Jaime Martinez-Urtaza
@jaimemurtaza.bsky.social
(Meta)genomics & evolution of human pathogens. Global health in a planet facing a climate emergency. All opinions are mine. Professor of Genetics at the Universitat Autònoma de Barcelona
Reposted by Jaime Martinez-Urtaza
Strain displacement in microbiomes via ecological competition
#microbes #ecology #microSky
www.nature.com/articles/s41...
#microbes #ecology #microSky
www.nature.com/articles/s41...
Strain displacement in microbiomes via ecological competition - Nature Microbiology
Mathematical modelling and experimental tests reveal principles that govern displacement of a resident strain by an invader in microbial communities.
www.nature.com
November 8, 2025 at 1:25 AM
Strain displacement in microbiomes via ecological competition
#microbes #ecology #microSky
www.nature.com/articles/s41...
#microbes #ecology #microSky
www.nature.com/articles/s41...
Reposted by Jaime Martinez-Urtaza
Hybridisation breaks species barriers in long-term coevolution of a cyanobacterial population.
buff.ly/EaJskBA
buff.ly/EaJskBA
November 2, 2025 at 11:28 PM
Hybridisation breaks species barriers in long-term coevolution of a cyanobacterial population.
buff.ly/EaJskBA
buff.ly/EaJskBA
Reposted by Jaime Martinez-Urtaza
New online! From clonality to complexity: a journey through microbial ecology and evolution
From clonality to complexity: a journey through microbial ecology and evolution
Nature Reviews Genetics, Published online: 30 October 2025; doi:10.1038/s41576-025-00910-6Jaime Martinez-Urtaza reflects on two papers by Smith et al., who found that bacteria exist along a continuum from clonal to recombining populations, and introduced the concept of an ‘epidemic’ microbial population structure.
www.nature.com
October 30, 2025 at 2:28 PM
New online! From clonality to complexity: a journey through microbial ecology and evolution
Reposted by Jaime Martinez-Urtaza
🚨 JUST PUBLISHED 🚨
⚠️ The 2025 @lancetcountdown.bsky.social report reveals climate change inaction is costing lives and livelihoods, and harming the economy.
❤️🩹 Protecting people’s health demands all hands on deck.
Read more: www.lancetcountdown.org/2025-report/ #LancetClimate25
⚠️ The 2025 @lancetcountdown.bsky.social report reveals climate change inaction is costing lives and livelihoods, and harming the economy.
❤️🩹 Protecting people’s health demands all hands on deck.
Read more: www.lancetcountdown.org/2025-report/ #LancetClimate25
October 29, 2025 at 12:23 AM
🚨 JUST PUBLISHED 🚨
⚠️ The 2025 @lancetcountdown.bsky.social report reveals climate change inaction is costing lives and livelihoods, and harming the economy.
❤️🩹 Protecting people’s health demands all hands on deck.
Read more: www.lancetcountdown.org/2025-report/ #LancetClimate25
⚠️ The 2025 @lancetcountdown.bsky.social report reveals climate change inaction is costing lives and livelihoods, and harming the economy.
❤️🩹 Protecting people’s health demands all hands on deck.
Read more: www.lancetcountdown.org/2025-report/ #LancetClimate25
Reposted by Jaime Martinez-Urtaza
Bacteria undergo rapid genetic changes that are selected by alterations in the human gut environment.
Learn more in a new #SciencePerspective: https://scim.ag/4qaRWNh
Learn more in a new #SciencePerspective: https://scim.ag/4qaRWNh
Natural directed evolution in gut microbiota
Bacteria undergo rapid genetic changes that are selected by alterations in the human gut environment
scim.ag
October 17, 2025 at 7:15 PM
Bacteria undergo rapid genetic changes that are selected by alterations in the human gut environment.
Learn more in a new #SciencePerspective: https://scim.ag/4qaRWNh
Learn more in a new #SciencePerspective: https://scim.ag/4qaRWNh
Reposted by Jaime Martinez-Urtaza
please read this thread - even if you don;t get time to read the paper!!!!! just the best - great work, really really great.
Delighted to see our paper studying the evolution of plasmids over the last 100 years, now out! Years of work by Adrian Cazares, also Nick Thomson @sangerinstitute.bsky.social - this version much improved over the preprint. Final version should be open access, apols.
Thread 1/n
Thread 1/n
September 25, 2025 at 9:48 PM
please read this thread - even if you don;t get time to read the paper!!!!! just the best - great work, really really great.
Reposted by Jaime Martinez-Urtaza
Delighted to announce that The International Meeting on the Biology of Vibrios will be back next year!
Vibrio2026 will be held in Berlin in September 13-16. See you there Vibriologists!
event.fourwaves.com/vibrio2026/p...
Vibrio2026 will be held in Berlin in September 13-16. See you there Vibriologists!
event.fourwaves.com/vibrio2026/p...
Vibrio2026: The International Meeting on the Biology of Vibrios
Fourwaves - Vibrio2026: The International Meeting on the Biology of Vibrios
event.fourwaves.com
September 18, 2025 at 6:24 PM
Delighted to announce that The International Meeting on the Biology of Vibrios will be back next year!
Vibrio2026 will be held in Berlin in September 13-16. See you there Vibriologists!
event.fourwaves.com/vibrio2026/p...
Vibrio2026 will be held in Berlin in September 13-16. See you there Vibriologists!
event.fourwaves.com/vibrio2026/p...
Reposted by Jaime Martinez-Urtaza
🚨 NEW: Climate change is already causing 30,000 deaths per year - a global annual economic loss of $100-350B USD - but the true damage is probably 10x higher. Out TODAY in Nature Climate Change: the first systematic look at the science of "health impact attribution" 🔓 www.nature.com/articles/s41...
September 17, 2025 at 11:57 AM
🚨 NEW: Climate change is already causing 30,000 deaths per year - a global annual economic loss of $100-350B USD - but the true damage is probably 10x higher. Out TODAY in Nature Climate Change: the first systematic look at the science of "health impact attribution" 🔓 www.nature.com/articles/s41...
Reposted by Jaime Martinez-Urtaza
Our “Less is more” story is out! 🚀 We reveal how gene loss shaped the adaptive evolution of pandemic Vibrio parahaemolyticus, highlight a potentially general mechanism across bacteria. Huge thanks @danielfalush.bsky.social @campy-bara.bsky.social @jaimemurtaza.bsky.social & all coauthors
Combination of large-scale phylogenomic analysis, mouse lethality experiments and bacterial growth assays shows sheds light on how a pandemic clone of Vibrio parahaemolyticus was able to spread worldwide
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Wave succession in the pandemic clone of Vibrio parahaemolyticus driven by gene loss - Nature Ecology & Evolution
A combination of large-scale phylogenomic analysis, mouse lethality experiments and bacterial growth assays shows that gene loss in the putrescine utilization pathway has enhanced biofilm formation an...
www.nature.com
August 27, 2025 at 1:06 PM
Our “Less is more” story is out! 🚀 We reveal how gene loss shaped the adaptive evolution of pandemic Vibrio parahaemolyticus, highlight a potentially general mechanism across bacteria. Huge thanks @danielfalush.bsky.social @campy-bara.bsky.social @jaimemurtaza.bsky.social & all coauthors
Reposted by Jaime Martinez-Urtaza
Combination of large-scale phylogenomic analysis, mouse lethality experiments and bacterial growth assays shows sheds light on how a pandemic clone of Vibrio parahaemolyticus was able to spread worldwide
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Wave succession in the pandemic clone of Vibrio parahaemolyticus driven by gene loss - Nature Ecology & Evolution
A combination of large-scale phylogenomic analysis, mouse lethality experiments and bacterial growth assays shows that gene loss in the putrescine utilization pathway has enhanced biofilm formation an...
www.nature.com
August 27, 2025 at 11:04 AM
Combination of large-scale phylogenomic analysis, mouse lethality experiments and bacterial growth assays shows sheds light on how a pandemic clone of Vibrio parahaemolyticus was able to spread worldwide
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Jaime Martinez-Urtaza
Beautiful work on the emergence of the pandemic clone of V. parahaemolyticus
Combination of large-scale phylogenomic analysis, mouse lethality experiments and bacterial growth assays shows sheds light on how a pandemic clone of Vibrio parahaemolyticus was able to spread worldwide
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Wave succession in the pandemic clone of Vibrio parahaemolyticus driven by gene loss - Nature Ecology & Evolution
A combination of large-scale phylogenomic analysis, mouse lethality experiments and bacterial growth assays shows that gene loss in the putrescine utilization pathway has enhanced biofilm formation an...
www.nature.com
August 27, 2025 at 11:21 AM
Beautiful work on the emergence of the pandemic clone of V. parahaemolyticus
Reposted by Jaime Martinez-Urtaza
How to get introgressed fragments in genomic data? Everything you always wanted to know you find in our review in @cp-trendsgenetics.bsky.social, led by Xin Huang:
doi.org/10.1016/j.ti...
doi.org/10.1016/j.ti...
July 24, 2025 at 2:04 AM
How to get introgressed fragments in genomic data? Everything you always wanted to know you find in our review in @cp-trendsgenetics.bsky.social, led by Xin Huang:
doi.org/10.1016/j.ti...
doi.org/10.1016/j.ti...
Reposted by Jaime Martinez-Urtaza
Really excited to share the first paper from my PhD - it’s all about assumptions in modelling and the history of early population genetics… 🧵
doi.org/10.1111/ahg....
doi.org/10.1111/ahg....
The History of the Panmictic Population Concept and Its Legacy in Contemporary Population Genetics
ABSTRACT The panmictic population concept is at the heart of population, evolutionary and conservation genetics. However, in nature, true panmictic populations are vanishingly rare. As an idea conce...
doi.org
August 1, 2025 at 10:48 PM
Really excited to share the first paper from my PhD - it’s all about assumptions in modelling and the history of early population genetics… 🧵
doi.org/10.1111/ahg....
doi.org/10.1111/ahg....
Reposted by Jaime Martinez-Urtaza
Long et al. integrate population genomics, experimental evolution, and environmental modeling to elucidate the evolutionary responses to climate change in Populus lasiocarpa.
This study has made the July cover of MBE.
🔗 doi.org/10.1093/molbev/msaf116
#evobio #molbio
This study has made the July cover of MBE.
🔗 doi.org/10.1093/molbev/msaf116
#evobio #molbio
July 20, 2025 at 6:13 AM
Long et al. integrate population genomics, experimental evolution, and environmental modeling to elucidate the evolutionary responses to climate change in Populus lasiocarpa.
This study has made the July cover of MBE.
🔗 doi.org/10.1093/molbev/msaf116
#evobio #molbio
This study has made the July cover of MBE.
🔗 doi.org/10.1093/molbev/msaf116
#evobio #molbio
Reposted by Jaime Martinez-Urtaza
Happy to share the preprint from here in Shanghai, together with @danielfalush.bsky.social, as well as with team Zhizhou Jia, Huqi Wen, and Zhe Xie!
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Evolution of hunt, kill, devour in a Vibrio ecospecies
Bacterial ecospecies are a recently recognized genetic structure that is hypothesized to arise by complex adaptation to a new niche. Using coadaptation analysis as a foundation for laboratory experime...
www.biorxiv.org
June 30, 2025 at 7:45 AM
Happy to share the preprint from here in Shanghai, together with @danielfalush.bsky.social, as well as with team Zhizhou Jia, Huqi Wen, and Zhe Xie!
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Jaime Martinez-Urtaza
Cleanifier: A fast and lightweight k-mer based tool to remove contamination in microbial sequence data. #MicrobialSequences #ContaminationRemoval #Kmers #Genomics #Bioinformatics @biorxivpreprint
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
July 1, 2025 at 8:31 AM
Cleanifier: A fast and lightweight k-mer based tool to remove contamination in microbial sequence data. #MicrobialSequences #ContaminationRemoval #Kmers #Genomics #Bioinformatics @biorxivpreprint
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Jaime Martinez-Urtaza
🥁NEW publication from our lab:
the largest meta-analysis of gut microbiome associations with CRC!
www.nature.com/articles/s41...
🧵⬇️
1/6
the largest meta-analysis of gut microbiome associations with CRC!
www.nature.com/articles/s41...
🧵⬇️
1/6
Pooled analysis of 3,741 stool metagenomes from 18 cohorts for cross-stage and strain-level reproducible microbial biomarkers of colorectal cancer - Nature Medicine
An analysis of 18 metagenomic datasets of individuals with colorectal cancer, adenomas and healthy controls yields improved cancer prediction accuracy based solely on gut metagenomics, as well as the ...
www.nature.com
June 3, 2025 at 10:43 AM
🥁NEW publication from our lab:
the largest meta-analysis of gut microbiome associations with CRC!
www.nature.com/articles/s41...
🧵⬇️
1/6
the largest meta-analysis of gut microbiome associations with CRC!
www.nature.com/articles/s41...
🧵⬇️
1/6
Reposted by Jaime Martinez-Urtaza
🚨 Out now!
Chronostrain - a method to profile low abundance strains in longitudinal microbiome samples 🦠💻
@travis.gibsonlab.io @younhk.bsky.social @gibsonlab.io @harvardmed.bsky.social @broadinstitute.org
#MicroSky 🦠 #MicrobiomeSky
www.nature.com/articles/s41...
Chronostrain - a method to profile low abundance strains in longitudinal microbiome samples 🦠💻
@travis.gibsonlab.io @younhk.bsky.social @gibsonlab.io @harvardmed.bsky.social @broadinstitute.org
#MicroSky 🦠 #MicrobiomeSky
www.nature.com/articles/s41...
Longitudinal profiling of low-abundance strains in microbiomes with ChronoStrain - Nature Microbiology
ChronoStrain accurately profiles low-abundance strains in longitudinal samples by jointly modelling nucleotide sequencing errors, strain presence/absence and the temporal information associated with e...
www.nature.com
May 6, 2025 at 6:54 PM
🚨 Out now!
Chronostrain - a method to profile low abundance strains in longitudinal microbiome samples 🦠💻
@travis.gibsonlab.io @younhk.bsky.social @gibsonlab.io @harvardmed.bsky.social @broadinstitute.org
#MicroSky 🦠 #MicrobiomeSky
www.nature.com/articles/s41...
Chronostrain - a method to profile low abundance strains in longitudinal microbiome samples 🦠💻
@travis.gibsonlab.io @younhk.bsky.social @gibsonlab.io @harvardmed.bsky.social @broadinstitute.org
#MicroSky 🦠 #MicrobiomeSky
www.nature.com/articles/s41...
Reposted by Jaime Martinez-Urtaza
Strain tracking in complex microbiomes using synteny analysis reveals per-species modes of evolution
@natbiotech.nature.com from @microbiome.bsky.social
www.nature.com/articles/s41...
@natbiotech.nature.com from @microbiome.bsky.social
www.nature.com/articles/s41...
Strain tracking in complex microbiomes using synteny analysis reveals per-species modes of evolution - Nature Biotechnology
The evolution of microbial strains is revealed by analyzing structural variation.
www.nature.com
May 17, 2025 at 7:35 AM
Strain tracking in complex microbiomes using synteny analysis reveals per-species modes of evolution
@natbiotech.nature.com from @microbiome.bsky.social
www.nature.com/articles/s41...
@natbiotech.nature.com from @microbiome.bsky.social
www.nature.com/articles/s41...
Reposted by Jaime Martinez-Urtaza
RAxML-NG v2.0 beta is here
github.com/amkozlov/rax...
Features
1. Difficulty prediction
academic.oup.com/mbe/article/...
2. Adaptive search academic.oup.com/mbe/article/...
3. Early Stop
www.biorxiv.org/content/10.1...
4. Model selection
5. Rapid bootstrapping academic.oup.com/mbe/article/...
github.com/amkozlov/rax...
Features
1. Difficulty prediction
academic.oup.com/mbe/article/...
2. Adaptive search academic.oup.com/mbe/article/...
3. Early Stop
www.biorxiv.org/content/10.1...
4. Model selection
5. Rapid bootstrapping academic.oup.com/mbe/article/...
Release RAxML-NG v2.0-beta2 · amkozlov/raxml-ng
Main new features
Adaptive tree search heuristic (Togkousidis 2023) , (Togkousidis 2024)
Multiple fast branch support measures
Integrated model testing
Full Changelog: 1.2.2...2.0-beta2
github.com
May 15, 2025 at 5:35 AM
RAxML-NG v2.0 beta is here
github.com/amkozlov/rax...
Features
1. Difficulty prediction
academic.oup.com/mbe/article/...
2. Adaptive search academic.oup.com/mbe/article/...
3. Early Stop
www.biorxiv.org/content/10.1...
4. Model selection
5. Rapid bootstrapping academic.oup.com/mbe/article/...
github.com/amkozlov/rax...
Features
1. Difficulty prediction
academic.oup.com/mbe/article/...
2. Adaptive search academic.oup.com/mbe/article/...
3. Early Stop
www.biorxiv.org/content/10.1...
4. Model selection
5. Rapid bootstrapping academic.oup.com/mbe/article/...
Reposted by Jaime Martinez-Urtaza
Detection of viral sequences at single-cell resolution identifies novel viruses associated with host gene expression changes - @lauraluebbert.com @lpachter.bsky.social go.nature.com/4lGrSY3
Detection of viral sequences at single-cell resolution identifies novel viruses associated with host gene expression changes - Nature Biotechnology
A workflow using conserved amino acid domains identifies viruses in sequence data at single-cell resolution.
go.nature.com
April 22, 2025 at 1:04 PM
Detection of viral sequences at single-cell resolution identifies novel viruses associated with host gene expression changes - @lauraluebbert.com @lpachter.bsky.social go.nature.com/4lGrSY3
Reposted by Jaime Martinez-Urtaza
New genomic & genetic insights into Mendel’s pea genes, including previously uncharacterised alleles
159 years after Mendel published his work, this is a real delight (especially for a geneticist)
🧪
@nature.com
www.nature.com/articles/s41...
159 years after Mendel published his work, this is a real delight (especially for a geneticist)
🧪
@nature.com
www.nature.com/articles/s41...
Genomic and genetic insights into Mendel’s pea genes - Nature
Characterization of the genetic architecture underlying the 7 pairs of contrasting traits studied by Mendel and the over 70 additional agronomic traits in pea (Pisum sativum) reveals their m...
www.nature.com
April 24, 2025 at 5:38 AM
New genomic & genetic insights into Mendel’s pea genes, including previously uncharacterised alleles
159 years after Mendel published his work, this is a real delight (especially for a geneticist)
🧪
@nature.com
www.nature.com/articles/s41...
159 years after Mendel published his work, this is a real delight (especially for a geneticist)
🧪
@nature.com
www.nature.com/articles/s41...
Reposted by Jaime Martinez-Urtaza
This new Hifiasm --ont option is amazing. It worked like a charm for us in the nanopore adaptive sampling based assembly paradigm we introduced in a preprint recently.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
April 19, 2025 at 2:31 AM
This new Hifiasm --ont option is amazing. It worked like a charm for us in the nanopore adaptive sampling based assembly paradigm we introduced in a preprint recently.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Jaime Martinez-Urtaza
Our rising seas. This is only going to get harder to ignore.
This NASA visualization was created by svs.gsfc.nasa.gov/5520/
This NASA visualization was created by svs.gsfc.nasa.gov/5520/
April 13, 2025 at 2:22 AM
Our rising seas. This is only going to get harder to ignore.
This NASA visualization was created by svs.gsfc.nasa.gov/5520/
This NASA visualization was created by svs.gsfc.nasa.gov/5520/
Reposted by Jaime Martinez-Urtaza
Ocean heat content (OHC) in 2024
Global full-depth OHC gain since 1960 reached a record 452 ± 77 zetajoules (ZJ) in 2024. OHC was 15 ± 9 ZJ higher than in 2023, primarily associated with warming in the Atlantic and Indian Oceans
1 ZJ = 1,000,000,000,000,000,000,000 J
www.nature.com/articles/s43...
Global full-depth OHC gain since 1960 reached a record 452 ± 77 zetajoules (ZJ) in 2024. OHC was 15 ± 9 ZJ higher than in 2023, primarily associated with warming in the Atlantic and Indian Oceans
1 ZJ = 1,000,000,000,000,000,000,000 J
www.nature.com/articles/s43...
Ocean heat content in 2024 - Nature Reviews Earth & Environment
Global full-depth ocean heat content (OHC) gain since 1960 reached a record 452 ± 77 ZJ in 2024. OHC was 15 ± 9 ZJ higher than in 2023, primarily associated with warming in the Atlantic and Indian Oce...
www.nature.com
April 13, 2025 at 6:18 AM
Ocean heat content (OHC) in 2024
Global full-depth OHC gain since 1960 reached a record 452 ± 77 zetajoules (ZJ) in 2024. OHC was 15 ± 9 ZJ higher than in 2023, primarily associated with warming in the Atlantic and Indian Oceans
1 ZJ = 1,000,000,000,000,000,000,000 J
www.nature.com/articles/s43...
Global full-depth OHC gain since 1960 reached a record 452 ± 77 zetajoules (ZJ) in 2024. OHC was 15 ± 9 ZJ higher than in 2023, primarily associated with warming in the Atlantic and Indian Oceans
1 ZJ = 1,000,000,000,000,000,000,000 J
www.nature.com/articles/s43...