Anna Cusco
@annacusco.bsky.social
Microbiome scientist | Metagenomics | Long-read sequencing
Postdoc at Big Data Biology Lab
Postdoc at Big Data Biology Lab
Pinned
Anna Cusco
@annacusco.bsky.social
· Sep 23
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...
www.biorxiv.org
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...
@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...
Reposted by Anna Cusco
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.
• 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
October 2, 2025 at 12:40 PM
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.
• Shanghai dog microbiome / @annacusco.bsky.social
• microbetag / @hariszaf.bsky.social
• invitation for the #MVIF 42 / @microbiomevif.bsky.social
& more.
Reposted by Anna Cusco
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.
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 23, 2025 at 11:24 AM
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.
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.
Reposted by Anna Cusco
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...
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
September 24, 2025 at 4:55 AM
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...
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...
@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...
www.biorxiv.org
September 23, 2025 at 11:24 AM
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...
@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...
Reposted by Anna Cusco
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...
Using ONT+Illumina, we get better MAGs than to corresponding species representative in public databases
doi.org/10.1101/2025...
September 18, 2025 at 12:01 PM
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...
Using ONT+Illumina, we get better MAGs than to corresponding species representative in public databases
doi.org/10.1101/2025...
Reposted by Anna Cusco
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
September 18, 2025 at 6:17 AM
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
Reposted by Anna Cusco
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%.
www.nature.com
July 24, 2025 at 12:55 PM
Genome-resolved long-read sequencing expands known microbial diversity across terrestrial habitats www.nature.com/articles/s41... #jcampubs
Reposted by Anna Cusco
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 🧵
July 16, 2025 at 9:59 PM
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 🧵
Reposted by Anna Cusco
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
May 16, 2025 at 10:55 AM
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
Reposted by Anna Cusco
argNorm is published now academic.oup.com/bioinformati...
April 17, 2025 at 4:57 AM
argNorm is published now academic.oup.com/bioinformati...
Reposted by Anna Cusco
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...
🔗 www.sciencedirect.com/science/arti...
March 31, 2025 at 1:26 AM
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...
🔗 www.sciencedirect.com/science/arti...
Reposted by Anna Cusco
#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
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
March 20, 2025 at 1:06 AM
#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
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
Reposted by Anna Cusco
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
Fully funded studentships available to work on a range of topics, from small proteins to developing computational tools to study the global microbiome
March 17, 2025 at 6:30 AM
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
Fully funded studentships available to work on a range of topics, from small proteins to developing computational tools to study the global microbiome
Reposted by Anna Cusco
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
@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
December 19, 2024 at 5:17 PM
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
@sjmcilroy.bsky.social, @benjwoodcroft.bsky.social, @jamesvolmer.bsky.social
doi.org/10.21203/rs....
🧵1/6
Reposted by Anna Cusco
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
...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
November 20, 2024 at 8:57 AM
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
...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
Reposted by Anna Cusco
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
Check out these people below and please let me know if you would like to be included!
go.bsky.app/6vPBEty
November 13, 2024 at 1:56 AM
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
Check out these people below and please let me know if you would like to be included!
go.bsky.app/6vPBEty
Reposted by Anna Cusco
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
🦠🧫🔬
Still learning to use bluesky and might have missed you, let me know if you would like to be included.
go.bsky.app/Fq36egy
October 19, 2024 at 4:09 PM
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
🦠🧫🔬
Still learning to use bluesky and might have missed you, let me know if you would like to be included.
go.bsky.app/Fq36egy
Reposted by Anna Cusco
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
If you're on it and don't want to be I will happily remove you
go.bsky.app/H5k2p2g
September 24, 2024 at 9:15 PM
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
If you're on it and don't want to be I will happily remove you
go.bsky.app/H5k2p2g
Reposted by Anna Cusco
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...
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
September 18, 2024 at 11:57 PM
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...
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...
Reposted by Anna Cusco
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
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
October 10, 2024 at 7:56 AM
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
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
Reposted by Anna Cusco
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
January 16, 2024 at 3:49 PM
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
Reposted by Anna Cusco
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!
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
January 15, 2024 at 8:53 AM
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!
Everyone is welcome!
Reposted by Anna Cusco
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...
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
www.biorxiv.org
December 29, 2023 at 3:01 AM
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...
As part of our ongoing efforts to understand small proteins in prokaryotes, we catalogued almost 1 billion sequences!
www.biorxiv.org/content/10.1...
Reposted by Anna Cusco
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 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/...
December 15, 2023 at 4:56 PM
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 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/...
Reposted by Anna Cusco
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)
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
December 20, 2023 at 9:09 AM
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)
This is a little tool to map ARG (antibiotic resistance gene) annotations from different tools to the same common ontology (ARO from CARD)