Anna Cusco
@annacusco.bsky.social
Microbiome scientist | Metagenomics | Long-read sequencing Postdoc at Big Data Biology Lab
. @annacusco.bsky.social welcomed Sarah Ahannach, Sandra Condori Catachura and Josiane Kenfack and had a rich conversation on collaboration, sisterhood, and #WomensHealth research! Thanks to @tosina.bsky.social, Marianna Bergamaschi, Merel van Gogh, and the podcast team. #CitizenScienceMonth 2/2
NEW #MVIFconversations: Episode 4 is about Isala – The power of sisterhood! ▶️ Spotify: open.spotify.com/episode/5Spk... ▶️ Amazon music: music.amazon.com/podcasts/81c... ▶️ Apple Music: podcasts.apple.com/us/podcast/m... ▶️ YouTube podcast: youtu.be/IsKTzFOs0J0 1/2
Episode 4 - Sarah Ahannach, Sandra Condori & Josiane Kenfack: “ISALA: The power of sisterhood"
Spotify video
open.spotify.com
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.
October 3, 2025
See you at the MVIF 42! Human gut microbiomeMicro-scale spatial metagenomics: revealing high-resolution spatial biogeography of gut microbiomes – Carlotta Pietroni – bioRxiv Animal microbiomeCaptur…
microbiomedigest.com
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...
BDB-Lab September 2025 Updates
Dogs and other microbiomes
bigdatabiology.substack.com
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...
Capturing global pet dog gut microbial diversity and hundreds of near-finished bacterial genomes by using long-read metagenomics in a Shanghai cohort
Pet dogs are considered part of the family, and understanding their gut microbiomes can provide insights into both animal and household health. Most comprehensive studies, however, relied on short-rea...
biorxiv.org
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
Genome-resolved long-read sequencing expands known microbial diversity across terrestrial habitats - Nature Microbiology
Nanopore sequencing of Danish soils and sediments yields genomes from over 15,000 microbial species, expanding the phylogenetic diversity of prokaryotes by 8%.
nature.com
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
Lyrebird (phage profiling)
Documentation for SingleM
wwood.github.io
argNorm is published now academic.oup.com/bioinformati...
argNorm: normalization of antibiotic resistance gene annotations to the Antibiotic Resistance Ontology (ARO)
AbstractSummary. Currently available and frequently used tools for annotating antimicrobial resistance genes (ARGs) in genomes and metagenomes provide resu
academic.oup.com
Svetlana Ugarcina Perovic@svetlanaup.bsky.social · 2y agoHey #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
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
Cassyni | Science starts with a seminar
Seamlessly organise, run and publish academic research seminars. Get started in minutes.
cassyni.com
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
GenomeFISH: genome-based fluorescence in situ hybridisation for strain-level visualisation of microbial communities
Fluorescence in situ hybridisation (FISH) is a powerful tool for visualising the spatial organisation of microbial communities. However, traditional FISH has several limitations, including limited p...
doi.org
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...
Why are bioinformatics results so full of false positives?
It's what the incentives
luispedro.substack.com
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
Survey: “A roadmap for fair reuse of public microbiome data”
This survey will inform a manuscript titled “A roadmap for fair reuse of public microbiome data”, the abstract of which and core figure (Figure 1) are included below. The manuscript in its current...
tinyurl.com
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!
Extremely Open Science Part 1 : introduction
#science #presentationLuis Pedro Coelho introduces the Extremely Open Science Project for 2024Links:- https://www.big-data-biology.org/extremely-open-science...
youtu.be
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...
A catalogue of small proteins from the global microbiome
bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution
biorxiv.org
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)
GitHub - BigDataBiology/argNorm: ARG normalization by mapping to the ARO ontology.
ARG normalization by mapping to the ARO ontology. Contribute to BigDataBiology/argNorm development by creating an account on GitHub.
github.com