Tom Hitch

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...

(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...

Virtual Colon: spatiotemporal modeling of metabolic interactions in a computational colonic environment

#mSystems from @kaletalab.bsky.social

journals.asm.org/doi/10.1128/...

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 💯

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...

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/...

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)

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...

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...

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

Bakta generally, but not tried with funkier genomes

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

Thanks for the mention 😁 The paper is out now in ISME Journal: academic.oup.com/ismej/advanc...

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...

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...

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!

GitHub - thh32/MiMiC2: A workflow for the creation of synthetic communities that are functionally representative of an ecosystem. A workflow for the creation of synthetic communities that are functionally representative of an ecosystem. - thh32/MiMiC2

MiMiC2 is available on GitHub and there are premade functional profiles for multiple collections of publicly accessible isolates: github.com/thh32/MiMiC2 7/7

Next we wanted to create SynComs that allow mechanistic studies of a disease, so we chose IBD. By comparing healthy and IBD metaGs we selected a SynCom for each. In germ-free mice we showed the IBD SynCom caused increased inflammation. 6/7

Using MiMiC2 we were able to create SynComs for a range of ecosystems, including the rumen of cows! We wondered our function-based approach would select a methanogen, since they are sub-dominant, but critical members. It did, along with diverse other members! 5/7

This comparison is done against ALL input metaGs, not a single metaG, allowing the SynComs to capture the variability within an ecosystem. Strains are also selected together, reducing functional redundancy between each other. 4/7

MiMiC2 addresses this by reducing both metaGs and isolate genomes down to the protein families they encode. Next, we can select strains that functional match our metaGs of interest. 3/7

SynComs are usually put together based on expert curation, but microbiota are functionally complex, and capturing that complexity in only a few strains is hard. Hence the idea "what if we used metagenomes (metaGs) to select the correct strains?" 2/7

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

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

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...

Thanks for the shout-out 😁

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...

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...

🌎👩‍🔬 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...

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 👇

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...

🧵 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...

Really cool dataset!

Congratulations on getting this out, can't wait to read the updated work in full!

well this is kinda cool 🦠✨

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.

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...

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