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Anna Cusco

@annacusco.bsky.social
763 followers 803 following 22 posts

Microbiome scientist | Metagenomics | Long-read sequencing Postdoc at Big Data Biology Lab

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Reposted by Anna Cusco
Microbiome Virtual International Forum @microbiomevif.bsky.social · 27/04/2026
. @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
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Microbiome Virtual International Forum @microbiomevif.bsky.social · 27/04/2026
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
open.spotify.com
Episode 4 - Sarah Ahannach, Sandra Condori & Josiane Kenfack: “ISALA: The power of sisterhood"
Spotify video
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Svetlana Ugarcina Perovic @svetlanaup.bsky.social · 02/10/2025
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.
microbiomedigest.com
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…
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Reposted by Anna Cusco
Anna Cusco @annacusco.bsky.social · 23/09/2025
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.
At Handan campus, Fudan University, Shanghai.Exploring the Great Wall near Beijing
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Anna Cusco @annacusco.bsky.social · 25/09/2025
That sounds great, thanks for sharing!
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Reposted by Anna Cusco
bigdatabiology.bsky.social @bigdatabiology.bsky.social · 24/09/2025
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...
bigdatabiology.substack.com
BDB-Lab September 2025 Updates
Dogs and other microbiomes
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Anna Cusco @annacusco.bsky.social · 24/09/2025
Thanks Steven! :)
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Anna Cusco @annacusco.bsky.social · 23/09/2025
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.
At Handan campus, Fudan University, Shanghai.Exploring the Great Wall near Beijing
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Anna Cusco @annacusco.bsky.social · 23/09/2025
I would like to thank all co-authors: Yiqian Duan, Fernando Gil, Alexei Chklovski, Nithya Kruthi, Shaojun Pan, Sofia Forslund, Susanne Lau, Ulrike Löber, Xing-Ming Zhao, and especially @luispedrocoelho.bsky.social And of course, all the dog owners and the main characters of this story🐶
The main characters of this story: the Shanghai pet dogs
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Anna Cusco @annacusco.bsky.social · 23/09/2025
All the generated data and resources are publicly available. You can play around with the Shanghai dog MAG catalog here: sh-dog-mags.big-data-biology.org where we added MAG basic information, ARGs annotation, and linked the 16S rRNA genes to MicrobeAtlas. More data at Zenodo & ENA.
Screenshot of https://sh-dog-mags.big-data-biology.org/
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Anna Cusco @annacusco.bsky.social · 23/09/2025
Using global dog gut microbiome data, we found that the living environment (household, colony, free-roaming) was the strongest factor shaping the gut microbiome composition. (This is consistent with the mapping results: higher mapping rates for pet dog vs. non-pet dog cohorts)
PCoA plot representing beta diversity (Bray-Curtis on log-transformed data).
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Anna Cusco @annacusco.bsky.social · 23/09/2025
In general, our species-level MAG representatives were more contiguous and had a higher quality than the reference genome assembly in public databases —especially regarding the presence of rRNA and mobile genetic elements, which are often missed in short-read assemblies.
Comparison of the representative species-level genome assemblies: canine long-read MAGs vs. public database representative (RefSeq or GenBank).
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Anna Cusco @annacusco.bsky.social · 23/09/2025
Our Shanghai dog catalogs proved to be globally representative🌍: over 90% of reads (median value) from pet dog cohorts in Germany, South Africa, and the USA mapped to them.
The Shanghai dog MAG catalog captures the majority of the microbial diversity of other pet dog cohorts living in households (median read mapping of >90%).
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Anna Cusco @annacusco.bsky.social · 23/09/2025
Let's go to some of the main messages: 🧬We recovered 2,676 MAGs from Shanghai dogs, ~72% were near-finished (high-quality regarding MIMAG criteria) & highly contiguous. ⭕We recovered 185 circular extrachromosomal elements like plasmids and viruses from the same dogs.
Total number of MAGs per sample, stratified by quality. Almost all the high-quality MAGs fulfilled the MIMAG criteria.
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Anna Cusco @annacusco.bsky.social · 23/09/2025
Each stool sample was deeply sequenced 🐶💩: 20 Gbp Illumina short-reads + (at least) 20 Gbp Nanopore long-reads per dog. That's a substantial throughput for assembling MAGs from complex metagenomes🧬!
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Anna Cusco @annacusco.bsky.social · 23/09/2025
We started by sharing questionnaires via WeChat 📲 and then collected 💩 samples from 51 pet dogs across Shanghai 🐶. Along the way, we met many doggies (& their humans)!
Sampling kit material for the Shanghai dog gut microbiome project
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Anna Cusco @annacusco.bsky.social · 23/09/2025
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...
biorxiv.org
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...
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Anna Cusco @annacusco.bsky.social · 23/09/2025
If you made it this far, thanks for reading. I hope you enjoyed the thread. I am currently looking for my next research adventure. If you have insights on the microbiome/microbial genomics🧬🦠 job market in Europe (academia and industry), or want to chat about this work, please reach out!
At Handan Campus, Fudan University, Shanghai.Exploring the Great Wall near Beijing
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Anna Cusco @annacusco.bsky.social · 23/09/2025
I would like to thank all co-authors: Yiqian Duan, Fernando Gil, Alexei Chklovski, Nithya Kruthi, Shaojun Pan, Sofia Forslund, Susanne Lau, Ulrike Löber, Xing-Ming Zhao, and especially @luispedrocoelho.bsky.social And of course, all the dog owners and the main characters of this story 🐶
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Anna Cusco @annacusco.bsky.social · 23/09/2025
All the generated data and resources are publicly available. You can play around with the Shanghai dog MAG catalog here: sh-dog-mags.big-data-biology.org where we have added MAG basic information, ARGs annotation, and linked 16S rRNA genes to MicrobeAtlas. More data at Zenodo and ENA.
Screenshot of https://sh-dog-mags.big-data-biology.org/
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Anna Cusco @annacusco.bsky.social · 23/09/2025
Using global dog gut microbiome data, we found that the living environment (household, colony, free-roaming) was the strongest factor shaping the gut microbiome composition. (This is consistent with previous mapping results to our catalog: higher mapping rates for pet dog vs. non-pet dog cohorts)
PCoA plot representing beta diversity (Bray-Curtis on log-transformed data). Green triangles indicate pet dogs in this study.
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Anna Cusco @annacusco.bsky.social · 23/09/2025
In general, our species-level MAG representatives were more contiguous and had a higher quality than the reference genome assembly in public databases —especially regarding the presence of rRNA and mobile genetic elements, which are often missed in short-read assemblies.
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Anna Cusco @annacusco.bsky.social · 23/09/2025
Our Shanghai dog catalogs proved to be globally representative🌍: over 90% of reads (median value) from pet dog cohorts in Germany, South Africa, and the USA mapped to them.
The Shanghai dog catalogs capture the majority of the microbial diversity of other pet dog cohorts living in households (median read mapping of >90%). The mapping is lower for non-pet cohorts (colony, shelter, or free-roaming dogs).
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Anna Cusco @annacusco.bsky.social · 23/09/2025
Let's go to some of the main messages: 🧬We recovered 2,676 MAGs from Shanghai dogs, ~72% were near-finished (high-quality regarding MIMAG criteria) and highly contiguous. ⭕Additionally, we retrieved 185 circular extrachromosomal elements like plasmids and viruses from the same dogs.
Shanghai dog catalogs: metagenome-assembled genomes & extrachromosomal elementsShanghai dog MAG catalog: total number of MAGs per sample, stratified by quality. Almost all the high-quality MAGs fulfilled the MIMAG criteria.
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Anna Cusco @annacusco.bsky.social · 23/09/2025
Each stool sample was deeply sequenced 🐶💩: 20 Gbp Illumina short-reads + (at least) 20 Gbp Nanopore long-reads per dog. That's a substantial throughput for assembling MAGs from complex metagenomes🧬!
Project overview
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Anna Cusco @annacusco.bsky.social · 23/09/2025
We started by sharing questionnaires via WeChat 📲 and then collected 💩 samples from 51 pet dogs across Shanghai 🐶. Along the way, we met many doggies (& their humans)!
Sampling material
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Reposted by Anna Cusco
Luis Pedro Coelho @luispedrocoelho.bsky.social · 18/09/2025
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...
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Reposted by Anna Cusco
bioRxiv Microbiology @biorxiv-microbiol.bsky.social · 18/09/2025
Capturing global pet dog gut microbial diversity and hundreds of near-finished bacterial genomes by using long-read metagenomics in a Shanghai cohort www.biorxiv.org/content/10.1101/202…
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Reposted by Anna Cusco
Cameron Thrash @jcamthrash.bsky.social · 24/07/2025
Genome-resolved long-read sequencing expands known microbial diversity across terrestrial habitats www.nature.com/articles/s41... #jcampubs
nature.com
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%.
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Ben J Woodcroft @benjwoodcroft.bsky.social · 16/07/2025
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 🧵
Logo for the Sandpiper website
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Rossen Zhao @rossenzhao.bsky.social · 16/05/2025
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
wwood.github.io
Lyrebird (phage profiling)
Documentation for SingleM
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Svetlana Ugarcina Perovic @svetlanaup.bsky.social · 17/04/2025
argNorm is published now academic.oup.com/bioinformati...
academic.oup.com
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
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Guillaume Méric @gmeric.bsky.social · 31/03/2025
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...
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Microbiome Virtual International Forum @microbiomevif.bsky.social · 20/03/2025
#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.com
Cassyni | Science starts with a seminar
Seamlessly organise, run and publish academic research seminars. Get started in minutes.
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bigdatabiology.bsky.social @bigdatabiology.bsky.social · 17/03/2025
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
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Pam Engelberts @pam-engelberts.bsky.social · 19/12/2024
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
doi.org
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...
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Microbiome Virtual International Forum @microbiomevif.bsky.social · 20/11/2024
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
mvif program december 2024
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Jan Claesen @claesengroup.bsky.social · 13/11/2024
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
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Anna Cusco @annacusco.bsky.social · 15/11/2024
Great resource, thanks Jan! I would like to be included, as well :) I work in animal-associated microbiomes, with a focus on dog microbiomes.
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Jan Claesen @claesengroup.bsky.social · 19/10/2024
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
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Binning Singletons @binningsingletons.com · 24/09/2024
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
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Luis Pedro Coelho @luispedrocoelho.bsky.social · 19/09/2024
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...
luispedro.substack.com
Why are bioinformatics results so full of false positives?
It's what the incentives
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Svetlana Ugarcina Perovic @svetlanaup.bsky.social · 10/10/2024
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
argnorm
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Roland Hatzenpichler @environmicrobio.bsky.social · 16/01/2024
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
tinyurl.com
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...
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Luis Pedro Coelho @luispedrocoelho.bsky.social · 15/01/2024
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!
youtu.be
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...
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Luis Pedro Coelho @luispedrocoelho.bsky.social · 29/12/2023
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...
biorxiv.org
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
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Ran Blekhman @blekhman.bsky.social · 15/12/2023
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/...
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Luis Pedro Coelho @luispedrocoelho.bsky.social · 20/12/2023
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.com
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.
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