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Reposted by Anna Cusco

Svetlana Ugarcina Perovic @svetlanaup.bsky.social · 6d

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

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Reposted by Anna Cusco

Anna Cusco @annacusco.bsky.social · 15d

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.

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Anna Cusco @annacusco.bsky.social · 13d

That sounds great, thanks for sharing!

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Reposted by Anna Cusco

bigdatabiology.bsky.social @bigdatabiology.bsky.social · 14d

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

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Anna Cusco @annacusco.bsky.social · 14d

Thanks Steven! :)

Anna Cusco @annacusco.bsky.social · 15d

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.

3 4

Anna Cusco @annacusco.bsky.social · 15d

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 · 15d

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 · 15d

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 · 15d

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 · 15d

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 · 15d

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 · 15d

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 · 15d

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 · 15d

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...

www.biorxiv.org

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Anna Cusco @annacusco.bsky.social · 15d

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!

1 1

Anna Cusco @annacusco.bsky.social · 15d

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 🐶

1

Anna Cusco @annacusco.bsky.social · 15d

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.

1

Anna Cusco @annacusco.bsky.social · 15d

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.

1

Anna Cusco @annacusco.bsky.social · 15d

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.

1

Anna Cusco @annacusco.bsky.social · 15d

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).

1

Anna Cusco @annacusco.bsky.social · 15d

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 elements

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

1

Anna Cusco @annacusco.bsky.social · 15d

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🧬!

1

Anna Cusco @annacusco.bsky.social · 15d

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)!

1 1

Reposted by Anna Cusco

Luis Pedro Coelho @luispedrocoelho.bsky.social · 20d

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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