Unfalsifiable by Design: A Year of Trying and Failing to Reproduce a Human Microbiome and Autism Study The myth of open data, reproducibility, responsibility, and accountability in science, and your role in it

How every layer of science's "self-correcting machinery" failed when Iva Veseli and I simply wanted to reproduce the findings of a high-profile study on gut microbiome and autism:

merenlab.org/2026/04/15/u...

Changes in antimicrobial resistance profiles of Escherichia coli and the metagenome on Dutch pig farms after antimicrobial usage interventions - npj Antimicrobials and Resistance npj Antimicrobials and Resistance - Changes in antimicrobial resistance profiles of Escherichia coli and the metagenome on Dutch pig farms after antimicrobial usage interventions

Just out in npj Antimicrobials & Resistance @natureportfolio.nature.com

www.nature.com/articles/s44...

We looked at what actually happens to AMR on pig farms when you reduce antimicrobial use through real-world, coaching-based interventions.

This is from 7 years ago (merenlab.org/2019/02/24/f...). We are talking about the same things today. We will be talking about the same things 7 years from now. There is no one to blame for this apart from ourselves. I find it very depressing.

Comprehensive benchmarking of metagenomic binning tools reveals key factors for improved genome recovery - Nature Communications Benchmarking metagenomic binning tools with simulated and real datasets reveals factors affecting genome recovery and provides practical guidelines for improving metagenome assembled genome reconstruc...

Comprehensive benchmarking of metagenomic binning tools reveals key factors for improved genome recovery www.nature.com/articles/s41... #jcampubs

Big win for South Norfolk: we’re getting HALF of England’s new dental training places.

I’ve raised this in Parliament and directly with ministers. After years of being overlooked, we are now front of the queue.

South Norfolk voted for change in 2024 and Labour has listened. More to come.

Don’t know why but I read it in trump’s voice in my head

Kagi (premium)

Systematic detection of abnormal samples reveals widespread mislabeling in metagenomic studies The human microbiome plays a critical role in health and disease, and its dynamic nature has made longitudinal sampling a key strategy for elucidating microbiome disease relationships. Although the gut microbiome generally stabilizes over time, a subset of samples frequently shows marked deviations from an individual baseline profile. We refer to these as abnormal samples. To analyze these abnormal samples, we developed a three stage workflow to identify and classify these abnormal samples to figure out the underlying causes of these abnormal samples. Moreover, we systematically investigated abnormal samples across 16 publicly available metagenomic datasets, comprising a total of 5,171 metagenomes. Our analysis revealed that abnormal samples are often the result of mislabeling during sample collection, processing, or sequencing. Of which, fecal samples from family are more likely mislabeled. We found evidence of mislabeling in 75% of longitudinal datasets, involving up to dozens of samples per study, and in 25% of randomly selected cross sectional datasets. Additional factors such as disease status (e.g., inflammatory bowel disease), sampling intervals, and sampling density may also contribute to sample abnormalities owing to true biological variations. These findings highlight that mislabeling is a common yet underrecognized issue in microbiome research. Our work underscores the importance of identifying and correcting abnormal samples to ensure data integrity in microbiome studies and provides a practical solution for quality control in large scale metagenomic datasets. ### Competing Interest Statement The authors have declared no competing interest. National Key R&D Program of China, 2024YFC3405800 General Program of the Natural Science Foundation of Fujian Province, 2023Y9116, 2024J01577 Government of Fuqing city, 2019B003 High-level Talents Research Start-up Project of Fujian Medical University, XRCZX2020037, XRCZX2022001, XRCZX2023030, XCRZX2023004, XRCZX2023005

Systematic detection of abnormal samples reveals widespread mislabeling in metagenomic studies | bioRxiv www.biorxiv.org/content/10.64898/2026.03...

The paper is about Excel spreadsheets, where I think it makes sense :)

YYYY-DD-MM is horrible, but YYYY-MM-DD (ISO 8601) is alphabetically sortable as string so it's a pass for me

Applications are open now!

You'll also benefit from the supervisory expertise of the brilliant Dipali Singh and @telatin.bsky.social

#mmbdtp #norwich #uea

A virus hiding inside bacteria may help explain colorectal cancer Scientists found an unexpected viral hitchhiker lurking inside a common gut bacterium – and it was twice as prevalent in people with colorectal cancer.

Scientists found an unexpected viral hitchhiker lurking inside a common gut bacterium – and it was twice as prevalent in people with colorectal cancer.

BRIG v1.0.0 Released — BLAST Ring Image Generator

This is dedicated to Joe Healey Who asked me many years ago to round up the version number to v1.

BRIG creates circular comparison images showing sequence similarity between a reference genome and multiple query sequences as concentric rings — […]

Interested in developing your skills in microbial 'omics? Consider joining us in Brest 🇫🇷, Oct. 10-24 for two weeks of intensive lectures an tutorial from top faculties and TA! maignienlab.gitlab.io/ebame/
Bonus: beautiful seascape and friendly spirit!

A Systematic Benchmark of Antibiotic Resistance Gene Detection Tools for Shotgun Metagenomic Datasets www.biorxiv.org/content/10.64898/2026.02...

RETRACTED: Integrative phylogenomics positions sponges at the root of the animal tree Determining whether sponges or ctenophores root the animal tree has important implications for understanding early animal evolution. Here, we examined support for these competing hypotheses by constru...

This is a beautiful case of how real science happens & serious scientists work. Kudos to both set of authors: “This has been a humbling experience, but one that speaks to the self-correcting nature of the scientific endeavor.” www.science.org/doi/10.1126/...

The preprint is available at www.biorxiv.org/content/10.6...

The bioinformatic method (Nextflow) is available at: workflowhub.eu/workflows/2080

ℹ Takeaway 1: sequencing depth and community complexity matter a lot. At low or uneven coverage, all tools struggle — even the ones we like and use ourselves.

ℹ Takeaway 2: speed vs sensitivity vs precision is a trade-off.
Some tools are fast and conservative.
Others are more sensitive but heavier.

💡 We also tried to control things that usually get mixed together:
– same unified ARG database for all the tools
– simulated data where we know what’s present
– coverage and complexity varied one at a time

That lets us see patterns, not absolutes.

Our goal wasn’t to crown a winner.

🔍 We asked a narrower question: how do different approaches behave when coverage and complexity change?

Each tool makes different trade-offs by design.

Metagenomic 💊 AMR detection is a genuinely hard problem.
Low coverage, uneven abundance, similar genes, and complex communities all make “ground truth” slippery.

So if results differ across tools, that’s often expected, not a failure.

How well do current tools detect antimicrobial resistance genes in metagenomes?

@sumeet-tiwari.bsky.social & team benchmarked 5 widely used methods across different sequencing coverages and community complexities, highlighting trade-offs between accuracy and computational cost.

UK ‘could lose generation of scientists’ with cuts to projects and research facilities UK’s research funding body says best scientists are taking posts overseas due to lack of job stability at home

More on the UKRI/STFC funding squeeze.
Significant quote: “It is clear that no UK university will want to open lecturer positions in curiosity-driven research if such lecturers would not be able to attract much national funding." KCL's Lucien Heurtier.

www.theguardian.com/science/2026...

Hugging Face – The AI community building the future. We’re on a journey to advance and democratize artificial intelligence through open source and open science.

Super excited to announce the release of gene and intergenic region annotation from the largest bacterial genome and MAG datasets available, including AllTheBacteria, GTDB, SPIRE, HRGM, mOTUs and MGnify - dereplicated and available from HuggingFace huggingface.co/AllTheBacteria

Washington Post lays off hundreds of staff after BEZOS wastes 75 MILLIONS on Melanias flop documentary

Information, gone. 👋

Important study highlighting the need for rigorous quality control during sequencing and the value of analyzing sequence read depth variation in assemblies.

Accurate plasmid reconstruction from metagenomics data using assembly–alignment graphs and contrastive learning - Nature Biotechnology PlasMAAG uses cross-sample information to improve plasmid reconstruction from metagenomic samples.

Accurate plasmid reconstruction from metagenomics data using assembly–alignment graphs and contrastive learning www.nature.com/articles/s41... #jcampubs

💻 Join us next week for Nextflow Training Week (Feb 9-13) - free online training for those new to @nextflow.io or looking to reinforce the basics.

👉 Register here: hubs.la/Q041v13y0

SeqFu dev - preview of `seqfu less` [coming with 1.24.0] YouTube video by Andrea Telatin

Meet seqfu less

youtu.be/e77tXBM6fRs?...

A social card with the text, "Senior Research Scientist Microbiome Assay and Metaproteomics, to support with day-to-day running of the Figeys lab, including line management, overseeing budgets and scientific direction. Salary: £45,450 to £56,750, Contract length: 2 years, Apply by 15 February 2026."

🆕 Vacancy! We are looking for a Senior Research Scientist to support with day-to-day running of @dfigeys.bsky.social lab, including line management of staff, overseeing budgets, and leading the scientific direction.

💷 £45,450 to £56,750
🗓️ Apply by 15 February 2026
➡️ buff.ly/UpcuEPa