Adam Blanchard
@addyblanch.bsky.social
Associate Professor in Computational Biology | University of Nottingham | School of Veterinary Medicine and Science | Deputy Head of Division
Microbial genomics | Antimicrobial Resistance | Metagenomics | Production Animal Health and Disease
Microbial genomics | Antimicrobial Resistance | Metagenomics | Production Animal Health and Disease
Reposted by Adam Blanchard
MAGdb: a comprehensive high quality MAGs repository for exploring microbial metagenome-assemble genomes. #MAGs #Metagenomics #MetagenomeAssembly #GenomeBiology
genomebiology.biomedcentral.com/articles/10....
genomebiology.biomedcentral.com/articles/10....
September 14, 2025 at 7:32 AM
MAGdb: a comprehensive high quality MAGs repository for exploring microbial metagenome-assemble genomes. #MAGs #Metagenomics #MetagenomeAssembly #GenomeBiology
genomebiology.biomedcentral.com/articles/10....
genomebiology.biomedcentral.com/articles/10....
Reposted by Adam Blanchard
Cool result: Transposon insertion sequencing reveals novel hypermutator genes in Acinetobacter baumannii
"Exposure of a transposon insertion mutant library to extended weak antibiotic selection ... revealed genes that indirectly increased fitness due to elevated general mutation rates"
"Exposure of a transposon insertion mutant library to extended weak antibiotic selection ... revealed genes that indirectly increased fitness due to elevated general mutation rates"
Transposon insertion sequencing reveals novel hypermutator genes in Acinetobacter baumannii | mBio
All organisms have the capacity for evolution through mutation. Bacteria with high
mutation rates have a survival advantage in some stressful environments because they
generate beneficial mutations mo...
journals.asm.org
June 29, 2025 at 4:58 AM
Cool result: Transposon insertion sequencing reveals novel hypermutator genes in Acinetobacter baumannii
"Exposure of a transposon insertion mutant library to extended weak antibiotic selection ... revealed genes that indirectly increased fitness due to elevated general mutation rates"
"Exposure of a transposon insertion mutant library to extended weak antibiotic selection ... revealed genes that indirectly increased fitness due to elevated general mutation rates"
Reposted by Adam Blanchard
What determines who a phage can infect?
We tackled this question for temperate phages of Klebsiella — a bacterial pathogen — using a genome-wide association study (GWAS) and a massive protein testing effort.
👇 A thread!
We tackled this question for temperate phages of Klebsiella — a bacterial pathogen — using a genome-wide association study (GWAS) and a massive protein testing effort.
👇 A thread!
June 26, 2025 at 7:13 AM
What determines who a phage can infect?
We tackled this question for temperate phages of Klebsiella — a bacterial pathogen — using a genome-wide association study (GWAS) and a massive protein testing effort.
👇 A thread!
We tackled this question for temperate phages of Klebsiella — a bacterial pathogen — using a genome-wide association study (GWAS) and a massive protein testing effort.
👇 A thread!
Another paper from the lab, trying to look at in vitro biological relevant phenotypes in essential genomes www.microbiologyresearch.org/content/jour...
In vitro determination of essential genes required by Streptococcus uberis to grow in a complex biological media relating to intramammary infection
Streptococcus uberis is a leading cause of bovine mastitis, a disease of significant economic impact to the dairy industry. Understanding the genetic factors essential for bacterial survival in milk a...
www.microbiologyresearch.org
June 18, 2025 at 1:46 PM
Another paper from the lab, trying to look at in vitro biological relevant phenotypes in essential genomes www.microbiologyresearch.org/content/jour...
New preprint up on the changes in the bovine virome though different life stages led by @milja001.bsky.social @ryancook94.bsky.social www.biorxiv.org/content/10.1...
Life-Stage Transitions Drive Distinct Gut Viral Communities in Dairy Cattle
Ruminant gut microbial communities profoundly influence host health and environmental impacts, yet their viral components remain poorly characterised across developmental transitions. Here, we analyse...
www.biorxiv.org
May 30, 2025 at 10:07 AM
New preprint up on the changes in the bovine virome though different life stages led by @milja001.bsky.social @ryancook94.bsky.social www.biorxiv.org/content/10.1...
Reposted by Adam Blanchard
Excited to share the first beta release of AMRrules at #ABPHM! (Poster 42 tonight)
interpretamr.github.io/AMRrules
interpretamr.github.io/AMRrules
May 22, 2025 at 9:35 AM
Excited to share the first beta release of AMRrules at #ABPHM! (Poster 42 tonight)
interpretamr.github.io/AMRrules
interpretamr.github.io/AMRrules
Reposted by Adam Blanchard
Myself and @yekwah.bsky.social are running our bacterial AMR databases and genotype prediction course again with @eventswcs.bsky.social. Completely free and study at your own pace.
Check out the course objectives below and sign up before June 9th to join us!
www.futurelearn.com/courses/anti...
Check out the course objectives below and sign up before June 9th to join us!
www.futurelearn.com/courses/anti...
Antimicrobial Databases and Genotype Prediction - Online Course - FutureLearn
Transform your understanding of antimicrobial resistance (AMR) and elevate your research or clinical practice with Wellcome Connecting Science.
www.futurelearn.com
May 22, 2025 at 11:39 AM
Myself and @yekwah.bsky.social are running our bacterial AMR databases and genotype prediction course again with @eventswcs.bsky.social. Completely free and study at your own pace.
Check out the course objectives below and sign up before June 9th to join us!
www.futurelearn.com/courses/anti...
Check out the course objectives below and sign up before June 9th to join us!
www.futurelearn.com/courses/anti...
Reposted by Adam Blanchard
New paper where we suggest bacteria in the honeybee stomach may be more interesting to study than generally thought.
doi.org/10.1007/s002...
doi.org/10.1007/s002...
Bacteria in Honeybee Crops Are Decoupled from Those in Floral Nectar and Bee Mouths - Microbial Ecology
Bacteria in the honeybee gut are a well-recognized factor affecting bee health. However, the primary focus of this research has been the hindgut, while the crop, or honey stomach, is assumed to be dom...
doi.org
May 22, 2025 at 2:17 PM
New paper where we suggest bacteria in the honeybee stomach may be more interesting to study than generally thought.
doi.org/10.1007/s002...
doi.org/10.1007/s002...
Interesting paper on novel bacteria isolated from the Phoenix Space Mission
microbiomejournal.biomedcentral.com/articles/10....
microbiomejournal.biomedcentral.com/articles/10....
Genomic insights into novel extremotolerant bacteria isolated from the NASA Phoenix mission spacecraft assembly cleanrooms - Microbiome
Background Human-designed oligotrophic environments, such as cleanrooms, harbor unique microbial communities shaped by selective pressures like temperature, humidity, nutrient availability, cleaning r...
microbiomejournal.biomedcentral.com
May 20, 2025 at 12:05 PM
Interesting paper on novel bacteria isolated from the Phoenix Space Mission
microbiomejournal.biomedcentral.com/articles/10....
microbiomejournal.biomedcentral.com/articles/10....
Reposted by Adam Blanchard
Super cool #bioinformatics tool alert: @widdowquinn.bsky.social group releases PyANI-plus, a flexible tool for exploring whole-genome similarity on large AND detailed scales. Walkthrough available below!
pyANI-plus walkthrough – pyANI-plus
pyani-plus.github.io
May 15, 2025 at 3:11 PM
Super cool #bioinformatics tool alert: @widdowquinn.bsky.social group releases PyANI-plus, a flexible tool for exploring whole-genome similarity on large AND detailed scales. Walkthrough available below!
Reposted by Adam Blanchard
Autocycler: long-read consensus assembly for bacterial genomes https://www.biorxiv.org/content/10.1101/2025.05.12.653612v1
May 15, 2025 at 8:47 PM
Autocycler: long-read consensus assembly for bacterial genomes https://www.biorxiv.org/content/10.1101/2025.05.12.653612v1
Reposted by Adam Blanchard
I've spent some time updating my two Nextflow-based bacterial QC pipelines (bacQC and bacQC-ONT). It'd be great to get some feedback.
github.com/avantonder/b...
github.com/avantonder/b...
github.com/avantonder/b...
github.com/avantonder/b...
GitHub - avantonder/bacQC-ONT: QC pipeline for ONT data
QC pipeline for ONT data. Contribute to avantonder/bacQC-ONT development by creating an account on GitHub.
github.com
March 6, 2025 at 10:47 AM
I've spent some time updating my two Nextflow-based bacterial QC pipelines (bacQC and bacQC-ONT). It'd be great to get some feedback.
github.com/avantonder/b...
github.com/avantonder/b...
github.com/avantonder/b...
github.com/avantonder/b...
Reposted by Adam Blanchard
New awesome Rust bioinformatics tool just dropped!
CoverM is published!
CoverM: Read alignment statistics for metagenomics academic.oup.com/bioinformati... #jcampubs
CoverM: Read alignment statistics for metagenomics academic.oup.com/bioinformati... #jcampubs
CoverM: Read alignment statistics for metagenomics
AbstractSummary. Genome-centric analysis of metagenomic samples is a powerful method for understanding the function of microbial communities. Calculating r
academic.oup.com
April 9, 2025 at 2:05 PM
New awesome Rust bioinformatics tool just dropped!
Reposted by Adam Blanchard
I'm really excited to share the postdoc I completed before joining PHG. It combines two great passions - bacteria and horses!!
Read more here: www.linkedin.com/posts/hayley... or go straight to the paper here: www.microbiologyresearch.org/content/jour...
Read more here: www.linkedin.com/posts/hayley... or go straight to the paper here: www.microbiologyresearch.org/content/jour...
Progressive evolution of Streptococcus equi from Streptococcus equi subsp.… | Hayley Wilson
I'm really excited to share this work with the world! As we know, academic research work will follow you even after you've left. So this is my post-doc project…
www.linkedin.com
March 31, 2025 at 10:35 AM
I'm really excited to share the postdoc I completed before joining PHG. It combines two great passions - bacteria and horses!!
Read more here: www.linkedin.com/posts/hayley... or go straight to the paper here: www.microbiologyresearch.org/content/jour...
Read more here: www.linkedin.com/posts/hayley... or go straight to the paper here: www.microbiologyresearch.org/content/jour...
Worth a read about a new antibiotic: pubmed.ncbi.nlm.nih.gov/39372947/
A Broad Spectrum Lasso Peptide Antibiotic Targeting the Bacterial Ribosome - PubMed
Lasso peptides, biologically active molecules with a distinct structurally constrained knotted fold, are natural products belonging to the class of ribosomally-synthesized and posttranslationally modi...
pubmed.ncbi.nlm.nih.gov
March 27, 2025 at 12:20 PM
Worth a read about a new antibiotic: pubmed.ncbi.nlm.nih.gov/39372947/
Reposted by Adam Blanchard
New work showing that multidrug-resistant 𝘈𝘤𝘪𝘯𝘦𝘵𝘰𝘣𝘢𝘤𝘵𝘦𝘳 𝘣𝘢𝘶𝘮𝘢𝘯𝘯𝘪𝘪 isn’t a scattered threat—it’s a structured epidemic!
A dominant super-lineage and a rising clade (2.5.6) are spreading worldwide, fueled by gene exchange.
Li et al. Nat Commun
#AMR #bacterialgenomics
www.nature.com/articles/s41...
A dominant super-lineage and a rising clade (2.5.6) are spreading worldwide, fueled by gene exchange.
Li et al. Nat Commun
#AMR #bacterialgenomics
www.nature.com/articles/s41...
Emergence and global spread of a dominant multidrug-resistant clade within Acinetobacter baumannii - Nature Communications
In this study, authors conduct a genomic analysis of 15,000 Acinetobacter baumannii isolates, revealing a dominant multidrug-resistant super-lineage (accounting for approximately 70% global isolates),...
www.nature.com
March 23, 2025 at 2:36 PM
New work showing that multidrug-resistant 𝘈𝘤𝘪𝘯𝘦𝘵𝘰𝘣𝘢𝘤𝘵𝘦𝘳 𝘣𝘢𝘶𝘮𝘢𝘯𝘯𝘪𝘪 isn’t a scattered threat—it’s a structured epidemic!
A dominant super-lineage and a rising clade (2.5.6) are spreading worldwide, fueled by gene exchange.
Li et al. Nat Commun
#AMR #bacterialgenomics
www.nature.com/articles/s41...
A dominant super-lineage and a rising clade (2.5.6) are spreading worldwide, fueled by gene exchange.
Li et al. Nat Commun
#AMR #bacterialgenomics
www.nature.com/articles/s41...
Reposted by Adam Blanchard
Incredibly excited to share that our manuscript was just published in @nature.com ! What a way to start the new year! 🎉
https://buff.ly/4gyYCzx
We present phylowave, a framework that enables to learn the fitness dynamics of pathogens from phylogenies.
🧵 A thread... 1/n
#IDSky #IDModelling
https://buff.ly/4gyYCzx
We present phylowave, a framework that enables to learn the fitness dynamics of pathogens from phylogenies.
🧵 A thread... 1/n
#IDSky #IDModelling
Learning the fitness dynamics of pathogens from phylogenies - Nature
Phylowave, an innovative phylogenetic approach, can identify the main circulating pathogen lineages with increased fitness and the associated genetic changes, enabling the timely identification of…
buff.ly
January 2, 2025 at 8:03 AM
Incredibly excited to share that our manuscript was just published in @nature.com ! What a way to start the new year! 🎉
https://buff.ly/4gyYCzx
We present phylowave, a framework that enables to learn the fitness dynamics of pathogens from phylogenies.
🧵 A thread... 1/n
#IDSky #IDModelling
https://buff.ly/4gyYCzx
We present phylowave, a framework that enables to learn the fitness dynamics of pathogens from phylogenies.
🧵 A thread... 1/n
#IDSky #IDModelling
Reposted by Adam Blanchard
This is very important -
shortening antibiotic treatment duration is a good way to reduce consumption
shortening antibiotic treatment duration is a good way to reduce consumption
Systematic review of antibiotic durations in @jac-amr.bsky.social
n=315 RCTs
85% demonstrated equivalence or non-inferiority of shorter therapy
Only 7% in ICU, 14% in LMIC, and 15% low risk of bias
academic.oup.com/jacamr/artic...
n=315 RCTs
85% demonstrated equivalence or non-inferiority of shorter therapy
Only 7% in ICU, 14% in LMIC, and 15% low risk of bias
academic.oup.com/jacamr/artic...
January 30, 2025 at 5:49 PM
This is very important -
shortening antibiotic treatment duration is a good way to reduce consumption
shortening antibiotic treatment duration is a good way to reduce consumption
Reposted by Adam Blanchard
An ICE, a PICI, and a phage walk into a cell… and start crosstalking. Interesting read on how MGEs juggle interactions like pros! 🦠
academic.oup.com/ismej/articl...
academic.oup.com/ismej/articl...
Escherichia coli phage-inducible chromosomal island aids helper phage replication and represses the locus of enterocyte effacement pathogenicity island
Abstract. In this study, we identify and characterize a novel phage-inducible chromosomal island (PICI) found in commensal Escherichia coli MP1. This novel
academic.oup.com
January 30, 2025 at 8:50 AM
An ICE, a PICI, and a phage walk into a cell… and start crosstalking. Interesting read on how MGEs juggle interactions like pros! 🦠
academic.oup.com/ismej/articl...
academic.oup.com/ismej/articl...
Latest publication with @virologyvet.bsky.social trying to make sense of viral/bacterial interactions in co-infections
www.mdpi.com/2076-0817/14...
www.mdpi.com/2076-0817/14...
Understanding the Molecular Interactions Between Influenza A Virus and Streptococcus Proteins in Co-Infection: A Scoping Review
Influenza A virus infections are known to predispose infected individuals to bacterial infections of the respiratory tract that result in co-infection with severe disease outcomes. Co-infections invol...
www.mdpi.com
January 24, 2025 at 10:29 AM
Latest publication with @virologyvet.bsky.social trying to make sense of viral/bacterial interactions in co-infections
www.mdpi.com/2076-0817/14...
www.mdpi.com/2076-0817/14...
Reposted by Adam Blanchard
PredCMB: Predicting changes in microbial metabolites based on the gene-metabolite network analysis of shotgun metagenome data academic.oup.com/bioinformati... #jcampubs
January 16, 2025 at 2:11 PM
PredCMB: Predicting changes in microbial metabolites based on the gene-metabolite network analysis of shotgun metagenome data academic.oup.com/bioinformati... #jcampubs
Reposted by Adam Blanchard
CompàreGenome: a command-line tool for genomic diversity estimation in prokaryotes and eukaryotes bmcbioinformatics.biomedcentral.com/articles/10.... #jcampubs
CompàreGenome: a command-line tool for genomic diversity estimation in prokaryotes and eukaryotes - BMC Bioinformatics
Background The increasing availability of sequenced genomes has enabled comparative analyses of various organisms. Numerous tools and online platforms have been developed for this purpose, facilitatin...
bmcbioinformatics.biomedcentral.com
January 16, 2025 at 2:12 PM
CompàreGenome: a command-line tool for genomic diversity estimation in prokaryotes and eukaryotes bmcbioinformatics.biomedcentral.com/articles/10.... #jcampubs
Reposted by Adam Blanchard
I thoroughly enjoyed this read. It put into words my own thought well. Definitely going to take up some of the suggestions.
Our paper on nurturing a #PositiveResearchCulture within your #research #team published by @wellcometrust.bsky.social gives useful tips for your lab. As well as making you a good team leader, nurturing culture pays off in building your science: 1/11
wellcomeopenresearch.org/articles/9-3...
wellcomeopenresearch.org/articles/9-3...
wellcomeopenresearch.org
January 15, 2025 at 4:47 PM
I thoroughly enjoyed this read. It put into words my own thought well. Definitely going to take up some of the suggestions.
Reposted by Adam Blanchard
New year, new assemblies!
I'm excited to announce Autocycler, my new tool for consensus assembly of long-read bacterial genomes!
It's the successor to Trycycler, designed to be faster and less reliant on user intervention.
Check it out: github.com/rrwick/Autoc...
(1/5)
I'm excited to announce Autocycler, my new tool for consensus assembly of long-read bacterial genomes!
It's the successor to Trycycler, designed to be faster and less reliant on user intervention.
Check it out: github.com/rrwick/Autoc...
(1/5)
Home
A tool for generating consensus long-read assemblies for bacterial genomes - rrwick/Autocycler
github.com
December 31, 2024 at 11:43 PM
New year, new assemblies!
I'm excited to announce Autocycler, my new tool for consensus assembly of long-read bacterial genomes!
It's the successor to Trycycler, designed to be faster and less reliant on user intervention.
Check it out: github.com/rrwick/Autoc...
(1/5)
I'm excited to announce Autocycler, my new tool for consensus assembly of long-read bacterial genomes!
It's the successor to Trycycler, designed to be faster and less reliant on user intervention.
Check it out: github.com/rrwick/Autoc...
(1/5)
Reposted by Adam Blanchard
DefensePredictor: A Machine Learning Model to Discover Novel Prokaryotic Immune Systems https://www.biorxiv.org/content/10.1101/2025.01.08.631726v1
January 9, 2025 at 8:18 AM
DefensePredictor: A Machine Learning Model to Discover Novel Prokaryotic Immune Systems https://www.biorxiv.org/content/10.1101/2025.01.08.631726v1