Annabel Klemets
@annabel-k.bsky.social
PhD student in @tartumicrobiome.bsky.social at the University of Tartu. Interested in early life microbiome development and microbiome-drug interactions | she/they 🌈 | banner photo: Joshua Fuller
Reposted by Annabel Klemets
Come and meet us at #EESMicrobiome in Heidelberg! We are excited to share our research with you 🥳
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September 16, 2025 at 3:32 PM
Come and meet us at #EESMicrobiome in Heidelberg! We are excited to share our research with you 🥳
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Reposted by Annabel Klemets
Interested in how it all began? Check out our paper about the Estonian Microbiome Cohort! ➡️ www.nature.com/articles/s41...
February 6, 2025 at 12:05 PM
Interested in how it all began? Check out our paper about the Estonian Microbiome Cohort! ➡️ www.nature.com/articles/s41...
Reposted by Annabel Klemets
The entire archive of CDC datasets can be found here.
HUGE shoutout to data archivists- this work is important 👏🙌🏻
archive.org/details/2025...
HUGE shoutout to data archivists- this work is important 👏🙌🏻
archive.org/details/2025...
February 1, 2025 at 6:33 PM
The entire archive of CDC datasets can be found here.
HUGE shoutout to data archivists- this work is important 👏🙌🏻
archive.org/details/2025...
HUGE shoutout to data archivists- this work is important 👏🙌🏻
archive.org/details/2025...
Thank you to organizers of the Research Days of Institute of Biomedicine and Translational Medicine for inviting me to present our project on type 2 diabetes medications and the gut microbiome. I really appreciate the feedback and questions. Find out more from the preprint: doi.org/10.1101/2024...
January 31, 2025 at 1:05 PM
Thank you to organizers of the Research Days of Institute of Biomedicine and Translational Medicine for inviting me to present our project on type 2 diabetes medications and the gut microbiome. I really appreciate the feedback and questions. Find out more from the preprint: doi.org/10.1101/2024...
Reposted by Annabel Klemets
Super proud of this paper on infant gut microbiome age coming from my lab. The paper has just been published with @springernature.bsky.social in @naturecomms.bsky.social. Read about it here: rdcu.be/d6cCw.
Early life microbial succession in the gut follows common patterns in humans across the globe
Nature Communications - Here, the authors perform a global analysis of over 3000 infant gut samples revealing a universal pattern of microbial changes over the first 1.5 years, with declines in...
rdcu.be
January 14, 2025 at 3:42 PM
Super proud of this paper on infant gut microbiome age coming from my lab. The paper has just been published with @springernature.bsky.social in @naturecomms.bsky.social. Read about it here: rdcu.be/d6cCw.
Reposted by Annabel Klemets
Thrilled to announce that Matthias Hülsmann's new perspective is now out in @naturemicrobiol.bsky.social! This exciting work is shaping how our group thinks about collective microbiome metabolism. Check it out! www.nature.com/articles/s41...
A framework for understanding collective microbiome metabolism - Nature Microbiology
This Perspective explores why microbiome members perform partial metabolism of substrates and suggests that proteome efficiency is a driver of collective microbiome metabolism.
www.nature.com
November 26, 2024 at 12:45 PM
Thrilled to announce that Matthias Hülsmann's new perspective is now out in @naturemicrobiol.bsky.social! This exciting work is shaping how our group thinks about collective microbiome metabolism. Check it out! www.nature.com/articles/s41...
Reposted by Annabel Klemets
1/ Keen to share the story of my postdoc research out in @natureportfolio.bsky.social! We built a massive resource characterizing the spatial landscape of the gut—and yes, we dug deep into the biology too. If you’ve got a minute, let me walk you through the story. 🧵👇
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Spatially restricted immune and microbiota-driven adaptation of the gut - Nature
Intestinal regionalization is characterized by robust and resilient structural cell states and the intestine can adapt to environmental stress in a spatially controlled manner through crosstalk betwee...
www.nature.com
November 21, 2024 at 10:21 PM
1/ Keen to share the story of my postdoc research out in @natureportfolio.bsky.social! We built a massive resource characterizing the spatial landscape of the gut—and yes, we dug deep into the biology too. If you’ve got a minute, let me walk you through the story. 🧵👇
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Annabel Klemets
More #NatureReviewsCancer updates 🚨
We recently launched a collection on the #microbiome in cancer. While its role is still debated, the collection presents a selection of articles from #SpringerNature journals to highlight our current understandings.🧫🦠
😀👉 bit.ly/48u8WFH
We recently launched a collection on the #microbiome in cancer. While its role is still debated, the collection presents a selection of articles from #SpringerNature journals to highlight our current understandings.🧫🦠
😀👉 bit.ly/48u8WFH
The microbiome in cancer
The gut microbiome plays a crucial role in cancer development and progression, by influencing the host immune system and metabolism.
www.nature.com
November 22, 2024 at 11:18 AM
More #NatureReviewsCancer updates 🚨
We recently launched a collection on the #microbiome in cancer. While its role is still debated, the collection presents a selection of articles from #SpringerNature journals to highlight our current understandings.🧫🦠
😀👉 bit.ly/48u8WFH
We recently launched a collection on the #microbiome in cancer. While its role is still debated, the collection presents a selection of articles from #SpringerNature journals to highlight our current understandings.🧫🦠
😀👉 bit.ly/48u8WFH
Reposted by Annabel Klemets
Your friends shape your microbiome — and so do their friends
Analysis of nearly 2,000 people living in remote villages in Honduras reveals who’s spreading gut microorganisms to whom.
www.nature.com/artic...
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Analysis of nearly 2,000 people living in remote villages in Honduras reveals who’s spreading gut microorganisms to whom.
www.nature.com/artic...
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Your friends shape your microbiome — and so do their friends
Nature - Analysis of nearly 2,000 people living in remote villages in Honduras reveals who’s spreading gut microorganisms to whom.
www.nature.com
November 23, 2024 at 8:36 AM
Your friends shape your microbiome — and so do their friends
Analysis of nearly 2,000 people living in remote villages in Honduras reveals who’s spreading gut microorganisms to whom.
www.nature.com/artic...
1/5
Analysis of nearly 2,000 people living in remote villages in Honduras reveals who’s spreading gut microorganisms to whom.
www.nature.com/artic...
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Reposted by Annabel Klemets
Results 10 yrs metagenomic sequencing for CNS infections www.nature.com/articles/s41...
Impressive.
Key take homes for me.
1) Time to result still long - addressable but a barrier currently.
2) 10% contamination.
3) Despite using cutting edge tests a "causative" organism found in only 15%.
Impressive.
Key take homes for me.
1) Time to result still long - addressable but a barrier currently.
2) 10% contamination.
3) Despite using cutting edge tests a "causative" organism found in only 15%.
November 13, 2024 at 5:15 PM
Results 10 yrs metagenomic sequencing for CNS infections www.nature.com/articles/s41...
Impressive.
Key take homes for me.
1) Time to result still long - addressable but a barrier currently.
2) 10% contamination.
3) Despite using cutting edge tests a "causative" organism found in only 15%.
Impressive.
Key take homes for me.
1) Time to result still long - addressable but a barrier currently.
2) 10% contamination.
3) Despite using cutting edge tests a "causative" organism found in only 15%.
Reposted by Annabel Klemets
Targeted protein evolution in the gut microbiome by diversity-generating retroelements
www.biorxiv.org/content/10.1...
Nice paper on diversity generating retroelements in the Bacteroides:
www.biorxiv.org/content/10.1...
Nice paper on diversity generating retroelements in the Bacteroides:
November 17, 2024 at 5:10 PM
Targeted protein evolution in the gut microbiome by diversity-generating retroelements
www.biorxiv.org/content/10.1...
Nice paper on diversity generating retroelements in the Bacteroides:
www.biorxiv.org/content/10.1...
Nice paper on diversity generating retroelements in the Bacteroides:
Reposted by Annabel Klemets
Reading: academic.oup.com/nar/advance-...
The mOTUs online database provides web-accessible genomic context to taxonomic profiling of microbial communities
The mOTUs online database provides web-accessible genomic context to taxonomic profiling of microbial communities
The mOTUs online database provides web-accessible genomic context to taxonomic profiling of microbial communities
Abstract. Determining the taxonomic composition (taxonomic profiling) is a fundamental task in studying environmental and host-associated microbial communi
academic.oup.com
November 18, 2024 at 7:28 AM
Reading: academic.oup.com/nar/advance-...
The mOTUs online database provides web-accessible genomic context to taxonomic profiling of microbial communities
The mOTUs online database provides web-accessible genomic context to taxonomic profiling of microbial communities
Reposted by Annabel Klemets
New paper from the lab out in Cell Systems. “Spatiotemporal dynamics during niche remodeling by super-colonizing microbiota in the mammalian gut”
www.cell.com/cell-systems...
www.cell.com/cell-systems...
Spatiotemporal dynamics during niche remodeling by super-colonizing microbiota in the mammalian gut
Fecal microbiota transplantation (FMT) therapies hold promise but suffer from variable
transplantation efficiencies. Here, we examine microbiome spatiotemporal dynamics
post-FMT with a super-colonizin...
www.cell.com
November 17, 2024 at 6:41 PM
New paper from the lab out in Cell Systems. “Spatiotemporal dynamics during niche remodeling by super-colonizing microbiota in the mammalian gut”
www.cell.com/cell-systems...
www.cell.com/cell-systems...
Reposted by Annabel Klemets
Estimates of microbiome heritability across hosts.
#Microbiome #NatureMicrobiology #BioSky #SciSky 🧪
www.nature.com/articles/s41...
#Microbiome #NatureMicrobiology #BioSky #SciSky 🧪
www.nature.com/articles/s41...
Estimates of microbiome heritability across hosts - Nature Microbiology
In this Perspective, Morris and Bohannan discuss heritability of microbiome-mediated traits across hosts and future research questions with implications for animal and plant breeding.
www.nature.com
November 16, 2024 at 11:18 AM
Estimates of microbiome heritability across hosts.
#Microbiome #NatureMicrobiology #BioSky #SciSky 🧪
www.nature.com/articles/s41...
#Microbiome #NatureMicrobiology #BioSky #SciSky 🧪
www.nature.com/articles/s41...
Reposted by Annabel Klemets
Incredible graphic - the myriad of ways that bacteria defend themselves against antibiotics.
14 resistance mechanisms, summarised by Idan Yelin & Roy Kishony in Cell
www.sciencedirect.com/science/arti...
14 resistance mechanisms, summarised by Idan Yelin & Roy Kishony in Cell
www.sciencedirect.com/science/arti...
November 13, 2024 at 12:46 PM
Incredible graphic - the myriad of ways that bacteria defend themselves against antibiotics.
14 resistance mechanisms, summarised by Idan Yelin & Roy Kishony in Cell
www.sciencedirect.com/science/arti...
14 resistance mechanisms, summarised by Idan Yelin & Roy Kishony in Cell
www.sciencedirect.com/science/arti...
Reposted by Annabel Klemets
Hot off the press: "Fecal microbial load is a major determinant of gut microbiome variation and a confounder for disease associations" www.sciencedirect.com/science/arti...
See below for @suguru-nishijima.bsky.social 's thread on the preprint!
#microsky #microbiome
See below for @suguru-nishijima.bsky.social 's thread on the preprint!
#microsky #microbiome
November 13, 2024 at 4:29 PM
Hot off the press: "Fecal microbial load is a major determinant of gut microbiome variation and a confounder for disease associations" www.sciencedirect.com/science/arti...
See below for @suguru-nishijima.bsky.social 's thread on the preprint!
#microsky #microbiome
See below for @suguru-nishijima.bsky.social 's thread on the preprint!
#microsky #microbiome
Reposted by Annabel Klemets
Excited to share our latest preprint on a novel computational tool to predict fecal microbial load solely from relative species profiles! Our study revealed that fecal microbial load is a substantial confounder in microbiome-disease association studies.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
March 19, 2024 at 11:41 AM
Excited to share our latest preprint on a novel computational tool to predict fecal microbial load solely from relative species profiles! Our study revealed that fecal microbial load is a substantial confounder in microbiome-disease association studies.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Annabel Klemets
Bluesky, I want to share with you one of my favourite papers:
November 9, 2024 at 4:23 PM
Bluesky, I want to share with you one of my favourite papers:
Reposted by Annabel Klemets
After editing, this very short letter to New Scientist is even shorter now. But I think it gets the point across! @faecalmatters.bsky.social
November 11, 2024 at 10:23 PM
After editing, this very short letter to New Scientist is even shorter now. But I think it gets the point across! @faecalmatters.bsky.social
Reposted by Annabel Klemets
Your hitchhiker's guide to microbiome studies:
journals.asm.org/doi/epub/10....
journals.asm.org/doi/epub/10....
November 12, 2024 at 5:05 PM
Your hitchhiker's guide to microbiome studies:
journals.asm.org/doi/epub/10....
journals.asm.org/doi/epub/10....
Reposted by Annabel Klemets
I'm new here, so I'll share our recent work here too 😁🧫
Using Tn-seq + live imaging in engineered airway organoids, we explored the fitness tradeoffs P. aeruginosa faces while growing and surviving antibiotic treatment on the mucosal surface.
Check it out: www.nature.com/articles/s41...
#MicroSky
Using Tn-seq + live imaging in engineered airway organoids, we explored the fitness tradeoffs P. aeruginosa faces while growing and surviving antibiotic treatment on the mucosal surface.
Check it out: www.nature.com/articles/s41...
#MicroSky
Pseudomonas aeruginosa faces a fitness trade-off between mucosal colonization and antibiotic tolerance during airway infection - Nature Microbiology
Tn-seq and live imaging of Pseudomonas aeruginosa during airway epithelial organoid infections reveal metabolic adaptations and trade-offs between growth and antibiotic tolerance in biofilm lifestyle,...
www.nature.com
November 11, 2024 at 3:57 PM
I'm new here, so I'll share our recent work here too 😁🧫
Using Tn-seq + live imaging in engineered airway organoids, we explored the fitness tradeoffs P. aeruginosa faces while growing and surviving antibiotic treatment on the mucosal surface.
Check it out: www.nature.com/articles/s41...
#MicroSky
Using Tn-seq + live imaging in engineered airway organoids, we explored the fitness tradeoffs P. aeruginosa faces while growing and surviving antibiotic treatment on the mucosal surface.
Check it out: www.nature.com/articles/s41...
#MicroSky
Reposted by Annabel Klemets
Welcome all (new) followers! Besides our work on probes & biosensors I'd like to share what I know about #Rstats and #DataViz. So I composed a book on data visualization with R & ggplot2 (it's work in progress).
Target audience = wet lab scientists.
Link: joachimgoedhart.github.io/DataViz-prot...
Target audience = wet lab scientists.
Link: joachimgoedhart.github.io/DataViz-prot...
DataViz protocols
This is an introduction to data visualization protocols for wet lab scientists
joachimgoedhart.github.io
November 12, 2024 at 7:12 PM
Welcome all (new) followers! Besides our work on probes & biosensors I'd like to share what I know about #Rstats and #DataViz. So I composed a book on data visualization with R & ggplot2 (it's work in progress).
Target audience = wet lab scientists.
Link: joachimgoedhart.github.io/DataViz-prot...
Target audience = wet lab scientists.
Link: joachimgoedhart.github.io/DataViz-prot...
Reposted by Annabel Klemets
[looking at Bluesky over the past 2 days] So this is what the Cambrian explosion must have felt like
November 11, 2024 at 10:17 PM
[looking at Bluesky over the past 2 days] So this is what the Cambrian explosion must have felt like
Reposted by Annabel Klemets
Human xenobiotic metabolism proteins have full-length and split homologs in the gut microbiome https://www.biorxiv.org/content/10.1101/2024.11.06.622278v1
Human xenobiotic metabolism proteins have full-length and split homologs in the gut microbiome https://www.biorxiv.org/content/10.1101/2024.11.06.622278v1
Xenobiotics, including pharmaceutical drugs, can be metabolized by both host and microbiota, in some
www.biorxiv.org
November 8, 2024 at 10:34 PM
Human xenobiotic metabolism proteins have full-length and split homologs in the gut microbiome https://www.biorxiv.org/content/10.1101/2024.11.06.622278v1
Hello, Bluesky! I'm Annabel, a PhD student in the Tartu Microbiome group led by Prof. Elin Org at the University of Tartu (EE).
I am interested in the long-term effects of medications on the gut microbiome and early-life microbiome development.
I also like photography, sci-fi, and crocheting 🌿
I am interested in the long-term effects of medications on the gut microbiome and early-life microbiome development.
I also like photography, sci-fi, and crocheting 🌿
November 9, 2024 at 4:43 PM
Hello, Bluesky! I'm Annabel, a PhD student in the Tartu Microbiome group led by Prof. Elin Org at the University of Tartu (EE).
I am interested in the long-term effects of medications on the gut microbiome and early-life microbiome development.
I also like photography, sci-fi, and crocheting 🌿
I am interested in the long-term effects of medications on the gut microbiome and early-life microbiome development.
I also like photography, sci-fi, and crocheting 🌿