Devin Holman
@devinholman.bsky.social
Microbiologist at Agriculture and Agri-Food Canada working on antimicrobial resistance and microbiomes in food producing-animals.
Reposted by Devin Holman
Awesome to see the transparent, systematic, and evidence-based approach behind the WHO Bacterial Priority Pathogens List 2024 out in the Lancet Infectious Diseases www.thelancet.com/journals/lan...
The WHO Bacterial Priority Pathogens List 2024: a prioritisation study to guide research, development, and public health strategies against antimicrobial resistance
The 2024 WHO BPPL is a key tool for prioritising research and development investments
and informing global public health policies to combat AMR. Gram-negative bacteria
and rifampicin-resistant M tuber...
www.thelancet.com
August 27, 2025 at 4:13 PM
Awesome to see the transparent, systematic, and evidence-based approach behind the WHO Bacterial Priority Pathogens List 2024 out in the Lancet Infectious Diseases www.thelancet.com/journals/lan...
Reposted by Devin Holman
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
June 21, 2025 at 7:59 PM
Hope this is useful - consensus statement "Guidelines for preventing and reporting contamination in low-biomass microbiome studies" rdcu.be/er3Io
Reposted by Devin Holman
High-quality metagenome assembly from nanopore reads with nanoMDBG www.biorxiv.org/content/10.1... 🧬🖥️🧪 github.com/GaetanBenoit...
April 25, 2025 at 3:31 PM
High-quality metagenome assembly from nanopore reads with nanoMDBG www.biorxiv.org/content/10.1... 🧬🖥️🧪 github.com/GaetanBenoit...
Reposted by Devin Holman
GTDB release 10 based on RefSeq 226 (R10-RS226) is live at gtdb.ecogenomic.org. This release covers 732,475 genomes (22% increase) and has 143,6141 species clusters (37% increase). Release notes at: forum.gtdb.ecogenomic.org/t/announcing.... Release statistics at: gtdb.ecogenomic.org/stats/r226.
GTDB - Genome Taxonomy Database
The Genome Taxonomy Database (GTDB) is an initiative to establish a standardised microbial taxonomy based on genome phylogeny.
gtdb.ecogenomic.org
April 18, 2025 at 7:13 PM
GTDB release 10 based on RefSeq 226 (R10-RS226) is live at gtdb.ecogenomic.org. This release covers 732,475 genomes (22% increase) and has 143,6141 species clusters (37% increase). Release notes at: forum.gtdb.ecogenomic.org/t/announcing.... Release statistics at: gtdb.ecogenomic.org/stats/r226.
Reposted by Devin Holman
From the Senior Editors of Microbiome - a blueprint for contemporary studies of microbiomes microbiomejournal.biomedcentral.com/articles/10.... @laurebindels.bsky.social
A blueprint for contemporary studies of microbiomes - Microbiome
This editorial piece co-authored by the Senior Editors at Microbiome aims to highlight current challenges in the field of environmental and host-associated microbiome research. We also take the opport...
microbiomejournal.biomedcentral.com
April 8, 2025 at 9:37 AM
From the Senior Editors of Microbiome - a blueprint for contemporary studies of microbiomes microbiomejournal.biomedcentral.com/articles/10.... @laurebindels.bsky.social
Reposted by Devin Holman
The overview of AMR that you always wanted (someone else to write) - amazing!
Truly brilliant paper with great figures! @lancetmicrobe.bsky.social
www.thelancet.com/journals/lan...
Truly brilliant paper with great figures! @lancetmicrobe.bsky.social
www.thelancet.com/journals/lan...
Antimicrobial resistance: a concise update
Antimicrobial resistance (AMR) is a serious threat to global public health, with approximately
5 million deaths associated with bacterial AMR in 2019. Tackling AMR requires a multifaceted
and cohesive...
www.thelancet.com
February 5, 2025 at 10:02 AM
The overview of AMR that you always wanted (someone else to write) - amazing!
Truly brilliant paper with great figures! @lancetmicrobe.bsky.social
www.thelancet.com/journals/lan...
Truly brilliant paper with great figures! @lancetmicrobe.bsky.social
www.thelancet.com/journals/lan...
Reposted by Devin Holman
And it’s been a while since I dipped my toe into the questions of what ‘species’ might mean for bacteria, and how they relate to ecology. But still interests me! genomebiology.biomedcentral.com/articles/10....
Relating ecological diversity to genetic discontinuity across bacterial species - Genome Biology
Background Genetic discontinuity represents abrupt breaks in genomic identity among species. Advances in genome sequencing have enhanced our ability to track and characterize genetic discontinuity in ...
genomebiology.biomedcentral.com
January 13, 2025 at 3:43 PM
And it’s been a while since I dipped my toe into the questions of what ‘species’ might mean for bacteria, and how they relate to ecology. But still interests me! genomebiology.biomedcentral.com/articles/10....
Reposted by Devin Holman
!!Come work with us!!
#ScienceJobs
Computational Biologist
Agriculture and Agri-Food Canada , BI-02.
Closing date: 28 Nov 2024
🔗 shorturl.at/eYCB8
Biologiste informaticien / biologiste informaticienne
Agriculture et Agroalimentaire Canada, BI-02
Date limite : 28 nov 2024
🔗 shorturl.at/WISJb
#ScienceJobs
Computational Biologist
Agriculture and Agri-Food Canada , BI-02.
Closing date: 28 Nov 2024
🔗 shorturl.at/eYCB8
Biologiste informaticien / biologiste informaticienne
Agriculture et Agroalimentaire Canada, BI-02
Date limite : 28 nov 2024
🔗 shorturl.at/WISJb
Computational Biologist
shorturl.at
November 20, 2024 at 4:17 PM
!!Come work with us!!
#ScienceJobs
Computational Biologist
Agriculture and Agri-Food Canada , BI-02.
Closing date: 28 Nov 2024
🔗 shorturl.at/eYCB8
Biologiste informaticien / biologiste informaticienne
Agriculture et Agroalimentaire Canada, BI-02
Date limite : 28 nov 2024
🔗 shorturl.at/WISJb
#ScienceJobs
Computational Biologist
Agriculture and Agri-Food Canada , BI-02.
Closing date: 28 Nov 2024
🔗 shorturl.at/eYCB8
Biologiste informaticien / biologiste informaticienne
Agriculture et Agroalimentaire Canada, BI-02
Date limite : 28 nov 2024
🔗 shorturl.at/WISJb
Reposted by Devin Holman
🚨🚨🚨 Looking for microbiome editors 🚨🚨🚨
Spectrum is a broad scope, open access ASM journal. We're currently looking for editors with an expertise in microbiome (early career welcome)!
If you're interested, please reach out to me or contact the journal directly:
journals.asm.org/journal/spec...
Spectrum is a broad scope, open access ASM journal. We're currently looking for editors with an expertise in microbiome (early career welcome)!
If you're interested, please reach out to me or contact the journal directly:
journals.asm.org/journal/spec...
Microbiology Spectrum Journal Homepage
Microbiology Spectrum is a a new open access journal that will publish research from all domains of basic, applied and clinical microbial sciences.
journals.asm.org
November 13, 2024 at 2:24 AM
🚨🚨🚨 Looking for microbiome editors 🚨🚨🚨
Spectrum is a broad scope, open access ASM journal. We're currently looking for editors with an expertise in microbiome (early career welcome)!
If you're interested, please reach out to me or contact the journal directly:
journals.asm.org/journal/spec...
Spectrum is a broad scope, open access ASM journal. We're currently looking for editors with an expertise in microbiome (early career welcome)!
If you're interested, please reach out to me or contact the journal directly:
journals.asm.org/journal/spec...
Reposted by Devin Holman
Your hitchhiker's guide to microbiome studies:
journals.asm.org/doi/epub/10....
journals.asm.org/doi/epub/10....
November 12, 2024 at 5:05 PM
Your hitchhiker's guide to microbiome studies:
journals.asm.org/doi/epub/10....
journals.asm.org/doi/epub/10....
Reposted by Devin Holman
NIAID releases alternative to BioRender, all illustrations freely available in public domain
bioart.niaid.nih.gov
bioart.niaid.nih.gov
October 30, 2024 at 2:46 PM
NIAID releases alternative to BioRender, all illustrations freely available in public domain
bioart.niaid.nih.gov
bioart.niaid.nih.gov
Reposted by Devin Holman
Florfenicol administration in piglets co-selects for multiple antimicrobial resistance genes https://www.biorxiv.org/content/10.1101/2024.06.03.597168v1
Florfenicol administration in piglets co-selects for multiple antimicrobial resistance genes https://www.biorxiv.org/content/10.1101/2024.06.03.597168v1
Florfenicol is a broad-spectrum phenicol antibiotic used in swine for various indications. However,
www.biorxiv.org
June 4, 2024 at 6:17 PM
Florfenicol administration in piglets co-selects for multiple antimicrobial resistance genes https://www.biorxiv.org/content/10.1101/2024.06.03.597168v1
Reposted by Devin Holman
This is a really interesting read, by Brian McGill (not on here?) on the state of play in scientific publishing in the field of ecology but is relevant to all academics
dynamicecology.wordpress.com/2024/04/29/t...
'Things are continuing to get worse and scientists are a lot to blame'
dynamicecology.wordpress.com/2024/04/29/t...
'Things are continuing to get worse and scientists are a lot to blame'
The state of academic publishing in 3 graphs, 6 trends, and 4 thoughts
Eleven years ago I shared a fairly heavily researched summary of the state of academic publishing. I mostly argued that OA (aka author pays) was a red herring and that we should really pay attention t...
dynamicecology.wordpress.com
April 29, 2024 at 3:55 PM
This is a really interesting read, by Brian McGill (not on here?) on the state of play in scientific publishing in the field of ecology but is relevant to all academics
dynamicecology.wordpress.com/2024/04/29/t...
'Things are continuing to get worse and scientists are a lot to blame'
dynamicecology.wordpress.com/2024/04/29/t...
'Things are continuing to get worse and scientists are a lot to blame'
Reposted by Devin Holman
GTDB release 9 based on RefSeq 220 (R09-RS220) is live at gtdb.ecogenomic.org. This release covers 596,859 genomes (48% increase) and has 113,104 species clusters (33% increase). Release notes at: forum.gtdb.ecogenomic.org/t/announcing.... Release statistics at: gtdb.ecogenomic.org/stats/r220.
GTDB - R220 Statistics
Statistics describing GTDB release R220.
gtdb.ecogenomic.org
April 24, 2024 at 5:19 AM
GTDB release 9 based on RefSeq 220 (R09-RS220) is live at gtdb.ecogenomic.org. This release covers 596,859 genomes (48% increase) and has 113,104 species clusters (33% increase). Release notes at: forum.gtdb.ecogenomic.org/t/announcing.... Release statistics at: gtdb.ecogenomic.org/stats/r220.
Reposted by Devin Holman
SingleM finally has a preprint associated with it!! I've juxtaposed two of their figures - that is a heck of a benchmark.
Assemble, but for an unassembled read-based perspective in environmental microbiomes, SingleM is a strong option.
Assemble, but for an unassembled read-based perspective in environmental microbiomes, SingleM is a strong option.
February 1, 2024 at 7:02 PM
SingleM finally has a preprint associated with it!! I've juxtaposed two of their figures - that is a heck of a benchmark.
Assemble, but for an unassembled read-based perspective in environmental microbiomes, SingleM is a strong option.
Assemble, but for an unassembled read-based perspective in environmental microbiomes, SingleM is a strong option.
Reposted by Devin Holman
Forecasting antimicrobial resistance evolution
#TrendsMicrobiol Opinion from Jens Wolff and colleagues
www.cell.com/trends/micro...
#TrendsMicrobiol Opinion from Jens Wolff and colleagues
www.cell.com/trends/micro...
January 19, 2024 at 8:22 AM
Forecasting antimicrobial resistance evolution
#TrendsMicrobiol Opinion from Jens Wolff and colleagues
www.cell.com/trends/micro...
#TrendsMicrobiol Opinion from Jens Wolff and colleagues
www.cell.com/trends/micro...
Reposted by Devin Holman
Are you a data creator/user in #metagenomics or other #omics? We’re working on standards for fair data reuse and would like your feedback. We welcome contributions by scientists from all career stages. 5-min anonymous survey here: shorturl.at/NOUW2 Please RT!
January 15, 2024 at 3:57 PM
Are you a data creator/user in #metagenomics or other #omics? We’re working on standards for fair data reuse and would like your feedback. We welcome contributions by scientists from all career stages. 5-min anonymous survey here: shorturl.at/NOUW2 Please RT!
Reposted by Devin Holman
In NEW Nature Reviews Microbiology article,
@fasnicar.bsky.social Andrew Maltez Thomas, Andrea Passerini @leviwaldron1.bsky.social and Nicola Segata cover the aspects that they consider most important to enable microbiologists to use machine learning.
www.nature.com/articles/s41...
1/2
@fasnicar.bsky.social Andrew Maltez Thomas, Andrea Passerini @leviwaldron1.bsky.social and Nicola Segata cover the aspects that they consider most important to enable microbiologists to use machine learning.
www.nature.com/articles/s41...
1/2
Machine learning for microbiologists - Nature Reviews Microbiology
In this Review, Segata, Waldron and colleagues discuss important key concepts of machine learning that are relevant to microbiologists and provide them with a set of tools essential to apply machine l...
www.nature.com
November 15, 2023 at 7:33 PM
In NEW Nature Reviews Microbiology article,
@fasnicar.bsky.social Andrew Maltez Thomas, Andrea Passerini @leviwaldron1.bsky.social and Nicola Segata cover the aspects that they consider most important to enable microbiologists to use machine learning.
www.nature.com/articles/s41...
1/2
@fasnicar.bsky.social Andrew Maltez Thomas, Andrea Passerini @leviwaldron1.bsky.social and Nicola Segata cover the aspects that they consider most important to enable microbiologists to use machine learning.
www.nature.com/articles/s41...
1/2