www.jbc.org

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Alex Arzamasov @arzamasovalex.bsky.social · Jul 18

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...

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...

link.springer.com

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Alex Arzamasov @arzamasovalex.bsky.social · Jul 18

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...

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

doi.org

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Alex Arzamasov @arzamasovalex.bsky.social · Jul 18

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...

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...

www.jbc.org

Reposted by Alex Arzamasov

Lucy Crouch @lucyicm.bsky.social · Jul 18

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...

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...

www.biorxiv.org

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Alex Arzamasov @arzamasovalex.bsky.social · Jul 12

Is the original 1924 article publicly available somewhere?

Reposted by Alex Arzamasov

Rauf Salamzade @raufs.bsky.social · Jul 11

Great to see our manuscript on skDER & CiDDER - programs for selection of representative microbial genomes - now published.

Please give them a try and if you have any feature requests or issues, just let us know.

www.microbiologyresearch.org/content/jour...

github.com/raufs/skDER

skDER and CiDDER: two scalable approaches for microbial genome dereplication

An abundance of microbial genomes have been sequenced in the past two decades. For fundamental comparative genomic investigations, where the goal is to determine the major gain and loss events shaping...

www.microbiologyresearch.org

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Reposted by Alex Arzamasov

vdecrecy.bsky.social @vdecrecy.bsky.social · Jun 18

The discovery of the missing Queuosine transporter is finally out. 15 years in the making with a combination of data mining and experimental validation performed by an international consortium funded by NIH and Irish agencies.
news.ufl.edu/2025/06/micr...

UF, Trinity College team cracks micronutrient mystery that could be key to brain health, cancer defense

Unlocking how our bodies absorb a micronutrient that we rely on for everything from healthy brain function to cancer defense.

news.ufl.edu

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