Yishay Pinto
@yishay.bsky.social
Computational biologist. Studying genomes of phages and microbes.
https://scholar.google.com/citations?user=nYRQiRMAAAAJ&hl=en
https://scholar.google.com/citations?user=nYRQiRMAAAAJ&hl=en
Pinned
Yishay Pinto
@yishay.bsky.social
· Nov 19
Sequencing-based analysis of microbiomes - Nature Reviews Genetics
In this Review, Pinto and Bhatt provide an overview of DNA-sequencing and RNA-sequencing approaches that can be used to study the composition, structure, and function of microbiomes and discuss the bi...
go.nature.com
1/ Our review on sequencing-based #microbiome analysis is in the Dec 24 issue of Nature Reviews Genetics. We explore DNA/RNA-sequencing approaches for studying microbiome structure and function, highlighting the biological insights sequencing-based microbiome research offers.
go.nature.com/3XFqonu
go.nature.com/3XFqonu
Reposted by Yishay Pinto
🚨New preprint out!
We present a foundational genomic resource of human gut microbiome viruses. It delivers high-quality, deeply curated data spanning taxonomy, predicted hosts, structures, and functions, providing a reference for gut virome research. (1/8)
www.biorxiv.org/content/10.1...
We present a foundational genomic resource of human gut microbiome viruses. It delivers high-quality, deeply curated data spanning taxonomy, predicted hosts, structures, and functions, providing a reference for gut virome research. (1/8)
www.biorxiv.org/content/10.1...
November 6, 2025 at 5:26 PM
🚨New preprint out!
We present a foundational genomic resource of human gut microbiome viruses. It delivers high-quality, deeply curated data spanning taxonomy, predicted hosts, structures, and functions, providing a reference for gut virome research. (1/8)
www.biorxiv.org/content/10.1...
We present a foundational genomic resource of human gut microbiome viruses. It delivers high-quality, deeply curated data spanning taxonomy, predicted hosts, structures, and functions, providing a reference for gut virome research. (1/8)
www.biorxiv.org/content/10.1...
Reposted by Yishay Pinto
🐝🦠 New paper: rdcu.be/eOf7A
Phages may drive microbial diversity, yet we often don’t even know how phages & bacteria correlate in nature. Our new study tackles this in the honeybee gut, thanks to the great work of PhD student @malickndiaye.bsky.social at @dmf-unil.bsky.social @fbm-unil.bsky.social
Phages may drive microbial diversity, yet we often don’t even know how phages & bacteria correlate in nature. Our new study tackles this in the honeybee gut, thanks to the great work of PhD student @malickndiaye.bsky.social at @dmf-unil.bsky.social @fbm-unil.bsky.social
Phage diversity mirrors bacterial strain diversity in the honey bee gut microbiota - Nature Communications
Authors analyse paired viral and bacterial shotgun metagenomics data from individual honeybee guts, revealing modular, nested phage–bacteria networks, with viral diversity mirroring bacterial strain c...
www.nature.com
November 4, 2025 at 8:36 PM
🐝🦠 New paper: rdcu.be/eOf7A
Phages may drive microbial diversity, yet we often don’t even know how phages & bacteria correlate in nature. Our new study tackles this in the honeybee gut, thanks to the great work of PhD student @malickndiaye.bsky.social at @dmf-unil.bsky.social @fbm-unil.bsky.social
Phages may drive microbial diversity, yet we often don’t even know how phages & bacteria correlate in nature. Our new study tackles this in the honeybee gut, thanks to the great work of PhD student @malickndiaye.bsky.social at @dmf-unil.bsky.social @fbm-unil.bsky.social
Reposted by Yishay Pinto
The average nucleotide identity (ANI) underpins how we map microbial diversity, compare species, and connect genomes to ecology.
I wrote a short piece reflecting on the discovery and significance of this metric (and really enjoyed digging into the context and story behind it!) #microsky 🧬
I wrote a short piece reflecting on the discovery and significance of this metric (and really enjoyed digging into the context and story behind it!) #microsky 🧬
Average nucleotide identity — the backbone of modern ecological genomics - Nature Reviews Genetics
In this Journal Club, Luis Orellana recalls a 2005 publication by Konstantinidis and Tiedje that introduced average nucleotide identity as a sequence-based metric to determine the relatedness between ...
www.nature.com
October 30, 2025 at 9:11 PM
The average nucleotide identity (ANI) underpins how we map microbial diversity, compare species, and connect genomes to ecology.
I wrote a short piece reflecting on the discovery and significance of this metric (and really enjoyed digging into the context and story behind it!) #microsky 🧬
I wrote a short piece reflecting on the discovery and significance of this metric (and really enjoyed digging into the context and story behind it!) #microsky 🧬
Fantastic piece of research that discovered the atypical lifestyle of the prototypic crAssphage. This project showcased so much determination, brilliance, and open-mindedness, proving that great discoveries are made by following the evidence wherever it leads.
The prototypic crAssphage is a linear phage-plasmid
New work demonstrates that C. communis, a ubiquitous human gut phage that evades conventional plaque-based isolation, predominately replicates as a low-copy linear phage-plasmid w/ broad host range
www.cell.com/cell-host-mi...
New work demonstrates that C. communis, a ubiquitous human gut phage that evades conventional plaque-based isolation, predominately replicates as a low-copy linear phage-plasmid w/ broad host range
www.cell.com/cell-host-mi...
The prototypic crAssphage is a linear phage-plasmid
Schmidtke et al. demonstrate that C. communis, a ubiquitous human gut phage that evades
conventional plaque-based isolation, predominately replicates as a low-copy linear
phage-plasmid with a broad ho...
www.cell.com
August 15, 2025 at 7:58 AM
Fantastic piece of research that discovered the atypical lifestyle of the prototypic crAssphage. This project showcased so much determination, brilliance, and open-mindedness, proving that great discoveries are made by following the evidence wherever it leads.
Reposted by Yishay Pinto
Phage people - does anyone have a lambda phage with a deletion/mutation in the integrase gene (unable to lysogenize)? If so, can you please share it with us to help us test a cool hypothesis?
Thanks!
Please RT. 🦠🙏
Thanks!
Please RT. 🦠🙏
a cartoon character from south park says " i m gonna need your help "
ALT: a cartoon character from south park says " i m gonna need your help "
media.tenor.com
April 18, 2025 at 9:10 AM
Phage people - does anyone have a lambda phage with a deletion/mutation in the integrase gene (unable to lysogenize)? If so, can you please share it with us to help us test a cool hypothesis?
Thanks!
Please RT. 🦠🙏
Thanks!
Please RT. 🦠🙏
Reposted by Yishay Pinto
Replicative selfish genetic elements are driving rapid pathogenic adaptation of Enterococcus faecium https://www.biorxiv.org/content/10.1101/2025.03.16.643550v1
March 17, 2025 at 3:16 AM
Replicative selfish genetic elements are driving rapid pathogenic adaptation of Enterococcus faecium https://www.biorxiv.org/content/10.1101/2025.03.16.643550v1
Talking about read-based methods to profile phages in metagenomes, check out Marker-MAGu by @miketisza.bsky.social —a marker gene-based method for identifying phages.
bsky.app/profile/natu...
bsky.app/profile/natu...
Check out my "tools of the trade" piece on Phanta! I cover the need it addresses (phage inclusion in microbiome studies), the features we prioritized (sensitivity & ease of use), our vision (phage profiling as the norm), and the future we envision.
Check it out and try Phanta!
tinyurl.com/ToTPhanta
Check it out and try Phanta!
tinyurl.com/ToTPhanta
Beyond bacteria: Phanta adds flavour to microbiome profiling with a focus on phages - Nature Reviews Immunology
In this Tools of the Trade article, Yishay Pinto describes a tool, called Phanta, that profiles phages alongside their bacterial hosts in microbiome analysis.
www.nature.com
January 31, 2025 at 3:13 AM
Talking about read-based methods to profile phages in metagenomes, check out Marker-MAGu by @miketisza.bsky.social —a marker gene-based method for identifying phages.
bsky.app/profile/natu...
bsky.app/profile/natu...
Check out my "tools of the trade" piece on Phanta! I cover the need it addresses (phage inclusion in microbiome studies), the features we prioritized (sensitivity & ease of use), our vision (phage profiling as the norm), and the future we envision.
Check it out and try Phanta!
tinyurl.com/ToTPhanta
Check it out and try Phanta!
tinyurl.com/ToTPhanta
Beyond bacteria: Phanta adds flavour to microbiome profiling with a focus on phages - Nature Reviews Immunology
In this Tools of the Trade article, Yishay Pinto describes a tool, called Phanta, that profiles phages alongside their bacterial hosts in microbiome analysis.
www.nature.com
January 28, 2025 at 7:48 PM
Check out my "tools of the trade" piece on Phanta! I cover the need it addresses (phage inclusion in microbiome studies), the features we prioritized (sensitivity & ease of use), our vision (phage profiling as the norm), and the future we envision.
Check it out and try Phanta!
tinyurl.com/ToTPhanta
Check it out and try Phanta!
tinyurl.com/ToTPhanta
Reposted by Yishay Pinto
This paper has been a long time coming: We looked at the genomes of historical bacterial samples over a century to look for trends of antibiotic resistance genes, finding multiple instances of them in infections before the age of antibiotics, but an increase in both frequency and mobility after
Genomic resistance in historical clinical isolates increased in frequency and mobility after the age of antibiotics https://www.biorxiv.org/content/10.1101/2025.01.16.633422v1
January 17, 2025 at 8:53 PM
This paper has been a long time coming: We looked at the genomes of historical bacterial samples over a century to look for trends of antibiotic resistance genes, finding multiple instances of them in infections before the age of antibiotics, but an increase in both frequency and mobility after
Reposted by Yishay Pinto
Starter pack for metagenomics and microbial genomics lovers.
go.bsky.app/MFipoLH
go.bsky.app/MFipoLH
November 15, 2024 at 2:51 AM
Starter pack for metagenomics and microbial genomics lovers.
go.bsky.app/MFipoLH
go.bsky.app/MFipoLH
Reposted by Yishay Pinto
I'm putting together a Microbial Bioinformatics starter pack to help get everyone connected in our community. Let me know if there are any bluesky users to be added and share so that twitter refugees can tune back in to the fantastic world microbes go.bsky.app/3ezLo7e
January 10, 2025 at 9:38 AM
I'm putting together a Microbial Bioinformatics starter pack to help get everyone connected in our community. Let me know if there are any bluesky users to be added and share so that twitter refugees can tune back in to the fantastic world microbes go.bsky.app/3ezLo7e
Reposted by Yishay Pinto
In the spirit of summaries, simple rules that, if everyone followed, would make academic publishing less painful in 2025.
As a reviewer:
*Separate major and minor comments
*Write your explicit recommendation in the "for authors" section
*If co-reviewing with trainees, read the paper yourself
1/2
As a reviewer:
*Separate major and minor comments
*Write your explicit recommendation in the "for authors" section
*If co-reviewing with trainees, read the paper yourself
1/2
Time for the annual peer-review summary! I did 46 peer reviews in 2024. A busier year than 2022-23, but still sub-2021 levels. This year I attempted to review revisions same-day, which worked ~75% of the time (the other 25% took way longer...).
December 31, 2024 at 9:43 PM
In the spirit of summaries, simple rules that, if everyone followed, would make academic publishing less painful in 2025.
As a reviewer:
*Separate major and minor comments
*Write your explicit recommendation in the "for authors" section
*If co-reviewing with trainees, read the paper yourself
1/2
As a reviewer:
*Separate major and minor comments
*Write your explicit recommendation in the "for authors" section
*If co-reviewing with trainees, read the paper yourself
1/2
Reposted by Yishay Pinto
Empathi: Embedding-based Phage Protein Annotation Tool by Hierarchical Assignment [new]
Empathi: Classifies phage proteins using embeddings, IDs multi-func.
Empathi: Classifies phage proteins using embeddings, IDs multi-func.
January 1, 2025 at 10:18 PM
Empathi: Embedding-based Phage Protein Annotation Tool by Hierarchical Assignment [new]
Empathi: Classifies phage proteins using embeddings, IDs multi-func.
Empathi: Classifies phage proteins using embeddings, IDs multi-func.
Reposted by Yishay Pinto
What a great way to end the year! ✨
Today in @cellpress.bsky.social we report the structure and function of the Shedu anti-phage defense system.
tinyurl.com/4crj6dnx
A long 🧵...
Today in @cellpress.bsky.social we report the structure and function of the Shedu anti-phage defense system.
tinyurl.com/4crj6dnx
A long 🧵...
December 31, 2024 at 3:38 PM
What a great way to end the year! ✨
Today in @cellpress.bsky.social we report the structure and function of the Shedu anti-phage defense system.
tinyurl.com/4crj6dnx
A long 🧵...
Today in @cellpress.bsky.social we report the structure and function of the Shedu anti-phage defense system.
tinyurl.com/4crj6dnx
A long 🧵...
Reposted by Yishay Pinto
Reposted by Yishay Pinto
We wrote a new review paper in @cp-trendsmicrobiol.bsky.social on recently developed bioinformatic tools that facilitate elucidating protein functions in the era of big genomics data.
www.sciencedirect.com/science/arti...
This is the 1st paper of 2 talented students Shani Cheskis and Avital Akerman.
www.sciencedirect.com/science/arti...
This is the 1st paper of 2 talented students Shani Cheskis and Avital Akerman.
Deciphering bacterial protein functions with innovative computational methods
Bacteria colonize every niche on Earth and play key roles in many environmental and host-associated processes. The sequencing revolution revealed the …
www.sciencedirect.com
December 30, 2024 at 6:02 AM
We wrote a new review paper in @cp-trendsmicrobiol.bsky.social on recently developed bioinformatic tools that facilitate elucidating protein functions in the era of big genomics data.
www.sciencedirect.com/science/arti...
This is the 1st paper of 2 talented students Shani Cheskis and Avital Akerman.
www.sciencedirect.com/science/arti...
This is the 1st paper of 2 talented students Shani Cheskis and Avital Akerman.
Reposted by Yishay Pinto
Reposted by Yishay Pinto
New paper from the Faber lab in @plosbiology.org characterizing the C. difficle ncRNA ModT, with effects on sporulation and the transition into stationary phase, evidence for RBP association -- and similar abundance to some ribosomal RNAs! 🧫🦠 journals.plos.org/plosbiology/...
The conserved noncoding RNA ModT coordinates growth and virulence in Clostridioides difficile
Bacterial non-coding RNAs influence various cellular functions and often have complex tertiary structures. This study characterizes ModT, a conserved ncRNA found in 2,500 bacterial species, found to r...
journals.plos.org
December 16, 2024 at 4:32 PM
New paper from the Faber lab in @plosbiology.org characterizing the C. difficle ncRNA ModT, with effects on sporulation and the transition into stationary phase, evidence for RBP association -- and similar abundance to some ribosomal RNAs! 🧫🦠 journals.plos.org/plosbiology/...
Reposted by Yishay Pinto
Feel like this paper slipped under the radar on ‘the other platform’ so giving it another airing here. Phage can significantly remodel the bacteriome in faecal samples - yet another confounder 🙄 www.sciencedirect.com/science/arti...
Dynamic nature of viral and bacterial communities in human faeces
Bacteriophages are a major component of the gut microbiome and are believed to play a role in establishment and stabilization of microbial communities…
www.sciencedirect.com
December 4, 2024 at 1:29 PM
Feel like this paper slipped under the radar on ‘the other platform’ so giving it another airing here. Phage can significantly remodel the bacteriome in faecal samples - yet another confounder 🙄 www.sciencedirect.com/science/arti...
Reposted by Yishay Pinto
Prophage induction contributes to alterations in the gut phageome during intestinal inflammation https://www.biorxiv.org/content/10.1101/2024.12.03.626644v1
Prophage induction contributes to alterations in the gut phageome during intestinal inflammation https://www.biorxiv.org/content/10.1101/2024.12.03.626644v1
Bacteriophages (phages) are abundant members of the gut microbiota and regulators of bacterial commu
www.biorxiv.org
December 4, 2024 at 2:18 AM
Prophage induction contributes to alterations in the gut phageome during intestinal inflammation https://www.biorxiv.org/content/10.1101/2024.12.03.626644v1
Reposted by Yishay Pinto
Exploring the diverse RNA #virome in urban freshwater ecosystems, this study uncovers novel viruses with recombinant genomes, expanding our knowledge of virus diversity. #Metagenomics #FreshwaterEcology #ViralDiversity
📄 doi.org/10.3390/micr...
EVBC👤: R. Zell
📄 doi.org/10.3390/micr...
EVBC👤: R. Zell
Metagenomic Analyses of Water Samples of Two Urban Freshwaters in Berlin, Germany, Reveal New Highly Diverse Invertebrate Viruses
In an attempt to explore the RNA viromes of two German rivers, we searched the virus particle contents of one 50 L water sample each from the Teltow Canal and the Havel River for viruses assumed to in...
doi.org
December 3, 2024 at 12:44 PM
Exploring the diverse RNA #virome in urban freshwater ecosystems, this study uncovers novel viruses with recombinant genomes, expanding our knowledge of virus diversity. #Metagenomics #FreshwaterEcology #ViralDiversity
📄 doi.org/10.3390/micr...
EVBC👤: R. Zell
📄 doi.org/10.3390/micr...
EVBC👤: R. Zell
Reposted by Yishay Pinto
Scientists, academics, researchers: We’re excited to share that @altmetric.com is now tracking mentions of your research on Bluesky! 🧪
There are already many articles for which there is more attention on Bluesky than on other comparable micro-blogging sites, meaning the academic community and the general public have clearly adopted Bluesky as one of its core places to disseminate and discuss new research.
A Place of Joy.
A Place of Joy.
December 3, 2024 at 2:10 PM
Scientists, academics, researchers: We’re excited to share that @altmetric.com is now tracking mentions of your research on Bluesky! 🧪
Reposted by Yishay Pinto
Excited to share our work on broadly effective phage-antibiotic cocktails. We report 4 cocktails that each work against 96% of 153 antibiotic resistant Pseudomonas isolates. Check it out here: www.nature.com/articles/s41... Congrats to Kevin Kim @KevinMinyo6651
A blueprint for broadly effective bacteriophage-antibiotic cocktails against bacterial infections - Nature Communications
The application of phage therapy for multidrug-resistant infections is mainly limited to personalized therapy due to the narrow host range of individual phages. Here, Kim et al. identify groups of pha...
www.nature.com
December 2, 2024 at 6:36 AM
Excited to share our work on broadly effective phage-antibiotic cocktails. We report 4 cocktails that each work against 96% of 153 antibiotic resistant Pseudomonas isolates. Check it out here: www.nature.com/articles/s41... Congrats to Kevin Kim @KevinMinyo6651
Reposted by Yishay Pinto
Identification and Mitigation of microbial contaminant reads from long-read metagenomic samples https://www.biorxiv.org/content/10.1101/2024.11.26.625374v1
Identification and Mitigation of microbial contaminant reads from long-read metagenomic samples https://www.biorxiv.org/content/10.1101/2024.11.26.625374v1
Metagenomic sequencing has revolutionized our understanding of microbial communities, but the presen
www.biorxiv.org
December 2, 2024 at 3:47 AM
Identification and Mitigation of microbial contaminant reads from long-read metagenomic samples https://www.biorxiv.org/content/10.1101/2024.11.26.625374v1