4.8 Article

MetaPhlAn 4 profiling of unknown species-level genome bins improves the characterization of diet-associated microbiome changes in mice

Related references

Note: Only part of the references are listed.
Article Biotechnology & Applied Microbiology

Extending and improving metagenomic taxonomic profiling with uncharacterized species using MetaPhlAn 4

Aitor Blanco-Miguez et al.

Summary: MetaPhlAn 4 integrates information from metagenome assemblies and microbial isolate genomes for more comprehensive metagenomic taxonomic profiling.

NATURE BIOTECHNOLOGY (2023)

Review Biochemistry & Molecular Biology

Cardiometabolic health, diet and the gut microbiome: a meta-omics perspective

Mireia Valles-Colomer et al.

Summary: Cardiometabolic diseases are closely related to the gut microbiome and diet, and high-throughput meta-omics techniques have the potential to reveal their intricate links. However, effective integration of these techniques and their application on large cohorts is still a challenge. This review discusses the potential of meta-omics technologies in improving cardiometabolic health and highlights recent large-scale efforts and insights provided.

NATURE MEDICINE (2023)

Article Microbiology

The Mouse Gastrointestinal Bacteria Catalogue enables translation between the mouse and human gut microbiotas via functional mapping

Benjamin S. Beresford-Jones et al.

Summary: This study constructed the Mouse Gastrointestinal Bacteria Catalogue (MGBC) to identify functionally equivalent taxa between the gut microbiotas of humans and mice. It also provided a publicly deposited collection of bacterial isolates to facilitate experimental investigation of individual commensal bacteria functions.

CELL HOST & MICROBE (2022)

Article Biochemical Research Methods

Comprehensive mouse microbiota genome catalog reveals major difference to its human counterpart

Silas Kieser et al.

Summary: This study created a comprehensive catalog of bacterial species commonly living in the gut of laboratory mice by analyzing all publicly available metagenomes. The catalog contains almost 42 thousand bacterial genomes from 1,573 species, of which 78.1% are uncultured. The researchers discovered that the microbial species in the gastrointestinal tracts of mice and humans are largely distinct.

PLOS COMPUTATIONAL BIOLOGY (2022)

Article Endocrinology & Metabolism

Fat and not sugar as the determining factor for gut microbiota changes, obesity, and related metabolic disorders in mice

Francesco Suriano et al.

Summary: Diet-induced obesity is associated with the development of type 2 diabetes, insulin resistance, metabolic inflammation, and stress. Different diets with varying sugar and fat content have distinct effects on obesity and related comorbidities, as well as the composition and diversity of gut microbiota. We found that high-fat diets promote obesity and diabetes progression, with specific changes in gut microbiota composition. These findings suggest that dietary macronutrients and gut microbiota composition play important roles in the development of an obese/diabetic state and metabolic inflammation.

AMERICAN JOURNAL OF PHYSIOLOGY-ENDOCRINOLOGY AND METABOLISM (2022)

Article Multidisciplinary Sciences

Neonatal antibiotic exposure impairs child growth during the first six years of life by perturbing intestinal microbial colonization

Atara Uzan-Yulzari et al.

Summary: Exposure to antibiotics in the neonatal period may affect growth development in boys but not girls, while antibiotic use later in childhood is associated with increased body mass index. Additionally, neonatal antibiotic exposure has long-term effects on gut microbiome, leading to growth impairment in boys during the first six years of life.

NATURE COMMUNICATIONS (2021)

Article Microbiology

An Expanded Gene Catalog of Mouse Gut Metagenomes

Jiahui Zhu et al.

Summary: The study established an expanded gene catalog of the mouse gut metagenome containing 5.8 million genes, identifying diet as a major contributor to differences in gut microbiota composition and functional potential.

MSPHERE (2021)

Review Cell Biology

Host-microbial interactions in the metabolism of different dietary fats

Katia S. Chadaideh et al.

Summary: Dietary fats can have different metabolic effects due to interactions with the gut microbiome, affecting digestion, energy gain, and inflammation. Incorporating host-microbial interactions into energetic models of human nutrition provides greater insight into the mechanisms of diet-induced metabolic diseases.

CELL METABOLISM (2021)

Article Biology

Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3

Francesco Beghini et al.

Summary: Culture-independent analyses of microbial communities have advanced significantly in the past decade, particularly due to the emergence of Shotgun Metagenomics. bioBakery 3, a newly developed toolset, enhances the accuracy and scope of taxonomic, functional, and phylogenetic profiling in microbial community studies by providing an expanding set of reference sequences.

ELIFE (2021)

Article Biotechnology & Applied Microbiology

Gut microbiota determines the social behavior of mice and induces metabolic and inflammatory changes in their adipose tissue

Oryan Agranyoni et al.

Summary: The study reveals distinct gut microbiota composition in dominant (Dom) and submissive (Sub) mice, with less diversity in Sub mice and unique taxa composition. Sub mice show lower body weight and higher expression of inflammation and metabolic-related eWAT adipokines. Fecal microbiota transplantation demonstrates the influence of microbiota on behavioral and physiological traits.

NPJ BIOFILMS AND MICROBIOMES (2021)

Article Biotechnology & Applied Microbiology

Microbiome meta-analysis and cross-disease comparison enabled by the SIAMCAT machine learning toolbox

Jakob Wirbel et al.

Summary: The SIAMCAT is a versatile R toolbox for ML-based comparative metagenomics that enhances model accuracy and disease specificity across different studies. Some biomarkers are found to be disease-specific, while others are applicable across multiple conditions.

GENOME BIOLOGY (2021)

Article Endocrinology & Metabolism

Blueberry proanthocyanidins and anthocyanins improve metabolic health through a gut microbiota-dependent mechanism in diet-induced obese mice

Arianne Morissette et al.

AMERICAN JOURNAL OF PHYSIOLOGY-ENDOCRINOLOGY AND METABOLISM (2020)

Article Immunology

High-Fat Diet Induced Alteration of Mice Microbiota and the Functional Ability to Utilize Fructooligosaccharide for Ethanol Production

Rajnish Prakash Singh et al.

FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY (2020)

Article Genetics & Heredity

The aging mouse microbiome has obesogenic characteristics

Dana Binyamin et al.

GENOME MEDICINE (2020)

Article Endocrinology & Metabolism

Altered Gut Microbiota Composition Is Associated With Back Pain in Overweight and Obese Individuals

Marloes Dekker Nitert et al.

FRONTIERS IN ENDOCRINOLOGY (2020)

Article Biology

Massive metagenomic data analysis using abundance-based machine learning

Zachary N. Harris et al.

BIOLOGY DIRECT (2019)

Article Multidisciplinary Sciences

Laboratory mice born to wild mice have natural microbiota and model human immune responses

Stephan P. Rosshart et al.

SCIENCE (2019)

Review Genetics & Heredity

A Review and Tutorial of Machine Learning Methods for Microbiome Host Trait Prediction

Yi-Hui Zhou et al.

FRONTIERS IN GENETICS (2019)

Article Multidisciplinary Sciences

A fiber-deprived diet disturbs the fine-scale spatial architecture of the murine colon microbiome

Alessandra Riva et al.

NATURE COMMUNICATIONS (2019)

Article Psychiatry

How to perform a meta-analysis with R: a practical tutorial

Sara Balduzzi et al.

EVIDENCE-BASED MENTAL HEALTH (2019)

Review Neurosciences

Leptin and the maintenance of elevated body weight

Warren W. Pan et al.

NATURE REVIEWS NEUROSCIENCE (2018)

Review Biotechnology & Applied Microbiology

Shotgun metagenomics, from sampling to analysis

Christopher Quince et al.

NATURE BIOTECHNOLOGY (2017)

Article Multidisciplinary Sciences

Meta-analysis of gut microbiome studies identifies disease-specific and shared responses

Claire Duvallet et al.

NATURE COMMUNICATIONS (2017)

Article Biochemistry & Molecular Biology

Wild Mouse Gut Microbiota Promotes Host Fitness and Improves Disease Resistance

Stephan P. Rosshart et al.

Article Biochemistry & Molecular Biology

Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation

Nuala A. O'Leary et al.

NUCLEIC ACIDS RESEARCH (2016)

Article Biochemical Research Methods

variancePartition: interpreting drivers of variation in complex gene expression studies

Gabriel E. Hoffman et al.

BMC BIOINFORMATICS (2016)

Article Multidisciplinary Sciences

Persistent microbiome alterations modulate the rate of post-dieting weight regain

Christoph A. Thaiss et al.

NATURE (2016)

Article Multidisciplinary Sciences

The Effect of Diet and Exercise on Intestinal Integrity and Microbial Diversity in Mice

Sara C. Campbell et al.

PLOS ONE (2016)

Article Biochemical Research Methods

Machine Learning Meta-analysis of Large Metagenomic Datasets: Tools and Biological Insights

Edoardo Pasolli et al.

PLOS COMPUTATIONAL BIOLOGY (2016)

Article Multidisciplinary Sciences

High fat diet drives obesity regardless the composition of gut microbiota in mice

Sylvie Rabot et al.

SCIENTIFIC REPORTS (2016)

Article Cell Biology

How informative is the mouse for human gut microbiota research?

Thi Loan Anh Nguyen et al.

DISEASE MODELS & MECHANISMS (2015)

Article Biotechnology & Applied Microbiology

A catalog of the mouse gut metagenome

Liang Xiao et al.

NATURE BIOTECHNOLOGY (2015)

Article Multidisciplinary Sciences

Metabolic and metagenomic outcomes from early-life pulsed antibiotic treatment

Yael R. Nobel et al.

NATURE COMMUNICATIONS (2015)

Article Biochemical Research Methods

Cross-study validation for the assessment of prediction algorithms

Christoph Bernau et al.

BIOINFORMATICS (2014)

Article Ecology

High-fat diet alters gut microbiota physiology in mice

Hannelore Daniel et al.

ISME JOURNAL (2014)

Article Gastroenterology & Hepatology

Modulation of the fecal bile acid profile by gut microbiota in cirrhosis

Genta Kakiyama et al.

JOURNAL OF HEPATOLOGY (2013)

Article Biochemistry & Molecular Biology

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

Christian Quast et al.

NUCLEIC ACIDS RESEARCH (2013)

Article Ecology

Forward selection of explanatory variables

F. Guillaume Blanchet et al.

ECOLOGY (2008)

Article Endocrinology & Metabolism

Role of selective leptin resistance in diet-induced obesity hypertension

K Rahmouni et al.

DIABETES (2005)

Article Computer Science, Artificial Intelligence

Random forests

L Breiman

MACHINE LEARNING (2001)