Philipp Engel

True! we did not discuss these parallels but will keep it in mind for the revision. Thank you!

Bottom line: priority effects strongly shape how gut communities form at the strain level in bees. This matters for understanding microbiome assembly… and for designing better probiotic strategies in beekeeping.

Result? Firstcomer strains dominated almost every time, indicating strong priority effects at the strain level. When we removed the firstcomer strain (“dropout” experiments), latecomers only partly took over, meaning both within-species and between-species interactions matter.

Honeybees are perfect for this 🐝: their gut microbiota has the same core species, but each bee carries different strains. We gave microbiota-depleted bees two microbial communities with the same 12 species but different strains, added in different orders.

We asked whether these priority effects also happen within species, where different bacterial strains compete for the same niche. If so, even similar environments could end up with very different microbial communities.

Gut microbes can vary a lot at the strain level between individuals, but we still don’t fully understand why. One big suspect: priority effects ⌛ — basically “first come, first served” in microbial colonization.

New preprint from our lab! www.biorxiv.org/content/10.1...
@aiswarya.bsky.social tested the role of priority effects in shaping the honeybee gut microbiota using an elegant combinatorial experimental design. A thread🧵....

Bottom line: priority effects strongly shape how gut communities form at the strain level in bees. This matters for understanding microbiome assembly… and for designing better probiotic strategies in beekeeping.

Result? Firstcomer strains dominated almost every time, suggesting strong priority effects at the strain level. When we removed the firstcomer strain (“dropout” experiments), latecomers only partly took over, meaning that both within-species and between-species interactions matter.

Honeybees are perfect for this: their gut microbiota has the same core species, but each bee carries different strains. We gave microbiota-depleted bees two microbial communities with the same 12 species but different strains, added in different orders.

We asked whether these priority effects also happen within species, where different bacterial strains compete for the same niche. If so, even similar environments could end up with very different microbial communities.

Gut microbes can vary a lot at the strain level between individuals, but we still don’t fully understand why. One big suspect: priority effects — basically “first come, first served” in microbial colonization.

Wow. Awesome news, Hassan. Congratulations!

Super cool to see this online. What a breakthrough! Congrats Alexander, Dorentina, and the whole team.

This project has been incredibly rewarding & fun. Funded through the @snf-fns.ch & with help from former senior researchers @germusthermophilus.bsky.social & Florent Mazel, Malick led the project from start to finish. A truly outstanding achievement by a highly talented PhD student. Congrats Malick.

Our findings show that honeybees offer a powerful model to study eco-evolutionary phage–bacteria dynamics. We now want to establish the directionality of these correlation patterns and probe both bottom-up and top-down regulatory mechanisms in the assembly of these gut communities. Stay tuned. 🦠🔄🐝

Viral and bacterial diversity were correlated, especially at the strain level and within the interaction network. This emphasizes that scale and resolution matter for detecting such correlations and may explain why past studies found mixed results.

The network showed a highly modular structure, with nested phage–bacteria interactions within modules, a hallmark of coevolution and fine-tuned host–phage associations. Modules mostly aligned with genus-level bacterial diversity, suggesting phages interact across species but stay within genera.

Malick managed to carry out paired metagenome sequencing of the viral particle fraction and the bacterial/host fraction of 49 individual honeybees. He then reconstructed the phage–bacteria interaction network using CRISPR spacer matches and genome homology, mapping who infects whom in the bee gut. 🧬

Phage diversity mirrors bacterial strain diversity in the honey bee gut microbiota - Nature Communications Authors analyse paired viral and bacterial shotgun metagenomics data from individual honeybee guts, revealing modular, nested phage–bacteria networks, with viral diversity mirroring bacterial strain c...

🐝🦠 New paper: rdcu.be/eOf7A
Phages may drive microbial diversity, yet we often don’t even know how phages & bacteria correlate in nature. Our new study tackles this in the honeybee gut, thanks to the great work of PhD student @malickndiaye.bsky.social at @dmf-unil.bsky.social @fbm-unil.bsky.social

Thanks for re-posting, Seth. Most of these bacteria are found almost exclusively in honeybees, suggesting that they have diversified within this host group, but not through strict co-speciation, but rather via frequent symbiont gains, losses, and host switches across different honeybee species.

... at @embl.org Heidelberg, the Cayman team in the Zeller lab; and @fbm-unil.bsky.social , Florent Mazel and the GTF.
This paper will enable future research on gut symbionts of native Asian honeybees, and we hope it advances our broader understanding of microbiota evolution in bees and beyond.🤞

Many thanks to everyone who supported this work! In Malaysia: our @snsf.ch Spirit grant collaborators Sze Huei Yek & Asha Pallujam (UMS, Monash U), the Nature Inspired team, the Orang Asli community, MY Bee Savior, & many beekeepers. At @ncbsbangalore.bsky.social India, Axel Brockmann & his team...

Unfortunately, we couldn't fully convince the reviewers/editors on this point, leading to a lengthy review process and ultimately a rather generic published title. We encourage you to read the bioRxiv preprint (10.1101/2024.09.11.612390) and the review documents shared with the final version.📝

It's widely accepted that bee gut bacteria co-diversified with their hosts, but this hasn't been tested, aside from a study on bumblebees (10.1111/mec.12209). Using a standard statistical framework, we found weak co-speciation signals & much less than reported for mammalian gut symbionts 🦍🐭👫🦠.

One of the biggest surprises? We found little evidence for co-speciation between hosts and their gut symbionts. Instead, we observed a dynamic pattern of symbiont gains, losses & replacements, leading to functional differences between host species. We see this as the paper's most important message 👇

Microbial communities were mostly host-specific, but not entirely. We found both specialist and generalist bacteria, even within the same bacterial genera. Interestingly, some generalists appeared host-specific only at the strain level, hinting at recent host switches.

Notably, the giant honeybee (Apis dorsata) hosted unique microbial taxa not found in the other species. Among them: Dysgonomonas species with a large set of pectin-degrading genes, suggesting a key role in pollen digestion. 🦠🏵️

We recovered thousands of metagenome-assembled bacterial genomes from these bees' metagenomes, uncovering surprising patterns in host–microbe relationships 🦠. We identified several novel bacterial species, expanding the known diversity of gut microbes in honeybees.... 🐝

Evolution of gut microbiota across honeybee species revealed by comparative metagenomics Nature Communications - Here, the authors perform metagenomic analysis of honeybee gut microbes, uncovering many previously unidentified species and host specific differences in composition and...

Happy to announce that our comparative metagenomic analysis of the gut microbiota of five honeybee species - spearheaded by @aiswarya.bsky.social - is finally published in a peer-reviewed journal! rdcu.be/eKMCs @fbm-unil.bsky.social @dmf-unil.bsky.social 🧵👇