Benjamin Coltman

Characterising complex metabolic responses in an engineered, cross-feeding microbial co-culture using quantitative proteomics Microbial communities play a key role in biogeochemical transformations in a wide range of ecosystems, but they also hold significant potential to enh…

Engineering synthetic co-cultures to be "needy" leads to unexpected consequences. We barely scratch the surface here, but get some interesting insights #biotech
🧪 www.sciencedirect.com/science/arti...

Interested in microbial proteins and their diversity? 🖥️🧬🦠

We have recently released the Amino Acid Sequence Toolkit (AASTK). AASTK is designed to work with the GlobDB to create and work with datasets of protein sequences.

AASTK currently consists of 4 tools:
- CASM
- PASR
- CUGO
- Meta

1/

Very excited about this, especially to work more closely with @patrickschimmel.bsky.social !
We will look at the establishment of gut and soil microbiomes following interventions through the lens of metabolic fluxes, and explore if there are shared principles of community assembly!

MRC instructs grant review boards to slash funding rates - Research Professional News Boards asked to recommend just three applications for funding, as BBSRC also suspends calls

Both MRC and BBSRC responsive modes now withdrawn until further notice. Existing applications unlikely to succeed (late 2025 round expecting 1-5% success rate).

Listen, I get that UKRI wants to pivot. But killing both at once is devastating.

Let's hope at least one opens by summer... #AcademicSky

We just released #anvio v9, "eunice" 🎉

This version represents over 2,000 changes in the codebase since v8, increasing the total number of programs in the anvi'o ecosystem to 176.

Read the release notes:

github.com/merenlab/anv...

Visit our up-to-date web page:

anvio.org

With the release of anvi'o v9, the 300k+ contigs databases available for download on the GlobDB website are now compatible with both the development version and the latest stable release (v9) of anvi'o.

More info:
globdb.org/news

Thanks #anvio team!
🖥️🧬🦠

We're excited to release metaTraits.embl.de! 🦠 Interactively explore 140+ 𝗺𝗶𝗰𝗿𝗼𝗯𝗶𝗮𝗹 𝗽𝗵𝗲𝗻𝗼𝘁𝘆𝗽𝗶𝗰 𝘁𝗿𝗮𝗶𝘁𝘀, harmonized & integrated from culture-derived collections 🔬 & genome-based predictions 🧬 for >2M MAGs & genomes.

Publication at NAR: doi.org/10.1093/nar/... @narjournal.bsky.social #microsky 🧵 1/8

microntology: a lightweight, data-driven controlled vocabulary to describe Earth's microbial habitats Summary. We introduce microntology v1.0, a pragmatic controlled vocabulary of 148 terms to describe microbial habitats and lifestyles, and provide manually curated microntology annotations for >300k m...

We just released a @biorxivpreprint.bsky.social describing the *microntology*, a lightweight controlled vocabulary that we have been using for a while to tag metagenomes with contextual data.

Study by @fullam.bsky.social @vishnuprasoodanan.bsky.social et al:

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www.biorxiv.org/content/10.6...

Merry X-SMASH!
My first first author paper is out on bioRxiv! 🖥

We present epsSMASH, a comprehensive and high-throughput tool for predicting exopolysaccharide (exoPS) biosynthetic gene clusters (BGCs) in bacterial genomes 🦠🧬🧫
1/8

New @fwf-at.bsky.social CoE Microplanet study introduces GlobDB globdb.org, a comprehensive database integrating 14 genomic catalogues providing consistent taxonomy for microbial species.
academic.oup.com/bioinformati...

Real-time simultaneous monitoring of multiple analytes in bacterial cultures | Applied and Environmental Microbiology Real-time monitoring of metabolites in bacterial cultures is crucial for advancing our understanding of microbial physiology, metabolic fluxes, and dynamic responses to environmental changes. This capability enables researchers to capture transient metabolic states that are often missed in endpoint measurements. The use of engineered periplasmic binding proteins as biosensors for this real-time metabolite monitoring represents a groundbreaking approach. By leveraging the natural specificity and high affinity of PBPs for small molecules, these biosensors can be engineered to detect a wide range of metabolites with exceptional sensitivity and temporal resolution. The integration of PBP-based biosensors into microbial research not only enhances our ability to study real-time metabolism but also provides a versatile tool for optimizing industrial bioprocesses and exploring bacterial infections and complex microbial ecosystems

Pretty cool! Engineered periplasmic binding proteins+fluorophore sensors (for sugars+AAs) are used to report real-time extracellular metabolite dynamics in E. coli + many others species after 24h in plate readers, showing hierarchical substrate use.
journals.asm.org/doi/full/10....

The Microflora Danica atlas of Danish environmental microbiomes - Nature Microflora Danica—an atlas of Danish environmental microbiomes—reveals that although human-disturbed habitats have high alpha diversity, species reoccur, revealing hidden homogeneity.

Microflora Danica: What can you learn from collecting and sequencing 10,000+ samples from a single country? Check out our new paper in @nature.com to find out. Incredible work led by Caitlin Singleton, Thomas B. N. Jensen, and Mads Albertsen from @aau.dk. 🦠🧫🧬
www.nature.com/articles/s41...

Most microbial diversity is uncultured. metaTraits bridges the gap by combining culture-based trait data (@bacdive.bsky.social, @bvbrc.bsky.social, JGI/GOLD/IMG) with predictions for MAGs and genomes (SPIRE, proGenomes). All trait summaries come with provenance and links to their original data. 4/8

Induced endosymbiosis between a fungus and bacterium reveals a shift from antagonism to commensalism - Nature Communications Gassler et al. implant a free-living bacterium into fungal cells to study early steps in the establishment of an endosymbiosis. They observe vertical transmission of the bacteria despite initial host ...

Induced endosymbiosis between a fungus and bacterium reveals a shift from antagonism to commensalism

@natcomms.nature.com by Thomas Gassler et al from Julia Vorholt

www.nature.com/articles/s41...

Ralstonia pickettii in the fungus Rhizopus microsporus

#Endofungal

This nice summary by @michiwagner4.bsky.social makes it easy to fit my post in a few characters.
Amplicon sequencing is still an affordable and quick way to get good insights into who lives in your samples. Our new primers make sure your vision is 20/20.
Try em, and contact me if you have questions!

A cloning strategy as depicted in the OpenCloning website

#OpenCloning is a an Open Source alternative to SnapGene/Benchling that supports automation and integration with other software

✅ Free
🔓 Open Source
🧬 More cloning methods than SnapGene
🤖 Can be automated with python
👨‍🔬 Built by a researcher — for researchers!

👉 Check it out at opencloning.org

🧫 Just out in Bioinformatics Advances: “GlobDB: A comprehensive species-dereplicated microbial genome resource.” 

Explore the full study: https://doi.org/10.1093/bioadv/vbaf280

Nice, thanks!

Modular in vivo engineering of the reductive methylaspartate cycles for synthetic CO2 fixation Biological carbon fixation is currently limited to seven naturally occurring pathways. Synthetic carbon fixation pathways have the potential to surpass aerobic natural pathways in efficiency, but none...

Newest preprint from our lab: a new family of promising synthetic CO2 fixation cycles that may outcompete the Calvin cycle and that Vittorio Rainaldi realized to a great extent in E. coli! Up to 11 heterologous enzymes in a cascade supporting CO2 fixation & growth! www.biorxiv.org/content/10.1...

GlobDB: a comprehensive species-dereplicated microbial genome resource AbstractMotivation. Over the past years, substantial numbers of microbial species’ genomes have been deposited outside of conventional INSDC databases.Resu

Our paper describing the GlobDB is now published in @bioinfoadv.bsky.social
doi.org/10.1093/bioa...

The GlobDB is the largest species dereplicated genome database currently available, containing 306,260 species representatives.
More information on globdb.org 1/5
🖥️🧬🦠

GlobDB is a great resource and is frequently of use in my research!

Developed and maintained by @daanspeth.bsky.social, I was glad to contribute in a small way. Have a look at Daan’s thread to find out more and let us know how you use it! >>

🚨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...

Last chance to turn it off.

On Monday, November 3rd, Microsoft will start using your LinkedIn data for AI training. And remember, you're opted in by default.

To toggle it off 👉 Account - Settings & Privacy > Data privacy > Data for Generative AI Improvement.

This week as part of the @pilzfestspiele.at - our group showed mycorrhizal fungal colonized roots, our culture collection, posters of results, and we had a massive turnout! People are becoming increasingly interested in fungi @cemess.bsky.social @ter-cemess.bsky.social

www.fungalecologylab.com

Looks interesting @nmjgeerlings.bsky.social

Use of paracetamol during pregnancy unchanged in the EU | European Medicines Agency (EMA) Paracetamol medicines can be used in pregnancy, in accordance with official recommendations

Paracetamol remains an important option to treat pain or fever in pregnant women.

Following rigorous assessment of the available scientific data, we find no evidence that taking paracetamol during pregnancy causes autism in children.

Read more 👉 www.ema.europa.eu/en/news/use-...

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...

It’s great to be at #mbkceesme2025 so far, hearing about all things microbial! It’s always rewarding to present one’s work and hear the community’s feedback. Thanks for the support @isme-microbes.bsky.social

Interested in the design of defined microbial communities for fundamental research and applications? Hope this work & tool will help you 👇 As always @tcahitch.bsky.social has been a driving factor ⭐⭐⭐! github.com/ClavelLab/Mi...; academic.oup.com/ismej/advanc...

Branched-chain amino acid assimilation promotes mixotrophy of ammonia-oxidizing archaeal sponge symbionts www.biorxiv.org/content/10.1... #jcampubs