Christian Diener
@cdiener.com
Lifelong relationship with microbes, now studying them for a living. Assistant Professor at MedUni Graz. Opinions are my own. He/him 🦠+💻=❤️
More socials at cdiener.com. Lab website at dienerlab.com.
More socials at cdiener.com. Lab website at dienerlab.com.
(2) a high specificity identification and quantification pipeline that reliably identifies metagenomic reads coming from food items even when those make up less than 0.001% of the total DNA
February 18, 2025 at 11:02 AM
(2) a high specificity identification and quantification pipeline that reliably identifies metagenomic reads coming from food items even when those make up less than 0.001% of the total DNA
(1) a linked food database of more than 400 food items that includes nutrition and genomic information with multiple fallback strategies (partial assemblies, higher ranks)
February 18, 2025 at 11:02 AM
(1) a linked food database of more than 400 food items that includes nutrition and genomic information with multiple fallback strategies (partial assemblies, higher ranks)
We also ran a proof-of-concept identifying foods and nutrients that were associated with the onset of metabolic disease in an adult cohort.
February 6, 2024 at 6:47 PM
We also ran a proof-of-concept identifying foods and nutrients that were associated with the onset of metabolic disease in an adult cohort.
Food genomic material was detected only in about half of infant stool samples but increased at the onset of solid food consumption and was ubiquitous in adult stool samples.
February 6, 2024 at 6:46 PM
Food genomic material was detected only in about half of infant stool samples but increased at the onset of solid food consumption and was ubiquitous in adult stool samples.
Using a decoy-aware mapping approach with additional consistency filtering we could show good sensitivity and specificity in simulated sequencing samples with a false positive rate around 1-10 reads per million.
February 6, 2024 at 6:46 PM
Using a decoy-aware mapping approach with additional consistency filtering we could show good sensitivity and specificity in simulated sequencing samples with a false positive rate around 1-10 reads per million.
Building a comprehensive genomic database for as many foods in FOODB as possible we could connect individual genomes to nutrient content. For now we can match 77% of all foods in FOODB with taxonomic information and the next version of the database will push this to 90%.
February 6, 2024 at 6:45 PM
Building a comprehensive genomic database for as many foods in FOODB as possible we could connect individual genomes to nutrient content. For now we can match 77% of all foods in FOODB with taxonomic information and the next version of the database will push this to 90%.
We also ran a proof-of-concept identifying foods and nutrients that were associated with the onset of metabolic disease in an adult cohort.
January 29, 2025 at 8:32 AM
We also ran a proof-of-concept identifying foods and nutrients that were associated with the onset of metabolic disease in an adult cohort.
Food genomic material was detected only in about half of infant stool samples but increased at the onset of solid food consumption and was ubiquitous in adult stool samples.
January 29, 2025 at 8:27 AM
Food genomic material was detected only in about half of infant stool samples but increased at the onset of solid food consumption and was ubiquitous in adult stool samples.
Using a decoy-aware mapping approach with additional consistency filtering we could show good sensitivity and specificity in simulated sequencing samples with a false positive rate around 1-10 reads per million.
January 29, 2025 at 8:21 AM
Using a decoy-aware mapping approach with additional consistency filtering we could show good sensitivity and specificity in simulated sequencing samples with a false positive rate around 1-10 reads per million.
Building a comprehensive genomic database for as many foods in FOODB as possible we could connect individual genomes to nutrient content. For now we can match 77% of all foods in FOODB with taxonomic information. The next version of the database will push this to 90%.
January 29, 2025 at 8:16 AM
Building a comprehensive genomic database for as many foods in FOODB as possible we could connect individual genomes to nutrient content. For now we can match 77% of all foods in FOODB with taxonomic information. The next version of the database will push this to 90%.
January 29, 2025 at 8:06 AM
October 20, 2023 at 5:29 PM
The final day of the 2023 ISB Microbiome series will start in 30m. Today we have a symposium packed with amazing speakers, so be there or be ▣. 🦠+💻=💕 Session 1 will feature @ceciliaNoecker
and @lab_maier
. #ISBMicro23 #microbiome @isbsci
and @lab_maier
. #ISBMicro23 #microbiome @isbsci
January 29, 2025 at 8:06 AM
The final day of the 2023 ISB Microbiome series will start in 30m. Today we have a symposium packed with amazing speakers, so be there or be ▣. 🦠+💻=💕 Session 1 will feature @ceciliaNoecker
and @lab_maier
. #ISBMicro23 #microbiome @isbsci
and @lab_maier
. #ISBMicro23 #microbiome @isbsci
The final day of the 2023 ISB Microbiome series will start in 30m. Today we have a symposium packed with amazing speakers, so be there or be ▣. 🦠+💻=💕 Session 1 will feature @cecilianoecker.bsky.social and Lisa Maier. #ISBMicro23 #microbiome
October 13, 2023 at 3:33 PM
The final day of the 2023 ISB Microbiome series will start in 30m. Today we have a symposium packed with amazing speakers, so be there or be ▣. 🦠+💻=💕 Session 1 will feature @cecilianoecker.bsky.social and Lisa Maier. #ISBMicro23 #microbiome
We will start day 2 of the Virtual ISB Microbiome course 2023 in 1h. Today, we will learn how to predict strain engraftment using metabolic modeling. isbscience.org/microbiome2023
The course will be based on Alex's preprint: doi.org/10.1101/2023.... 🦠+💻=💕
#microbiome #ISBMicro23
The course will be based on Alex's preprint: doi.org/10.1101/2023.... 🦠+💻=💕
#microbiome #ISBMicro23
October 12, 2023 at 3:17 PM
We will start day 2 of the Virtual ISB Microbiome course 2023 in 1h. Today, we will learn how to predict strain engraftment using metabolic modeling. isbscience.org/microbiome2023
The course will be based on Alex's preprint: doi.org/10.1101/2023.... 🦠+💻=💕
#microbiome #ISBMicro23
The course will be based on Alex's preprint: doi.org/10.1101/2023.... 🦠+💻=💕
#microbiome #ISBMicro23
We will start day 2 of the ISB Microbiome course 2023 in 1h. Today, let's learn how to predict strain engraftment using metabolic modeling. 🦠=💕 https://isbscience.org/microbiome2023
The course will be based on Alex's preprint:...
The course will be based on Alex's preprint:...
January 29, 2025 at 8:06 AM
We will start day 2 of the ISB Microbiome course 2023 in 1h. Today, let's learn how to predict strain engraftment using metabolic modeling. 🦠=💕 https://isbscience.org/microbiome2023
The course will be based on Alex's preprint:...
The course will be based on Alex's preprint:...
Only 45 minutes left until we start our Virtual ISB Microbiome course 2023. Can't wait to meet all the participants and chat with you about the course. 🦠+💻=💕. isbscience.org/microbiome2023 #microbiome #microbiomesky
October 11, 2023 at 3:21 PM
Only 45 minutes left until we start our Virtual ISB Microbiome course 2023. Can't wait to meet all the participants and chat with you about the course. 🦠+💻=💕. isbscience.org/microbiome2023 #microbiome #microbiomesky
Only 45 minutes left until we start our Virtual ISB Microbiome course 2023. Can't wait to meet all the participants and chat with you about the course. 🦠+💻=💕. https://isbscience.org/microbiome2023 #microbiome
January 29, 2025 at 8:06 AM
Only 45 minutes left until we start our Virtual ISB Microbiome course 2023. Can't wait to meet all the participants and chat with you about the course. 🦠+💻=💕. https://isbscience.org/microbiome2023 #microbiome
Back in Europe for a bit. Climate sure is something else here 🥵
January 29, 2025 at 8:06 AM
Back in Europe for a bit. Climate sure is something else here 🥵
Alex also showed that his strategy can reproduce the success of a recently published probiotic cocktail to prevent C. diff infection by @VedantaBio and predicts that its mechanism of action is blockage of the C. diff niche. #noxp
January 29, 2025 at 8:52 AM
Alex also showed that his strategy can reproduce the success of a recently published probiotic cocktail to prevent C. diff infection by @VedantaBio and predicts that its mechanism of action is blockage of the C. diff niche. #noxp
Looking at this a bit more, one surprising thing is that C. diff uptake fluxes clustered into 3-4 distinct metabolic niches that were correlated with C. diff. growth and were highly reproducible across thousands of samples. #noxp
January 29, 2025 at 8:42 AM
Looking at this a bit more, one surprising thing is that C. diff uptake fluxes clustered into 3-4 distinct metabolic niches that were correlated with C. diff. growth and were highly reproducible across thousands of samples. #noxp
This also worked when modeling individuals with recurrent C. diff infection receiving FMTs, where he could correctly predict the susceptible state before treatment and the return to normal levels after. #noxp
January 29, 2025 at 8:32 AM
This also worked when modeling individuals with recurrent C. diff infection receiving FMTs, where he could correctly predict the susceptible state before treatment and the return to normal levels after. #noxp
The cool thing about this is that you can predict pathogen invasion potential even for a microbiome that does not contain the pathogen at all 🤯 #noxp
January 29, 2025 at 8:21 AM
The cool thing about this is that you can predict pathogen invasion potential even for a microbiome that does not contain the pathogen at all 🤯 #noxp
How do you get around that? Use a steady state method that predicts growth rates that look like they could have come from a dynamic model, for instance by enriching for growth rates that can be reached easily from inoculation. #noxp
January 29, 2025 at 8:22 AM
How do you get around that? Use a steady state method that predicts growth rates that look like they could have come from a dynamic model, for instance by enriching for growth rates that can be reached easily from inoculation. #noxp
One issue is the objective itself. One can formulate a community-wide growth rate, but that is rarely maximized in the real world, creating uncertainty in the growth rate and flux predictions. #noxp
January 29, 2025 at 8:11 AM
One issue is the objective itself. One can formulate a community-wide growth rate, but that is rarely maximized in the real world, creating uncertainty in the growth rate and flux predictions. #noxp