Tom Hitch
@tcahitch.bsky.social
Bioinformatician focused on the gut microbiome. Post-doc at Uniklinik RWTH Aachen within the AG Clavel group. He/Him/They
Want to delineate genera? We have been optimising POCP, and propose POCPu, which stops the 'double counting' of proteins in POCP by only allowing unique matches. We also speed up, and benchmarked, the analysis using DIAMOND; peerj.com/articles/202... (now implemented in Protologger)
Fast and robust estimate of bacterial genus novelty using the percentage of conserved proteins with unique matches (POCPu)
Accurate taxonomic assignment of bacterial genomes is essential for identifying novel taxa and for stable classification to enable robust comparison between studies. Bacterial genus delineation relies...
peerj.com
November 14, 2025 at 9:31 AM
Want to delineate genera? We have been optimising POCP, and propose POCPu, which stops the 'double counting' of proteins in POCP by only allowing unique matches. We also speed up, and benchmarked, the analysis using DIAMOND; peerj.com/articles/202... (now implemented in Protologger)
Reposted by Tom Hitch
Is the human microbiome a source for hospital-associated infections (HAI) and are any genetic changes associated with HAI? In our new preprint, we longitudinally reconstruct the evolutionary processes within the human microbiome leading up to HAI: doi.org/10.1101/2025...
Colonization, translocation, and evolution of opportunistic pathogens during hospital-associated infections
Many commensal bacteria that peacefully reside in the human microbiome are also able to cause acute opportunistic infections. Emerging evidence suggests that within-host evolution contributes to infec...
doi.org
October 27, 2025 at 9:25 AM
Is the human microbiome a source for hospital-associated infections (HAI) and are any genetic changes associated with HAI? In our new preprint, we longitudinally reconstruct the evolutionary processes within the human microbiome leading up to HAI: doi.org/10.1101/2025...
Reposted by Tom Hitch
Come and do a PhD with me! Are you looking for a PhD project at the intersection of #microbiome and #food science? This project, in collaboration with ADM milling, will explore novel microbiome targeted food ingredients
🎓 #PhDPosition !
🍽️ The impact of innovative food ingredients on the human gut microbiome and health with Dr Fred Warren @starchlab.bsky.social
📅Apply by 2 December
➡️ buff.ly/k1KEcfL
🍽️ The impact of innovative food ingredients on the human gut microbiome and health with Dr Fred Warren @starchlab.bsky.social
📅Apply by 2 December
➡️ buff.ly/k1KEcfL
October 14, 2025 at 4:01 PM
Come and do a PhD with me! Are you looking for a PhD project at the intersection of #microbiome and #food science? This project, in collaboration with ADM milling, will explore novel microbiome targeted food ingredients
Reposted by Tom Hitch
How to design new synthetic microbial communities? It's a huge question we're still deeply exploring 🦠
Check out this new preprint by @tcahitch.bsky.social & @tclavel.bsky.social! They developed an function-directed approach using metagenomic to build better SynComs.
www.biorxiv.org/content/10.1...
Check out this new preprint by @tcahitch.bsky.social & @tclavel.bsky.social! They developed an function-directed approach using metagenomic to build better SynComs.
www.biorxiv.org/content/10.1...
Function-Based Selection of Synthetic Communities Enables Mechanistic Microbiome Studies
Understanding the complex interactions between microbes and their environment requires robust model systems such as synthetic communities (SynComs). We developed a functionally directed approach to ge...
www.biorxiv.org
September 28, 2025 at 10:52 AM
How to design new synthetic microbial communities? It's a huge question we're still deeply exploring 🦠
Check out this new preprint by @tcahitch.bsky.social & @tclavel.bsky.social! They developed an function-directed approach using metagenomic to build better SynComs.
www.biorxiv.org/content/10.1...
Check out this new preprint by @tcahitch.bsky.social & @tclavel.bsky.social! They developed an function-directed approach using metagenomic to build better SynComs.
www.biorxiv.org/content/10.1...
Reposted by Tom Hitch
New article on equitable reuse of public sequencing data, published in @natmicrobiol.nature.com!
Led by the Data reuse core team @lhug.bsky.social @environmicrobio.bsky.social Cristina Moraru, @geomicrosoares.bsky.social, @folker.bsky.social and with Anke Heyer and The Data Reuse Consotrium!
Led by the Data reuse core team @lhug.bsky.social @environmicrobio.bsky.social Cristina Moraru, @geomicrosoares.bsky.social, @folker.bsky.social and with Anke Heyer and The Data Reuse Consotrium!
September 26, 2025 at 7:34 PM
New article on equitable reuse of public sequencing data, published in @natmicrobiol.nature.com!
Led by the Data reuse core team @lhug.bsky.social @environmicrobio.bsky.social Cristina Moraru, @geomicrosoares.bsky.social, @folker.bsky.social and with Anke Heyer and The Data Reuse Consotrium!
Led by the Data reuse core team @lhug.bsky.social @environmicrobio.bsky.social Cristina Moraru, @geomicrosoares.bsky.social, @folker.bsky.social and with Anke Heyer and The Data Reuse Consotrium!
The main work from my time in Aachen is now out 🎉 if you have wanted to make a SynCom that captures the functional-landscape of microbiota, MiMiC2 makes that possible based on metagenomic data! 1/7 doi.org/10.1093/isme...
Function-Based Selection of Synthetic Communities Enables Mechanistic Microbiome Studies
Abstract. Understanding the complex interactions between microbes and their environment requires robust model systems such as synthetic communities (SynCom
doi.org
September 24, 2025 at 1:22 PM
The main work from my time in Aachen is now out 🎉 if you have wanted to make a SynCom that captures the functional-landscape of microbiota, MiMiC2 makes that possible based on metagenomic data! 1/7 doi.org/10.1093/isme...
Reposted by Tom Hitch
It’s also timely to present about SynCom design considering the recent work from @tcahitch.bsky.social @tclavel.bsky.social. I highly recommend reading!
academic.oup.com/ismej/advanc...
academic.oup.com/ismej/advanc...
Function-Based Selection of Synthetic Communities Enables Mechanistic Microbiome Studies
Abstract. Understanding the complex interactions between microbes and their environment requires robust model systems such as synthetic communities (SynCom
academic.oup.com
September 23, 2025 at 3:12 PM
It’s also timely to present about SynCom design considering the recent work from @tcahitch.bsky.social @tclavel.bsky.social. I highly recommend reading!
academic.oup.com/ismej/advanc...
academic.oup.com/ismej/advanc...
Reposted by Tom Hitch
Excellent article on quantitative production of fermentation products by the microbiota. Key takeaway: microbial fermentation products may be more important in mice than humans, amplifying microbiome effects in mice. www.cell.com/cell/fulltex...
Quantifying the varying harvest of fermentation products from the human gut microbiota
Fermentation products are the most abundant gut microbial metabolites absorbed by
the host, with important dose-dependent consequences for health. In this study, we
present a systems-level analysis in...
www.cell.com
September 22, 2025 at 7:49 AM
Excellent article on quantitative production of fermentation products by the microbiota. Key takeaway: microbial fermentation products may be more important in mice than humans, amplifying microbiome effects in mice. www.cell.com/cell/fulltex...
Reposted by Tom Hitch
🌎👩🔬 For 15+ years biology has accumulated petabytes (million gigabytes) of🧬DNA sequencing data🧬 from the far reaches of our planet.🦠🍄🌵
Logan now democratizes efficient access to the world’s most comprehensive genetics dataset. Free and open.
doi.org/10.1101/2024...
Logan now democratizes efficient access to the world’s most comprehensive genetics dataset. Free and open.
doi.org/10.1101/2024...
September 3, 2025 at 8:39 AM
🌎👩🔬 For 15+ years biology has accumulated petabytes (million gigabytes) of🧬DNA sequencing data🧬 from the far reaches of our planet.🦠🍄🌵
Logan now democratizes efficient access to the world’s most comprehensive genetics dataset. Free and open.
doi.org/10.1101/2024...
Logan now democratizes efficient access to the world’s most comprehensive genetics dataset. Free and open.
doi.org/10.1101/2024...
Reposted by Tom Hitch
Really pleased to see this study led by @raymondkiu.bsky.social now published in @natcomms.nature.com!
We show that probiotics help modulate the preterm infant 👶#microbiome - to reduce ARGs, lower MDR bacteria 🦠 & increase beneficial Bifido ✨
Huge team effort!
www.nature.com/articles/s41...
We show that probiotics help modulate the preterm infant 👶#microbiome - to reduce ARGs, lower MDR bacteria 🦠 & increase beneficial Bifido ✨
Huge team effort!
www.nature.com/articles/s41...
August 17, 2025 at 11:54 PM
Really pleased to see this study led by @raymondkiu.bsky.social now published in @natcomms.nature.com!
We show that probiotics help modulate the preterm infant 👶#microbiome - to reduce ARGs, lower MDR bacteria 🦠 & increase beneficial Bifido ✨
Huge team effort!
www.nature.com/articles/s41...
We show that probiotics help modulate the preterm infant 👶#microbiome - to reduce ARGs, lower MDR bacteria 🦠 & increase beneficial Bifido ✨
Huge team effort!
www.nature.com/articles/s41...
Reposted by Tom Hitch
Go and check out the pre-print of the landscape-scale tree microbiome study from the Future Oak project. Huge amounts of efforts and talent went into this work, with a pinch of "this is crazy, but we can do it". Well done @jamesemcdonald.bsky.social @cenococcum.bsky.social et al. Thread below 👇
🧵 New preprint alert!
From the Future Oak project, led by @cenococcum.bsky.social
Landscape-scale impacts of environment and disease on the tree microbiome 🌳🦠
www.biorxiv.org/content/10.1...
From the Future Oak project, led by @cenococcum.bsky.social
Landscape-scale impacts of environment and disease on the tree microbiome 🌳🦠
www.biorxiv.org/content/10.1...
Environment and disease have tissue-specific effects on the tree microbiome
Trees are essential for ecosystem function, but due to their long lifespan, are disproportionately impacted by climate change and disease. Tree-associated microbiota are critical for tree health and r...
www.biorxiv.org
August 16, 2025 at 11:35 AM
Go and check out the pre-print of the landscape-scale tree microbiome study from the Future Oak project. Huge amounts of efforts and talent went into this work, with a pinch of "this is crazy, but we can do it". Well done @jamesemcdonald.bsky.social @cenococcum.bsky.social et al. Thread below 👇
Reposted by Tom Hitch
🧵 New preprint alert!
From the Future Oak project, led by @cenococcum.bsky.social
Landscape-scale impacts of environment and disease on the tree microbiome 🌳🦠
www.biorxiv.org/content/10.1...
From the Future Oak project, led by @cenococcum.bsky.social
Landscape-scale impacts of environment and disease on the tree microbiome 🌳🦠
www.biorxiv.org/content/10.1...
Environment and disease have tissue-specific effects on the tree microbiome
Trees are essential for ecosystem function, but due to their long lifespan, are disproportionately impacted by climate change and disease. Tree-associated microbiota are critical for tree health and r...
www.biorxiv.org
August 16, 2025 at 6:48 AM
🧵 New preprint alert!
From the Future Oak project, led by @cenococcum.bsky.social
Landscape-scale impacts of environment and disease on the tree microbiome 🌳🦠
www.biorxiv.org/content/10.1...
From the Future Oak project, led by @cenococcum.bsky.social
Landscape-scale impacts of environment and disease on the tree microbiome 🌳🦠
www.biorxiv.org/content/10.1...
Reposted by Tom Hitch
well this is kinda cool 🦠✨
New pre-print from my group - project led by PhD student Michael Hoffert. We set out on a daunting mission to generate a 'periodic table' of bacterial diversity (1/6) www.biorxiv.org/content/10.1...
A periodic table of bacteria?: Mapping bacterial diversity in trait space
Bacterial diversity can be overwhelming. There is an ever-expanding number of bacterial taxa being discovered, but many of these taxa remain uncharacterized with unknown traits and environmental prefe...
www.biorxiv.org
July 18, 2025 at 7:46 PM
well this is kinda cool 🦠✨
Reposted by Tom Hitch
New RESOURCE!
Integrative genomic reconstruction reveals heterogeneity in carbohydrate utilization across human gut bifidobacteria
@arzamasovalex.bsky.social @drlarsbode.bsky.social Andrei Osterman, Jeff Gordon & co
#microbiomesky #microsky
www.nature.com/articles/s41...
Integrative genomic reconstruction reveals heterogeneity in carbohydrate utilization across human gut bifidobacteria
@arzamasovalex.bsky.social @drlarsbode.bsky.social Andrei Osterman, Jeff Gordon & co
#microbiomesky #microsky
www.nature.com/articles/s41...
Integrative genomic reconstruction reveals heterogeneity in carbohydrate utilization across human gut bifidobacteria - Nature Microbiology
A comprehensive genomic analysis reveals species- and strain-level heterogeneity in carbohydrate utilization potential across bifidobacteria of human origin.
www.nature.com
July 16, 2025 at 11:31 AM
New RESOURCE!
Integrative genomic reconstruction reveals heterogeneity in carbohydrate utilization across human gut bifidobacteria
@arzamasovalex.bsky.social @drlarsbode.bsky.social Andrei Osterman, Jeff Gordon & co
#microbiomesky #microsky
www.nature.com/articles/s41...
Integrative genomic reconstruction reveals heterogeneity in carbohydrate utilization across human gut bifidobacteria
@arzamasovalex.bsky.social @drlarsbode.bsky.social Andrei Osterman, Jeff Gordon & co
#microbiomesky #microsky
www.nature.com/articles/s41...
Reposted by Tom Hitch
Our friends @thehesslab.bsky.social are actively looking for postdoctoral researchers interested in anerobic microbiology, and studying the rumen microbiome. #microbiologists #bioinformatics #microbiomes
Check out their website: hesslab.com
Check out their website: hesslab.com
Hess Laboratory – Systems Microbiology & Natural Products Research
hesslab.com
July 16, 2025 at 5:14 AM
Our friends @thehesslab.bsky.social are actively looking for postdoctoral researchers interested in anerobic microbiology, and studying the rumen microbiome. #microbiologists #bioinformatics #microbiomes
Check out their website: hesslab.com
Check out their website: hesslab.com
Reposted by Tom Hitch
An update to my recent pre-print:
Start right to end right: authentic open reading frame selection matters
has just gone online. In it, we look at the effect of mis-annotating an ORF on a spliced gene's predicted protein structure.
www.biorxiv.org/content/10.1...
Start right to end right: authentic open reading frame selection matters
has just gone online. In it, we look at the effect of mis-annotating an ORF on a spliced gene's predicted protein structure.
www.biorxiv.org/content/10.1...
July 13, 2025 at 11:30 AM
An update to my recent pre-print:
Start right to end right: authentic open reading frame selection matters
has just gone online. In it, we look at the effect of mis-annotating an ORF on a spliced gene's predicted protein structure.
www.biorxiv.org/content/10.1...
Start right to end right: authentic open reading frame selection matters
has just gone online. In it, we look at the effect of mis-annotating an ORF on a spliced gene's predicted protein structure.
www.biorxiv.org/content/10.1...
Reposted by Tom Hitch
🧪🌾 VACANCIES - Are you looking for a postdoc or group leader opportunity?
Come and work with us at @umeaplantsciencecentre.se 🌱!
🍀 We have currently several job openings available. Take a look on our homepage and apply:
www.upsc.se/jobs.html
#PlantSciJobs #plantscience #hiring
Come and work with us at @umeaplantsciencecentre.se 🌱!
🍀 We have currently several job openings available. Take a look on our homepage and apply:
www.upsc.se/jobs.html
#PlantSciJobs #plantscience #hiring
July 9, 2025 at 1:37 PM
🧪🌾 VACANCIES - Are you looking for a postdoc or group leader opportunity?
Come and work with us at @umeaplantsciencecentre.se 🌱!
🍀 We have currently several job openings available. Take a look on our homepage and apply:
www.upsc.se/jobs.html
#PlantSciJobs #plantscience #hiring
Come and work with us at @umeaplantsciencecentre.se 🌱!
🍀 We have currently several job openings available. Take a look on our homepage and apply:
www.upsc.se/jobs.html
#PlantSciJobs #plantscience #hiring
Reposted by Tom Hitch
UK Gut-Immune-Brain Axis Network+
We are building a UK-wide interdisciplinary research community to advance the mechanistic understanding of the gut-immune-brain axis. Join our network to find out about our UK-wide launch event, where we will announce #funding opportunities
www.giba-uk.org
We are building a UK-wide interdisciplinary research community to advance the mechanistic understanding of the gut-immune-brain axis. Join our network to find out about our UK-wide launch event, where we will announce #funding opportunities
www.giba-uk.org
Home | Giba Network UK | Gut Immune Brain Axis Network
Gut Immune Brain Axis Network (GIBA Network)
www.giba-uk.org
July 3, 2025 at 10:54 AM
UK Gut-Immune-Brain Axis Network+
We are building a UK-wide interdisciplinary research community to advance the mechanistic understanding of the gut-immune-brain axis. Join our network to find out about our UK-wide launch event, where we will announce #funding opportunities
www.giba-uk.org
We are building a UK-wide interdisciplinary research community to advance the mechanistic understanding of the gut-immune-brain axis. Join our network to find out about our UK-wide launch event, where we will announce #funding opportunities
www.giba-uk.org
Reposted by Tom Hitch
Curious about plasmid biology? Our latest paper is out now in Nature Communications! 🚨
doi.org/10.1038/s414...
We analyzed thousands of diverse bacterial plasmids to shed light for the first time on a key aspect of plasmid biology: plasmid copy number. 1/7 👇
doi.org/10.1038/s414...
We analyzed thousands of diverse bacterial plasmids to shed light for the first time on a key aspect of plasmid biology: plasmid copy number. 1/7 👇
Universal rules govern plasmid copy number - Nature Communications
Plasmids exhibit a broad range of sizes and copies per cell, and these two parameters appear to be negatively correlated. Here, Ramiro-Martínez et al. analyse the copy number of thousands of diverse b...
doi.org
July 2, 2025 at 10:07 AM
Curious about plasmid biology? Our latest paper is out now in Nature Communications! 🚨
doi.org/10.1038/s414...
We analyzed thousands of diverse bacterial plasmids to shed light for the first time on a key aspect of plasmid biology: plasmid copy number. 1/7 👇
doi.org/10.1038/s414...
We analyzed thousands of diverse bacterial plasmids to shed light for the first time on a key aspect of plasmid biology: plasmid copy number. 1/7 👇
Reposted by Tom Hitch
www.nature.com/articles/s41... Our new paper on the risks and socio-demographic dimensions of antibiotic resistance in the human gut is now out in @natcomms.nature.com!
Variation and prognostic potential of the gut antibiotic resistome in the FINRISK 2002 cohort - Nature Communications
Here, in a representative cohort of 7,095 Finnish adults, the authors reveal that gut antibiotic resistance is shaped not only by antibiotic use but also by the microbiome, diet, lifestyle, household ...
www.nature.com
July 2, 2025 at 5:30 AM
www.nature.com/articles/s41... Our new paper on the risks and socio-demographic dimensions of antibiotic resistance in the human gut is now out in @natcomms.nature.com!
Reposted by Tom Hitch
Go and check out the great review by @xinmingxu.bsky.social and collaborators in this issue, and also shout-out to @evolvedbiofilm.bsky.social for supporting amazing science art actually made by a real humans and not AI!
July issue of @cp-trendsmicrobiol.bsky.social is now online, with our review by @xinmingxu.bsky.social @neftalyl.bsky.social on Composing a microbial symphony and a matching cover illustration by @lizahaart.bsky.social
#SynCom #PlantMicrobiome #MicrobiomeEcology at #LeidenBiology
#SynCom #PlantMicrobiome #MicrobiomeEcology at #LeidenBiology
July 1, 2025 at 4:12 PM
Go and check out the great review by @xinmingxu.bsky.social and collaborators in this issue, and also shout-out to @evolvedbiofilm.bsky.social for supporting amazing science art actually made by a real humans and not AI!
Reposted by Tom Hitch
Beautiful new review paper in preprint bridging microbial ecology and classic ecology led by Maggie Vogel, @olimeacock.bsky.social and @annasophieweiss.bsky.social, also by @juliensluneau.bsky.social and @lambdapp.bsky.social from our lab (not me :)) ecoevorxiv.org/repository/v...
Bridging the scales: what can microbial ecologists learn from classic ecology?
ecoevorxiv.org
July 1, 2025 at 8:25 AM
Beautiful new review paper in preprint bridging microbial ecology and classic ecology led by Maggie Vogel, @olimeacock.bsky.social and @annasophieweiss.bsky.social, also by @juliensluneau.bsky.social and @lambdapp.bsky.social from our lab (not me :)) ecoevorxiv.org/repository/v...
Reposted by Tom Hitch
The team's first preprint is out!
Led by
@vishnuprasoodanan.bsky.social & @omaistrenko.bsky.social , we asked a question (almost) as old as microbiology: how many prokaryotic species exist on Earth? More specifically, how much diversity is "hiding" in existing metagenomic data?
A 🧵.
Led by
@vishnuprasoodanan.bsky.social & @omaistrenko.bsky.social , we asked a question (almost) as old as microbiology: how many prokaryotic species exist on Earth? More specifically, how much diversity is "hiding" in existing metagenomic data?
A 🧵.
A census of hidden and discoverable microbial diversity beyond genome-centric approaches https://www.biorxiv.org/content/10.1101/2025.06.26.661807v1
June 27, 2025 at 8:10 PM
The team's first preprint is out!
Led by
@vishnuprasoodanan.bsky.social & @omaistrenko.bsky.social , we asked a question (almost) as old as microbiology: how many prokaryotic species exist on Earth? More specifically, how much diversity is "hiding" in existing metagenomic data?
A 🧵.
Led by
@vishnuprasoodanan.bsky.social & @omaistrenko.bsky.social , we asked a question (almost) as old as microbiology: how many prokaryotic species exist on Earth? More specifically, how much diversity is "hiding" in existing metagenomic data?
A 🧵.
Reposted by Tom Hitch
🚨 Job Alert at RBG Kew! We are looking for Lab Research Assistants in genomics to join our Fungarium Sequencing Project! Do you like Fungi? Do you want to develop new -omics techniques? Interested in historical collections? Join the team! Posts to start ASAP. Apply here:https://lnkd.in/e2BpWJpA
June 25, 2025 at 10:58 AM
🚨 Job Alert at RBG Kew! We are looking for Lab Research Assistants in genomics to join our Fungarium Sequencing Project! Do you like Fungi? Do you want to develop new -omics techniques? Interested in historical collections? Join the team! Posts to start ASAP. Apply here:https://lnkd.in/e2BpWJpA
Reposted by Tom Hitch
Ever wondered why proton pump inhibitors raise the risk of C. diff infections? Is it due to pH shifts or direct antibacterial effects on the gut microbiome? We think it’s the pH. 🧪💡 Dive into Julia & Patrick’s new paper for the full story! 📖👇 #Microbiome #PPI
doi.org/10.1080/1949...
doi.org/10.1080/1949...
Proton-pump inhibitors increase C. difficile infection risk by altering pH rather than by affecting the gut microbiome based on a bioreactor model
Clostridioides difficile infections often occur after antibiotic use, but they have also been linked to proton-pump inhibitor (PPI) therapy. The underlying mechanism – whether infection risk is due...
doi.org
June 17, 2025 at 12:32 PM
Ever wondered why proton pump inhibitors raise the risk of C. diff infections? Is it due to pH shifts or direct antibacterial effects on the gut microbiome? We think it’s the pH. 🧪💡 Dive into Julia & Patrick’s new paper for the full story! 📖👇 #Microbiome #PPI
doi.org/10.1080/1949...
doi.org/10.1080/1949...