4.8 Article

Kernel-based genetic association analysis for microbiome phenotypes identifies host genetic drivers of beta-diversity

Related references

Note: Only part of the references are listed.
Article Multidisciplinary Sciences

Gut Ruminococcaceae levels at baseline correlate with risk of antibiotic-associated diarrhea

Xiaoqiong Gu et al.

Summary: Antibiotic-associated diarrhea (AAD) is a common issue in patients receiving antibiotic treatment. Differences in the gut microbiome may influence the development of AAD. Lower levels of gut Ruminococcaceae and decreased microbial diversity may be associated with the occurrence of AAD. The levels of Faecalibacterium prausnitzii at baseline can predict the likelihood of AAD.

ISCIENCE (2022)

Article Genetics & Heredity

MicrobiomeGWAS: A Tool for Identifying Host Genetic Variants Associated with Microbiome Composition

Xing Hua et al.

Summary: This article introduces a method to investigate the association between host genetic variations and microbiome composition through sequencing the highly variable regions of 16S rRNA genes. The authors develop a statistical framework and software package to identify host genetic variants associated with microbiome beta diversity and improve the accuracy of p-value approximations by correcting for skewness and kurtosis. The method is validated using lung tissue samples and shows preliminary evidence of an association between lung cancer risk SNPs and microbiome composition.

GENES (2022)

Article Genetics & Heredity

Large-scale association analyses identify host factors influencing human gut microbiome composition

Alexander Kurilshikov et al.

Summary: The study revealed significant effects of host genetic variation on microbial composition, with the lactase (LCT) gene locus showing an age-dependent association with Bifidobacterium abundance. Other associations, while suggestive, were enriched for taxa with high heritability and for genes expressed in the intestine and brain.

NATURE GENETICS (2021)

Article Cell Biology

A genome-wide association study for gut metagenome in Chinese adults illuminates complex diseases

Xiaomin Liu et al.

Summary: This study demonstrates the significant genetic influence on the gut microbiome, which plays a key role in human health and diseases. Analysis revealed abundant signals associated with the gut microbiome in metabolic, neurological, and immunological functions, with potential genetic attributes to enterotypes. Gender stratification led to differential associations, and a two-stage metagenome genome-wide association studies emphasized the importance of considering both microbiome and GWAS studies in understanding human health and diseases.

CELL DISCOVERY (2021)

Article Microbiology

Commensal Clostridiales strains mediate effective anti-cancer immune response against solid tumors

Ana Montalban-Arques et al.

Summary: Despite the overall success of T cell checkpoint inhibitors in cancer treatment, research has found that certain commensal species of gut microbiota associated with lower tumor burden and are significantly reduced in CRC patients. Oral application of specific Clostridiales strains can prevent and even treat CRC successfully in mouse models, outperforming anti-PD-1 therapy in some cases. This indicates the potential of gut bacteria as a novel stand-alone therapy against solid tumors.

CELL HOST & MICROBE (2021)

Review Cell Biology

Interaction between microbiota and immunity in health and disease

Danping Zheng et al.

CELL RESEARCH (2020)

Article Genetics & Heredity

Multi-SKAT: General framework to test for rare-variant association with multiple phenotypes

Diptavo Dutta et al.

GENETIC EPIDEMIOLOGY (2019)

Article Genetics & Heredity

ACAT: A Fast and Powerful p Value Combination Method for Rare-Variant Analysis in Sequencing Studies

Yaowu Liu et al.

AMERICAN JOURNAL OF HUMAN GENETICS (2019)

Article Multidisciplinary Sciences

ZFR coordinates crosstalk between RNA decay and transcription in innate immunity

Nazmul Haque et al.

NATURE COMMUNICATIONS (2018)

Editorial Material Microbiology

Earth Microbiome Project and Global Systems Biology

Jack A. Gilbert et al.

MSYSTEMS (2018)

Article Multidisciplinary Sciences

Environment dominates over host genetics in shaping human gut microbiota

Daphna Rothschild et al.

NATURE (2018)

Article Microbiology

Microbiome Datasets Are Compositional: And This Is Not Optional

Gregory B. Gloor et al.

FRONTIERS IN MICROBIOLOGY (2017)

Article Gastroenterology & Hepatology

The gut microbiota and host health: a new clinical frontier

Julian R. Marchesi et al.

Article Genetics & Heredity

A Statistical Approach for Testing Cross-Phenotype Effects of Rare Variants

K. Alaine Broadaway et al.

AMERICAN JOURNAL OF HUMAN GENETICS (2016)

Article Microbiology

Genetic Determinants of the Gut Microbiome in UK Twins

Julia K. Goodrich et al.

CELL HOST & MICROBE (2016)

Review Immunology

Genetic variation in IBD: progress, clues to pathogenesis and possible clinical utility

Byong Duk Ye et al.

EXPERT REVIEW OF CLINICAL IMMUNOLOGY (2016)

Article Genetics & Heredity

The effect of host genetics on the gut microbiome

Marc Jan Bonder et al.

NATURE GENETICS (2016)

Review Biotechnology & Applied Microbiology

Lower Level of Bacteroides in the Gut Microbiota Is Associated with Inflammatory Bowel Disease: A Meta-Analysis

Yingting Zhou et al.

BIOMED RESEARCH INTERNATIONAL (2016)

Article Microbiology

Interpreting Prevotella and Bacteroides as biomarkers of diet and lifestyle

Anastassia Gorvitovskaia et al.

MICROBIOME (2016)

Article Genetics & Heredity

Testing in Microbiome-Profiling Studies with MiRKAT, the Microbiome Regression-Based Kernel Association Test

Ni Zhao et al.

AMERICAN JOURNAL OF HUMAN GENETICS (2015)

Article Multidisciplinary Sciences

A global reference for human genetic variation

David M. Altshuler et al.

NATURE (2015)

Article Multidisciplinary Sciences

Genome-Wide Association Studies of the Human Gut Microbiota

Emily R. Davenport et al.

PLOS ONE (2015)

Article Biotechnology & Applied Microbiology

Host genetic variation impacts microbiome composition across human body sites

Ran Blekhman et al.

GENOME BIOLOGY (2015)

Article Biochemical Research Methods

Cosi2: an efficient simulator of exact and approximate coalescent with selection

Ilya Shlyakhter et al.

BIOINFORMATICS (2014)

Article Gastroenterology & Hepatology

The Microbiome in Inflammatory Bowel Disease: Current Status and the Future Ahead

Aleksandar D. Kostic et al.

GASTROENTEROLOGY (2014)

Article Computer Science, Artificial Intelligence

Distance-Based Analysis of Variance: Approximate Inference

Christopher Minas et al.

STATISTICAL ANALYSIS AND DATA MINING (2014)

Proceedings Paper Mathematics, Applied

Kernel Methods for Regression Analysis of Microbiome Compositional Data

Jun Chen et al.

TOPICS IN APPLIED STATISTICS (2013)

Article Gastroenterology & Hepatology

Linkage of gut microbiome with cognition in hepatic encephalopathy

Jasmohan S. Bajaj et al.

AMERICAN JOURNAL OF PHYSIOLOGY-GASTROINTESTINAL AND LIVER PHYSIOLOGY (2012)

Review Biochemistry & Molecular Biology

The Impact of the Gut Microbiota on Human Health: An Integrative View

Jose C. Clemente et al.

Article Multidisciplinary Sciences

Human gut microbiome viewed across age and geography

Tanya Yatsunenko et al.

NATURE (2012)

Article Biotechnology & Applied Microbiology

Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment

Xochitl C. Morgan et al.

GENOME BIOLOGY (2012)

Article Genetics & Heredity

Rare-Variant Association Testing for Sequencing Data with the Sequence Kernel Association Test

Michael C. Wu et al.

AMERICAN JOURNAL OF HUMAN GENETICS (2011)

Review Medicine, General & Internal

Interleukin-23: A key cytokine in inflammatory diseases

Emilie Duvallet et al.

ANNALS OF MEDICINE (2011)

Article Multidisciplinary Sciences

Enterotypes of the human gut microbiome

Manimozhiyan Arumugam et al.

NATURE (2011)

Article Public, Environmental & Occupational Health

Design and Implementation of the Hispanic Community Health Study/Study of Latinos

Paul D. Sorlie et al.

ANNALS OF EPIDEMIOLOGY (2010)

Article Genetics & Heredity

MaCH: Using Sequence and Genotype Data to Estimate Haplotypes and Unobserved Genotypes

Yun Li et al.

GENETIC EPIDEMIOLOGY (2010)

Article Multidisciplinary Sciences

Disordered Microbial Communities in the Upper Respiratory Tract of Cigarette Smokers

Emily S. Charlson et al.

PLOS ONE (2010)

Article Genetics & Heredity

MAST3: a novel IBD risk factor that modulates TLR4 signaling

C. Labbe et al.

GENES AND IMMUNITY (2008)

Article Genetics & Heredity

Functional variants in the B-cell gene BANK1 are associated with systemic lupus erythematosus

Sergey V. Kozyrev et al.

NATURE GENETICS (2008)

Article Biotechnology & Applied Microbiology

Quantitative and qualitative beta diversity measures lead to different insights into factors that structure microbial communities

Catherine A. Lozupone et al.

APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2007)

Article Multidisciplinary Sciences

A genome-wide association study identifies IL23R as an inflammatory bowel disease gene

Richard H. Duerr et al.

SCIENCE (2006)

Article Biotechnology & Applied Microbiology

UniFrac: a new phylogenetic method for comparing microbial communities

C Lozupone et al.

APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2005)

Article Genetics & Heredity

Identification of a variant associated with adult-type hypolactasia

NS Enattah et al.

NATURE GENETICS (2002)