Tom Hitch

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 👇🏻

Anyone know where you can buy acrolein for electron microscopy? Apparently it must be stabilised with either hydrochinon or hydroquinon-monomethylether 🫠

I would caution this since GTDB placement isn't enough taxonomic evidence to propose a new species, multiple lines of evidence should be obtained to corroborate the proposed taxonomy.

Hmmm I would probably go with "many are proposed species in GTDB, represented by only MAGs and for which no cultured representative exists". Although GTDB also contains SAGs so genomes instead of MAGs might be better

We do GENUS sp. as Paul suggests, it highlights it's an unknown species and gives the taxonomic assignment

This Research Experiences for Undergraduates (REU) program is funded by the National Science Foundation to create "points of entry" for students interested in research. Students apply from across the country to spend 10 weeks in Bozeman, Montana this summer (May 26, 2026 - August 1, 2026). Admitted students are paired with a faculty mentor, who serves as an advisor for a student's summer project. Each student receives a stipend ($7000 for 10 wks). Travel compensation, room, and board are also provided. Our program leverages MSU’s unique microbiology expertise, focusing specifically on microbes living with little or no oxygen (like those in the hot springs of nearby Yellowstone). Low oxygen microbes are essential to human and ecosystem health. They influence (or control) such processes as the breakdown of food in the GI tract, removal of toxins from our bodies and the environment, and production of greenhouse gases. They are also models for understanding the origins of life on this planet, and the potential for life on other planets. A key goal of our program is to recruit students from schools with limited research infrastructure. Being in Montana, a state with a vibrant Native American community, we are particularly interested in applications from students at tribal colleges. However, ANYONE with an interest in microbiology - or biology/science in general - can and should apply. If willing and able, please share/tweet/spread the word far and wide. Applications are due February 14, 2026. Full details can be found through our website http://www.montana.edu/mbi/reu/

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

Ok, then I think BacDive is probably your best bet. I think they have an API and also link to alternative strain IDs that have been used along with genomes for the strains. Lorenz who heads it is also super helpful 😁 good luck!

Microbes in total or just bacteria? DSMZ have done the best job I know off for creating resources like BacDive or StrainInfo, but I'm pretty sure they are bacteria specific and might lack strains that weren't ever deposited in a culture collection

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...

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

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....

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...

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...