iiinova — where your digital self keeps evolving

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.

120

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.

100

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.

100

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.

100

bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution

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🧵....

biorxiv.org

| bioRxiv

1188

000

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.

100

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.

200

100

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.

100

Wow. Awesome news, Hassan. Congratulations!

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

020

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.

020

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. 🧬

120

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.

130

... 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.🤞

130

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...

130

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.

120

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.... 🐝

Philipp Engel @pengellab.bsky.social · 16/09/2025

Fascinating work and a fun 🧵 about the ‘behind the paper’!

010

Philipp Engel @pengellab.bsky.social · 18/02/2025

We are looking for a bioinformatician with expertise in microbiome data analysis join our team at the University of Lausanne. The successful candidate will lead and support research projects within nccr-microbiomes.ch. More details here: shorturl.at/mC46o . Please share with potential candidates.

shorturl.at

Opportunités de carrière : Research Associate position in bioinformatics support (22124)

11321

Philipp Engel @pengellab.bsky.social · 05/02/2025

We are looking for a postdoc in bioinformatics interested in broad questions about the ecology and evolution of host-associated microbiomes using social bees as model. Please share with potential candidates and if interested apply here: career5.successfactors.eu/career?caree...

career5.successfactors.eu

Career Opportunities: Postdoctoral position in bioinformatics/gut microbiota ecology and evolution (22087)

02624

Reposted by Philipp Engel

Mark A. Hanson @hansonmark.bsky.social · 13/11/2024

I am hiring! PhD studentship available through the SWbio DTP. The interested student will investigate the evolution of innate immune signalling in a model species group. Infection biology & #Drosophila genetics combined! #ImmunoSky #AcademicSky More info: mahansonresearch.weebly.com/blog/phd-stu...

mahansonresearch.weebly.com

PhD studentship! Deadline Dec 11th 2024

SWbio application link: https://www.swbio.ac.uk/biomolecular-and-biophysical-studies/ For inquiries, please email: m.hanson@exeter.ac.uk Based in: University of Exeter, Penryn, Cornwall, UK....

13128

Reposted by Philipp Engel

Jack A Gilbert @gilbertjacka.bsky.social · 11/11/2024

CALL TO ACTION: By publishing this Editorial concurrently across journals, we are demanding immediate, tangible steps that harness the power of microbiology and the expertise of researchers and policymakers to safeguard the planet for future generations. doi.org/10.1128/msys...

doi.org

Microbial solutions must be deployed against climate catastrophe | mSystems

This paper is a call to action. By publishing concurrently across journals like an emergency bulletin, we are not merely making a plea for awareness about climate change. Instead, we are demanding imm...

11818

Philipp Engel @pengellab.bsky.social · 06/11/2024

PhD position available in our lab in 🇨🇭! Interested in microbial ecology and evolution in the context of #Symbiosis, #Microbiota, #Bees? Like to analyze shotgun metagenomics data with the possibility for fieldwork and experiments? This is for you. Apply here: shorturl.at/swHf1 #SymbioSky

shorturl.at

Opportunités de carrière : PhD position in gut microbiota ecology and evolution (21945)

04245

Philipp Engel @pengellab.bsky.social · 06/11/2024

Super nice work Omaya! Congrats.