4.5 Article

Vertebrate host phylogeny influences gut archaeal diversity

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Article Biochemical Research Methods

Struo: a pipeline for building custom databases for common metagenome profilers

Jacobo de la Cuesta-Zuluaga et al.

BIOINFORMATICS (2020)

Article Agriculture, Dairy & Animal Science

Review: Comparative methane production in mammalian herbivores

M. Clauss et al.

ANIMAL (2020)

Article Agriculture, Dairy & Animal Science

Influential factors on the composition of the conventionally raised broiler gastrointestinal microbiomes

K. M. Feye et al.

POULTRY SCIENCE (2020)

Review Microbiology

Diversity, ecology and evolution of Archaea

Brett J. Baker et al.

NATURE MICROBIOLOGY (2020)

Review Microbiology

The host-associated archaeome

Guillaume Borrel et al.

NATURE REVIEWS MICROBIOLOGY (2020)

Article Biochemical Research Methods

clustermq enables efficient parallelization of genomic analyses

Michael Schubert

BIOINFORMATICS (2019)

Article Environmental Sciences

Newly designed 16S rRNA metabarcoding primers amplify diverse and novel archaeal taxa from the environment

Mohammad Bahram et al.

ENVIRONMENTAL MICROBIOLOGY REPORTS (2019)

Article Multidisciplinary Sciences

Host diet and evolutionary history explain different aspects of gut microbiome diversity among vertebrate clades

Nicholas D. Youngblut et al.

NATURE COMMUNICATIONS (2019)

Review Genetics & Heredity

Host and Microbiome Genome-Wide Association Studies: Current State and Challenges

Denis Awany et al.

FRONTIERS IN GENETICS (2019)

Article Multidisciplinary Sciences

Comprehensive skin microbiome analysis reveals the uniqueness of human skin and evidence for phylosymbiosis within the class Mammalia

Ashley A. Ross et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2018)

Review Biochemistry & Molecular Biology

Archaea Are Interactive Components of Complex Microbiomes

Christine Moissl-Eichinger et al.

TRENDS IN MICROBIOLOGY (2018)

Article Ecology

RRPP: An R package for fitting linear models to high-dimensional data using residual randomization

Michael L. Collyer et al.

METHODS IN ECOLOGY AND EVOLUTION (2018)

Article Biotechnology & Applied Microbiology

A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life

Donovan H. Parks et al.

NATURE BIOTECHNOLOGY (2018)

Article Microbiology

The Distal Gut Bacterial Community of Some Primates and Carnivora

Xiu Chen et al.

CURRENT MICROBIOLOGY (2018)

Review Microbiology

Bathyarchaeota: globally distributed metabolic generalists in anoxic environments

Zhichao Zhou et al.

FEMS MICROBIOLOGY REVIEWS (2018)

Article Biochemistry & Molecular Biology

metaSPAdes: a new versatile metagenomic assembler

Sergey Nurk et al.

GENOME RESEARCH (2017)

Article Zoology

The Effects of Captivity on the Mammalian Gut Microbiome

Valerie J. McKenzie et al.

INTEGRATIVE AND COMPARATIVE BIOLOGY (2017)

Article Biochemistry & Molecular Biology

TimeTree: A Resource for Timelines, Timetrees, and Divergence Times

Sudhir Kumar et al.

MOLECULAR BIOLOGY AND EVOLUTION (2017)

Article Biochemistry & Molecular Biology

Intergenomic evolution and metabolic cross-talk between rumen and thermophilic autotrophic methanogenic archaea

M. Bharathi et al.

MOLECULAR PHYLOGENETICS AND EVOLUTION (2017)

Letter Biotechnology & Applied Microbiology

MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets

Martin Steinegger et al.

NATURE BIOTECHNOLOGY (2017)

Article Multidisciplinary Sciences

Unraveling the processes shaping mammalian gut microbiomes over evolutionary time

Mathieu Groussin et al.

NATURE COMMUNICATIONS (2017)

Article Microbiology

Unexplored Archaeal Diversity in the Great Ape Gut Microbiome

Kasie Raymann et al.

MSPHERE (2017)

Article Ecology

paco: implementing Procrustean Approach to Cophylogeny in R

Matthew C. Hutchinson et al.

METHODS IN ECOLOGY AND EVOLUTION (2017)

Article Computer Science, Artificial Intelligence

Bracken: estimating species abundance in metagenomics data

Jennifer Lu et al.

PEERJ COMPUTER SCIENCE (2017)

Article Statistics & Probability

cooccur: Probabilistic Species Co-Occurrence Analysis inR

Daniel M. Griffith et al.

Journal of Statistical Software (2016)

Review Biochemistry & Molecular Biology

Microbiome evolution along divergent branches of the vertebrate tree of life: what is known and unknown

Timothy J. Colston et al.

MOLECULAR ECOLOGY (2016)

Article Biochemical Research Methods

DADA2: High-resolution sample inference from Illumina amplicon data

Benjamin J. Callahan et al.

NATURE METHODS (2016)

Article Biochemistry & Molecular Biology

Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees

Ivica Letunic et al.

NUCLEIC ACIDS RESEARCH (2016)

Article Multidisciplinary Sciences

Cospeciation of gut microbiota with hominids

Andrew H. Moeller et al.

SCIENCE (2016)

Article Ecology

iNEXT: an R package for rarefaction and extrapolation of species diversity (Hill numbers)

T. C. Hsieh et al.

METHODS IN ECOLOGY AND EVOLUTION (2016)

Article Ecology

phylosignal: an R package to measure, test, and explore the phylogenetic signal

Francois Keck et al.

ECOLOGY AND EVOLUTION (2016)

Article Automation & Control Systems

zCompositions - R Package for multivariate imputation of left-censored data under a compositional approach

Javier Palarea-Albaladejo et al.

CHEMOMETRICS AND INTELLIGENT LABORATORY SYSTEMS (2015)

Article Microbiology

Bacterial diversity along a 2600 km river continuum

Domenico Savio et al.

ENVIRONMENTAL MICROBIOLOGY (2015)

Article Biochemistry & Molecular Biology

Human Genetics Shape the Gut Microbiome

Julia K. Goodrich et al.

Review Microbiology

Ecology and characteristics of methanogenic archaea in animals and humans

Suwat Saengkerdsub et al.

CRITICAL REVIEWS IN MICROBIOLOGY (2014)

Article Ecology

Diet and body temperature in mammals and birds

Andrew Clarke et al.

GLOBAL ECOLOGY AND BIOGEOGRAPHY (2014)

Article Gastroenterology & Hepatology

Archaea and the human gut: New beginning of an old story

Nadia Gaci et al.

WORLD JOURNAL OF GASTROENTEROLOGY (2014)

Review Ecology

The Epidemiology and Evolution of Symbionts with Mixed-Mode Transmission

Dieter Ebert

ANNUAL REVIEW OF ECOLOGY, EVOLUTION, AND SYSTEMATICS, VOL 44 (2013)

Article Biochemistry & Molecular Biology

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

Kazutaka Katoh et al.

MOLECULAR BIOLOGY AND EVOLUTION (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 Physiology

Comparative Digestive Physiology

William H. Karasov et al.

COMPREHENSIVE PHYSIOLOGY (2013)

Article Biotechnology & Applied Microbiology

Contribution of lateral gene transfer to the gene repertoire of a gut-adapted methanogen

Mor N. Lurie-Weinberger et al.

GENOMICS (2012)

Article Biochemistry & Molecular Biology

Primer3-new capabilities and interfaces

Andreas Untergasser et al.

NUCLEIC ACIDS RESEARCH (2012)

Article Biotechnology & Applied Microbiology

Differences in the Rumen Methanogen Populations of Lactating Jersey and Holstein Dairy Cows under the Same Diet Regimen

Erin E. King et al.

APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2011)

Article Multidisciplinary Sciences

Pan-genome of the dominant human gut-associated archaeon, Methanobrevibacter smithii, studied in twins

Elizabeth E. Hansen et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2011)

Article Multidisciplinary Sciences

FastTree 2-Approximately Maximum-Likelihood Trees for Large Alignments

Morgan N. Price et al.

PLOS ONE (2010)

Article Ecology

Phylogenetic signal and linear regression on species data

Liam J. Revell

METHODS IN ECOLOGY AND EVOLUTION (2010)

Article Biochemical Research Methods

BLAST plus : architecture and applications

Christiam Camacho et al.

BMC BIOINFORMATICS (2009)

Article Microbiology

The Mth60 fimbriae of Methanothermobacter thermoautotrophicus are functional adhesins

Christine Thoma et al.

ENVIRONMENTAL MICROBIOLOGY (2008)

Article Multidisciplinary Sciences

The influence of sex, handedness, and washing on the diversity of hand surface bacteria

Noah Fierer et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2008)

Article Biochemistry & Molecular Biology

SILVA:: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB

Elmar Pruesse et al.

NUCLEIC ACIDS RESEARCH (2007)

Article Computer Science, Interdisciplinary Applications

The ecodist package for dissimilarity-based analysis of ecological data

Sarah C. Goslee et al.

JOURNAL OF STATISTICAL SOFTWARE (2007)

Article Biochemical Research Methods

APE: Analyses of Phylogenetics and Evolution in R language

E Paradis et al.

BIOINFORMATICS (2004)

Article Biochemistry & Molecular Biology

RevTrans: multiple alignment of coding DNA from aligned amino acid sequences

R Wernersson et al.

NUCLEIC ACIDS RESEARCH (2003)

Article Biotechnology & Applied Microbiology

Rapid detection and quantification of members of the archaeal community by quantitative PCR using fluorogenic probes

K Takai et al.

APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2000)