New #MicrobiomeDigest is OUT microbiomedigest.com/2025/10/02/o... • Shanghai dog microbiome / @annacusco.bsky.social • microbetag / @hariszaf.bsky.social • invitation for the #MVIF 42 / @microbiomevif.bsky.social & more.

If you made it this far, thanks for reading. I hope you enjoyed it. I am currently looking for my next research adventure. If you have insights on the microbiome/microbial genomics job market in Europe (academia & industry), or want to chat about this work, please reach out.

September 2025 updates! A focus on Anna's preprint, but several other updates too, including Faith Adegoke joining us to work on AMR and several other preprints bigdatabiology.substack.com/p/bdb-lab-se...

Finally, the results of my postdoc at the @bigdatabiology.bsky.social lab in Shanghai see the light! The work includes my three favorite things research-wise: 🦠 microbiome, 🧬 long-reads, and 🐶 dogs. See our new preprint: www.biorxiv.org/content/10.1...

Full thread will come later, but @annacusco.bsky.social's preprint on the dog pet gut microbiome is out! Using ONT+Illumina, we get better MAGs than to corresponding species representative in public databases doi.org/10.1101/2025...

Capturing global pet dog gut microbial diversity and hundreds of near-finished bacterial genomes by using long-read metagenomics in a Shanghai cohort https://www.biorxiv.org/content/10.1101/2025.09.17.676595v1

Genome-resolved long-read sequencing expands known microbial diversity across terrestrial habitats www.nature.com/articles/s41... #jcampubs

Out in @natbiotech.nature.com: Metagenome taxonomy profilers usually ignore unknown species. SingleM is an accurate profiler which doesn't, even detecting phyla with no MAGs. Profiles of 700,000 metagenomes at sandpiper.qut.edu.au. A 🧵

First code release of "SingleM for dsDNA phage"! Lyrebird scans metagenomic reads for marker genes to give a “phage community profile”. It detects many novel phages, many more than standard contig-centric methods. @benjwoodcroft.bsky.social @emerge-bii.bsky.social wwood.github.io/singlem/Lyrebird

argNorm is published now academic.oup.com/bioinformati...

Dominant taxa in microbiomes are obviously important but here's a discussion on low abundance taxa that are highly persisting/prevalent. We can see a lot of these in metagenomics, often obscured by a high false negative rate. 🔗 www.sciencedirect.com/science/arti...

#MVIF.37 is LIVE in the Pacific time-zones! Let's talk about Microbiome! The speakers are will be live for Q&A. Join at: cassyni.com/s/mvif-3 Today's backstage team: @aroneys.bsky.social @annacusco.bsky.social @pamferretti.bsky.social @azufre451.bsky.social @kruthirao.bsky.social @JoseCaparros

We are looking for PhD students! Fully funded studentships available to work on a range of topics, from small proteins to developing computational tools to study the global microbiome

Excited to share GenomeFISH: genome-based fluorescence in situ hybridisation for strain-level visualisation of microbial communities. @sjmcilroy.bsky.social, @benjwoodcroft.bsky.social, @jamesvolmer.bsky.social doi.org/10.21203/rs.... 🧵1/6

It's Wednesday! ...and #MVIF 34 program is out! 🤩 ⭐️MicroTalks: 🇹🇼 Ha T. Doan 🇦🇺 Vedanth Ramji ⭐️ Keynote: 🇺🇸 Sean Gibbons @gibbological.bsky.social ⭐️Selected talks: 🇯🇵 Yuya Kiguchi 🇦🇺 Kurtis Budden 🇨🇭 Amit Halkhoree (#Roche) Registration: cassyni.com/s/mvif-34

Wow, Bluesky really took off in the last couple of days! The first microbiome starter pack is full now and I started a second one with non-overlapping profiles. Check out these people below and please let me know if you would like to be included! go.bsky.app/6vPBEty

Hi everyone, I tried assembling a Microbiome & friends starter pack. 🦠🧫🔬 Still learning to use bluesky and might have missed you, let me know if you would like to be included. go.bsky.app/Fq36egy

I made a starter pack to help recent emigrees from Twitter If you're on it and don't want to be I will happily remove you go.bsky.app/H5k2p2g

Why are bioinformatics results so full of false positives? I've been thinking about this for a few years: the incentives in the field are to produce false positives luispedro.substack.com/p/why-are-bi...

Hey #AMR people, the argNorm preprint is now available on #QUT ePrints: eprints.qut.edu.au/252448 We* designed a tool for normalizing ARG annotations across currently popular tools & dbs. *@svetlanaup.bsky.social Vedanth Ramji Hui Chong Yiqian Duan Finlay Maguire @luispedrocoelho.bsky.social 1/6

Please share: Are you a data creator/user in #metagenomics or other #omics? We’re working on standards for fair data reuse and would like your feedback. We welcome contributions by scientists from all career stages. 5-min anonymous survey here: tinyurl.com/y5kwytpd

New experiment: I will work on a project (starting question: what antibiotic resistance genes co-occur in genomes/metagenomes and does it matter?) completely in the open Everyone is welcome!

New preprint: A catalogue of small proteins from the global microbiome! As part of our ongoing efforts to understand small proteins in prokaryotes, we catalogued almost 1 billion sequences! www.biorxiv.org/content/10.1...

More diverse microbiome communities provide protection against infection, but how? New paper in Science shows this is achieved by nutrient blocking -- diverse communities will consume all the nutrients an incoming pathogen needs to colonize www.science.org/doi/10.1126/...

New release of argNorm This is a little tool to map ARG (antibiotic resistance gene) annotations from different tools to the same common ontology (ARO from CARD)