It is crucial to be aware that infectious agents are an important preventable cause of #cancer globally. A new study provides a comprehensive picture of cancer burden attributable to infections. 🧪 #Science #Health 1- www.scientificamerican.com/article/one-... 2- www.thelancet.com/journals/lan...

Completely honoured to win the Research and Impact award at Norwich Medical School. It would not be possible without the supportive environment beside me. So thank you to everyone else in the community and congratulations to the other winners of the day!

Daniel Brewer@danbrewer.bsky.social · 3mo ago

Excellent day of prizes yesterday. First up, we have @abrahamgihawi.bsky.social who was awarded "Winner - Research and Impact" at the Norwich Medical School Staff Awards 2026.

Predicting oxygen levels in microbial habitats using a metagenome-based approach #microbiology #metagenomics #oxygen @asm.org doi.org/10.1128/msys...

Predicting oxygen levels in microbial habitats using a metagenome-based approach | mSystems

Oxygen is one of the most important environmental variables affecting microbial activity and composition, but is often difficult to measure in situ. We developed a tool, OxyMetaG, that leverages differences in bacterial gene content across known aerobic and anaerobic taxa to predict the oxygen level of a given sample directly from shotgun metagenomic reads. OxyMetaG works on samples with low sequencing depth and avoids computationally expensive genome assembly, which often captures only a fraction of the microbial community in a given environment. With OxyMetaG, bacteria can be used as bioindicators of oxygen availability over broader time scales than just a single measurement and provide crucial environmental context in cases where oxygen has not been or cannot be measured. OxyMetaG is publicly available and can be used to answer a wide variety of ecological questions in both environmental and host-associated systems.

doi.org

Nine (not so simple) steps: a practical guide to using machine learning in microbial ecology Step 1: Determine whether machine learning is necessary or even worth doing journals.asm.org/doi/10.1128/...

Nine (not so simple) steps: a practical guide to using machine learning in microbial ecology | mBio

Microbial ecologists are increasingly turning to machine learning (ML) models to better identify and predict meaningful biological patterns and relationships in molecular microbial community data (inc...

journals.asm.org

Rapid genomic data release and analysis from DRC and Uganda public health teams on Bundibugyo Ebola outbreak confirms new spillover: virological.org/t/initial-ge... - sequences shared via @pathoplexus.org

Initial genomes from May 2026 Bundibugyo Virus Disease Outbreak in the Democratic Republic of the Congo and Uganda

Initial genomes from May 2026 Bundibugyo Virus Disease Outbreak in the Democratic Republic of the Congo and Uganda, reveal a new spillover event Context On 15 May 2026, the Ministry of Public Health, ...

virological.org

In terms of what cures are being lost: - Epstein-Barr virus is perhaps the major trigger for multiple sclerosis - herpes simplex virus causes cold sores, genital herpes, infections in babies, deadly meningitis - shingles virus causes an intensely painful disease

Our new paper, where we use metabolic modeling to show Fusobacterium grows faster in colorectal tumor vs normal tissue microenvironments, and use computational + experimental approach to find specific metabolic pathways driving host-microbiome interactions in cancer www.biorxiv.org/content/10.6...

The time of day for cancer immunotherapy is associated with major outcomes. Early is better. Results from a randomized trial of lung cancer, backs up the importance of our circadian rhythm and immune system www.nature.com/articles/s41...

Breast milk isn't just nutrition – it delivers live bacterial strains that colonize the infant gut and persist for months. Happy to share our new paper, where we used metagenomics to track bacterial strains between 195 mother-infant pairs over the first 6 months of life: doi.org/10.1038/s414...

Assembly of the infant gut microbiome and resistome are linked to bacterial strains in mother’s milk - Nature Communications

Here, with metagenomic analyses on longitudinal samples collected from 195 mother-infant pairs, the authors show that the breast milk microbiome contributes to infant gut assembly through bacterial st...

doi.org

🚨🚨Publication alert🚨🚨 First paper of 2026! We review recent developments in molecular & genetic biomarkers in prostate cancer active surveillance. NIHR Clinical fellow Stephanie Smith @drstephsmith.bsky.social leading the charge. Open access 🧬👇 doi.org/10.3390/gene...

Tumor bacterial burden dictates immunotherapy fate in head & neck cancer @natcancer.nature.com www.nature.com/articles/s43... @clevelandclinic.bsky.social @mskcancercenter.bsky.social @mdanderson.bsky.social @xrtgenomics.bsky.social www.nature.com/articles/s43... www.nature.com/articles/s43...

Troubleshooting common errors in assemblies of long-read metagenomes - @merenbey.bsky.social @banfieldlab.bsky.social go.nature.com/44P7nSm

Troubleshooting common errors in assemblies of long-read metagenomes - Nature Biotechnology

Long-read sequence assemblies from metagenomes contain frequent errors.

go.nature.com

Use of Metagenomic Reference Materials to Compare Lysis and Extraction Methods Against a Known Input https://www.biorxiv.org/content/10.64898/2025.12.31.697245v1

Now out in @asm.org #mSystems! journals.asm.org/doi/10.1128/... Congratulations to Robert and thanks to all collaborators. See thread below for a summary of the work, exploring the use of cross-species coexpression analyses to predict primary and secondary metabolic interactions in microbiomes.

Using cross-species co-expression to predict metabolic interactions in microbiomes | mSystems

An improved mechanistic understanding of microbial interactions can guide targeted interventions or inform the rational design of microbial communities to optimize them for applications such as pathog...

journals.asm.org

Marnix Medema@marnixmedema.bsky.social · last yr.

New preprint out by #RobertKoetsier, the first of his PhD project, on assessing the use of cross-species coexpression analysis to identify primary and secondary metabolic interactions in microbiomes: www.biorxiv.org/content/10.1...

Yeeeesh

Willem van Schaik@wvschaik.bsky.social · 11mo ago

Wow 'MHRA-led study reveals major inconsistencies in global microbiome research' www.gov.uk/government/n... 'Species identification varied from 63% to 100% accuracy across different methods, meaning that some laboratories failed to detect a third of the bacterial species present in the sample'

“Bin Chicken” is now published in Nature Methods! It substantially improves genome recovery through rational coassembly 🧬🖥️. Applied to public 🌍 metagenomes, we recovered 24,000 novel species 🦠, including 6 new phyla. doi.org/10.1038/s415... @benjwoodcroft.bsky.social @rhysnewell.bsky.social 🧵1/6

Know metagenomics and could spare 2 mins? I'm applying for funding to build a visual repository for metagenomic classification data (not sequence data). To support the application, I have a short 2 minute survey and it would be a big help if you could fill it in: docs.google.com/forms/d/e/1F...

🚀 TaxSEA v1.2 is now live in #Bioconductor release 3.22! TaxSEA brings enrichment testing to #metagenomics data. Just like GSEA does for transcriptomics making #microbiome & #microbiota results biologically interpretable, fast, and reproducible. We've added new DBs & features in 1.2 👇 🧵

Dear community, Bakta needs your help! To further improve the functional annotation of "hypothetical" CDS, me and @gbouras13.bsky.social, we are looking for the worst Bakta-annotated bacterial genomes ;-) (1/2)

📣 Speakers announced for the Oral Tissue Collaborative (OTC) Symposium Register now to join either in person or online for the event on the future of oral tissue biorepositories 🗓️ 10 October Register by 3 October ⤵️

Oral Tissue Collaborative (OTC) Symposium: Building Excellence in Oral Tissue Biobanking - Quadram Institute

This symposium brings together leading experts, researchers, and practitioners in the field of oral tissue biobanking

buff.ly

Delighted to finally announce a preprint describing the Q100 project! “A complete diploid human genome benchmark for personalized genomics” For which we finished HG002 to near-perfect accuracy: www.biorxiv.org/content/10.1... 🧵[1/14]

A complete diploid human genome benchmark for personalized genomics

Human genome resequencing typically involves mapping reads to a reference genome to call variants; however, this approach suffers from both technical and reference biases, leaving many duplicated and ...

biorxiv.org

Spacedust: a tool for de novo identification of conserved gene clusters from metagenomic data. @ruoshiz.bsky.social @milot.bsky.social www.nature.com/articles/s41...

De novo discovery of conserved gene clusters in microbial genomes with Spacedust - Nature Methods

This work presents Spacedust, a tool for de novo identification of conserved gene clusters from metagenomic data.

nature.com

Finding microbes in cancer sequencing data has been controversial. Are we seeing real biology… or just contamination + batch effects?

Two papers in today's issue of @nature.com ‬: 1) we assemble 65 genomes to near completion, including centromeres and the MHC. tinyurl.com/3huhax6w. 2) we sequence 1,019 genomes from the 1kGP with long reads, revealing SVs down to low allele frequencies tinyurl.com/wbx3we9x.

Complex genetic variation in nearly complete human genomes - Nature

Using sequencing and haplotype-resolved assembly of 65 diverse human genomes, complex regions including the major histocompatibility complex and centromeres are analysed.

tinyurl.com

About 18 months ago we held a @microbiologysociety.org meeting in Glasgow to discuss the thorny topic of #microbial #taxonomy and #nomenclature - and now you can read what we talked about :D #microbiology #controversy doi.org/10.1099/ijse...

‘What’s in a name? Fit-for-purpose bacterial nomenclature’: meeting report

Rapid and economical DNA sequencing has resulted in a revolution in phylogenomics. The impact of changes in nomenclature can be perceived as an absolute necessity of scientific rigour, coupled with th...

doi.org

Hope this is useful - consensus statement "Guidelines for preventing and reporting contamination in low-biomass microbiome studies" rdcu.be/er3Io

Guidelines for preventing and reporting contamination in low-biomass microbiome studies

Nature Microbiology - In this Consensus Statement, the authors outline strategies for processing, analysing and interpreting low-biomass microbiome samples, and provide recommendations to minimize...

rdcu.be

I'm happy to announce the latest release of the GlobDB, available at globdb.org. The GlobDB is a database of "species dereplicated" microbial genomes, and as of release 226 contains twice the number of species-representative genomes (306,260) than the latest GTDB release.

BakRep – a searchable large-scale web repository for bacterial genomes, characterizations and metadata www.microbiologyresearch.org/content/jour... 🧬🖥️ Nextflow code: github.com/ag-computati...

New preprint! Autocycler is a tool for long-read consensus assembly of bacterial genomes. It's like Trycycler but can be run fully automated (without any human intervention). www.biorxiv.org/content/10.1... (1/6)

Autocycler: long-read consensus assembly for bacterial genomes

Motivation Long-read sequencing enables complete bacterial genome assemblies, but individual assemblers are imperfect and often produce sequence-level and structural errors. Consensus assembly using T...

biorxiv.org

The human pangenome continues to grow and improve! Release 2 is here! Click through for the details, but this is a pretty amazing dataset including not just the phased assemblies, but PacBio HiFi, ONT Ultralong, Dovetail/Illumina Hi-C, PacBio Kinnex, and Illumina WGS for all samples

Human Pangenome Reference Consortium@humanpangenome.bsky.social · last yr.

📢 HPRC Release 2 is here! Now with phased genomes from 200+ individuals, a 5x increase from Release 1. Explore sequencing data, assemblies, annotations & alignments in our interactive data explorer ⬇️: humanpangenome.org/hprc-data-re...