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| Item Type: | Preprint |
|---|---|
| Title: | Capturing global pet dog gut microbial diversity and hundreds of near-finished bacterial genomes by using long-read metagenomics in a Shanghai cohort |
| Creators: |
Cusco, Anna  ORCID: https://orcid.org/0000-0002-9574-5755, Duan, Yiqian ORCID: https://orcid.org/0000-0002-8046-9831, Gil, Fernando, Chklovski, Alexei, Kruthi, Nithya ORCID: https://orcid.org/0000-0002-4149-0400, Pan, Shaojun, Forslund, Sofia ORCID: https://orcid.org/0000-0003-4285-6993, Lau, Susanne ORCID: https://orcid.org/0000-0002-5189-4265, Löber, Ulrike ORCID: https://orcid.org/0000-0001-7468-9531, Zhao, Xinmging and Coelho, Luis Pedro ORCID: https://orcid.org/0000-0002-9280-7885
|
| Abstract: | 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-read sequencing, resulting in fragmented MAGs that miss mobile elements, antimicrobial-resistance genes, and ribosomal genes. Here, we applied deep long-read metagenomics (polished with short-reads) to fecal samples from 51 urban pet dogs in Shanghai, generating 2,676 MAGs—representing 320 bacterial species—, of which ∼72% achieved near-finished quality, often improving on the corresponding reference public genome. Comparisons with external datasets showed that our Shanghai-based MAG catalog is representative of pet dogs worldwide (median read mapping of >90%). Moreover, we recovered circular extrachromosomal elements, including those linked to antimicrobial resistance, which were also detected in external dog gut datasets. In conclusion, we provide a high-quality reference resource and demonstrate the power of deep long-read metagenomics to resolve microbial diversity in complex host-associated microbiomes. |
| Keywords: | Animals, Dogs |
| Source: | bioRxiv |
| Publisher: | Cold Spring Harbor Laboratory Press |
| Article Number: | 2025.09.17.676595 |
| Date: | 17 September 2025 |
| Official Publication: | https://doi.org/10.1101/2025.09.17.676595 |
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