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Tom Hitch @tcahitch.bsky.social · 3d

Bakta generally, but not tried with funkier genomes

Tom Hitch @tcahitch.bsky.social · 10d

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

Abstract. Understanding the complex interactions between microbes and their environment requires robust model systems such as synthetic communities (SynCom

academic.oup.com

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Reposted by Tom Hitch

Mizrahi Lab @mizrahilab.bsky.social · 10d

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...

www.biorxiv.org

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Reposted by Tom Hitch

Alex Probst @alexjprobst.bsky.social · 11d

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!

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Tom Hitch @tcahitch.bsky.social · 14d

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

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

github.com

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Tom Hitch @tcahitch.bsky.social · 14d

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

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Tom Hitch @tcahitch.bsky.social · 14d

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

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Tom Hitch @tcahitch.bsky.social · 14d

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

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Tom Hitch @tcahitch.bsky.social · 14d

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

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Tom Hitch @tcahitch.bsky.social · 14d

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

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Tom Hitch @tcahitch.bsky.social · 14d

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

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Reposted by Tom Hitch

Benjamin Coltman @bcoltman.bsky.social · 15d

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

2 2 5

Tom Hitch @tcahitch.bsky.social · 15d

Thanks for the shout-out 😁

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Reposted by Tom Hitch

Christoph Kaleta @kaletalab.bsky.social · 16d

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

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Reposted by Tom Hitch

Rayan Chikhi @rayanchikhi.bsky.social · Sep 3

🌎👩‍🔬 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...

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Reposted by Tom Hitch

Hall Lab @halllab.bsky.social · Aug 17

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...

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Reposted by Tom Hitch

Marine C. Cambon @marccamb.bsky.social · Aug 16

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 · Aug 16

🧵 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...

www.biorxiv.org

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Reposted by Tom Hitch

James McDonald @jamesemcdonald.bsky.social · Aug 16

🧵 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...

www.biorxiv.org

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Tom Hitch @tcahitch.bsky.social · Aug 15

Really cool dataset!

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Tom Hitch @tcahitch.bsky.social · Aug 6

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

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Reposted by Tom Hitch

April Hayes @aprilhayes.bsky.social · Jul 18

well this is kinda cool 🦠✨

Noah Fierer @noahfierer.bsky.social · Jul 18

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

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Reposted by Tom Hitch

Nature Microbiology @natmicrobiol.nature.com · Jul 16

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 - Nature Microbiology

A comprehensive genomic analysis reveals species- and strain-level heterogeneity in carbohydrate utilization potential across bifidobacteria of human origin.

www.nature.com

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Reposted by Tom Hitch

Diamond Lab @diamondlab.bsky.social · Jul 16

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

Hess Laboratory – Systems Microbiology & Natural Products Research

hesslab.com

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Reposted by Tom Hitch

James Lloyd 🧬 @jamespblloyd.bsky.social · Jul 13

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...

Protein structures, mostly unstructured. Three of them. First is complete and the other two are truncations. The rightmost is a very small truncation.

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Reposted by Tom Hitch

Umeå Plant Science Centre @umeaplantsciencecentre.se · Jul 9

🧪🌾 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

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