Reposted by Alison MatherQuadram Institute @quadraminstitute.bsky.social · 07/09/2026Would you like to join us as a Group Leader in Microbes and Food Safety? The priorities for the research programme are to reduce enduring and emerging threats to the safety of UK food supplies. 💷 Competitive 🗓️ Apply by 30 September 2026 ➡️ buff.ly/CG8vwJK 138
Reposted by Alison MatherHall Lab @halllab.bsky.social · 07/01/2026Happy 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...edzz.fa.em3.oraclecloud.comResearch Fellow - Department of Microbes, Infection and Microbiomes - 106849 - Grade 7To 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... 11118
Reposted by Alison MatherAldert Zomer @aldertzomer.bsky.social · 08/12/20258/ 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.jpiamr.euMEGAISurv – JPIAMRJPIAMR is a global collaborative organisation and platform, engaging 28 nations to curb antimicrobial resistance (AMR) with a One Health approach. 021
Reposted by Alison MatherAldert Zomer @aldertzomer.bsky.social · 08/12/20257/ 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. 111
Reposted by Alison MatherAldert Zomer @aldertzomer.bsky.social · 08/12/20256/ 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. 101
Reposted by Alison MatherAldert Zomer @aldertzomer.bsky.social · 08/12/20255/ 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. 111
Reposted by Alison MatherAldert Zomer @aldertzomer.bsky.social · 08/12/20254/ 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. 101
Reposted by Alison MatherAldert Zomer @aldertzomer.bsky.social · 08/12/20253/ 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. 111
Reposted by Alison MatherAldert Zomer @aldertzomer.bsky.social · 08/12/20252/ 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. 111
Reposted by Alison MatherAldert Zomer @aldertzomer.bsky.social · 08/12/20251/ 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. 131
Alison Mather @alisonmather.bsky.social · 08/12/2025A 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 093
Reposted by Alison MatherQuadram Institute @quadraminstitute.bsky.social · 27/10/2025🆕 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 012
Reposted by Alison MatherQuadram Institute @quadraminstitute.bsky.social · 27/10/2025🆕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 113
Reposted by Alison MatherFanny Wegner @fwegner.bsky.social · 13/10/2025📣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 152
Reposted by Alison MatherKate Baker @ksbakes.bsky.social · 31/07/2025Was 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...nature.comFrom farm to factory to fork - Nature MicrobiologyA 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. 1208
Reposted by Alison MatherQuadram Institute @quadraminstitute.bsky.social · 18/03/2025🎓 #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 133
Reposted by Alison MatherRaymond Kiu @raymondkiu.bsky.social · 03/01/2025Starting 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 #pretermbiorxiv.orgImpact of early life antibiotic and probiotic treatment on gut microbiome and resistome of very-low-birth-weight preterm infantsPreterm 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... 11913
Reposted by Alison MatherMartin Hunt @martibartfast.bsky.social · 29/11/2024I 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.iotna.readthedocs.ioTNA documentation — TNA 0.0.1 documentation 917569
Reposted by Alison MatherJamie Hall @jpjhall.bsky.social · 07/11/2023🚨#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... 03140
Reposted by Alison MatherMarco Galardini @mgalactus.bsky.social · 06/11/2023The 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... 01120
Reposted by Alison MatherLeo Martins (he/him) @leomrtns.bsky.social · 21/10/2023Come 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... 2915
Reposted by Alison MatherZamin Iqbal @zaminiqbal.bsky.social · 18/10/2023PhD 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... 04856
Reposted by Alison MatherZamin Iqbal @zaminiqbal.bsky.social · 19/10/2023PhD 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... 11014
Reposted by Alison MatherProfessor Lesley Hoyles @bugsinyourguts.bsky.social · 19/10/2023PhD 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. #MicrobiomeSkyntu.ac.ukHost–microbiota interactions in pancreatic cancer: determining whether they exist, and their influ...Discover our PhD Studentship opportunities in the School of Science and Technology 0811
Alison Mather @alisonmather.bsky.social · 19/10/2023PhD opportunity with me and Mark Webber! Some microbial genomics, some molecular biology, all fun. Apply here: buff.ly/3FjzrzS 01116