Abraham Gihawi

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 ;-)

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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

📣 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 ⤵️

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 ...

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]

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.

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...

Many thanks to @danbrewer.bsky.social for your support and guidance through the years and to the other co-authors, funders, @genomicsengland.bsky.social and patients that made this work possible.

The landscape of microbial associations in human cancer Differences between cancer types, infectious disease, and potential prognostic markers are uncovered by studying microbes within cancer DNA.

We demonstrate some microbial patterns hold real clinical promise — from detecting infectious disease to uncovering potential prognostic markers.

Read more here 👉 www.science.org/doi/10.1126/...

Comprehensive analysis of microbial content in whole-genome sequencing samples from The Cancer Genome Atlas project An analysis of TCGA whole-genome sequencing samples yields a comprehensive resource for investigating the role of microbes in cancer.

We also see the same patterns in other datasets:
📊 PCAWG
📊 TCGA - Cleaner signals produced by a fantastic paper today from Peter Ge, @stevensalzberg.bsky.social & team)

www.science.org/doi/10.1126/...

The results hold up across methods:
✅ Conventional statistics
✅ Machine learning
✅ Dimensionality reduction

In our new paper, we dig into Genomics England’s 100,000 Genomes Project.

We find distinct microbial signals in colorectal cancer (and to a lesser extent oral cancer)

Some microbes are well known in cancer:
🦠 Hepatitis → liver cancer
🦠 HPV → cervical & oral cancers
But beyond these, can microbial DNA really help distinguish tumour types?

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

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.

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.

‘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...

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...

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...

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

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...

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...

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...
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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

This is important work for the exciting next stage of metagenomics #MicroSky

A natural experiment on the effect of herpes zoster vaccination on dementia - Nature Using a natural experiment that avoids common bias concerns, this study finds that the live-attenuated shingles vaccine reduced the probability of a new dementia diagnosis within a follow-up period of...

Very compelling study showing the association between herpes zoster vaccination and dementia prevention. The authors leveraged a unique cohort for this natural experiment which shows a reduction in dementia risk of 20% in vaccinated individuals. #MedSky #IDSky 🧪
www.nature.com/articles/s41...

If you generate, or use MAGs, you should really read the work we have done benchmarking their limitations. Using complex mock communities (70 species), we assessed how deeply you need to sequence to accurately conduct common metaG analyses. Webwere shocked to see even HQ MAGs are often chimeric!

🧫🧪 "Ten species comprise half of the bacteriology literature,
leaving most species unstudied."
'Model' gram - and gram + (Escherichia coli and Bacillus subtitles) + human pathogens
www.biorxiv.org/content/10.1...

CroCoDeEL: accurate control-free detection of cross-sample contamination in metagenomic data Metagenomic sequencing provides profound insights into microbial communities, but it is often compromised by technical biases, including cross-sample contamination. This underexplored phenomenon arise...

1/9 🚨 New preprint alert!

Frustrated by strange results with your metagenomic data?

Meet CroCoDeEL, an accurate, easy-to-use tool to detect and quantify cross-sample contamination—no need for negative controls or sample positions!

🔗 doi.org/10.1101/2025...

Today we report that an engineered skin bacterium, swabbed gently on the head of a mouse, can unleash a potent antibody response against a pathogen. Could lead to topical vaccines that are applied in a cream. @djenetbousbaine.bsky.social led the charge... @natureportfolio.bsky.social 1/55

This seems odd. A cancer microbiome machine learning paper that uses data from the retracted Poore et al. 2020 Nature paper has been published just last week in mSystems. Some of the claims seem very strong. Also, it seems to have been accepted four days after submission.

🧬 & 🖥️ #microbiome

This has been a long journey and I think it's the correct outcome. Thanks to everyone that has been involved, especially @abrahamgihawi.bsky.social who has been investigating this since his PhD days, and Steven Salzberg for really raising the analysis and awareness to another level.

🧬🖥️

Aggressive prostate cancer in African men: are microbes involved? Investigating decontamination, microbiomes and human genomics (BREWER_U24MMB) at University of East Anglia on FindAPhD.com PhD Project - Aggressive prostate cancer in African men: are microbes involved? Investigating decontamination, microbiomes and human genomics (BREWER_U24MMB) at University of East Anglia, listed on Fi...

Great PhD opportunity available with us. Bacteria, bioinformatics, lab work, ancestry, and prostate cancer. Fully funded for those eligible for UK fees. Deadline 15th April.

buff.ly/43AZD4k

@ueamedical.bsky.social
🧬🖥️🩺 #microbiome

Contact me or @abrahamgihawi.bsky.social for more details.

New review paper out today in Journal of Medical Biology "Cancer invasion and anaerobic bacteria: new insights into mechanisms". Great work by Rachel Hurst, with @abrahamgihawi.bsky.social, John Wain, and Colin Cooper.

doi.org/10.1099/jmm....

New paper by Pat Schloss about rarefaction is definitely worth a read for microbiome aficionados

journals.asm.org/doi/10.1128/...

Well... Depends on your audience I suppose!

We have a few good threads summarising key points:
twitter.com/AbrahamGihaw...

twitter.com/StevenSalzbe...

twitter.com/ProfBootyPhD...

Lots of errors stacking up. I'm actually hoping to give a talk at your institution in the next month or two!