Philipp Engel
@pengellab.bsky.social
Microbiologist at UNIL Switzerland, interested in Microbiota-host interactions, symbiosis, evolution and genomics, and social bees
engelbeelab.com
engelbeelab.com
Reposted by Philipp Engel
New preprint! 🐝 We engineered a bacterial biosensor to reveal micron-scale arabinose gradients in the honeybee gut. Congratulations to Audam and all co-authors. Great collaboration with @pengellab.bsky.social as part of the NCCR Microbiomes at @fbm-unil.bsky.social
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Engineered symbiont biosensor maps micron-scale sugar gradients in the honeybee gut
The honeybee gut microbiota plays a key role in shaping host health and susceptibility to disease. Yet, the nutrient environment it experiences within the gut remains poorly characterized. In particul...
www.biorxiv.org
December 17, 2025 at 9:14 AM
New preprint! 🐝 We engineered a bacterial biosensor to reveal micron-scale arabinose gradients in the honeybee gut. Congratulations to Audam and all co-authors. Great collaboration with @pengellab.bsky.social as part of the NCCR Microbiomes at @fbm-unil.bsky.social
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
True! we did not discuss these parallels but will keep it in mind for the revision. Thank you!
November 26, 2025 at 7:04 AM
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.
November 25, 2025 at 9:29 PM
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.
November 25, 2025 at 9:29 PM
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.
November 25, 2025 at 9:29 PM
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.
November 25, 2025 at 9:29 PM
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.
November 25, 2025 at 9:29 PM
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🧵....
@aiswarya.bsky.social tested the role of priority effects in shaping the honeybee gut microbiota using an elegant combinatorial experimental design. A thread🧵....
| bioRxiv
bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution
www.biorxiv.org
November 25, 2025 at 9:29 PM
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🧵....
@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.
November 25, 2025 at 9:16 PM
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.
November 25, 2025 at 9:16 PM
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.
November 25, 2025 at 9:16 PM
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.
November 25, 2025 at 9:16 PM
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.
November 25, 2025 at 9:16 PM
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!
November 25, 2025 at 1:23 PM
Wow. Awesome news, Hassan. Congratulations!
Super cool to see this online. What a breakthrough! Congrats Alexander, Dorentina, and the whole team.
November 25, 2025 at 12:55 PM
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.
November 4, 2025 at 8:36 PM
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. 🦠🔄🐝
November 4, 2025 at 8:36 PM
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.
November 4, 2025 at 8:36 PM
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.
November 4, 2025 at 8:36 PM
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. 🧬
November 4, 2025 at 8:36 PM
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. 🧬
🐝🦠 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
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
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...
www.nature.com
November 4, 2025 at 8:36 PM
🐝🦠 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
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.
October 14, 2025 at 9:23 PM
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.🤞
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.🤞
October 14, 2025 at 7:04 PM
... 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.🤞
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...
October 14, 2025 at 7:04 PM
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.📝
October 14, 2025 at 7:04 PM
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.📝