Excited to share our new study out in Nature Communications. We mapped the composition of the human breast #milk #microbiome and showed that microbes present in breast milk directly contribute to the assembly of the #infant gut microbiome in the first months of life. www.nature.com/articles/s41...

Unique bifunctional α-sialidase/β-N-acetylgalactosaminidase from Bifidobacterium bifidum acting on the Sda antigen www.jbc.org/article/S002... #microsky #microbiomesky

Our new paper on high-throughput isolation of Bifidobacterium just got published! A very nice adventure starting with the supervision of @lamhaiha.bsky.social, a talented intern, and a nice collab with our BSight expert @isaacyueyuan.bsky.social! Stay tuned for more isolation and Bifido work! :)

💾 Prokka 1.15.6 is released! This is the last major release of Prokka. But don't be sad, because @oschwengers.bsky.social already has an excellent replacement called Bakta you can migrate to. #bioinformatics #microbiology #genomics github.com/tseemann/pro...

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 www.pnas.org/doi/10.1073/...

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...

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!

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 🧵👇

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...

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...

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

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...

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

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...

A great blog post by @math-rachel.bsky.social on this preprint describing failures of an ML approach for gene annotation: rachel.fast.ai/posts/2025-0... www.biorxiv.org/content/10.1... "how challenging (or even impossible) it can be to evaluate AI claims in work outside our own area of expertise"

I often flag genomic predictions of SCFA production that clash with “textbook” data. But sometimes it’s the experimental claims that raise eyebrows. This recent paper reports propionate (!) and butyrate (!!) production by Bif. longum ssp. infantis (it shouldn't make either doi.org/10.3168/jds....

Great resource! A small note on Bifidobacterium hominis: the description mentions "predicted starch utilization and propionate production", but bifidobacteria don’t produce propionate, and this species lacks extracellular alpha-amylases for starch degradation. Hope this can be refined in the future!

Diversity and prevalence of Anaerostipes in the human gut microbiota https://www.biorxiv.org/content/10.1101/2025.05.01.651700v1

I got hit by some rather sudden and extreme financial hardship so if anyone is in need of remote wetlab contract research, strictly BSL1, do let me know. Currently scrambling for gigs. Plant, Bacterial, Archaeal Non-model Bioeng Custom Lab Hardware Turn Key Genetic Design Please repost for reach 💚

Small amounts of misassembly can have disproportionate effects on pangenome-based metagenomic analyses journals.asm.org/doi/full/10.... #jcampubs

I am very happy (and anxious) to share with you our most recent work in which we evaluated four of the most popular long-read assemblers, www.biorxiv.org/content/10.1... and tell you just a little bit about it in the following 🧵

GTDB release 10 based on RefSeq 226 (R10-RS226) is live at gtdb.ecogenomic.org. This release covers 732,475 genomes (22% increase) and has 143,6141 species clusters (37% increase). Release notes at: forum.gtdb.ecogenomic.org/t/announcing.... Release statistics at: gtdb.ecogenomic.org/stats/r226.

Nice paper led by Aruto Nakajima (Katayama lab) that provides mechanistic insights on 2'-fucosyllactose (2'FL) and other HMO utilization by Clostridium perfringens. There also some cool data on in vitro competition for 2'FL with different Bifidobacterium species www.tandfonline.com/doi/full/10....

DNA-utilization loci enable exogenous DNA metabolism in gut Bacteroidales https://www.biorxiv.org/content/10.1101/2025.03.18.642099v1

Interested in the influence of the infant microbiome on health? Quickly interrogating non-model organisms using omic approaches? A new publication, describing genome-scale resources in bifidobacteria, is now available online: doi.org/10.1016/j.ce... #microbiome #microsky

New insights into the substrate-specificity of transporters in Bifidobacterium longum subsp. infantis

Very important work showing that many human gut bacteria can metabolize various human milk oligosaccharides (HMOs)

Super excited to share our latest research on how HMOs shape the post-weaned gut microbiota! Huge thanks to our incredible team, this wouldn’t have been possible without their dedication and expertise @emmaallen-vercoe.bsky.social @drlarsbode.bsky.social

Difficult to focus on science during these times, but if you have the bandwidth, our study on zol is now out in NAR: academic.oup.com/nar/article/... GitHub: github.com/Kalan-Lab/zol Please give the software a try and let us know if you have any feedback! And stay tuned for new features...

New paper out today from the lab on Akkermansia muciniphila 🦠and how it breaks down host glycans! Very proud of my group, especially @cassiebakshani.bsky.social who did an amazing job. @naturemicrobiol.bsky.social www.nature.com/articles/s41...

Selective utilization of medicinal polysaccharides by human gut Bacteroides and Parabacteroides species #microbiomesky #microsky

Characterization of Bifidobacterium bifidum growth and metabolism on whey protein phospholipid concentrate #micobiomesky #microsky www.sciencedirect.com/science/arti...

New specific comment on the use of newer scientific names for species. TL;DR a reminder that once a name is validly published, it can always be used. You don't *have* to use a new name just because someone published it. zenodo.org/records/1461...

Tungsten is utilized for lactate consumption and SCFA production by a dominant human gut microbe Eubacterium limosum #microsky #microbiomesky www.pnas.org/doi/10.1073/...

Very nice study on polysaccharide utilization in Segatella copri #microbiomesky #microsky journals.asm.org/doi/full/10....

Check out this 1 min video on using zol + cgcg for scalable visualization of evo info across 1000s of homologous gene cluster instances (e.g. BGCs, phages, plasmids, defense islands, etc.) as network graphs. Github: github.com/Kalan-Lab/zol Docs: github.com/Kalan-Lab/zo... #secmet #phage #genomics

Nice to see such a large proteomic dataset from the human gut. However, certain functional annotation results seem odd to me. E.g., Bacteroides thetaiotaomicron does not produce butyrate; Bifidobacterium longum does not produce propionate and vitamin B5 (1/2)

Not all gum arabic structures are the same. The study describes the degradation mechanism of gum arabic from Acacia seyal by Bifidobacterium catenulatum subsp. catenulatum www.sciencedirect.com/science/arti...

Degradation mechanism of difructose dianhydride III in Blautia species link.springer.com/article/10.1...

Happy to share a preprint with the results of my PhD work on creating a comprehensive genomic encyclopedia of carbohydrate metabolism in human-colonizing bifidobacteria. TL;DR: there's tons of variability. A thread with results (1/) www.biorxiv.org/content/10.1...

I was reading this new review about human milk oligosaccharide (HMO) utilization strategies by various gut bacteria (including bifidobacteria) and noticed some errors on which I want to comment, mainly because they persist in the literature (1/7)