Tom Hitch
@tcahitch.bsky.social
Assistant Professor at The Chinese University of Hong Kong focused on how we can control the human gut microbiota to improve human health. He/Him/They
Dear microbiome enthusiasts: I'm excited to be moving my lab to New York University this fall (& the NYU Institute for Engineering Health); with joint-appointment @isbscience.org I'm hiring a postdoc @ NYU to look at diet-driven evolution in the gut: apply.interfolio.com/189980 Please share! 🦠🤓
Apply - Interfolio {{$ctrl.$state.data.pageTitle}} - Apply - Interfolio
apply.interfolio.com
PhD advert for the new lab in Hong Kong! We are hiring a PhD student to merge large-scale metagenomics with 3D structural analysis and immunology. If you have experience in any of these areas and are motivated to learn the others, get in contact; lnkd.in/ggr3T4sQ
PhD advert for the new lab in Hong Kong! We are hiring a PhD student to merge large-scale metagenomics with 3D structural analysis and immunology. If you have experience in any of these areas and are motivated to learn the others, get in contact; www.aic.cuhk.edu.hk/web/wp-conte...
Excellent work by our one and only #CharliePauvert. We use it in all our high-throughput anaerobic cultivation projects. More to come... 💫
Bioinformatics Advances@bioinfoadv.bsky.social · last mo.🔬 New paper in Bioinformatics Advances: "maldipickr dereplicates microbial MALDI-TOF spectra to facilitate multiplexed isolation" Find it here: https://doi.org/10.1093/bioadv/vbag171 Authors include: @tclavel.bsky.social
🚨 #INFOGUT2026 meeting has started! WG leaders welcome you ✨ Andrea Gianotti Stéphanie Blanquet Lorenzo Nissen Clarisse Nobre Lidia Tomas Lucie Etienne Thomas Hitch @tcahitch.bsky.social Enrique Carrillo Alice Ponsero Laure-Alix Clerbaux Pilar Acedo @pilaracedo.bsky.social
🚨 INFOGUT FREE webinar 🗓️ 30 March @ 11.00 CET 🗣️ Prof Tom Van de Wiele (Ghent University) will share his cutting-edge expertise on #invitro technologies for mimicking the #human #microbiome in the small #intestine. 👉 Open to everyone on Teams lnkd.in/eHZ6X8iz
This link will take you to a page that’s not on LinkedIn
lnkd.in
Delighted to see our work on the impact of drought on the oak microbiome featured on the cover of @cp-cellhostmicrobe.bsky.social Link to the article below this post 👇🏻
Cell Host & Microbe@cp-cellhostmicrobe.bsky.social · 6mo agoOur February issue--now live--is deeply rooted in exciting new microbiology! On the cover: Microbial communities associated with semi-mature oak trees are remarkably resilient in the face of environmental challenges. www.cell.com/cell-host-mi...
Anyone know where you can buy acrolein for electron microscopy? Apparently it must be stabilised with either hydrochinon or hydroquinon-monomethylether 🫠
Friends, please help spread the word about our microbiology REU program at Montana State University. www.montana.edu/mbi/reu/ Each student receives a stipend ($7000 for 10 wks). Travel compensation, room, and board are also provided. Details in the attached pic--Feb 14 deadline 🧫🧪🦠#microsky
Very happy and proud that our paper “Effector–host interactome map links type III secretion systems in healthy gut microbiomes to immune modulation” is out today in #NatureMicrobiology @natmicrobiol.nature.com Paper 👉 t1p.de/v42xb #microbiome #commensal #pathomechanism #T3SS #immune #health #IBD
Effector–host interactome map links type III secretion systems in healthy gut microbiomes to immune modulation - Nature Microbiology
Large-scale computational and in vitro analyses identify commensal type III secretion systems and substrates in the human gut microbiome that can interact with human proteins to modulate immune pathwa...
t1p.de
Last chance to apply for our funded PhD opportunity. w. Prof. Fredric Coulon @ Cranfield University. This will investigate expansion of ML models for AMR phenotype detection to agriculture settings to create a sensor-ready hit list. Detail here: www.findaphd.com/phds/project...
From Genomic Context to Sensor Design: Computational Identification of AMR Biomarkers in Agriculture (project at Queen's University Belfast) at University of Reading on FindAPhD.com
PhD Project - From Genomic Context to Sensor Design: Computational Identification of AMR Biomarkers in Agriculture (project at Queen's University Belfast) at University of Reading, listed on FindAPhD....
findaphd.com
(1/7) Excited that the Virtual Colon, an extension of BacArena for modeling the spatiostructural environment of the colon, is now out at mSystems. Kudos to @maringos.bsky.social and for leading this work! @crc1182.bsky.social @uni-kiel.de iel.de Link: journals.asm.org/doi/full/10....
Virtual Colon: spatiotemporal modeling of metabolic interactions in a computational colonic environment | mSystems
Interactions between the human body and gut microbes are crucial for health and disease. We present the Virtual Colon, an extension of the individual-based microbiome modeling approach BacArena that m...
journals.asm.org
Virtual Colon: spatiotemporal modeling of metabolic interactions in a computational colonic environment #mSystems from @kaletalab.bsky.social journals.asm.org/doi/10.1128/...
Virtual Colon: spatiotemporal modeling of metabolic interactions in a computational colonic environment | mSystems
Interactions between the human body and gut microbes are crucial for health and disease. We present the Virtual Colon, an extension of the individual-based microbiome modeling approach BacArena that m...
journals.asm.org
The pre print of my PhD research is out! 📣 Check it out for some cool results on high-throuhput microbial isolation, #SynComs and #Tree #Microbiome 🌳🧫 doi.org/10.1101/2025... #PhDone 💯
Large-scale culturing of the tree microbiome enables targeted disease suppression
The tree microbiome is essential for host health and pathogen suppression. Synthetic microbial communities (SynComs) are emerging as important tools to understand microbiome dynamics and engineer micr...
doi.org
James McDonald@jamesemcdonald.bsky.social · 9mo ago🧵 1/ New preprint alert! From the FUTURE OAK project, led by the super talented @alejandra1909.bsky.social Large-scale culturing of the tree microbiome enables targeted disease suppression Here's what we found... 👇 www.biorxiv.org/content/10.1...
We are delighted to let you know that your Plants, People, Planet article 'Demystifying Fungal Systematics: A Gateway to Fungal Literacy and Societal/Ecological Relevance Through Familiar Species' has been published on Early View. nph.onlinelibrary.wiley.com/doi/10.1002/...
Demystifying fungal systematics: A gateway to fungal literacy and societal/ecological relevance through familiar species
Fungal systematics can feel overwhelming given the vast species diversity within this kingdom, with numerous subgroups at every taxonomic rank. This often creates a disconnect between the undertsnidn...
nph.onlinelibrary.wiley.com
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
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
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
Quadram Institute@quadraminstitute.bsky.social · 10mo ago🎓 #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
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...
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...
biorxiv.org
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!
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
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...
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
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...
cell.com
🌎👩🔬 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...
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...
Impact of early life antibiotic and probiotic treatment on gut microbiome and resistome of very-low-birth-weight preterm infants - Nature Communications
Here, the authors show that giving probiotics to very low birth weight preterm babies can help reduce harmful antibiotic-resistant bacteria in the gut and support the development of a healthier microb...
nature.com
Hall Lab @halllab.bsky.social · 2y agoSo excited to see this preprint out! Huge congrats to @raymondkiu.bsky.social on bringing this preterm microbiome study together with some really neat well-controlled clinical subgroups & analysis. As always we couldn't do this without amazing team members & collaborators! Check out details below 👇
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 👇
James McDonald@jamesemcdonald.bsky.social · 12mo ago🧵 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...
🧵 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...
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...
biorxiv.org
