Lilian Caesar
@liliancaesar.bsky.social
Postdoc at Newton Lab (@IUBiology). Eco-evolution of symbiosis. Microbiomes | Bees | Virus, Bact, Fungi. https://liliancaesar.com/
Pinned
Lilian Caesar
@liliancaesar.bsky.social
· Dec 22
Spatial segregation and cross-kingdom interactions drive stingless bee hive microbiome assembly
Nature Communications - Here, the authors characterize the microbiome assembly across an entire stingless bee colony, revealing site-adapted within-hive communities, and showing that nest...
rdcu.be
Our manuscript on the microbiome of a stingless bee hive is out! 🦠🐝 So excited! Here’s a short thread with some findings, going from the assembly of a consistent multi-kingdom microbiome to discussions on host traits that contribute to it. Please take a look and share : ) rdcu.be/eVNFJ
Reposted by Lilian Caesar
www.growkudos.com/publications...
New work with @ckarakoc.bsky.social and @shoestrapped.bsky.social in @pnas.org
New work with @ckarakoc.bsky.social and @shoestrapped.bsky.social in @pnas.org
The hidden energy cost of cellular dormancy
Many organisms survive harsh environments by switching into special survival modes. Some bacteria do this by forming spores—dormant, highly resilient cells that can persist for years or even centuries...
www.growkudos.com
February 9, 2026 at 5:56 PM
www.growkudos.com/publications...
New work with @ckarakoc.bsky.social and @shoestrapped.bsky.social in @pnas.org
New work with @ckarakoc.bsky.social and @shoestrapped.bsky.social in @pnas.org
Reposted by Lilian Caesar
Happy to share a preprint—the last chapter of my dissertation with @mcsymbiont.bsky.social and Co—on what happens when bacterial endosymbionts accumulate huge numbers of pseudogenes during early genome reduction.
www.biorxiv.org/content/10.6...
www.biorxiv.org/content/10.6...
February 8, 2026 at 2:08 AM
Happy to share a preprint—the last chapter of my dissertation with @mcsymbiont.bsky.social and Co—on what happens when bacterial endosymbionts accumulate huge numbers of pseudogenes during early genome reduction.
www.biorxiv.org/content/10.6...
www.biorxiv.org/content/10.6...
Reposted by Lilian Caesar
NEW: Registration is now FREE for graduate students and postdocs for the 14th Annual Yosemite Symbiosis workshop. THANKS to the Gordon and Betty Moore Foundation! Space is limited. Learn more and REGISTER here: snri.ucmerced.edu/form/symbios...
February 8, 2026 at 5:29 PM
NEW: Registration is now FREE for graduate students and postdocs for the 14th Annual Yosemite Symbiosis workshop. THANKS to the Gordon and Betty Moore Foundation! Space is limited. Learn more and REGISTER here: snri.ucmerced.edu/form/symbios...
Reposted by Lilian Caesar
Applications close for this 4-year postdoc on Feb 9th (2 days!). The associated post for a technician should be online next week 👀
🐜 4-year #postdoc position in the @socialfluids.bsky.social lab @camzoology.bsky.social investigating metabolic cooperation between bodies in a BBSRC-funded project.
www.cam.ac.uk/jobs/postdoc...
#ants #socialtransfers #sociallytransferredmaterials #autophagy #socialinsects #aging #job (🧵1/n)
www.cam.ac.uk/jobs/postdoc...
#ants #socialtransfers #sociallytransferredmaterials #autophagy #socialinsects #aging #job (🧵1/n)
Postdoctoral Research Associate (Fixed Term)
Applications are invited for a Postdoctoral Research Associate to join the Social Fluids Laboratory (https://leboeuflab.com) led by Dr Adria LeBoeuf in the Department of Zoology
www.cam.ac.uk
February 7, 2026 at 11:16 AM
Applications close for this 4-year postdoc on Feb 9th (2 days!). The associated post for a technician should be online next week 👀
Reposted by Lilian Caesar
Review in #ProcB - Flower constancy in #pollinators: a bouquet of agendas shapes interactions among mutualistic partners #OpenAccess @chrisleduck.bsky.social royalsocietypublishing.org/rspb/article...
February 6, 2026 at 9:46 AM
Review in #ProcB - Flower constancy in #pollinators: a bouquet of agendas shapes interactions among mutualistic partners #OpenAccess @chrisleduck.bsky.social royalsocietypublishing.org/rspb/article...
Reposted by Lilian Caesar
Accurate plasmid reconstruction from metagenomics data using assembly–alignment graphs and contrastive learning www.nature.com/articles/s41... #jcampubs
Accurate plasmid reconstruction from metagenomics data using assembly–alignment graphs and contrastive learning - Nature Biotechnology
PlasMAAG uses cross-sample information to improve plasmid reconstruction from metagenomic samples.
www.nature.com
February 4, 2026 at 8:20 PM
Accurate plasmid reconstruction from metagenomics data using assembly–alignment graphs and contrastive learning www.nature.com/articles/s41... #jcampubs
Reposted by Lilian Caesar
Want to ride the front of the wave of all-things-microbiology; field work, cultivation, microscopy, molecular, bioinformatics and AI tools? Me too!
Please join us @mblscience.bsky.social for the 2026 Summer Microbial Diversity Course!
Applications due soon.
www.mbl.edu/education/ad...
Please join us @mblscience.bsky.social for the 2026 Summer Microbial Diversity Course!
Applications due soon.
www.mbl.edu/education/ad...
Microbial Diversity | Marine Biological Laboratory
The goal of the course is to teach professors, postdocs and advanced graduate students how to discover, cultivate, and isolate diverse microorganisms catalyzing a breadth of chemical transformations, ...
www.mbl.edu
February 2, 2026 at 9:58 PM
Want to ride the front of the wave of all-things-microbiology; field work, cultivation, microscopy, molecular, bioinformatics and AI tools? Me too!
Please join us @mblscience.bsky.social for the 2026 Summer Microbial Diversity Course!
Applications due soon.
www.mbl.edu/education/ad...
Please join us @mblscience.bsky.social for the 2026 Summer Microbial Diversity Course!
Applications due soon.
www.mbl.edu/education/ad...
Reposted by Lilian Caesar
Happy to share my solo-authored Perspective "An Interpretation, Survey, and Outlook of Microbial Macroecology"! Making time these last few months to take stock of the patterns us microbial ecologists examine + models we invoke has been invaluable. Feedback welcome!
ecoevorxiv.org/repository/v...
ecoevorxiv.org/repository/v...
January 28, 2026 at 8:22 PM
Happy to share my solo-authored Perspective "An Interpretation, Survey, and Outlook of Microbial Macroecology"! Making time these last few months to take stock of the patterns us microbial ecologists examine + models we invoke has been invaluable. Feedback welcome!
ecoevorxiv.org/repository/v...
ecoevorxiv.org/repository/v...
Reposted by Lilian Caesar
Join our first Social Transfer Network General Assembly on Wednesday, February 4th!
15h UK / UTC+0; 16h Europe / UTC+1; 7h US West coast / UTC-8
This is your chance to connect, catch up, and have your voice heard as we reflect on the past year and look ahead to what's next for our community.
15h UK / UTC+0; 16h Europe / UTC+1; 7h US West coast / UTC-8
This is your chance to connect, catch up, and have your voice heard as we reflect on the past year and look ahead to what's next for our community.
January 29, 2026 at 3:53 PM
Join our first Social Transfer Network General Assembly on Wednesday, February 4th!
15h UK / UTC+0; 16h Europe / UTC+1; 7h US West coast / UTC-8
This is your chance to connect, catch up, and have your voice heard as we reflect on the past year and look ahead to what's next for our community.
15h UK / UTC+0; 16h Europe / UTC+1; 7h US West coast / UTC-8
This is your chance to connect, catch up, and have your voice heard as we reflect on the past year and look ahead to what's next for our community.
Reposted by Lilian Caesar
Calling all OrthoFinder users!
We’ve just released GLADE, a tool to infer gene gains, losses, duplications, and ancestral genomes across a phylogeny.
GLADE runs directly on OrthoFinder results.
www.biorxiv.org/content/10.6...
github.com/lauriebelch/...
(1/10)
We’ve just released GLADE, a tool to infer gene gains, losses, duplications, and ancestral genomes across a phylogeny.
GLADE runs directly on OrthoFinder results.
www.biorxiv.org/content/10.6...
github.com/lauriebelch/...
(1/10)
www.biorxiv.org
January 29, 2026 at 12:07 PM
Calling all OrthoFinder users!
We’ve just released GLADE, a tool to infer gene gains, losses, duplications, and ancestral genomes across a phylogeny.
GLADE runs directly on OrthoFinder results.
www.biorxiv.org/content/10.6...
github.com/lauriebelch/...
(1/10)
We’ve just released GLADE, a tool to infer gene gains, losses, duplications, and ancestral genomes across a phylogeny.
GLADE runs directly on OrthoFinder results.
www.biorxiv.org/content/10.6...
github.com/lauriebelch/...
(1/10)
Reposted by Lilian Caesar
Registration is open for the inaugural GRC conference in the Function of Evolving Systems. Aug 9-14, 2026, Waterville Valley. Truly stellar speaker lineup. Student/postdoc fellowships are available! Please come join us! www.grc.org/function-of-... @joybergelson.bsky.social
www.grc.org
January 29, 2026 at 3:03 PM
Registration is open for the inaugural GRC conference in the Function of Evolving Systems. Aug 9-14, 2026, Waterville Valley. Truly stellar speaker lineup. Student/postdoc fellowships are available! Please come join us! www.grc.org/function-of-... @joybergelson.bsky.social
Reposted by Lilian Caesar
How and when can internal conflicts tear an individual organism apart?
That’s the question at the heart of this new paper.
Great thread by lead author @martijnschenkel.bsky.social below.
That’s the question at the heart of this new paper.
Great thread by lead author @martijnschenkel.bsky.social below.
NEW PAPER with @arvidagren.bsky.social and Manus Patten on evolutionary reversions in individuality now out (as an advance article) at @jevbio.bsky.social (see academic.oup.com/jeb/advance-...). Thread below! [1/8]
.
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Evolutionary transitions and reversions in individuality
Abstract. Biological individuality exists in different forms—unicellular, multicellular, colonial, etc.—which have arisen through evolutionary transitions
academic.oup.com
January 28, 2026 at 6:59 PM
How and when can internal conflicts tear an individual organism apart?
That’s the question at the heart of this new paper.
Great thread by lead author @martijnschenkel.bsky.social below.
That’s the question at the heart of this new paper.
Great thread by lead author @martijnschenkel.bsky.social below.
Reposted by Lilian Caesar
New paper by Saskia Wilmsen and me just came out BioEssays:
A new classification framework to understand evolutionary transitions in individuality
Please find the OA paper here:
onlinelibrary.wiley.com/doi/10.1002/...
A new classification framework to understand evolutionary transitions in individuality
Please find the OA paper here:
onlinelibrary.wiley.com/doi/10.1002/...
A New Classification Framework to Understand Evolutionary Transitions in Individuality
Classifying biological entities based on whether and how the two fundamental aspects physiological and evolutionary components are represented yields six types of structural organization. The resulti...
onlinelibrary.wiley.com
January 27, 2026 at 4:21 PM
New paper by Saskia Wilmsen and me just came out BioEssays:
A new classification framework to understand evolutionary transitions in individuality
Please find the OA paper here:
onlinelibrary.wiley.com/doi/10.1002/...
A new classification framework to understand evolutionary transitions in individuality
Please find the OA paper here:
onlinelibrary.wiley.com/doi/10.1002/...
Reposted by Lilian Caesar
Another product from Dr. Ying-Chih 'Ella' Chuang's time in my lab - bacteria that excrete purines are better equipped to tolerate inhibitory effects of purines, suggesting a physiological basis behind some cross-feeding interactions. www.biorxiv.org/content/10.6...
January 23, 2026 at 3:05 PM
Another product from Dr. Ying-Chih 'Ella' Chuang's time in my lab - bacteria that excrete purines are better equipped to tolerate inhibitory effects of purines, suggesting a physiological basis behind some cross-feeding interactions. www.biorxiv.org/content/10.6...
Reposted by Lilian Caesar
🥁 NEW
Our study on infant gut microbiome and #straintransmission is now published in @nature.com:
doi.org/10.1038/s415...
1/10
Our study on infant gut microbiome and #straintransmission is now published in @nature.com:
doi.org/10.1038/s415...
1/10
Baby-to-baby strain transmission shapes the developing gut microbiome - Nature
A metagenomic survey of babies attending the first year of nursery detected extensive baby-to-baby microbial strain transmission, pointing to social interactions in infancy as crucial drivers of infan...
doi.org
January 21, 2026 at 6:24 PM
🥁 NEW
Our study on infant gut microbiome and #straintransmission is now published in @nature.com:
doi.org/10.1038/s415...
1/10
Our study on infant gut microbiome and #straintransmission is now published in @nature.com:
doi.org/10.1038/s415...
1/10
Reposted by Lilian Caesar
✨ Latest exciting story of the group in @nature.com. Here, we go beyond SNPs and built a species-wide atlas of genetic variants in yeast. With >1,000 near T2T genomes, we show how large genomic variations affect trait diversity.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
From genotype to phenotype with 1,086 near telomere-to-telomere yeast genomes - Nature
A newly compiled atlas of species-wide structural variants and gene-based and graph pangenomes derived from highly complete assemblies of genomes from 1,086 natural isolates enable integrative genome-...
www.nature.com
October 16, 2025 at 7:49 AM
✨ Latest exciting story of the group in @nature.com. Here, we go beyond SNPs and built a species-wide atlas of genetic variants in yeast. With >1,000 near T2T genomes, we show how large genomic variations affect trait diversity.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Lilian Caesar
Join #MVIF 45 cassyni.com/s/mvif-45
and #MeetTheSpeakers
🇺🇸 Lilian Caesar (@liliancaesar.bsky.social) will discuss how space and species sculpt stingless bee microbiomes!
and #MeetTheSpeakers
🇺🇸 Lilian Caesar (@liliancaesar.bsky.social) will discuss how space and species sculpt stingless bee microbiomes!
January 19, 2026 at 9:40 AM
Join #MVIF 45 cassyni.com/s/mvif-45
and #MeetTheSpeakers
🇺🇸 Lilian Caesar (@liliancaesar.bsky.social) will discuss how space and species sculpt stingless bee microbiomes!
and #MeetTheSpeakers
🇺🇸 Lilian Caesar (@liliancaesar.bsky.social) will discuss how space and species sculpt stingless bee microbiomes!
Reposted by Lilian Caesar
#MVIF 45 starts tomorrow, with
🇳🇵 Bishwash Thapa
🇮🇷 Zahra Nezamivand Chegini
🇨🇭 Sara Mitri (@saramitri.bsky.social)
🇺🇸 Lilian Caesar (@liliancaesar.bsky.social)
🇮🇹 Haseeb Manzoor
🇦🇹 Laurenz Holcik (@laurenz0908.bsky.social)
Free registration: cassyni.com/s/mvif-45
See you 👋
🇳🇵 Bishwash Thapa
🇮🇷 Zahra Nezamivand Chegini
🇨🇭 Sara Mitri (@saramitri.bsky.social)
🇺🇸 Lilian Caesar (@liliancaesar.bsky.social)
🇮🇹 Haseeb Manzoor
🇦🇹 Laurenz Holcik (@laurenz0908.bsky.social)
Free registration: cassyni.com/s/mvif-45
See you 👋
January 19, 2026 at 9:59 AM
#MVIF 45 starts tomorrow, with
🇳🇵 Bishwash Thapa
🇮🇷 Zahra Nezamivand Chegini
🇨🇭 Sara Mitri (@saramitri.bsky.social)
🇺🇸 Lilian Caesar (@liliancaesar.bsky.social)
🇮🇹 Haseeb Manzoor
🇦🇹 Laurenz Holcik (@laurenz0908.bsky.social)
Free registration: cassyni.com/s/mvif-45
See you 👋
🇳🇵 Bishwash Thapa
🇮🇷 Zahra Nezamivand Chegini
🇨🇭 Sara Mitri (@saramitri.bsky.social)
🇺🇸 Lilian Caesar (@liliancaesar.bsky.social)
🇮🇹 Haseeb Manzoor
🇦🇹 Laurenz Holcik (@laurenz0908.bsky.social)
Free registration: cassyni.com/s/mvif-45
See you 👋
Reposted by Lilian Caesar
Breast milk isn't just nutrition – it delivers live bacterial strains that colonize the infant gut and persist for months.
Happy to share our new paper, where we used metagenomics to track bacterial strains between 195 mother-infant pairs over the first 6 months of life:
doi.org/10.1038/s414...
Happy to share our new paper, where we used metagenomics to track bacterial strains between 195 mother-infant pairs over the first 6 months of life:
doi.org/10.1038/s414...
Assembly of the infant gut microbiome and resistome are linked to bacterial strains in mother’s milk - Nature Communications
Here, with metagenomic analyses on longitudinal samples collected from 195 mother-infant pairs, the authors show that the breast milk microbiome contributes to infant gut assembly through bacterial st...
doi.org
January 18, 2026 at 8:35 PM
Breast milk isn't just nutrition – it delivers live bacterial strains that colonize the infant gut and persist for months.
Happy to share our new paper, where we used metagenomics to track bacterial strains between 195 mother-infant pairs over the first 6 months of life:
doi.org/10.1038/s414...
Happy to share our new paper, where we used metagenomics to track bacterial strains between 195 mother-infant pairs over the first 6 months of life:
doi.org/10.1038/s414...
Reposted by Lilian Caesar
Community conservatism is widespread across microbial phyla and environments www.nature.com/articles/s41... #jcampubs
Community conservatism is widespread across microbial phyla and environments - Nature Ecology & Evolution
This study reveals that closely related microorganisms tend to inhabit similar communities across all major environments and phyla. The authors term this phenomenon ‘community conservatism’, extending...
www.nature.com
January 16, 2026 at 5:02 PM
Community conservatism is widespread across microbial phyla and environments www.nature.com/articles/s41... #jcampubs
Reposted by Lilian Caesar
Are you a graduate student or postdoc who wants to apply your science to policy?
The Gulf Research Program’s Science Policy Fellowship provides experience for one year on the staff of federal, state, local, NGO in the Gulf region and impt networking.
www.nationalacademies.org/programs/GUL...
The Gulf Research Program’s Science Policy Fellowship provides experience for one year on the staff of federal, state, local, NGO in the Gulf region and impt networking.
www.nationalacademies.org/programs/GUL...
Gulf Research Program Science Policy Fellowships
The Gulf Research Program’s Science Policy Fellowship helps scientists hone their skills by putting them to practice for the benefit of Gulf Coast communities and ecosystems. Fellows gain first-hand e...
www.nationalacademies.org
January 15, 2026 at 8:14 PM
Are you a graduate student or postdoc who wants to apply your science to policy?
The Gulf Research Program’s Science Policy Fellowship provides experience for one year on the staff of federal, state, local, NGO in the Gulf region and impt networking.
www.nationalacademies.org/programs/GUL...
The Gulf Research Program’s Science Policy Fellowship provides experience for one year on the staff of federal, state, local, NGO in the Gulf region and impt networking.
www.nationalacademies.org/programs/GUL...
Reposted by Lilian Caesar
Phold's manuscript is now available @narjournal.bsky.social thanks to @susiegriggo.bsky.social @npbhavya.bsky.social @vijinim.bsky.social @linsalrob.bsky.social @martinsteinegger.bsky.social @milot.bsky.social @eunbelivable.bsky.social & others not on bsky #phagesky academic.oup.com/nar/article/...
January 14, 2026 at 5:10 AM
Phold's manuscript is now available @narjournal.bsky.social thanks to @susiegriggo.bsky.social @npbhavya.bsky.social @vijinim.bsky.social @linsalrob.bsky.social @martinsteinegger.bsky.social @milot.bsky.social @eunbelivable.bsky.social & others not on bsky #phagesky academic.oup.com/nar/article/...
Reposted by Lilian Caesar
New preprint out!
How do host regulate ancient symbioses to optimise benefits across environments? Using 🐜, we show hosts actively regulate symbionts, flexibly switching between symbiont-derived and environmental nutrients to thrive under changing diets.
👏 Well done Phoebe and team!
How do host regulate ancient symbioses to optimise benefits across environments? Using 🐜, we show hosts actively regulate symbionts, flexibly switching between symbiont-derived and environmental nutrients to thrive under changing diets.
👏 Well done Phoebe and team!
www.biorxiv.org
January 13, 2026 at 4:25 PM
New preprint out!
How do host regulate ancient symbioses to optimise benefits across environments? Using 🐜, we show hosts actively regulate symbionts, flexibly switching between symbiont-derived and environmental nutrients to thrive under changing diets.
👏 Well done Phoebe and team!
How do host regulate ancient symbioses to optimise benefits across environments? Using 🐜, we show hosts actively regulate symbionts, flexibly switching between symbiont-derived and environmental nutrients to thrive under changing diets.
👏 Well done Phoebe and team!
Reposted by Lilian Caesar
Last days to submit your cool symbiosis abstracts to our cool symbiosis-astrobiology session at #AbSciCon26!!!
Our session on symbiosis and biointeractions for the #Astrobiology meeting #AbSciCon26 was accepted! Please share widely and submit your abstract by 14 of January 2026; Let's put more biology into Astrobiology!
agu.confex.com/agu/abscicon...
agu.confex.com/agu/abscicon...
January 12, 2026 at 6:43 PM
Last days to submit your cool symbiosis abstracts to our cool symbiosis-astrobiology session at #AbSciCon26!!!
Reposted by Lilian Caesar
🚨vConTACT3 now in Nature Biotechnology:
- >95% agreement with ICTV for known viruses
- Classifies both prokaryotic and eukaryotic viruses
- Extends beyond genus → subfamily, family & order
- Systematically assigns taxonomy to tens of thousands of previously unclassified viruses
- >95% agreement with ICTV for known viruses
- Classifies both prokaryotic and eukaryotic viruses
- Extends beyond genus → subfamily, family & order
- Systematically assigns taxonomy to tens of thousands of previously unclassified viruses
January 12, 2026 at 4:34 PM
🚨vConTACT3 now in Nature Biotechnology:
- >95% agreement with ICTV for known viruses
- Classifies both prokaryotic and eukaryotic viruses
- Extends beyond genus → subfamily, family & order
- Systematically assigns taxonomy to tens of thousands of previously unclassified viruses
- >95% agreement with ICTV for known viruses
- Classifies both prokaryotic and eukaryotic viruses
- Extends beyond genus → subfamily, family & order
- Systematically assigns taxonomy to tens of thousands of previously unclassified viruses