Christoph Kaleta
@kaletalab.bsky.social
Medical Systems Biology research group - Constraint-based modelling - Modelling of host-microbiome-interactions - Systems Biology of Aging
Pinned
1/3 We're hiring! Join us as a PhD student in metabolic microbiome modeling within @spp2474.bsky.social — help uncover the microbiome’s dark matter alongside top microbiome labs across Germany! @uni-kiel.de
jobs.uksh.de/job/Kiel-PhD...
jobs.uksh.de/job/Kiel-PhD...
Reposted by Christoph Kaleta
This is really cool and important.
Some of the longest-lived organisms on Earth aren’t whales, trees or corals, but microbes buried deep in the earth. This eye-opening essay examines the slowest lives on Earth, asking what such lives mean for how we define life itself @karenlloyd.bsky.social
The discovery of aeonophiles expands our definition of life | Aeon Essays
The discovery of organisms that have been alive for many thousands of years requires a revolution in how we understand life
buff.ly
December 18, 2025 at 4:56 PM
This is really cool and important.
Reposted by Christoph Kaleta
📍Our paper is out!📍
Here, we show the development of a GC-MS/MS method for the quantification of 120 compounds produced by gut bacteria, including short-chain fatty acids, indols, nucleotides, organic acids, and amino acid derivatives.
Check it out!
link.springer.com/article/10.1...
Here, we show the development of a GC-MS/MS method for the quantification of 120 compounds produced by gut bacteria, including short-chain fatty acids, indols, nucleotides, organic acids, and amino acid derivatives.
Check it out!
link.springer.com/article/10.1...
Development of a GC-MS/MS method to quantify 120 gut microbiota-derived metabolites - Analytical and Bioanalytical Chemistry
The gut microbiota produces metabolites that are important for host physiology and have critical roles in the development of diseases, such as metabolic disorders, cardiovascular diseases, and cancer....
link.springer.com
December 16, 2025 at 10:56 AM
📍Our paper is out!📍
Here, we show the development of a GC-MS/MS method for the quantification of 120 compounds produced by gut bacteria, including short-chain fatty acids, indols, nucleotides, organic acids, and amino acid derivatives.
Check it out!
link.springer.com/article/10.1...
Here, we show the development of a GC-MS/MS method for the quantification of 120 compounds produced by gut bacteria, including short-chain fatty acids, indols, nucleotides, organic acids, and amino acid derivatives.
Check it out!
link.springer.com/article/10.1...
Highly interesting work identifying commonly targeted enzymes for production improvement of target compounds across literature by dan1elmachado.bsky.social: www.biorxiv.org/content/10.6...
A database of over 15.000 strain design publications reveals a conserved set of metabolic engineering targets across microbial hosts and products
Microbial biotechnology has the potential to address several societal issues through the sustainable production of industrially relevant compounds. Despite decades of successful cases, rational engine...
www.biorxiv.org
December 17, 2025 at 9:39 AM
Highly interesting work identifying commonly targeted enzymes for production improvement of target compounds across literature by dan1elmachado.bsky.social: www.biorxiv.org/content/10.6...
Reposted by Christoph Kaleta
A database of over 15.000 strain design publications reveals a conserved set of metabolic engineering targets across microbial hosts and products https://www.biorxiv.org/content/10.64898/2025.12.15.694291v1
December 17, 2025 at 7:02 AM
A database of over 15.000 strain design publications reveals a conserved set of metabolic engineering targets across microbial hosts and products https://www.biorxiv.org/content/10.64898/2025.12.15.694291v1
Reposted by Christoph Kaleta
New preprint out! Using ~75k environmental OTUs + 77 fossil calibrations, we reconstructed a Proterozoic timeline of eukaryote evolution. Our results show crown eukaryotes were already diversifying >1.6 Ga, long before the first undisputed fossils (~1.05 Ga).
🔗 DOI: www.biorxiv.org/content/10.6...
🔗 DOI: www.biorxiv.org/content/10.6...
December 15, 2025 at 8:19 AM
New preprint out! Using ~75k environmental OTUs + 77 fossil calibrations, we reconstructed a Proterozoic timeline of eukaryote evolution. Our results show crown eukaryotes were already diversifying >1.6 Ga, long before the first undisputed fossils (~1.05 Ga).
🔗 DOI: www.biorxiv.org/content/10.6...
🔗 DOI: www.biorxiv.org/content/10.6...
Reposted by Christoph Kaleta
"One small molecule for man, one giant leap for mankind with obesity"
sciencedirect.com/science/arti...
But the very high amounts of drug in pills relative to injectable peptides, due to such poor bioavailability, means we need to be watchful for new side effects when these pills get widely used
sciencedirect.com/science/arti...
But the very high amounts of drug in pills relative to injectable peptides, due to such poor bioavailability, means we need to be watchful for new side effects when these pills get widely used
One small molecule for man, one giant leap for mankind with obesity
The ATTAIN-1 trial launches a new era in obesity care. Orforglipron, the first oral small-molecule GLP-1 receptor agonist to complete a phase 3 clinic…
sciencedirect.com
December 12, 2025 at 9:30 PM
"One small molecule for man, one giant leap for mankind with obesity"
sciencedirect.com/science/arti...
But the very high amounts of drug in pills relative to injectable peptides, due to such poor bioavailability, means we need to be watchful for new side effects when these pills get widely used
sciencedirect.com/science/arti...
But the very high amounts of drug in pills relative to injectable peptides, due to such poor bioavailability, means we need to be watchful for new side effects when these pills get widely used
Reposted by Christoph Kaleta
Denmark just mapped its entire environmental microbiome. More than 10,000 samples revealing hidden, dominant nitrifiers that shape fertilizer use, water quality, and climate impact. A national microbiome atlas could transform sustainable agriculture across Europe.
#AMR
www.nature.com/articles/s41...
#AMR
www.nature.com/articles/s41...
The Microflora Danica atlas of Danish environmental microbiomes - Nature
Microflora Danica—an atlas of Danish environmental microbiomes—reveals that although human-disturbed habitats have high alpha diversity, species reoccur, revealing hidden homogeneity.
www.nature.com
December 5, 2025 at 10:52 AM
Denmark just mapped its entire environmental microbiome. More than 10,000 samples revealing hidden, dominant nitrifiers that shape fertilizer use, water quality, and climate impact. A national microbiome atlas could transform sustainable agriculture across Europe.
#AMR
www.nature.com/articles/s41...
#AMR
www.nature.com/articles/s41...
Reposted by Christoph Kaleta
I'm very happy to share our latest manuscript published today in @nature.com !!
➡️ doi.org/10.1038/s415...
We analyzed data from over 34,000 participants in the US and UK, revealing strong associations between specific gut bacteria and markers of cardiometabolic health and dietary habits.
➡️ doi.org/10.1038/s415...
We analyzed data from over 34,000 participants in the US and UK, revealing strong associations between specific gut bacteria and markers of cardiometabolic health and dietary habits.
December 10, 2025 at 5:26 PM
I'm very happy to share our latest manuscript published today in @nature.com !!
➡️ doi.org/10.1038/s415...
We analyzed data from over 34,000 participants in the US and UK, revealing strong associations between specific gut bacteria and markers of cardiometabolic health and dietary habits.
➡️ doi.org/10.1038/s415...
We analyzed data from over 34,000 participants in the US and UK, revealing strong associations between specific gut bacteria and markers of cardiometabolic health and dietary habits.
Reposted by Christoph Kaleta
Is the human microbiome a source for hospital-associated infections (HAI) and are any genetic changes associated with HAI? In our new preprint, we longitudinally reconstruct the evolutionary processes within the human microbiome leading up to HAI: doi.org/10.1101/2025...
Colonization, translocation, and evolution of opportunistic pathogens during hospital-associated infections
Many commensal bacteria that peacefully reside in the human microbiome are also able to cause acute opportunistic infections. Emerging evidence suggests that within-host evolution contributes to infec...
doi.org
October 27, 2025 at 9:25 AM
Is the human microbiome a source for hospital-associated infections (HAI) and are any genetic changes associated with HAI? In our new preprint, we longitudinally reconstruct the evolutionary processes within the human microbiome leading up to HAI: doi.org/10.1101/2025...
Reposted by Christoph Kaleta
Controlled settings may offer limited insight into the complexities of ageing in natural and variable ecosystems, and why (and how) ageing patterns vary so widely across individuals, populations, and species.
We call for more research on ecology of ageing!
onlinelibrary.wiley.com/doi/10.1111/...
We call for more research on ecology of ageing!
onlinelibrary.wiley.com/doi/10.1111/...
Ecological Perspectives on Aging
Controlled settings may offer limited insight into the complexities of aging in natural and variable ecosystems. Artwork by Zahida Sultanova.
onlinelibrary.wiley.com
December 5, 2025 at 11:13 AM
Controlled settings may offer limited insight into the complexities of ageing in natural and variable ecosystems, and why (and how) ageing patterns vary so widely across individuals, populations, and species.
We call for more research on ecology of ageing!
onlinelibrary.wiley.com/doi/10.1111/...
We call for more research on ecology of ageing!
onlinelibrary.wiley.com/doi/10.1111/...
Reposted by Christoph Kaleta
New preprint:
www.biorxiv.org/content/10.6...
www.biorxiv.org/content/10.6...
Pyocyanin produced by Pseudomonas aeruginosa Creates Legacy Effects That Boost Antibiotic Resistance Evolution in Enterococci
Polymicrobial infections are small communities of multiple interacting bacterial species. Interactions among constituent species may modify the growth of community members in the presence of antibioti...
www.biorxiv.org
December 5, 2025 at 2:27 PM
New preprint:
www.biorxiv.org/content/10.6...
www.biorxiv.org/content/10.6...
Reposted by Christoph Kaleta
💬 Beim zweiten Research Festival der Medizinischen Fakultät der #UniKiel standen der interdisziplinäre Austausch und die Forschung des wissenschaftlichen Nachwuchses im Mittelpunkt:
🔗: https://www.uni-kiel.de/de/detailansicht/news/206-researchfestival
📷: Kerstin Nees/Felix Lürssen, Uni Kiel
🔗: https://www.uni-kiel.de/de/detailansicht/news/206-researchfestival
📷: Kerstin Nees/Felix Lürssen, Uni Kiel
December 5, 2025 at 2:46 PM
💬 Beim zweiten Research Festival der Medizinischen Fakultät der #UniKiel standen der interdisziplinäre Austausch und die Forschung des wissenschaftlichen Nachwuchses im Mittelpunkt:
🔗: https://www.uni-kiel.de/de/detailansicht/news/206-researchfestival
📷: Kerstin Nees/Felix Lürssen, Uni Kiel
🔗: https://www.uni-kiel.de/de/detailansicht/news/206-researchfestival
📷: Kerstin Nees/Felix Lürssen, Uni Kiel
Reposted by Christoph Kaleta
Our latest, led by the inimitable Chris Kay "Dated gene duplications elucidate the evolutionary assembly of eukaryotes" in which we used gene duplications to test hypotheses of eukaryogenesis. TLDR? They're all wrong. With @tweethinking.bsky.social @anya1.bsky.social @ssolo.bsky.social Davide Pisani
Dated gene duplications elucidate the evolutionary assembly of eukaryotes - Nature
Analysis of eukaryotic gene sequences using a relaxed molecular clock methodology indicate that eukaryotes emerged 3.0–2.25 billion years ago as a result of mitochondrial endosymbiosis with complex ar...
www.nature.com
December 3, 2025 at 5:05 PM
Our latest, led by the inimitable Chris Kay "Dated gene duplications elucidate the evolutionary assembly of eukaryotes" in which we used gene duplications to test hypotheses of eukaryogenesis. TLDR? They're all wrong. With @tweethinking.bsky.social @anya1.bsky.social @ssolo.bsky.social Davide Pisani
Reposted by Christoph Kaleta
Nature research paper: Dated gene duplications elucidate the evolutionary assembly of eukaryotes
go.nature.com/4azJDF8
go.nature.com/4azJDF8
Dated gene duplications elucidate the evolutionary assembly of eukaryotes - Nature
Analysis of eukaryotic gene sequences using a relaxed molecular clock methodology indicate that eukaryotes emerged 3.0–2.25 billion years ago as a result of mitochondrial endosymbiosis with complex archaea that already possessed an elaborated cytoskeleton, membrane trafficking, endomembrane, phagocytotic machinery and a nucleus.
go.nature.com
December 5, 2025 at 9:18 AM
Nature research paper: Dated gene duplications elucidate the evolutionary assembly of eukaryotes
go.nature.com/4azJDF8
go.nature.com/4azJDF8
1/3 We're hiring! Join us as a PhD student in metabolic microbiome modeling within @spp2474.bsky.social — help uncover the microbiome’s dark matter alongside top microbiome labs across Germany! @uni-kiel.de
jobs.uksh.de/job/Kiel-PhD...
jobs.uksh.de/job/Kiel-PhD...
December 5, 2025 at 7:57 AM
1/3 We're hiring! Join us as a PhD student in metabolic microbiome modeling within @spp2474.bsky.social — help uncover the microbiome’s dark matter alongside top microbiome labs across Germany! @uni-kiel.de
jobs.uksh.de/job/Kiel-PhD...
jobs.uksh.de/job/Kiel-PhD...
Reposted by Christoph Kaleta
Looks interesting: “A host-centric view of the microbiota metabolome” www.cell.com/immunity/abs...
A host-centric view of the microbiota metabolome
Our current understanding of microbial-host communication is largely based on context-dependent
examples and anecdotes. Yamada and Palm present a teleological framework that organizes
microbial metabo...
www.cell.com
December 3, 2025 at 8:47 PM
Looks interesting: “A host-centric view of the microbiota metabolome” www.cell.com/immunity/abs...
Reposted by Christoph Kaleta
Excited to see our work published. Thanks for the support, Johannes Zimmermann, Jan Taubenheim, @kaletalab.bsky.social and our funding bodies.
(1/7) Excited that the Virtual Colon, an extension of BacArena for modeling the spatiostructural environment of the colon, is now out at mSystems. Kudos to @maringos.bsky.social and for leading this work! @crc1182.bsky.social @uni-kiel.de iel.de Link: journals.asm.org/doi/full/10....
Virtual Colon: spatiotemporal modeling of metabolic interactions in a computational colonic environment | mSystems
Interactions between the human body and gut microbes are crucial for health and disease.
We present the Virtual Colon, an extension of the individual-based microbiome modeling
approach BacArena that m...
journals.asm.org
December 4, 2025 at 11:34 AM
Excited to see our work published. Thanks for the support, Johannes Zimmermann, Jan Taubenheim, @kaletalab.bsky.social and our funding bodies.
Reposted by Christoph Kaleta
Faecal metabolites as a readout of habitual diet capture dietary interactions with the gut microbiome.
By integrating faecal metabolomics, metagenomics, and dietary data Falchi et al. show that faecal metabolites capture mediations between diet and the gut microbiome
www.nature.com/articles/s41...
By integrating faecal metabolomics, metagenomics, and dietary data Falchi et al. show that faecal metabolites capture mediations between diet and the gut microbiome
www.nature.com/articles/s41...
Faecal metabolites as a readout of habitual diet capture dietary interactions with the gut microbiome - Nature Communications
Here, by integrating faecal metabolomics, metagenomics, and habitual dietary data of two large human cohorts, the authors show that faecal metabolites reflect diet and gut microbiome interactions, pre...
www.nature.com
December 4, 2025 at 11:10 AM
Faecal metabolites as a readout of habitual diet capture dietary interactions with the gut microbiome.
By integrating faecal metabolomics, metagenomics, and dietary data Falchi et al. show that faecal metabolites capture mediations between diet and the gut microbiome
www.nature.com/articles/s41...
By integrating faecal metabolomics, metagenomics, and dietary data Falchi et al. show that faecal metabolites capture mediations between diet and the gut microbiome
www.nature.com/articles/s41...
Reposted by Christoph Kaleta
Excited to share our new @natecoevo.nature.com
paper. We identified microbes found across nearly all ruminants that act as the functional backbone of both the rumen ecosystem and the host, with major implications for food security and climate change mitigation. (1/8)
www.nature.com/articles/s41...
paper. We identified microbes found across nearly all ruminants that act as the functional backbone of both the rumen ecosystem and the host, with major implications for food security and climate change mitigation. (1/8)
www.nature.com/articles/s41...
December 3, 2025 at 4:00 PM
Excited to share our new @natecoevo.nature.com
paper. We identified microbes found across nearly all ruminants that act as the functional backbone of both the rumen ecosystem and the host, with major implications for food security and climate change mitigation. (1/8)
www.nature.com/articles/s41...
paper. We identified microbes found across nearly all ruminants that act as the functional backbone of both the rumen ecosystem and the host, with major implications for food security and climate change mitigation. (1/8)
www.nature.com/articles/s41...
(1/7) Excited that the Virtual Colon, an extension of BacArena for modeling the spatiostructural environment of the colon, is now out at mSystems. Kudos to @maringos.bsky.social and for leading this work! @crc1182.bsky.social @uni-kiel.de iel.de Link: journals.asm.org/doi/full/10....
Virtual Colon: spatiotemporal modeling of metabolic interactions in a computational colonic environment | mSystems
Interactions between the human body and gut microbes are crucial for health and disease.
We present the Virtual Colon, an extension of the individual-based microbiome modeling
approach BacArena that m...
journals.asm.org
December 4, 2025 at 7:54 AM
(1/7) Excited that the Virtual Colon, an extension of BacArena for modeling the spatiostructural environment of the colon, is now out at mSystems. Kudos to @maringos.bsky.social and for leading this work! @crc1182.bsky.social @uni-kiel.de iel.de Link: journals.asm.org/doi/full/10....
Reposted by Christoph Kaleta
HGMT: a database of human gut microbiota for tumors and immunotherapy response. #GutMicrobiota #TumorSample #Metagenomics #ImmunotherapyTreated #GenomeBiology 🧪🧬 🖥️
link.springer.com/article/10.1...
link.springer.com/article/10.1...
December 3, 2025 at 11:30 AM
HGMT: a database of human gut microbiota for tumors and immunotherapy response. #GutMicrobiota #TumorSample #Metagenomics #ImmunotherapyTreated #GenomeBiology 🧪🧬 🖥️
link.springer.com/article/10.1...
link.springer.com/article/10.1...
👇Three days left to apply👇
1/4 🌍 We are looking for a passionate #PhD student in #Metabolic #Microbiome #Modeling in the Marie Skłodowska-Curie Doctoral Network MenoBrain. Join us at one of Europe’s microbiome research hubs and push the boundaries of microbiome science! @uni-kiel.de
🔗 www.uniklinikum-jena.de/menobrain/en...
🔗 www.uniklinikum-jena.de/menobrain/en...
November 27, 2025 at 11:09 AM
👇Three days left to apply👇
Reposted by Christoph Kaleta
1/4 🌍 We are looking for a passionate #PhD student in #Metabolic #Microbiome #Modeling in the Marie Skłodowska-Curie Doctoral Network MenoBrain. Join us at one of Europe’s microbiome research hubs and push the boundaries of microbiome science! @uni-kiel.de
🔗 www.uniklinikum-jena.de/menobrain/en...
🔗 www.uniklinikum-jena.de/menobrain/en...
October 9, 2025 at 7:04 AM
1/4 🌍 We are looking for a passionate #PhD student in #Metabolic #Microbiome #Modeling in the Marie Skłodowska-Curie Doctoral Network MenoBrain. Join us at one of Europe’s microbiome research hubs and push the boundaries of microbiome science! @uni-kiel.de
🔗 www.uniklinikum-jena.de/menobrain/en...
🔗 www.uniklinikum-jena.de/menobrain/en...
Reposted by Christoph Kaleta
New data that supports metformin as a potential intervention to reduce #LongCovid www.authorea.com/users/100423...
Metformin at the time of Covid-19 infection and risk of Long Covid: A Target Trial Emulation Study
Background: Our objective was to evaluate metformin prescribed at the time of SARS-CoV-2 infection on the risk of developing Long Covid (LC) in electronic health record data. Methods: We conducted a n...
www.authorea.com
November 26, 2025 at 7:12 PM
New data that supports metformin as a potential intervention to reduce #LongCovid www.authorea.com/users/100423...
Highly interesting note of caution about research on the link between autism and the microbiome. Summary adapted from the article: Across many fields, we’ve learned that a lot of smoke doesn’t necessarily mean there’s any real fire. www.sciencedirect.com/science/arti...
Conceptual and methodological flaws undermine claims of a link between the gut microbiome and autism
The idea that the gut microbiome causally contributes to autism has gained currency in the scientific literature and popular press. Support for this h…
www.sciencedirect.com
November 20, 2025 at 8:52 AM
Highly interesting note of caution about research on the link between autism and the microbiome. Summary adapted from the article: Across many fields, we’ve learned that a lot of smoke doesn’t necessarily mean there’s any real fire. www.sciencedirect.com/science/arti...