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Bahtiyar Yilmaz @bahtiyil.bsky.social · 03/08/2026

Thanks a lot! Our study just added one more piece to the puzzle!

Bahtiyar Yilmaz @bahtiyil.bsky.social · 03/08/2026

However, our findings suggest that even when donor microbes gain access to the recipient gut, durable engraftment remains highly selective, implying that ecological compatibility rather than simply available niche space is a major determinant of long-term persistence.

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Bahtiyar Yilmaz @bahtiyil.bsky.social · 03/08/2026

That’s an excellent point. Broad-spectrum antibiotic preconditioning has indeed been explored, particularly in recurrent C. difficile FMT, to reduce colonization resistance.

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Bahtiyar Yilmaz @bahtiyil.bsky.social · 03/08/2026

🙏We are also deeply grateful to the reviewers, whose thoughtful and constructive suggestions helped us make the story substantially more complete and compelling.

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Bahtiyar Yilmaz @bahtiyil.bsky.social · 03/08/2026

I would say the existing microbial communities are the major driving force of the FMT rejections. Of course most likely host contributes as well unfortunately we didn’t have host associated samples to include analysis. That would be pretty cool to close the loop.

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Bahtiyar Yilmaz @bahtiyil.bsky.social · 03/08/2026

At single-nucleotide resolution FMT is a bottleneck: diversity contracts, few lineages get through. Remission tracked with donor strains replacing residents, not with taxonomic reshuffling. Screen donors at strain level, not for raw diversity. doi.org/10.1016/j.ce...

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Bahtiyar Yilmaz @bahtiyil.bsky.social · 03/08/2026

So just do it again? Two patients had 5 and 2 rounds of FMT. Donor species kept arriving, leaving, and being replaced by different ones. Median survival: 2 rounds. A revolving door, not a build-up. Repeat dosing built species-level memory but never broke the strain barrier.

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Bahtiyar Yilmaz @bahtiyil.bsky.social · 03/08/2026

Even the microbes that leave do real work. Function recovered faster than taxonomy: 757 pathway restorations, 64% delivered by donor taxa - many of which later vanished. Tryptophan and B-vitamin pathways rose most in patients who reached remission.

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Bahtiyar Yilmaz @bahtiyil.bsky.social · 03/08/2026

Now the twist. Finding a donor species in a patient does not mean the donor's strain moved in. Of 465 species-level colonization events, only 22 were genetically donor-identical. For Lachnospiraceae: 5 out of 161. Right species name. Wrong organism underneath.

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Bahtiyar Yilmaz @bahtiyil.bsky.social · 03/08/2026

We rebuilt 3,748 genomes from stool and tracked 252 species found only in the donor. 61.9% never established. Just 16.7% were still there at week 8. Failure wasn't random: some families stuck reliably, while Lachnospiraceae, the gut's dominant clade, mostly didn't.

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Bahtiyar Yilmaz @bahtiyil.bsky.social · 03/08/2026

Zoom out and FMT looks like a win. Recipient guts gained diversity and drifted toward the donor community by weeks 4 and 8 - but never arrived. Everyone parked somewhere in between. That community-level similarity was hiding what happens underneath.

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Bahtiyar Yilmaz @bahtiyil.bsky.social · 03/08/2026

A stool transplant delivers billions of microbes into a sick gut. Almost none move in for good. We followed donor-recipient pairs from whole communities down to single nucleotides, and found the gut runs a ruthless strain-level filter. Out now in Cell Reports 🧵 www.cell.com/cell-reports...

cell.com

Strain-level ecological filtering governs microbial colonization of the human gut

Baertschi et al. demonstrate that microbiota transplantation functions as a selective ecological filter. Although donor species frequently appear, only specific lineages achieve stable strain integrat...

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Reposted by Bahtiyar Yilmaz

Universität Bern @unibe.ch · 04/11/2025

An international consortium, led by #unibern & @inselgruppe.bsky.social have launched the first comprehensive atlas of the mouse gut microbiome: mediarelations.unibe.ch/media_releas... @medfacultyunibe.bsky.social @dbmr-unibe.bsky.social @bahtiyil.bsky.social

Landmark Study: The first comprehensive atlas of the mouse gut microbiome contributes to better reproducibility in animal experiments and thus a reduction in the need for them.

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Bahtiyar Yilmaz @bahtiyil.bsky.social · 04/07/2025

Huge congratulations to my brilliant students Isabel Bärtschi (co-supervised by Andrew Macpherson) and Sebastian Jordi (co-supervised by Benjamin Misselwitz) for their well-deserved recognition. It’s incredibly rewarding to see young researchers grow and be celebrated for their contributions.

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Reposted by Bahtiyar Yilmaz

Segata Lab @cibiocm.bsky.social · 06/06/2025

Join us at #EESMicrobiome! Organisers Mani Arumugam (#uni_copenhagen), Ami Bhatt (@stanfordpress.bsky.social), Peer Bork (@borklab.bsky.social) and Nicola Segata (#CIBIO_UniTrento) look forward to welcoming #microbiome scientists in September at @embl.org! @events.embl.org

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Bahtiyar Yilmaz @bahtiyil.bsky.social · 10/05/2025

Excited to share one of our latest reviews, along with the cover of Trends in Biotechnology by Mete Duman! In our review, together with Prof. Fatih Inci and his team, we dive into how organ-on-a-chip technology is revolutionizing IBD research @unibe.ch @dbmr-unibe.bsky.social 📄 lnkd.in/dZWst3bp

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