@bigdatabiology.bsky.social
New paper led by Daniel Howard & Simon Phipps: why breastfeeding protects infants against severe lung infections. Milk osteopontin reshapes the infant gut microbiome → Lactobacillaceae → phenyllactic acid → dendritic cell development in liver & lung → disease tolerance doi.org/10.1016/j.ce...
Redirecting
doi.org
It's out! Excited to present the Great Barrier Reef Microbial Genomes Database (GBR-MGD), a comprehensive DB of 1000s of high-quality prokaryote, virus, plasmid, and chromosome-level eukaryote MAGs using Nanopore long reads. Subthreads incoming. Please share widely. 🙂 www.nature.com/articles/s41...
The planktonic microbiome of the Great Barrier Reef - Nature
The Great Barrier Reef Microbial Genomes Database compiles prokaryotic, viral and eukaryotic genomes from seawater collected from the Great Barrier Reef, providing a rich resource for the study of mar...
nature.com
We updated our companion website to the elusive resistome paper to be more responsive (it's 100% client side now) You can generate all the alternative plots that we could not get into the paper: arg-pipelines.big-data-biology.org
ARG Pipeline Explorer — The Elusive Resistome
Interactive companion to "The elusive resistome": compare 10 antibiotic-resistance-gene detection pipelines across 13 habitats and 278M genes.
arg-pipelines.big-data-biology.org
New newsletter with updates from the group! Focus is on Juan's preprint on the elusive resistome bigdatabiology.substack.com/p/updates-fo...
BDB-Lab June 2026 Updates
The elusive resistome and upcoming travel/conferences
bigdatabiology.substack.com
A bit delayed announcement, but we recently released SemiBin 2.30! No big new features, but it contains a large number of small fixes and improvements (include having had all major LLMs audit and improve the code) bioconda & pypi packages have been updated too github.com/BigDataBiolo...
Release Version 2.3.0 · BigDataBiology/SemiBin
This release bundles a large number of bug fixes (several of which fix silent correctness issues in training and clustering), removes the deprecated SemiBin1 command, and includes many documentatio...
github.com
This is an incredibly relevant preprint. Your favourite pipeline and/or AMR gene database cannot be considered authoritative, but neither can others.
@bigdatabiology.bsky.social · 3mo agoHow well do ARG detection pipelines agree when applied to the same data? Spoiler: not very well. In our new preprint, we ran 10 pipelines on 270M microbial unigenes from GMGCv1. The same data can support conflicting biological conclusions! 🧵 www.biorxiv.org/content/10.6...
How well do ARG detection pipelines agree when applied to the same data? Spoiler: not very well. In our new preprint, we ran 10 pipelines on 270M microbial unigenes from GMGCv1. The same data can support conflicting biological conclusions! 🧵 www.biorxiv.org/content/10.6...
The elusive resistome: a global comparison reveals large discrepancies among detection pipelines
Identifying antibiotic resistance genes (ARGs) from metagenomic data is critical for studying antimicrobial resistance across microbial communities and pathogens. However, there is no standardized methodology for ARG annotation. Here, we compare ten commonly used ARG detection pipelines by analysing over 270 million prokaryotic genes from the Global Microbial Gene Catalogue across 13 distinct habitats. We observed up to a 45-fold difference in the number of reported ARGs, with a mean Jaccard index of only 16% between pipelines. Pipeline selection profoundly impacted downstream biological interpretations, with drastic changes to estimates of ARG relative abundance and richness, to the characterization of pan- and core-resistomes, and to the class-level composition of the inferred resistome. ARG detection pipelines make different, defensible trade-offs, and no single approach should be treated as authoritative. Therefore, users should justify and communicate choices carefully, as our analyses show that, taken uncritically, the same data can support conflicting biological and ecological interpretations. ### Competing Interest Statement The authors have declared no competing interest. National Health and Medical Research Council of Australia (NHMRC), 2031902 Australian Research Council (ARC), FT230100724 International Development Research Centre (IDRC), 109304-001 Deutsche Forschungsgemeinschaft (DFG), FO1279/6-1 Bundesministerium für Bildung und Forschung (BMBF), F01KI1909A, 01KI2404B Swedish Research Council (VR), 2024-06123, 2019-00299, 2023-01721 Knut and Alice Wallenberg Foundation, KAW 2020.0239 Swedish Foundation for Strategic Research, FFL21-0174
biorxiv.org
The elusive resistome: a global comparison reveals large discrepancies among detection pipelines https://www.biorxiv.org/content/10.64898/2026.05.11.724158v1
Our work on 'hidden diversity' in unbinned contigs is now published in @natmicrobiol.nature.com : www.nature.com/articles/s41... See the linked threads for more details!
Unbinned contigs expand known diversity in the global microbiome - Nature Microbiology
Re-analysis of over 92,000 metagenomes reveals hundreds of thousands of previously undescribed Bacterial and Archaeal clades hidden in plain sight.
nature.com
Sebastian Schmidt@tsbschm.bsky.social · 9mo agoWe've updated our recent @biorxivpreprint.bsky.social on 'Hidden but discoverable diversity in the global microbiome', led by @vishnuprasoodanan.bsky.social & @omaistrenko.bsky.social www.biorxiv.org/content/10.1...
Urban soils are a small part of the world and lack the glamour of the wilderness or the economic importance of agriculture, but as most people live in cities, they are very important Our latest preprint using long-read metagenomics reveals massive hidden diversity and function in city soils 🧵
Quarterly updates from the group! Focus is our latest work on urban soil microbiomes. They are far richer than might be expected. Our latest work using long-read metagenomics reveals massive hidden diversity and function in city soils bigdatabiology.substack.com/p/bdb-lab-ma...
BDB-Lab March 2026 Updates
What lurks in urban soil microbiomes
bigdatabiology.substack.com
We released GMSC-mapper v0.2.0! GMSC-mapper queries the Global Microbial smORFs Catalog to find and annotate small proteins from metagenomic data github.com/BigDataBiolo...
GitHub - BigDataBiology/GMSC-mapper
Contribute to BigDataBiology/GMSC-mapper development by creating an account on GitHub.
github.com
Jug 2.5.0 is out! Jug is a Python framework for parallel & reproducible computation. Write plain Python, run it across many processes or machines with no message-passing code. pip install jug --upgrade (Or use the conda-forge packages with conda/pixi)
New Year updates from the group with a focus on Anil Pokhrel who is working on metagenomics for food security! bigdatabiology.substack.com/p/bdb-lab-ja...
BDB-Lab January 2026 Updates
New Year!
bigdatabiology.substack.com
It's time for the 2025 Gibbons Lab Research Roundup! Yeehaw! 🤠 @isbscience.org In these dark times, let the joy of scientific discovery and trainee success be your balm ❤️🩹 🧵...
Today I had the pleasure of meeting the 🇵🇹 Microbiome HD Lab Great to see Bich Ngoc Do's work on the Portuguese gut resistome data using argNorm (github.com/BigDataBiolo... by @bigdatabiology.bsky.social). Impressive, methodical research! @anasalmeida.bsky.social thank you for the invitation!
🔬 Call to create junior research groups at the Institut Pasteur Focus: Infectious diseases, host-microbe interactions, vaccines Special interest: AI methodologies 📅 Deadline: Feb 9, 2026 👥 2-12 years post-PhD Apply now 📝 research.pasteur.fr/en/call/crea... #JobOpportunity #Research
Creation of new junior research groups at the Institut Pasteur - Call for applications 2026 - Research
The Institut Pasteur is launching an international call to recruit new junior research group leaders leveraging cutting-edge transdisciplinary approaches to exploring infectious diseases, host-microbe...
research.pasteur.fr
New version of macrel released (v1.6.0) The biggest change is internal, using a much better approach to saving and loading models (thus removing the dependency on particular versions of scikit-learn) A few other bugfixes were included github.com/BigDataBiolo...
GitHub - BigDataBiology/macrel: Predict AMPs in (meta)genomes and peptides
Predict AMPs in (meta)genomes and peptides. Contribute to BigDataBiology/macrel development by creating an account on GitHub.
github.com
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 🐶
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
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...
biorxiv.org
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
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...
New paper in collaboration with the @asantoslopez.bsky.social lab! www.biorxiv.org/content/10.1...
Plasmids promote antimicrobial resistance through Insertion Sequence-mediated gene inactivation
Antimicrobial Resistance (AMR) is a major threat to public health. Plasmids are mobile genetic elements that can rapidly spread across bacterial populations, promoting the dissemination of AMR genes i...
biorxiv.org
Jorge Sastre Domínguez@jorgesastred.bsky.social · 12mo agoNew paper out! 🔈🔈📣📣 Plasmids promote antimicrobial resistance through Insertion Sequence-mediated gene inactivation. Combining experimental and computational approaches, we unveil how two of the most prevalent bacterial MGE accelerate the evolution of AMR. 🧵👇🏻 www.biorxiv.org/content/10.1...
Quarterly updates from the Lab! This June, the focus is on Alexandre Areias Castro, who is working on metabolic modeling of the microbiome with the aim of giving us a new view on microbial composition, focused of "functional roles" instead of taxonomy bigdatabiology.substack.com/p/bdb-lab-up...
New version of argNorm! Will be available frombioconda & funcscan in the next few days We fixed how NCBI genes were being handled. It is a fundamentally more principled way and should fix a few corner cases (particularly if data has been run through hARMonization) pypi.org/project/argn...
argnorm
Normalize antibiotic resistance genes (ARGs) results by using the ARO ontology (developed by CARD).
pypi.org
Anyone from Europe wants to spend 2 years in sunny Queensland working on the global microbiome? Get in touch (even if all you have right now is a vague idea, just email early)! We also have a lot of friends in Europe for the return phase. marie-sklodowska-curie-actions.ec.europa.eu/calls/msca-p...
MSCA Postdoctoral Fellowships 2025
MSCA Postdoctoral Fellowships enhance the creative and innovative potential of researchers holding a PhD and who wish to acquire new skills through advanced training, international, interdisciplinary ...
marie-sklodowska-curie-actions.ec.europa.eu
