Our faculty has a particularly interesting PhD position open on antimicrobial resistance, effects of antibiotics treatment on the microbiome and resistome, restoration of the equine microbiome using FMT.
www.uu.nl/en/organisat...
Please contact Mathijs Theelen, email address in the link below.
www.uu.nl/en/organisat...
Please contact Mathijs Theelen, email address in the link below.
PhD candidate in Equine Intestinal Microbiome and Resistome
Join this PhD project to study how the equine gut microbiome and resistome can improve gastrointestinal health and combat antimicrobial resistance.
www.uu.nl
February 24, 2026 at 12:10 PM
Our faculty has a particularly interesting PhD position open on antimicrobial resistance, effects of antibiotics treatment on the microbiome and resistome, restoration of the equine microbiome using FMT.
www.uu.nl/en/organisat...
Please contact Mathijs Theelen, email address in the link below.
www.uu.nl/en/organisat...
Please contact Mathijs Theelen, email address in the link below.
Our metagenomic study describing the impact of agricultural and urban practices on antimicrobial resistance genes (resistome) in rivers is out!
www.sciencedirect.com/science/arti...
www.sciencedirect.com/science/arti...
April 14, 2024 at 9:08 AM
Our metagenomic study describing the impact of agricultural and urban practices on antimicrobial resistance genes (resistome) in rivers is out!
www.sciencedirect.com/science/arti...
www.sciencedirect.com/science/arti...
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
#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...
www.biorxiv.org
January 3, 2025 at 5:03 PM
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
#resistome #amr #microbiome #preterm
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/...
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/...
December 8, 2025 at 10:00 AM
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/...
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/...
More details to follow later, but this has been in the works for almost 6 years, so it is great to finally see it in preprint form:
"The elusive resistome: a global comparison reveals large discrepancies among detection pipelines"
www.biorxiv.org/content/10.6...
"The elusive resistome: a global comparison reveals large discrepancies among detection pipelines"
www.biorxiv.org/content/10.6...
www.biorxiv.org
May 13, 2026 at 6:25 AM
More details to follow later, but this has been in the works for almost 6 years, so it is great to finally see it in preprint form:
"The elusive resistome: a global comparison reveals large discrepancies among detection pipelines"
www.biorxiv.org/content/10.6...
"The elusive resistome: a global comparison reveals large discrepancies among detection pipelines"
www.biorxiv.org/content/10.6...
#Microplastics Mobile resistome
Guruge and Goswami, et al., #Plastiome: Plastisphere-enriched mobile #resistome in aquatic environments. Journal of Hazardous Materials, 471, Article 134353.
orbit.dtu.dk/en/publicati...
Guruge and Goswami, et al., #Plastiome: Plastisphere-enriched mobile #resistome in aquatic environments. Journal of Hazardous Materials, 471, Article 134353.
orbit.dtu.dk/en/publicati...
March 20, 2025 at 12:49 PM
#Microplastics Mobile resistome
Guruge and Goswami, et al., #Plastiome: Plastisphere-enriched mobile #resistome in aquatic environments. Journal of Hazardous Materials, 471, Article 134353.
orbit.dtu.dk/en/publicati...
Guruge and Goswami, et al., #Plastiome: Plastisphere-enriched mobile #resistome in aquatic environments. Journal of Hazardous Materials, 471, Article 134353.
orbit.dtu.dk/en/publicati...
We started with a simple question: which tool and db should we use for resistome profiling in the EMBARK project?
That question sent us down a rabbit hole.
Different ARG annotation pipelines don't just give different ARG numbers, they give you different resistome profiles.
1/3
That question sent us down a rabbit hole.
Different ARG annotation pipelines don't just give different ARG numbers, they give you different resistome profiles.
1/3
May 15, 2026 at 10:52 AM
We started with a simple question: which tool and db should we use for resistome profiling in the EMBARK project?
That question sent us down a rabbit hole.
Different ARG annotation pipelines don't just give different ARG numbers, they give you different resistome profiles.
1/3
That question sent us down a rabbit hole.
Different ARG annotation pipelines don't just give different ARG numbers, they give you different resistome profiles.
1/3
The Mycobacterium tuberculosis long-chain fatty acid resistome reveals the universal stress protein TB15.3 as essential for infection https://www.biorxiv.org/content/10.1101/2025.04.14.648703v1
April 15, 2025 at 4:16 AM
The Mycobacterium tuberculosis long-chain fatty acid resistome reveals the universal stress protein TB15.3 as essential for infection https://www.biorxiv.org/content/10.1101/2025.04.14.648703v1
[Publication] The article "Symbiotoxicity and infectious diseases: A proposed conceptual framework linking the exposome, microbiome, resistome, and infection risk" is now available.
www.sciencedirect.com/science/arti...
#IDsky #Symbiotoxicity #Microbiome #Infections #Resistome #Exposome
www.sciencedirect.com/science/arti...
#IDsky #Symbiotoxicity #Microbiome #Infections #Resistome #Exposome
www.sciencedirect.com
October 1, 2026 at 7:48 AM
[Publication] The article "Symbiotoxicity and infectious diseases: A proposed conceptual framework linking the exposome, microbiome, resistome, and infection risk" is now available.
www.sciencedirect.com/science/arti...
#IDsky #Symbiotoxicity #Microbiome #Infections #Resistome #Exposome
www.sciencedirect.com/science/arti...
#IDsky #Symbiotoxicity #Microbiome #Infections #Resistome #Exposome
Variation and prognostic potential of the gut antibiotic resistome in a population-based cohort www.nature.com/articles/s41...
We look at the risks and sociodemographic aspects of antimicrobial resistance, and its association with recent global urbanization and middle-class growth.
We look at the risks and sociodemographic aspects of antimicrobial resistance, and its association with recent global urbanization and middle-class growth.
July 5, 2025 at 9:43 AM
Variation and prognostic potential of the gut antibiotic resistome in a population-based cohort www.nature.com/articles/s41...
We look at the risks and sociodemographic aspects of antimicrobial resistance, and its association with recent global urbanization and middle-class growth.
We look at the risks and sociodemographic aspects of antimicrobial resistance, and its association with recent global urbanization and middle-class growth.
Lin et al.
Climate warming fuels the global antibiotic resistome by altering soil bacterial traits
www.nature.com/articles/s41...
Climate warming fuels the global antibiotic resistome by altering soil bacterial traits
www.nature.com/articles/s41...
Climate warming fuels the global antibiotic resistome by altering soil bacterial traits - Nature Ecology & Evolution
A combination of metagenomic data from experimental and natural warming with microbial culturing experiments shows that warming increases the potential of evolution of antibiotic resistance in soil ba...
www.nature.com
August 6, 2025 at 8:50 PM
Lin et al.
Climate warming fuels the global antibiotic resistome by altering soil bacterial traits
www.nature.com/articles/s41...
Climate warming fuels the global antibiotic resistome by altering soil bacterial traits
www.nature.com/articles/s41...
The elusive resistome: a global comparison reveals large discrepancies among detection pipelines https://www.biorxiv.org/content/10.64898/2026.05.11.724158v1
May 13, 2026 at 5:46 AM
The elusive resistome: a global comparison reveals large discrepancies among detection pipelines https://www.biorxiv.org/content/10.64898/2026.05.11.724158v1
Of all the -omes neologisms, i think Resistome is my favourite one! www.cell.com/trends/paras...
Predicting Plasmodium drug resistance through in vitro evolution
Knowledge about the resistibility and targets of compounds critically informs antimalarial
drug development. Luth et al. systematically analyzed the resistome of Plasmodium
falciparum through in vitro...
www.cell.com
March 6, 2025 at 3:07 PM
Of all the -omes neologisms, i think Resistome is my favourite one! www.cell.com/trends/paras...
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
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/...
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/...
December 8, 2025 at 10:51 AM
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
The tetracycline resistome is shaped by selection for specific resistance mechanisms by each antibiotic generation
by Blake et al. (@washumedicine.bsky.social) in @naturecomms.bsky.social
www.nature.com/articles/s41...
by Blake et al. (@washumedicine.bsky.social) in @naturecomms.bsky.social
www.nature.com/articles/s41...
The tetracycline resistome is shaped by selection for specific resistance mechanisms by each antibiotic generation - Nature Communications
Bacteria can use different mechanisms to become resistant to the same antibiotic class. Here, the authors study bacterial strains that express genes conferring tetracycline resistance via different me...
www.nature.com
February 14, 2025 at 9:17 AM
The tetracycline resistome is shaped by selection for specific resistance mechanisms by each antibiotic generation
by Blake et al. (@washumedicine.bsky.social) in @naturecomms.bsky.social
www.nature.com/articles/s41...
by Blake et al. (@washumedicine.bsky.social) in @naturecomms.bsky.social
www.nature.com/articles/s41...
Fascinating preprint by Leo Lahti (@antagomir.bsky.social) and colleagues
'Population variation and prognostic potential of gut antibiotic resistome'
7,095 Finns with 17-year follow-up 'prognostic potential of resistome comparable to blood pressure for mortality'
www.medrxiv.org/content/10.1...
'Population variation and prognostic potential of gut antibiotic resistome'
7,095 Finns with 17-year follow-up 'prognostic potential of resistome comparable to blood pressure for mortality'
www.medrxiv.org/content/10.1...
Population variation and prognostic potential of gut antibiotic resistome
medRxiv - The Preprint Server for Health Sciences
www.medrxiv.org
September 12, 2024 at 7:27 PM
Fascinating preprint by Leo Lahti (@antagomir.bsky.social) and colleagues
'Population variation and prognostic potential of gut antibiotic resistome'
7,095 Finns with 17-year follow-up 'prognostic potential of resistome comparable to blood pressure for mortality'
www.medrxiv.org/content/10.1...
'Population variation and prognostic potential of gut antibiotic resistome'
7,095 Finns with 17-year follow-up 'prognostic potential of resistome comparable to blood pressure for mortality'
www.medrxiv.org/content/10.1...
Selective expansion of gut #antibiotic resistome and underlying #pathways involved in type 1 diabetes #iMetaOmics onlinelibrary.wiley.com/doi/full/10.... #T1D #MedTwitter #microbiome #antibiotics
Selective expansion of gut antibiotic resistome and underlying pathways involved in type 1 diabetes
Selective expansion of gut antibiotic resistance genes (including glycopeptides, tetracyclines, macrolide-lincosamide-streptogramins, and beta-lactams) was observed in type 1 diabetic rats. Interesti...
onlinelibrary.wiley.com
March 14, 2025 at 1:14 PM
Selective expansion of gut #antibiotic resistome and underlying #pathways involved in type 1 diabetes #iMetaOmics onlinelibrary.wiley.com/doi/full/10.... #T1D #MedTwitter #microbiome #antibiotics
Our new advanced wastewater treatment paper in npj Clean Water:
Reusable immobilised quaternary ammonium particles reduce microbial and resistome burdens without promoting resistance selection during wastewater post-treatment
www.nature.com/articles/s41...
Reusable immobilised quaternary ammonium particles reduce microbial and resistome burdens without promoting resistance selection during wastewater post-treatment
www.nature.com/articles/s41...
Reusable immobilised quaternary ammonium particles reduce microbial and resistome burdens without promoting resistance selection during wastewater post-treatment - npj Clean Water
npj Clean Water - Reusable immobilised quaternary ammonium particles reduce microbial and resistome burdens without promoting resistance selection during wastewater post-treatment
www.nature.com
May 13, 2026 at 10:09 AM
Our new advanced wastewater treatment paper in npj Clean Water:
Reusable immobilised quaternary ammonium particles reduce microbial and resistome burdens without promoting resistance selection during wastewater post-treatment
www.nature.com/articles/s41...
Reusable immobilised quaternary ammonium particles reduce microbial and resistome burdens without promoting resistance selection during wastewater post-treatment
www.nature.com/articles/s41...
Global health risks lurking in livestock resistome | Science Advances www.science.org/doi/10.1126/...
Global health risks lurking in livestock resistome
A risk-assessment framework uncovers the global health risks associated with livestock resistomes.
www.science.org
July 2, 2025 at 6:37 AM
Global health risks lurking in livestock resistome | Science Advances www.science.org/doi/10.1126/...
Engineering soil with phages to fight #AMR. Very cool.
"Harnessing phage consortia to mitigate the soil antibiotic resistome by targeting keystone taxa Streptomyces"
by Hanpeng Liao et al. in @microbiomej.bsky.social
microbiomejournal.biomedcentral.com/articles/10....
"Harnessing phage consortia to mitigate the soil antibiotic resistome by targeting keystone taxa Streptomyces"
by Hanpeng Liao et al. in @microbiomej.bsky.social
microbiomejournal.biomedcentral.com/articles/10....
Harnessing phage consortia to mitigate the soil antibiotic resistome by targeting keystone taxa Streptomyces - Microbiome
Background Antimicrobial resistance poses a substantial and growing threat to global health. While antibiotic resistance genes (ARGs) are tracked most closely in clinical settings, their spread remain...
microbiomejournal.biomedcentral.com
June 2, 2025 at 7:05 AM
Engineering soil with phages to fight #AMR. Very cool.
"Harnessing phage consortia to mitigate the soil antibiotic resistome by targeting keystone taxa Streptomyces"
by Hanpeng Liao et al. in @microbiomej.bsky.social
microbiomejournal.biomedcentral.com/articles/10....
"Harnessing phage consortia to mitigate the soil antibiotic resistome by targeting keystone taxa Streptomyces"
by Hanpeng Liao et al. in @microbiomej.bsky.social
microbiomejournal.biomedcentral.com/articles/10....
Happy to have participated in this beautiful work on the human gut resistome in populations exposed to minimal anthropogenic pollution 🥳. Do not miss it!
We are pleased to share our last article rdcu.be/fabhM. It offers the most comprehensive analysis so far of Ab+non-Ab resistance genes in human gut microbiome, using an Indigenous population (low industrialization, chronic Hg exposure from gold mining) 6/6👇
The antimicrobial gut resistome of the Wayampi reveals a shared background of antibiotic and metal resistance genes with industrialized populations, underscoring the “robust-yet-fragile” architecture ...
rdcu.be
March 26, 2026 at 2:12 PM
Happy to have participated in this beautiful work on the human gut resistome in populations exposed to minimal anthropogenic pollution 🥳. Do not miss it!
🆕💫PROTECT RCT
Ceftriaxone to prevent early-onset pneumonia in comatose patients after out-of-hospital cardiac arrest: a pilot randomized controlled trial and resistome assessment (PROTECT) #IDsky #EMIMCC @pulmcrit.bsky.social
journal.chestnet.org/article/S001...
Ceftriaxone to prevent early-onset pneumonia in comatose patients after out-of-hospital cardiac arrest: a pilot randomized controlled trial and resistome assessment (PROTECT) #IDsky #EMIMCC @pulmcrit.bsky.social
journal.chestnet.org/article/S001...
Ceftriaxone to prevent early-onset pneumonia in comatose patients after out-of-hospital cardiac arrest: a pilot randomized controlled trial and resistome assessment (PROTECT)
This trial was inconclusive regarding the impact of ceftriaxone prophylaxis to reduce
the incidence of EOP after OHCA but ceftriaxone was associated with less frequent
administration of open-label ant...
journal.chestnet.org
August 28, 2025 at 10:19 PM
🆕💫PROTECT RCT
Ceftriaxone to prevent early-onset pneumonia in comatose patients after out-of-hospital cardiac arrest: a pilot randomized controlled trial and resistome assessment (PROTECT) #IDsky #EMIMCC @pulmcrit.bsky.social
journal.chestnet.org/article/S001...
Ceftriaxone to prevent early-onset pneumonia in comatose patients after out-of-hospital cardiac arrest: a pilot randomized controlled trial and resistome assessment (PROTECT) #IDsky #EMIMCC @pulmcrit.bsky.social
journal.chestnet.org/article/S001...
Quero volver ser tuiteira aquí pero todo o que quero comentar xa está posto na rede social fascista e resístome a copiarme.
November 10, 2024 at 4:26 PM
Quero volver ser tuiteira aquí pero todo o que quero comentar xa está posto na rede social fascista e resístome a copiarme.
𝐆𝐥𝐨𝐛𝐚𝐥 𝐬𝐭𝐮𝐝𝐲: 𝐥𝐢𝐯𝐞𝐬𝐭𝐨𝐜𝐤 𝐦𝐚𝐧𝐮𝐫𝐞 = 𝐨𝐩𝐞𝐧 𝐩𝐚𝐧-𝐫𝐞𝐬𝐢𝐬𝐭𝐨𝐦𝐞
Contains nearly all known AMR genes + huge diversity of unknown ones—more per cell than sewage, soils, or human feces—reservoirs directly connectable to human pathogens
“𝙒𝙝𝙖𝙩 𝙝𝙖𝙥𝙥𝙚𝙣𝙨 𝙤𝙣 𝙛𝙖𝙧𝙢𝙨 𝙙𝙤𝙚𝙨𝙣’𝙩 𝙨𝙩𝙖𝙮 𝙤𝙣 𝙛𝙖𝙧𝙢𝙨”
www.science.org/doi/10.1126/...
Contains nearly all known AMR genes + huge diversity of unknown ones—more per cell than sewage, soils, or human feces—reservoirs directly connectable to human pathogens
“𝙒𝙝𝙖𝙩 𝙝𝙖𝙥𝙥𝙚𝙣𝙨 𝙤𝙣 𝙛𝙖𝙧𝙢𝙨 𝙙𝙤𝙚𝙨𝙣’𝙩 𝙨𝙩𝙖𝙮 𝙤𝙣 𝙛𝙖𝙧𝙢𝙨”
www.science.org/doi/10.1126/...
Global health risks lurking in livestock resistome
A risk-assessment framework uncovers the global health risks associated with livestock resistomes.
www.science.org
June 30, 2025 at 4:33 PM
𝐆𝐥𝐨𝐛𝐚𝐥 𝐬𝐭𝐮𝐝𝐲: 𝐥𝐢𝐯𝐞𝐬𝐭𝐨𝐜𝐤 𝐦𝐚𝐧𝐮𝐫𝐞 = 𝐨𝐩𝐞𝐧 𝐩𝐚𝐧-𝐫𝐞𝐬𝐢𝐬𝐭𝐨𝐦𝐞
Contains nearly all known AMR genes + huge diversity of unknown ones—more per cell than sewage, soils, or human feces—reservoirs directly connectable to human pathogens
“𝙒𝙝𝙖𝙩 𝙝𝙖𝙥𝙥𝙚𝙣𝙨 𝙤𝙣 𝙛𝙖𝙧𝙢𝙨 𝙙𝙤𝙚𝙨𝙣’𝙩 𝙨𝙩𝙖𝙮 𝙤𝙣 𝙛𝙖𝙧𝙢𝙨”
www.science.org/doi/10.1126/...
Contains nearly all known AMR genes + huge diversity of unknown ones—more per cell than sewage, soils, or human feces—reservoirs directly connectable to human pathogens
“𝙒𝙝𝙖𝙩 𝙝𝙖𝙥𝙥𝙚𝙣𝙨 𝙤𝙣 𝙛𝙖𝙧𝙢𝙨 𝙙𝙤𝙚𝙨𝙣’𝙩 𝙨𝙩𝙖𝙮 𝙤𝙣 𝙛𝙖𝙧𝙢𝙨”
www.science.org/doi/10.1126/...