Andrea Quagliariello
@microquaglia.bsky.social
Reposted by Andrea Quagliariello
So happy to share this! Bacteriocins were first discovered over 100 years ago, but what do they actually do? We look at >1000 bacteriocin plasmids and find links to virulence and antimicrobial resistance, and frequent bacteriocin sharing in Enterobacteriaceae.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Bacterial warfare is associated with virulence and antimicrobial resistance - Nature Communications
Bacteria employ a range of competition systems that deliver toxins to inhibit competing strains. This study shows that these systems are particularly important for the ecology of virulent and antibiot...
www.nature.com
November 9, 2025 at 4:51 PM
Reposted by Andrea Quagliariello
This new study takes a closer look at eukaryotic reference genomes. 🧬 By mapping microbial-like regions across thousands of plant & animal assemblies, it helps make ancient eDNA analyses more accurate. #MetagenomicsMonday #SPAAM #aDNA #metagenomics #eDNA
doi.org/10.1093/giga...
doi.org/10.1093/giga...
Improving taxonomic inference from ancient environmental metagenomes by masking microbial-like regions in reference genomes
Abstract. Ancient environmental DNA is increasingly vital for reconstructing past ecosystems, particularly when paleontological and archaeological tissue r
doi.org
November 10, 2025 at 8:01 AM
This new study takes a closer look at eukaryotic reference genomes. 🧬 By mapping microbial-like regions across thousands of plant & animal assemblies, it helps make ancient eDNA analyses more accurate. #MetagenomicsMonday #SPAAM #aDNA #metagenomics #eDNA
doi.org/10.1093/giga...
doi.org/10.1093/giga...
Reposted by Andrea Quagliariello
DNA from Napoleon’s 1812 army identifies the pathogens likely responsible for the army’s demise during their Russian retreat. www.cell.com/current-biol...
Nicolás Rascovan & colleagues
@currentbiology.bsky.social
Nicolás Rascovan & colleagues
@currentbiology.bsky.social
October 24, 2025 at 3:00 PM
DNA from Napoleon’s 1812 army identifies the pathogens likely responsible for the army’s demise during their Russian retreat. www.cell.com/current-biol...
Nicolás Rascovan & colleagues
@currentbiology.bsky.social
Nicolás Rascovan & colleagues
@currentbiology.bsky.social
Reposted by Andrea Quagliariello
A new Species Survival Commission (SSC) has been established by the International Union for Conversation of Nature (IUCN). Microbiota Vault collaborators are among the founding members: doi.org/10.1038/s415...
Launching the IUCN Microbial Conservation Specialist Group as a global safeguard for microbial biodiversity - Nature Microbiology
Nature Microbiology - Launching the IUCN Microbial Conservation Specialist Group as a global safeguard for microbial biodiversity
doi.org
October 2, 2025 at 11:14 AM
A new Species Survival Commission (SSC) has been established by the International Union for Conversation of Nature (IUCN). Microbiota Vault collaborators are among the founding members: doi.org/10.1038/s415...
Reposted by Andrea Quagliariello
What lived in Arctic Norway ~80,000 years ago? ❄️🦌 Ancient sediments from a cave reveal 46 taxa of mammals, birds & fish — a unique cold-adapted coastal ecosystem. #MetagenomicsMonday #SPAAM #aDNA
doi.org/10.1073/pnas...
doi.org/10.1073/pnas...
A 75,000-y-old Scandinavian Arctic cave deposit reveals past faunal diversity and paleoenvironment | PNAS
During the last glacial period (~118 to 11.7 ka), the Arctic has been characterized by a major redistribution of flora and fauna as a consequence o...
doi.org
September 29, 2025 at 7:02 AM
What lived in Arctic Norway ~80,000 years ago? ❄️🦌 Ancient sediments from a cave reveal 46 taxa of mammals, birds & fish — a unique cold-adapted coastal ecosystem. #MetagenomicsMonday #SPAAM #aDNA
doi.org/10.1073/pnas...
doi.org/10.1073/pnas...
For those engaged in studies on the hologenome and its relevance to One Health
www.alocongress.com/pangenome2025
www.alocongress.com/pangenome2025
PANGENOME2025
The biology of prokaryotic cells is directly dependent on the differential gene pools that characterize each cell or strain. This has been a fundamental aspect of epidemiology for delimiting outbreaks...
www.alocongress.com
September 11, 2025 at 12:30 PM
For those engaged in studies on the hologenome and its relevance to One Health
www.alocongress.com/pangenome2025
www.alocongress.com/pangenome2025
Reposted by Andrea Quagliariello
In the now published study doi.org/10.1111/1755..., @markella-morait.bsky.social shows just how widespread dental calculus is and how to make to work for your favourite #mammal. #metagenomics #aDNA #museums
September 8, 2025 at 5:29 PM
In the now published study doi.org/10.1111/1755..., @markella-morait.bsky.social shows just how widespread dental calculus is and how to make to work for your favourite #mammal. #metagenomics #aDNA #museums
Reposted by Andrea Quagliariello
#MetagenomicsMonday A new study shares 174 archaeological dental calculus metagenomes from across the UK, spanning multiple periods. With rich metadata and rigorous quality control, the dataset opens new doors to exploring ancient microbiome through time.
doi.org/10.1016/j.di...
doi.org/10.1016/j.di...
An extensive archaeological dental calculus dataset spanning 5000 years for ancient human oral microbiome research
Archaeological dental calculus can provide detailed insights into the ancient human oral microbiome. We offer a multi-period, multi-site, ancient shot…
doi.org
September 8, 2025 at 7:36 AM
#MetagenomicsMonday A new study shares 174 archaeological dental calculus metagenomes from across the UK, spanning multiple periods. With rich metadata and rigorous quality control, the dataset opens new doors to exploring ancient microbiome through time.
doi.org/10.1016/j.di...
doi.org/10.1016/j.di...
Reposted by Andrea Quagliariello
My new @science.org editorial on the role of scientists in defending democracy is out today. As authoritarianism takes hold in the US, we must fight for the democratic principles that enable a free society and scientists have a key role. I hope you'll join us.
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Scientists’ role in defending democracy
The United States’ democratic leadership, commitment to freedom of expression, and investment in the pursuit of knowledge have long enabled its preeminence in science and technology. Yet today we are ...
www.science.org
August 14, 2025 at 6:36 PM
My new @science.org editorial on the role of scientists in defending democracy is out today. As authoritarianism takes hold in the US, we must fight for the democratic principles that enable a free society and scientists have a key role. I hope you'll join us.
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Reposted by Andrea Quagliariello
Perspective @natcomms.nature.com
A reconceptualized framework for human microbiome transmission in early life
www.nature.com/articles/s41...
A reconceptualized framework for human microbiome transmission in early life
www.nature.com/articles/s41...
August 15, 2025 at 2:41 AM
Perspective @natcomms.nature.com
A reconceptualized framework for human microbiome transmission in early life
www.nature.com/articles/s41...
A reconceptualized framework for human microbiome transmission in early life
www.nature.com/articles/s41...
I strongly recommend considering this opportunity to work with a great scientist and friend in an exceptional place.
I am starting a computational lab at LIOS, Riga, Latvia, and going to recruit a few people. Please DM if you are interested in a postdoc or PhD position in my Metabolic Research Group within the TARGETWISE project. I can highly recommend Riga, it is a beautiful city with very good living conditions.
July 23, 2025 at 5:01 PM
I strongly recommend considering this opportunity to work with a great scientist and friend in an exceptional place.
Reposted by Andrea Quagliariello
Detailed atlas reveals how #pesticides affect gut #bacteria and hints at #probiotic interventions ...
| #toxic | #microbes | #chemicals | #inflammation | Via @sciencex.bsky.social
| #toxic | #microbes | #chemicals | #inflammation | Via @sciencex.bsky.social
Detailed atlas reveals how pesticides affect gut bacteria and hints at probiotic interventions
While emerging evidence suggests pesticides can be toxic to the mix of microorganisms in the digestive system, a new study is the first to map changes to specific gut bacteria based on interactions between...
medicalxpress.com
June 30, 2025 at 5:00 AM
Detailed atlas reveals how #pesticides affect gut #bacteria and hints at #probiotic interventions ...
| #toxic | #microbes | #chemicals | #inflammation | Via @sciencex.bsky.social
| #toxic | #microbes | #chemicals | #inflammation | Via @sciencex.bsky.social
Reposted by Andrea Quagliariello
The Microbiota Vault Initiative: Safeguarding Earth's microbial heritage for future generations
#Microbiomes4Life @gilbertjacka.bsky.social
https://bit.ly/4kifmvX
#Microbiomes4Life @gilbertjacka.bsky.social
https://bit.ly/4kifmvX
June 27, 2025 at 11:13 AM
The Microbiota Vault Initiative: Safeguarding Earth's microbial heritage for future generations
#Microbiomes4Life @gilbertjacka.bsky.social
https://bit.ly/4kifmvX
#Microbiomes4Life @gilbertjacka.bsky.social
https://bit.ly/4kifmvX
Reposted by Andrea Quagliariello
Single-tooth prediction of childhood caries:
• Dental plaque microbiota patterns in children are predictive of tooth-specific caries development.
• Spatial-MiC model, integrating microbial and spatial data, improves caries forecasting with 93% accuracy
www.cell.com/cell-host-mi...
• Dental plaque microbiota patterns in children are predictive of tooth-specific caries development.
• Spatial-MiC model, integrating microbial and spatial data, improves caries forecasting with 93% accuracy
www.cell.com/cell-host-mi...
June 18, 2025 at 12:45 PM
Single-tooth prediction of childhood caries:
• Dental plaque microbiota patterns in children are predictive of tooth-specific caries development.
• Spatial-MiC model, integrating microbial and spatial data, improves caries forecasting with 93% accuracy
www.cell.com/cell-host-mi...
• Dental plaque microbiota patterns in children are predictive of tooth-specific caries development.
• Spatial-MiC model, integrating microbial and spatial data, improves caries forecasting with 93% accuracy
www.cell.com/cell-host-mi...
Reposted by Andrea Quagliariello
Let us introduce a new subspecies:
✨Catenibacterium mitsuokai subsp. tridentinum✨
Plus, we also propose a taxonomic reclassification of publicly available reference genomes belonging to the C. mitsuokai sp.
More details ⬇️
www.microbiologyresearch.org/content/jour...
✨Catenibacterium mitsuokai subsp. tridentinum✨
Plus, we also propose a taxonomic reclassification of publicly available reference genomes belonging to the C. mitsuokai sp.
More details ⬇️
www.microbiologyresearch.org/content/jour...
Description of Catenibacterium mitsuokai subsp. tridentinum subsp. nov., an anaerobic bacterium isolated from human faeces, and emended description of C. mitsuokai
A recent metagenomic survey has revealed an unknown bacterial clade within the Catenibacterium mitsuokai species to be significantly more prevalent in non-urbanized populations, compared to urbanized ...
www.microbiologyresearch.org
June 4, 2025 at 10:31 AM
Let us introduce a new subspecies:
✨Catenibacterium mitsuokai subsp. tridentinum✨
Plus, we also propose a taxonomic reclassification of publicly available reference genomes belonging to the C. mitsuokai sp.
More details ⬇️
www.microbiologyresearch.org/content/jour...
✨Catenibacterium mitsuokai subsp. tridentinum✨
Plus, we also propose a taxonomic reclassification of publicly available reference genomes belonging to the C. mitsuokai sp.
More details ⬇️
www.microbiologyresearch.org/content/jour...
NIH funding supporting the HMMER and Infernal software projects has been terminated. NIH states that our work, as well as all other federally funded research at Harvard, is of no benefit to the US.
May 29, 2025 at 7:43 AM
Reposted by Andrea Quagliariello
The UK Health Security Agency has released an updated antimicrobial stewardship tool to guide healthcare professionals in prescribing the most appropriate antimicrobial to patients to preserve antimicrobial efficacy. Find out more microb.io/452uTvL 👈 #KnockingOutAMR
Antibiotic 'Access' list updated for the UK
UKHSA has published an updated antimicrobial stewardship tool
microb.io
May 28, 2025 at 9:02 AM
The UK Health Security Agency has released an updated antimicrobial stewardship tool to guide healthcare professionals in prescribing the most appropriate antimicrobial to patients to preserve antimicrobial efficacy. Find out more microb.io/452uTvL 👈 #KnockingOutAMR
Reposted by Andrea Quagliariello
Genetic compatibility and environmental co-occurrence drive the dissemination of #AntibioticResistance genes
Co-occurrence of bacteria in the human #microbiome and #wastewater contributes to gene transfer
Co-occurrence of bacteria in the human #microbiome and #wastewater contributes to gene transfer
Genetic compatibility and ecological connectivity drive the dissemination of antibiotic resistance genes - Nature Communications
The dynamics of antimicrobial resistance gene transfer remain unclear. Here, by integrating bacterial genome and metagenome data with machine learning the authors show that genetic incompatibility is a main limiting factor, while co-occurrence of bacteria in the human microbiome and wastewater contributes to gene transfer.
bit.ly
May 26, 2025 at 8:48 AM
Genetic compatibility and environmental co-occurrence drive the dissemination of #AntibioticResistance genes
Co-occurrence of bacteria in the human #microbiome and #wastewater contributes to gene transfer
Co-occurrence of bacteria in the human #microbiome and #wastewater contributes to gene transfer
Reposted by Andrea Quagliariello
New online! A gut fungus protects the liver
A gut fungus protects the liver
Nature Reviews Microbiology, Published online: 21 May 2025; doi:10.1038/s41579-025-01194-7This study reports that that a gut fungus produces a secondary metabolite that protects against metabolic disease in mice.
www.nature.com
May 21, 2025 at 11:29 AM
New online! A gut fungus protects the liver
Reposted by Andrea Quagliariello
Save the date! Understanding and Predicting Microbial Evolutionary Dynamics 2025 will be held on 26-27 November in Liverpool: microb.io/MicroEvo25 #MicroEvo25
Understanding and predicting microbial evolutionary dynamics - 2025 meeting
26 - 27 November 2025 - Liverpool, UK
microb.io
May 6, 2025 at 8:01 AM
Save the date! Understanding and Predicting Microbial Evolutionary Dynamics 2025 will be held on 26-27 November in Liverpool: microb.io/MicroEvo25 #MicroEvo25
Reposted by Andrea Quagliariello
Did you know gut bacteria make vitamins? 🦠💊In #MMBR, discover mechanisms of microbiota vitamin biosynthesis, how interactions between microbiota members contribute to vitamin production, the role of diet and more. Read the review: asm.social/2mF
April 17, 2025 at 6:52 PM
Did you know gut bacteria make vitamins? 🦠💊In #MMBR, discover mechanisms of microbiota vitamin biosynthesis, how interactions between microbiota members contribute to vitamin production, the role of diet and more. Read the review: asm.social/2mF
Reposted by Andrea Quagliariello
🚨 Machine learning for multi-omics integration course with @oskolkov.bsky.social
This course covers key ML methods for integrating multi-omics data. Participants will learn how to apply supervised, unsupervised, and ML techniques to biological datasets.
www.physalia-courses.org/courses-work...
This course covers key ML methods for integrating multi-omics data. Participants will learn how to apply supervised, unsupervised, and ML techniques to biological datasets.
www.physalia-courses.org/courses-work...
Machine Learning for Multi-Omics Integration
9-11 June 2025 To foster international participation, this course will be held online
www.physalia-courses.org
April 10, 2025 at 6:47 AM
🚨 Machine learning for multi-omics integration course with @oskolkov.bsky.social
This course covers key ML methods for integrating multi-omics data. Participants will learn how to apply supervised, unsupervised, and ML techniques to biological datasets.
www.physalia-courses.org/courses-work...
This course covers key ML methods for integrating multi-omics data. Participants will learn how to apply supervised, unsupervised, and ML techniques to biological datasets.
www.physalia-courses.org/courses-work...
Reposted by Andrea Quagliariello
If you use Kraken for profiling microbial / environmental / ancient metagenomic data, please check this preprint where I benchmark filtering strategies of Kraken outputs on simulated microbial and environmental metagenomic samples, and provide recommendations for optimal filtering thresholds
April 10, 2025 at 6:57 AM
If you use Kraken for profiling microbial / environmental / ancient metagenomic data, please check this preprint where I benchmark filtering strategies of Kraken outputs on simulated microbial and environmental metagenomic samples, and provide recommendations for optimal filtering thresholds
Reposted by Andrea Quagliariello
Now online! 🖥️🧬🦠
A computational framework to integrate microbial GWAS and single-cell RNA-sequencing profiles of 24 human organs reveals interactions between the host cells and microbes
#MicroSky
www.nature.com/articles/s41...
A computational framework to integrate microbial GWAS and single-cell RNA-sequencing profiles of 24 human organs reveals interactions between the host cells and microbes
#MicroSky
www.nature.com/articles/s41...
Integrating microbial GWAS and single-cell transcriptomics reveals associations between host cell populations and the gut microbiome - Nature Microbiology
A computational framework to integrate microbial GWAS and single-cell RNA-sequencing profiles of 24 human organs reveals interactions between the host cells and microbes.
www.nature.com
April 7, 2025 at 11:42 AM
Now online! 🖥️🧬🦠
A computational framework to integrate microbial GWAS and single-cell RNA-sequencing profiles of 24 human organs reveals interactions between the host cells and microbes
#MicroSky
www.nature.com/articles/s41...
A computational framework to integrate microbial GWAS and single-cell RNA-sequencing profiles of 24 human organs reveals interactions between the host cells and microbes
#MicroSky
www.nature.com/articles/s41...
Reposted by Andrea Quagliariello
Delighted our study (7+ years in the making) is out today in Nature. In a nutshell, 48 hours of antibiotics in week 1 led to impaired vaccine responses up to 15 months later in infants. We show (in-vivo) a probiotic can fix it #microbiome #science #immunology
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Bifidobacteria support optimal infant vaccine responses - Nature
Neonatal antibiotic use is shown to reduce immune response to infant vaccines, accompanied by reduced abundance of Bifidobacteria in the gut microbiota, with experiments in mice indicating that probio...
www.nature.com
April 2, 2025 at 11:33 PM
Delighted our study (7+ years in the making) is out today in Nature. In a nutshell, 48 hours of antibiotics in week 1 led to impaired vaccine responses up to 15 months later in infants. We show (in-vivo) a probiotic can fix it #microbiome #science #immunology
www.nature.com/articles/s41...
www.nature.com/articles/s41...