Anna Cusco

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…

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.

At Handan campus, Fudan University, Shanghai.

Exploring the Great Wall near Beijing

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.

That sounds great, thanks for sharing!

BDB-Lab September 2025 Updates Dogs and other microbiomes

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...

Thanks Steven! :)

At Handan campus, Fudan University, Shanghai.

Exploring the Great Wall near Beijing

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.

The main characters of this story: the Shanghai pet dogs

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🐶

Screenshot of https://sh-dog-mags.big-data-biology.org/

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.

PCoA plot representing beta diversity (Bray-Curtis on log-transformed data).

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)

Comparison of the representative species-level genome assemblies: canine long-read MAGs vs. public database representative (RefSeq or GenBank).

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.

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%).

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.

Total number of MAGs per sample, stratified by quality. Almost all the high-quality MAGs fulfilled the MIMAG criteria.

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.

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🧬!

Sampling kit material for the Shanghai dog gut microbiome project

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)!

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...

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...

At Handan Campus, Fudan University, Shanghai.

Exploring the Great Wall near Beijing

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!

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 🐶

Screenshot of https://sh-dog-mags.big-data-biology.org/

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.

PCoA plot representing beta diversity (Bray-Curtis on log-transformed data). Green triangles indicate pet dogs in this study.

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)

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.

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).

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.

Shanghai dog catalogs: metagenome-assembled genomes & extrachromosomal elements

Shanghai dog MAG catalog: total number of MAGs per sample, stratified by quality. Almost all the high-quality MAGs fulfilled the MIMAG criteria.

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.

Project overview

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🧬!

Sampling material

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)!

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 - 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%.

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

Logo for the Sandpiper website

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...