Looking forward
13–15 October: Luis will be in Houston for the SMBE Satellite Meeting: Evolutionary Biochemistry of Insect Antimicrobial Peptides.
23-24 October: Luis will be at the Queensland Immunology Networking Symposium.
15-18 December: Luis will be at the 19th International Conference on Data and Text Mining in Biomedical Informatics (DTMBIO 2025) in Muju, Republic of Korea.
If you are at any of these events, please come and say Hi!
Focus of the Quarter: long-read metagenomics on Shanghai pet dogs by Anna Cuscó
The Shanghai Dog Gut microbiome project was first featured in the BDB newsletter in January 2023. At that time, I had just received my own funding from the National Natural Science Foundation of China (RFIS-I grant). The main idea was to explore the gut microbiome of Shanghai pet dogs using long-read metagenomics —a project that combined three of my favorite research themes: microbiomes, long-reads, and dogs. The main results have now been released as a preprint:
Capturing global pet dog gut microbial diversity and hundreds of near-finished bacterial genomes by using long-read metagenomics in a Shanghai cohort by Anna Cuscó, Yiqian Duan, Fernando Gil, Alexei Chklovski, Nithya Kruthi, Shaojun Pan, Sofia Forslund, Susanne Lau, Ulrike Löber, Xing-Ming Zhao, and Luis Pedro Coelho (bioRxiv preprint 2025)
We collected 51 fecal samples from Shanghai pet dogs and deeply sequenced each of them —20 Gbp of short-read and at least 20 Gbp of long-read data per sample. We also gathered information about the dogs’ environment, lifestyle, and other characteristics through owner questionnaires.
Here are a few results that I want to highlight:
We present a catalog of 2,676 MAGs from Shanghai dogs: ~72% were near-finished quality (high-quality regarding MIMAG criteria1) and highly contiguous. Additionally, we present a catalog of 185 circular extrachromosomal elements like plasmids and viruses, from the same dogs.
Our Shanghai dog catalogs proved to be globally representative: over 90% of reads from pet dog cohorts in Germany, South Africa2, and the USA3 mapped to them.
In general, our species-level MAG representatives were more contiguous and presented 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.
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 mapping results to our catalogs: we observed higher mapping rates for pet dog cohorts compared to non-pet dog cohorts.
All the generated data and resources are freely available. You might want to start by checking our Shanghai Dog MAG Catalog website, which is aimed at visually exploring the MAGs. Each entry has MAG basic information, ARGs annotation, and even 16S rRNA genes linked to MicrobeAtlas entries. Everything, including extrachromosomal elements, smORFs, gene catalogs, annotation files, is available on a Zenodo repository.
This project has been quite a journey from start to finish, and I am happy to finally share the results with the scientific community. As I complete my international postdoc in China, I am now preparing for my next career step in Europe, with a strong interest in applied research in microbiome or microbial genomics. Thus, if you have insights into opportunities in academia or industry, or if you would simply like to exchange ideas about this work, I would be glad to connect. You can reach me directly, or find me on LinkedIn or Bluesky.
Other updates
People
Faith Adegoke joined our group as a PhD student. Faith will be supervised by Luis & Juan and will work on as part of the SEARCHER project. Her research is focused on investigating the proximity of mobile genetic elements to antibiotic resistance genes to better understand their genetic context. Her work will develop computational methods for risk categorisation of these genes. Welcome, Faith!
Preprints
Beyond Anna’s dog preprint (focus of the quarter), we posted several preprint this quarter.
Abundance Estimation for Metagenomic Binning (AEMB) preprint by Shaojun Pan is now posted on bioRxiv! This describes functionality available on SemiBin2 and strobealign to make abundance estimation much faster.
Antimicrobial resistance in wastewater preprint “Persistence of High‑Risk Antimicrobial Resistance Genes in Extracellular DNA Along an Urban Wastewater‑River Continuum”, led by former lab member John P. Makumbi, is online on SSRN. It describes how extracellular DNA may play a role in the transmission of antibiotic resistance genes.
Microbial consensus manuscript, “A census of hidden and discoverable microbial diversity beyond genome-centric approaches” co-authored by Luis, was deposited on bioRxiv. We show that we are not getting close to saturation in terms of how much microbial diversity there is in the world.
Software & Tools
argNorm v1.1.0 released: This update adds genomic RefSeq IDs to NCBI mappings and adopts accession-only matching. Thus, reduces inconsistencies in gene names and one-to-many ARO mappings. As a reminder, argNorm maps results from multiple antibiotic resistance tools to a common ontology, see (Ugarcina Perovic, Ramji, et al., Bioinformatics, 2025).
We released SPIREpy-a Python package and command-line tool to interact with SPIRE: Searchable Planetary-scale mIcrobiome REsource4 and a partner tool to interact with ProGenomes.
Talks & Presentations
14-17 July: Anna presented a poster on long‑read metagenomics of Shanghai pet dogs at FEMS Micro Milan.
20–24 July: Luis presented an abstract on dog gut microbiome work at “ISMB/ECCB 2025: Intelligent Systems for Molecular Biology & European Conference on Computational Biology.”
17–22 August: Luis was a speaker at Decoding Microproteins Across Evolution and Disease, Gordon Research Conference.
9 September: Luis presented at mVIF: Cataloging the global microbiome. Very big data for small things
16–19 September: Luis delivered a talk at the EMBL Human Microbiome Symposium.
High-quality regarding MIMAG criteria means >90% completeness, <5% contamination, the presence of ribosomal genes, and at least 18 out of 20 tRNAs. See Bowers, R. M. et al. Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea. Nat. Biotechnol. 35, 725–731 (2017)
Data from Yarlagadda, K. et al. Geographically diverse canid sampling provides novel insights into pre-industrial microbiomes. Proc. R. Soc. B. 289, 20220052 (2022).
Data from Tanprasertsuk, J. et al. Heterogeneity of gut microbial responses in healthy household dogs transitioning from an extruded to a mildly cooked diet. PeerJ 9, e11648 (2021).
Thomas S B Schmidt, et al., SPIRE: a Searchable, Planetary-scale mIcrobiome REsource, Nucleic Acids Research, Volume 52, Issue D1, 5 January 2024, Pages D777–D783.
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