Happy New Year – new role! 🎉 We’re looking for a PostDoc to join us in @halllab.bsky.social @unibirmingham.bsky.social. Full-time, fixed-term to March 2028. Note tight closing date: 11 Jan 2026. CV + cover letter (submit via portal). Further details 👇 edzz.fa.em3.oraclecloud.com/hcmUI/Candid...

Research Fellow - Department of Microbes, Infection and Microbiomes - 106849 - Grade 7

To create and contribute to the creation of knowledge by undertaking a specified range of activities as part of an Investigator project funded by Wellcome, focusing on understanding microbial and diet...

edzz.fa.em3.oraclecloud.com

8/ Authored by Aldert Zomer, Sam Nooij, Cailean Carter, and Alison Mather (@alisonmather.bsky.social). Supported by the JPIAMR MEGAISurv project: jpiamr.eu/projects/meg... Thanks to all contributing to strengthening mutation-focused AMR surveillance in metagenomic data.

7/ The code is open-source, with both a web-based interface and the full repository available: Web tool: klif.uu.nl/metapointfin... GitHub: github.com/aldertzomer/... Feedback on extending reference sets and integrating the approach into surveillance pipelines is welcome.

6/ We applied the tool to public datasets on fluoroquinolone, β-lactam, and rifamycin resistance, showing how mutation-level profiling resolves discrepancies between phenotypes and gene-only predictions.

5/ In benchmarks using simulated reads (100–5000 bp), MetaPointFinder outperformed existing mutation mappers and showed strong recovery of mutation-positive reads, particularly from long-read metagenomes.

4/ The outputs enable calculation of both relative abundance of mutation-driven AMR and the proportion of resistant reads among all reads mapping to a locus (WT + R). Metrics can be summarised at read, gene, or antibiotic-class level, extending metagenomic resistome profiling beyond gene presence.

3/ MetaPointFinder performs read-level protein and DNA alignment (DIAMOND + KMA) against curated AMRFinder mutation references. A custom scoring engine evaluates each substitution, enabling accurate detection across both long- and short-read datasets.

2/ In metagenomic data, most AMR tools detect only acquired genes, while point mutations in gyrA, parC, folA, rpoB, 23S rRNA and others are major drivers of resistance. These variants are rarely quantified because they require precise alignment and position-specific evaluation.

1/ Our preprint on MetaPointFinder is online: www.biorxiv.org/content/10.6... Current resistome profiling has a major gap: it misses mutation-driven AMR, even though chromosomal mutations underpin resistance to key antimicrobials. MetaPointFinder addresses this at the read level in metagenomes.

A new tool we’ve developed to identify AMR-associated SNPs in short- and long-read metagenome data….allows a greater understanding of the total resistome of a sample

Aldert Zomer@aldertzomer.bsky.social · 8mo ago

MetaPointFinder: A new approach for detecting mutation-driven antimicrobial resistance directly from metagenomic reads. Fills a major gap in current resistome profiling by capturing chromosomal AMR mutations that metagenome tools miss. github.com/aldertzomer/...

🆕 We’re looking for a motivated candidate to investigate whether differences in E. coli types increase risk of UTIs in pregnancy. This will help inform better patient care 🧪 🗓️ Apply by 6 January 2025 ➡️https://buff.ly/sFpuQWo @alisonmather.bsky.social

🆕We’re looking for a motivated candidate to examine drivers and evolutionary factors influencing antimicrobial resistance in pigs from Brazil🐖 🗓️ Apply by 6 January 2025 ➡️https://buff.ly/sFpuQWo @alisonmather.bsky.social

📣Call for abstracts — WBF 2026, Session NEX5: “Microbial communities as One Health drivers.” Davos, 14–19 Jun 2026. Community-level mechanisms, AMR & practical interventions (experimental/computational/interventional). Deadline: 18 Nov 2025 → tinyurl.com/4un5a8a4 #OneHealth #Microbiome #AMR

Was great to put the dream team back together for a commentary on this with @alisonmather.bsky.social very cool study on AMR flow through food production chains in Europe www.nature.com/articles/s41...

From farm to factory to fork - Nature Microbiology

A recent study has examined the flow of antimicrobial resistance genes in food production using nearly 2,000 metagenomes, indicating a potential role for contamination in processing facilities.

nature.com

Nature Microbiology@natmicrobiol.nature.com · last yr.

#NewResearch 'The food-associated resistome is shaped by processing and production environments' by @nmquijada.bsky.social and co-workers. #MicroSky 🦠 www.nature.com/articles/s41...

🎓 #PhDPosition ! 🤰 Understanding the relationship between the maternal microbiome and fetal growth restriction with Professor Mark Webber @webberma.bsky.social and Professor Alison Mather @alisonmather.bsky.social 📅Apply by Monday 14 April ➡️ buff.ly/QL3JFtg

Starting the new year with a new pre-print from the Hall Lab @halllab.bsky.social looking at the impact of empirical antibiotics on gut microbiome and resistome of both probiotic and non-probiotic supplemented VLBW preterm infants: www.biorxiv.org/content/10.1... #resistome #amr #microbiome #preterm

Impact of early life antibiotic and probiotic treatment on gut microbiome and resistome of very-low-birth-weight preterm infants

Preterm infants (<37 weeks’ gestation) are often administered broad-spectrum antibiotics in hospitals due to their vulnerability to severe morbidity, including necrotising enterocolitis and sepsis. Ho...

biorxiv.org

I just made a first release of TNA - new tool to compare 2 bacterial genomes. Is shamelessly inspired by ACT, but should be simpler to use. Drag-n-drop two genomes: it runs BLAST for you and then you can visualize. For Mac, Windows 11, Linux tna.readthedocs.io

🚨#PhD opportunity!🚨Do plasmids help soil microbiomes adapt to climate change? Join me and Raj Whitlock to investigate, using the world's longest-running climate experiment 🌾🥵🦠 Please share, and get in touch if you are interested! www.findaphd.com/phds/project...

The HZI will hire up to twenty (20!) tenure-track research groups under the broad topic of "Microbial Stargazing" (🦠🌌). The first round of 4 positions is now open; the call closes on the 10th of December. Please share! www.helmholtz-hzi.de/en/career/jo...

Come work with us! The Quadram is in search of a Head of Bioinformatics to lead and cultivate a specialised bioinformatics core support team. Applications Close 04 December 2023 quadram.ac.uk/vacancies/he...

PhD studentship with myself and Ed Feil at the University of Bath looking at the evolution and epidemiology of plasmids - in particular looking at plasmid fusions/hybrids/recombinants. Lots of fun bioinformatics! Open to UK or international students. #microsky www.findaphd.com/phds/project...

PhD studentship (co-sup with Ed Feil, collaborators incl. Edze Westra): using GWAS to find bacterial susceptibility loci to phage infection, and machine learning for prediction. Amazing dataset, great application for machine learning www.findaphd.com/phds/project...

PhD available with me at NTU. Metabolomics and cell-line work (... maybe some microbiota ...). Open to UK and international students. Host–microbiota interactions in pancreatic cancer: determining whether they exist, and their influence on disease Please RT. #MicrobiomeSky

Host–microbiota interactions in pancreatic cancer: determining whether they exist, and their influ...

Discover our PhD Studentship opportunities in the School of Science and Technology

ntu.ac.uk

PhD opportunity with me and Mark Webber! Some microbial genomics, some molecular biology, all fun. Apply here: buff.ly/3FjzrzS