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Reposted by Abraham Gihawi

Oliver Schwengers @oschwengers.bsky.social · 2d

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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Reposted by Abraham Gihawi

Quadram Institute @quadraminstitute.bsky.social · 13d

📣 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

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Reposted by Abraham Gihawi

Adam Phillippy @aphillippy.bsky.social · 15d

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 ...

www.biorxiv.org

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Nature Methods @natmethods.nature.com · 22d

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.

www.nature.com

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Abraham Gihawi @abrahamgihawi.bsky.social · Sep 3

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.

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Abraham Gihawi @abrahamgihawi.bsky.social · Sep 3

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/...

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.

www.science.org

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Abraham Gihawi @abrahamgihawi.bsky.social · Sep 3

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/...

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.

www.science.org

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Abraham Gihawi @abrahamgihawi.bsky.social · Sep 3

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

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Abraham Gihawi @abrahamgihawi.bsky.social · Sep 3

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)

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Abraham Gihawi @abrahamgihawi.bsky.social · Sep 3

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?

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Abraham Gihawi @abrahamgihawi.bsky.social · Sep 3

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

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Reposted by Abraham Gihawi

Tobias Marschall @tobiasmar.bsky.social · Jul 23

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

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Leighton Pritchard @widdowquinn.bsky.social · Jul 23

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

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Noah Fierer @noahfierer.bsky.social · Jun 21

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

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Reposted by Abraham Gihawi

Daan Speth @daanspeth.bsky.social · Jun 10

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.

home | GlobDB

globdb.org

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Stephen Turner @stephenturner.us · Jun 4

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

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Reposted by Abraham Gihawi

Ryan Wick @rrwick.bsky.social · May 21

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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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...

www.biorxiv.org

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Reposted by Abraham Gihawi

Adam Phillippy @aphillippy.bsky.social · May 12

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 · May 12

📢 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...

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Mike Lee @astrobiomike.org · Apr 28

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

Florian Trigodet @floriantrigodet.bsky.social · Apr 28

I am very happy (and anxious) to share with you our most recent work in which we evaluated four of the most popular long-read assemblers,

www.biorxiv.org/content/10.1...

and tell you just a little bit about it in the following 🧵

Assemblies of long-read metagenomes suffer from diverse errors

Genomes from metagenomes have revolutionised our understanding of microbial diversity, ecology, and evolution, propelling advances in basic science, biomedicine, and biotechnology. Assembly algorithms...

www.biorxiv.org

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BK. Titanji @boghuma.bsky.social · Apr 2

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...

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...

www.nature.com

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Tom Hitch @tcahitch.bsky.social · Mar 28

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!

bioRxivpreprint @biorxivpreprint.bsky.social · Mar 28

Benchmarking of shotgun sequencing depth highlights strain-level limitations of metagenomic analysis https://www.biorxiv.org/content/10.1101/2025.03.27.645659v1

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Allan Konopka @hamatsa50.bsky.social · Mar 6

🧫🧪 "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...

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Reposted by Abraham Gihawi

Guillaume GAUTREAU @guigau.bsky.social · Jan 20

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...

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...

doi.org

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Michael Fischbach @mfgrp.bsky.social · Dec 11

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

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Daniel Brewer @danbrewer.bsky.social · Dec 2

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

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