James McDonald

📢 New preprint is out on bioRxiv 📢:

How much does virome prep influence our view of the human gut virome?

Short answer: a lot.

Long answer:
doi.org/10.1101/2025...

Different methods lead to distinct community structures, richness, and major virus-host abundance patterns.

🧵 1/5

Thanks, Sofia! Hope all is well

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 💯

11/ 📄 feedback welcome!
🔬 Huge thanks to our amazing team, collaborators and funders! @marccamb.bsky.social @cenococcum.bsky.social @drcarriebrady.bsky.social @bpettifor.bsky.social
BBSRC, NERC, DEFRA, Scottish Government.

10/ Our work shows the potential of microbiome-based interventions for trees, just like those emerging in agriculture and human health. 🌍

9/ This shows that tree microbiomes can be engineered to suppress disease — a promising strategy for forest health and conservation. 🌲🛡️

8/ We then inoculated oak seedlings and logs with a disease-suppressive SynCom before pathogen challenge. The results were striking:
📉 Brenneria goodwinii (oak pathogen) ↓ 56% (seedlings), ↓ 71% (logs)
📉 Gibbsiella quercinecans (oak pathogen) ↓ 87% (seedlings), ↓ 95% (logs)

7/ Next, we assembled synthetic microbial communities (SynComs) from these isolates. In vitro tests showed they could suppress oak pathogens. 🧪

6/ We screened 22,000 isolates on agar plates for their ability to suppress oak pathogens linked to Acute Oak Decline - 341 of the isolates showed strong pathogen suppression. 💪🌱

5/ These isolates belonged to taxonomic groups that represented 61% of the total bacterial and 87% of total fungal sequences found in oak trees, based on 16S rRNA gene and ITS sequencing, respectively. A major resource for tree microbiome research! 🌳🦠

4/ We processed tree tissue samples for isolation in the field within a few hours of collection to maximise chances of culturing key microbiota, using our mobile lab setup.

3/ We built a culture collection of >30,000 bacterial and fungal isolates from 150 oak trees across 30 sites in Britain — the largest culture collections of its kind🌿

2/ Trees rely on their microbiome for health and resilience, but are increasingly impacted by disease. We asked ‘can we engineer these microbial communities to fight disease?’ 🌳🦠.

2/ Trees rely on their microbiome for health and resilience, but are increasingly impacted by disease. We asked ‘can we engineer these microbial communities to fight disease?’ 🌳🦠.

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...

🧵 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...

So pleased to see this Bex! Huge congratulations!!

Really cool paper!

Brilliant picture

Had a great week at #PSM2025 - excellent science, great organisation, and super friendly people. Really enjoyed presenting our work on the oak microbiome and leaving here with lots of ideas for future work and collaborations. Thanks @vcarryon.bsky.social & team for organising @microsos.bsky.social

A pause on the live posts from @evolvedbiofilm.bsky.social as he is on stage giving the next presentation at #PSM2025 on single species and community living of Bacillus on plants @microsos.bsky.social

Thank you, Dirk-Jan! We indeed enjoyed it with our Birmingham-Leiden collaboration group!
(Not tapas but restaurant part)

-with @marccamb.bsky.social @jamesemcdonald.bsky.social @xinmingxu.bsky.social and María Negre Rodríguez

@vcarryon.bsky.social opening #PSM2025

Great to be at #PMS2025 in Malaga. Looking forward to 5 days of science and giving a presentation on our group’s work on Thursday (session 4)

New paper: Dried soil bacteria enter dormancy with "frozen" RNA & metabolite profiles—but water vapor alone can wake them up!

#Microbiology #SoilScience #Dormancy #ClimateChange #MicroSky

Have research, results, or ideas to share with the microbial ecology community? Don’t miss your chance to present it at #MMEG2025 - abstract submissions close 2 November!

📨 Submit your abstract: appliedmicrobiology.org/ems-event-ca...

Really Nice work by @evolvedbiofilm.bsky.social and colleagues

MMEG is coming to @unibirmingham.bsky.social in December - look out for some exciting announcements about the programme in the next few weeks! Abstract submission and registration is open 👇🏻

Save the Date: #MMEG2025 is coming to Birmingham!

Join us on 15–16 December 2025 for the 31st edition of MMEG. This year's event is your chance to:
🔬 Share your research
🤝 Connect with peers
🦠 Discover the latest in molecular microbial ecology

Register now: appliedmicrobiology.org/ems-event-ca...

You watched it!

New preprint from the lab by Adele Pioppi on her #NNF_INTERACT project

Successive cultivation under drought selects for specific microbiome members in the wheat rhizosphere

www.biorxiv.org/content/10.1...