Publications by authors named "Nicholas D Youngblut"

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Infection with gut parasites correlates with gut microbiome diversity across human populations in Africa.
Mirabeau M Ngwese, Bayode R Adegbite, Jeannot F Zinsou, J Liam Fitzstevens, Victor T Schmidt, Nicholas D Youngblut

Gut Microbes· December 2025

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Obesity is the main driver of altered gut microbiome functions in the metabolically unhealthy.
Jacobo de la Cuesta-Zuluaga, Kelsey E Huus, Nicholas D Youngblut, Juan S Escobar, Ruth E Ley

Gut Microbes· December 2023

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An integrated systems biology approach reveals differences in formate metabolism in the genus .
Isabella Casini, Tim McCubbin, Sofia Esquivel-Elizondo, Guillermo G Luque, Daria Evseeva, Nicholas D Youngblut

iScience· October 2023

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ResMiCo: Increasing the quality of metagenome-assembled genomes with deep learning.
Olga Mineeva, Daniel Danciu, Bernhard Schölkopf, Ruth E Ley, Gunnar Rätsch, Nicholas D Youngblut

PLoS Comput Biol· May 2023

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Silent recognition of flagellins from human gut commensal bacteria by Toll-like receptor 5.
Sara J Clasen, Michael E W Bell, Andrea Borbón, Du-Hwa Lee, Zachariah M Henseler, Nicholas D Youngblut

Sci Immunol· January 2023

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Interpreting tree ensemble machine learning models with endoR.
Albane Ruaud, Niklas Pfister, Ruth E Ley, Nicholas D Youngblut

PLoS Comput Biol· December 2022

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Bacterial community dynamics explain carbon mineralization and assimilation in soils of different land-use history.
Samuel E Barnett, Nicholas D Youngblut, Daniel H Buckley

Environ Microbiol· November 2022

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Tracing Carbon Metabolism with Stable Isotope Metabolomics Reveals the Legacy of Diverse Carbon Sources in Soil.
Roland C Wilhelm, Samuel E Barnett, Tami L Swenson, Nicholas D Youngblut, Chantal N Koechli

Appl Environ Microbiol· November 2022

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Incorporating genome-based phylogeny and functional similarity into diversity assessments helps to resolve a global collection of human gut metagenomes.
Nicholas D Youngblut, Jacobo de la Cuesta-Zuluaga, Ruth E Ley

Environ Microbiol· September 2022

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Codiversification of gut microbiota with humans.
Taichi A Suzuki, J Liam Fitzstevens, Victor T Schmidt, Hagay Enav, Kelsey E Huus, Nicholas D Youngblut

Science· September 2022

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Vertebrate host phylogeny influences gut archaeal diversity.
Nicholas D Youngblut, Georg H Reischer, Silke Dauser, Sophie Maisch, Chris Walzer

Nat Microbiol· November 2021

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Multisubstrate DNA stable isotope probing reveals guild structure of bacteria that mediate soil carbon cycling.
Samuel E Barnett, Nicholas D Youngblut, Chantal N Koechli, Daniel H Buckley

Proc Natl Acad Sci U S A· November 2021

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Struo2: efficient metagenome profiling database construction for ever-expanding microbial genome datasets.
Nicholas D Youngblut, Ruth E Ley

PeerJ· September 2021

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Free-Living, Psychrotrophic Bacteria of the Genus Are Descendants of Pathobionts.
Daphne K Welter, Albane Ruaud, Zachariah M Henseler, Hannah N De Jong, Peter van Coeverden de Groot, Nicholas D Youngblut

mSystems· April 2021

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Reclassification of as comb. nov. based on whole genome analysis.
Xiaoying Liu, Jessica L Sutter, Jacobo de la Cuesta-Zuluaga, Jillian L Waters, Nicholas D Youngblut

Int J Syst Evol Microbiol· April 2021

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Genomic Insights into Adaptations of Trimethylamine-Utilizing Methanogens to Diverse Habitats, Including the Human Gut.
Jacobo de la Cuesta-Zuluaga, Tim D Spector, Nicholas D Youngblut, Ruth E Ley

mSystems· February 2021

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Large-Scale Metagenome Assembly Reveals Novel Animal-Associated Microbial Genomes, Biosynthetic Gene Clusters, and Other Genetic Diversity.
Nicholas D Youngblut, Jacobo de la Cuesta-Zuluaga, Georg H Reischer, Silke Dauser, Nathalie Schuster

mSystems· November 2020

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Strain-Level Analysis of spp. from Gut Microbiomes of Adults with Differing Lactase Persistence Genotypes.
Victor Schmidt, Hagay Enav, Timothy D Spector, Nicholas D Youngblut, Ruth E Ley

mSystems· September 2020

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Data Analysis for DNA Stable Isotope Probing Experiments Using Multiple Window High-Resolution SIP.
Samuel E Barnett, Nicholas D Youngblut, Daniel H Buckley

Methods Mol Biol· June 2020

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DeepMAsED: evaluating the quality of metagenomic assemblies.
Olga Mineeva, Mateo Rojas-Carulla, Ruth E Ley, Bernhard Schölkopf, Nicholas D Youngblut

Bioinformatics· May 2020

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Struo: a pipeline for building custom databases for common metagenome profilers.
Jacobo de la Cuesta-Zuluaga, Ruth E Ley, Nicholas D Youngblut

Bioinformatics· April 2020

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Syntrophy via Interspecies H Transfer between and Underlies Their Global Cooccurrence in the Human Gut.
Albane Ruaud, Sofia Esquivel-Elizondo, Jacobo de la Cuesta-Zuluaga, Jillian L Waters, Largus T Angenent, Nicholas D Youngblut

mBio· February 2020

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Soil characteristics and land-use drive bacterial community assembly patterns.
Samuel E Barnett, Nicholas D Youngblut, Daniel H Buckley

FEMS Microbiol Ecol· January 2020

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Host diet and evolutionary history explain different aspects of gut microbiome diversity among vertebrate clades.
Nicholas D Youngblut, Georg H Reischer, William Walters, Nathalie Schuster, Chris Walzer

Nat Commun· May 2019

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Human Salivary Amylase Gene Copy Number Impacts Oral and Gut Microbiomes.
Angela C Poole, Julia K Goodrich, Nicholas D Youngblut, Guillermo G Luque, Albane Ruaud

Cell Host Microbe· April 2019

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