In our new publication in Environmental Microbiology, we explore the use of genome-level phylogenies and also genome-derived functional information for assessing alpha and beta diversity. Given the large number of microbial genomes that are now available, we sought to assess...
In our new preprint (Ruaud et al., 2022), we introduce endoR: an R-package to interpret machine learning models. We also present the application of endoR to human gut metagenomes to identify associations between H2 producers and methanogens in the human...
Congratulations to all doctoral students that presented their work, especially Andrea Borbon, Mirabeau Mbong, and Yihua Liu who were also recognized for the local MPI community among the finest. Andrea got the second place among the best posters presentations with...
Archaea are often mistaken as bacteria, given that both are small, single-cell organisms. However, archaea are as genetically different from bacteria as humans are from bacteria. While archaea are found in most environments, including the human gut microbiome, relatively little...
In this YouTube video, Nick Youngblut and colleagues discuss their latest work on the Archaea of the vertebrate gut. Read the original research paper in Nature Microbiology, and the less technical summary on our MPI blog.
...
Ever wonder if H. pylori was the only gut microbe that tracked human population as they migrated out of Africa? Here we show evidence that others did too! By matching human genotype data to gut metagenome data, Taichi Suzuki, Liam...
Check out Hagay Enav’s new tool, SynTracker, for comparing microbial strains using comparative synteny. It requires remarkably small fractions of genomes to do so, and is good at ignoring differences in strains at the SNP level.
...
Here, doctoral student Michael Bell prepares samples for the Cryo-EM. Please see the Join Us page for more details!
...
The 1929 Nobel Prize was given for pyrotherapy: heating people up to 41C to kill the Treponema causing syphilis. Ever wonder what fever does to the body’s microbiome? Post Doc Dr. Kelsey Huss has looked into it, and written a...
We have a new Doctor! Last week, Albane Ruaud defended her thesis titled “Analysis of human gut metagenomes for the prediction of host traits with tree ensemble machine learning models”, for which she was awarded the Magna Cum Laude distinction....
This week saw our newest pre-print arrive on bioRxiv! Postdoc Stacey Heaver shows that inositol lipid production is more widespread in bacteria than previously thought and identifies two pathways for their production in Bacteroides thetaiotaomicron (B. theta). Inositol lipids are...
Welter et al.’s analysis of the evolutionary history of Psychrobacter is out in mSystems. Her phylogenomic analysis, combined with the outcome of >10,000 growth tests, indicates that the psychrophiles in this genus are descendants of warm host-associated ancestors. More about...
Our contribution to encouraging bacterial classification to match phylogeny is in this pitch to rename Catabacter as Christensenella, based on whole genome analysis of isolates by Xiaoying Liu – pubished in the International Journal of Systematic and Evolutionary Microbiology.
...
Daphne Welter is our second graduate student to have defended during the pandemic. She presented her thesis entitled “Insights into the ecology and evolutionary history of the bacterial genus Psychrobacter”. mSystems published her paper during her presentation as an Editor’s...
The Otto Bayer Award came with a cartoon! Thank you to the Bayer Foundation for a very nice event.
...
Methanomassiliicoccales are lesser known members of the human gut archaeome that use methylated amines, including trimethylamine, in methane production. A new study, led by grad student Jacobo de la Cuesta-Zuluaga and published in mSystems, assessed the abundances of these methanogens...
The Bayer Foundation announced today that Ruth Ley is the 2020 recipient of the Otto Bayer Award. We are very grateful to the foundation for this recognition of the lab’s work. Read the announcement here: https://www.bayer-foundation.com/otto-bayer-award-goes-ruth-ley
...
In this review, Taichi Suzuki takes on the challenge of thinking through how the microbiome can play a role in the process of human genetic adaptation to new environments. When humans spread out across the globe they encountered new diets,...
Last week the institute held its annual PhD symposium online, to great success. Congratulations to Tanja Schön for winning Best Poster, Michael Bell for winning Best Short Talk, and Albane Ruaud for Runner-Up in the Long Talk category. The 2020...
https://www.biorxiv.org/content/10.1101/2020.11.10.376293v1 The Archaea remain more mysterious than the Bacteria as they are comparatively under-studied. This is changing thanks for next generation sequencing. However, little is known about archaeal communities associated with vertebrates, especially due to strong Bacteria-biases of standard “universal”...
In our new publication in Environmental Microbiology, we explore the use of genome-level phylogenies and also genome-derived functional information for assessing alpha and beta diversity. Given the large number of microbial genomes that are now available, we sought to assess...
In our new preprint (Ruaud et al., 2022), we introduce endoR: an R-package to interpret machine learning models. We also present the application of endoR to human gut metagenomes to identify associations between H2 producers and methanogens in the human...
Congratulations to all doctoral students that presented their work, especially Andrea Borbon, Mirabeau Mbong, and Yihua Liu who were also recognized for the local MPI community among the finest. Andrea got the second place among the best posters presentations with...
Archaea are often mistaken as bacteria, given that both are small, single-cell organisms. However, archaea are as genetically different from bacteria as humans are from bacteria. While archaea are found in most environments, including the human gut microbiome, relatively little...
In this YouTube video, Nick Youngblut and colleagues discuss their latest work on the Archaea of the vertebrate gut. Read the original research paper in Nature Microbiology, and the less technical summary on our MPI blog.
... Ever wonder if H. pylori was the only gut microbe that tracked human population as they migrated out of Africa? Here we show evidence that others did too! By matching human genotype data to gut metagenome data, Taichi Suzuki, Liam...
Check out Hagay Enav’s new tool, SynTracker, for comparing microbial strains using comparative synteny. It requires remarkably small fractions of genomes to do so, and is good at ignoring differences in strains at the SNP level.
... Here, doctoral student Michael Bell prepares samples for the Cryo-EM. Please see the Join Us page for more details!
... The 1929 Nobel Prize was given for pyrotherapy: heating people up to 41C to kill the Treponema causing syphilis. Ever wonder what fever does to the body’s microbiome? Post Doc Dr. Kelsey Huss has looked into it, and written a...
We have a new Doctor! Last week, Albane Ruaud defended her thesis titled “Analysis of human gut metagenomes for the prediction of host traits with tree ensemble machine learning models”, for which she was awarded the Magna Cum Laude distinction....
This week saw our newest pre-print arrive on bioRxiv! Postdoc Stacey Heaver shows that inositol lipid production is more widespread in bacteria than previously thought and identifies two pathways for their production in Bacteroides thetaiotaomicron (B. theta). Inositol lipids are...
Welter et al.’s analysis of the evolutionary history of Psychrobacter is out in mSystems. Her phylogenomic analysis, combined with the outcome of >10,000 growth tests, indicates that the psychrophiles in this genus are descendants of warm host-associated ancestors. More about...
Our contribution to encouraging bacterial classification to match phylogeny is in this pitch to rename Catabacter as Christensenella, based on whole genome analysis of isolates by Xiaoying Liu – pubished in the International Journal of Systematic and Evolutionary Microbiology.
... Daphne Welter is our second graduate student to have defended during the pandemic. She presented her thesis entitled “Insights into the ecology and evolutionary history of the bacterial genus Psychrobacter”. mSystems published her paper during her presentation as an Editor’s...
The Otto Bayer Award came with a cartoon! Thank you to the Bayer Foundation for a very nice event.
... Methanomassiliicoccales are lesser known members of the human gut archaeome that use methylated amines, including trimethylamine, in methane production. A new study, led by grad student Jacobo de la Cuesta-Zuluaga and published in mSystems, assessed the abundances of these methanogens...
The Bayer Foundation announced today that Ruth Ley is the 2020 recipient of the Otto Bayer Award. We are very grateful to the foundation for this recognition of the lab’s work. Read the announcement here: https://www.bayer-foundation.com/otto-bayer-award-goes-ruth-ley
... In this review, Taichi Suzuki takes on the challenge of thinking through how the microbiome can play a role in the process of human genetic adaptation to new environments. When humans spread out across the globe they encountered new diets,...
Last week the institute held its annual PhD symposium online, to great success. Congratulations to Tanja Schön for winning Best Poster, Michael Bell for winning Best Short Talk, and Albane Ruaud for Runner-Up in the Long Talk category. The 2020...
https://www.biorxiv.org/content/10.1101/2020.11.10.376293v1 The Archaea remain more mysterious than the Bacteria as they are comparatively under-studied. This is changing thanks for next generation sequencing. However, little is known about archaeal communities associated with vertebrates, especially due to strong Bacteria-biases of standard “universal”...