4.8 Article

Phylogenetic Comparative Approach Reveals Evolutionary Conservatism, Ancestral Composition, and Integration of Vertebrate Gut Microbiota

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。
Review Biochemistry & Molecular Biology

Avian gut microbiomes taking flight

Kasun H. Bodawatta et al.

Summary: Research on the gut microbiomes of birds is crucial for understanding their ecological functions and evolution, as well as for avian conservation and host health monitoring.

TRENDS IN MICROBIOLOGY (2022)

Review Ecology

Cophylogenetic Methods to Untangle the Evolutionary History of Ecological Interactions

Wade Dismukes et al.

Summary: This review organizes currently available cophylogenetic methods into three categories and provides a framework for empiricists investigating the macroevolution of symbioses. It also offers recommendations for the development of next-generation cophylogenetic models.

ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS (2022)

Review Biochemistry & Molecular Biology

Does Intraspecific Variation in rDNA Copy Number Affect Analysis of Microbial Communities?

Anton Lavrinienko et al.

Summary: Variation in rDNA copy number is a common response to environmental change, complicating the analysis of rDNA amplicon sequence data. It is emphasized that interpreting amplicon sequence data in light of possible interspecific and intraspecific variation, and examining the potential plasticity in rDNA copy number is important to understand how microbial communities are structured in heterogeneous environments.

TRENDS IN MICROBIOLOGY (2021)

Review Microbiology

Colonization resistance: metabolic warfare as a strategy against pathogenic Enterobacteriaceae

Nicolas G. Shealy et al.

Summary: The intestine is a complex bacterial ecosystem that provides immune education, nutrition, and protection against pathogens. Symbiotic interactions between the host and microbiome occur through metabolic crosstalk, with microbiota inhibiting pathogen colonization through diverse metabolic pathways, while pathogens disrupt the microbiome to gain a metabolic advantage. This review discusses the role of microbiota metabolites in colonization resistance and the metabolic mechanisms used by pathogens to outcompete commensal microbes.

CURRENT OPINION IN MICROBIOLOGY (2021)

Article Ecology

Quantitative Interspecific Approach to the Stylosphere: Patterns of Bacteria and Fungi Abundance on Passerine Bird Feathers

Maria del Mar Labrador et al.

Summary: Feathers are habitats for a variety of microorganisms, with abundances varying among individuals and species, likely influenced by environmental factors and interactions between bacteria and fungi.

MICROBIAL ECOLOGY (2021)

Article Ecology

Bacterial microbiota similarity between predators and prey in a blue tit trophic network

Helene Dion-Phenix et al.

Summary: This study investigated the relations among host microbiota across a trophic network in wild communities. Results showed that hosts from adjacent trophic levels had more similar bacterial microbiota, and sharing the same habitat increased similarity in bacterial microbiota among hosts. The main drivers of bacterial microbiota variation differed across spatial scales within each trophic level, indicating complex factors shaping microbiota composition.

ISME JOURNAL (2021)

Article Biochemistry & Molecular Biology

Evolutionary signal in the gut microbiomes of 74 bird species from Equatorial Guinea

Darien C. Capunitan et al.

MOLECULAR ECOLOGY (2020)

Review Biology

Ecological and evolutionary mechanisms underlying patterns of phylosymbiosis in host-associated microbial communities

Kevin D. Kohl

PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES (2020)

Article Microbiology

Microbiomes, Community Ecology, and the Comparative Method

Sarah M. Hird

MSYSTEMS (2019)

Article Biochemistry & Molecular Biology

Characterizing symbiont inheritance during host-microbiota evolution: Application to the great apes gut microbiota

Benoit Perez-Lamarque et al.

MOLECULAR ECOLOGY RESOURCES (2019)

Review Ecology

Untangling the Multiple Ecological Radiations of Early Mammals

David M. Grossnickle et al.

TRENDS IN ECOLOGY & EVOLUTION (2019)

Article Ecology

Evolutionary and Ecological Consequences of Gut Microbial Communities

Nancy A. Moran et al.

Annual Review of Ecology Evolution and Systematics (2019)

Article Biochemistry & Molecular Biology

Rates of gut microbiome divergence in mammals

Alex H. Nishida et al.

MOLECULAR ECOLOGY (2018)

Review Microbiology

Best practices for analysing microbiomes

Rob Knight et al.

NATURE REVIEWS MICROBIOLOGY (2018)

Article Multidisciplinary Sciences

The evolution of the host microbiome as an ecosystem on a leash

Kevin R. Foster et al.

NATURE (2017)

Article Multidisciplinary Sciences

A communal catalogue reveals Earth's multiscale microbial diversity

Luke R. Thompson et al.

NATURE (2017)

Article Multidisciplinary Sciences

Unraveling the processes shaping mammalian gut microbiomes over evolutionary time

Mathieu Groussin et al.

NATURE COMMUNICATIONS (2017)

Review Multidisciplinary Sciences

Cross-species comparisons of host genetic associations with the microbiome

Julia K. Goodrich et al.

SCIENCE (2016)

Article Multidisciplinary Sciences

Host genotype and age shape the leaf and root microbiomes of a wild perennial plant

Maggie R. Wagner et al.

NATURE COMMUNICATIONS (2016)

Review Microbiology

Microbiota and Host Nutrition across Plant and Animal Kingdoms

Stephane Hacquard et al.

CELL HOST & MICROBE (2015)

Article Evolutionary Biology

Comparative Analysis of Principal Components Can be Misleading

Josef C. Uyeda et al.

SYSTEMATIC BIOLOGY (2015)

Review Biotechnology & Applied Microbiology

Proteobacteria: microbial signature of dysbiosis in gut microbiota

Na-Ri Shin et al.

TRENDS IN BIOTECHNOLOGY (2015)

Article Ecology

mvMORPH: an R package for fitting multivariate evolutionary models to morphometric data

Julien Clavel et al.

METHODS IN ECOLOGY AND EVOLUTION (2015)

Article Microbiology

Comparative Gut Microbiota of 59 Neotropical Bird Species

Sarah M. Hird et al.

Frontiers in Microbiology (2015)

Article Biochemistry & Molecular Biology

Stability and phylogenetic correlation in gut microbiota: lessons from ants and apes

Jon G. Sanders et al.

MOLECULAR ECOLOGY (2014)

Article Multidisciplinary Sciences

Diet rapidly and reproducibly alters the human gut microbiome

Lawrence A. David et al.

NATURE (2014)

Article Multidisciplinary Sciences

Dietary specializations and diversity in feeding ecology of the earliest stem mammals

Pamela G. Gill et al.

NATURE (2014)

Article Gastroenterology & Hepatology

Proteobacteria-specific IgA regulates maturation of the intestinal microbiota

Julie Mirpuri et al.

GUT MICROBES (2014)

Article Multidisciplinary Sciences

Animals in a bacterial world, a new imperative for the life sciences

Margaret McFall-Ngai et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2013)

Article Multidisciplinary Sciences

The global diversity of birds in space and time

W. Jetz et al.

NATURE (2012)

Article Ecology

phytools: an R package for phylogenetic comparative biology (and other things)

Liam J. Revell

METHODS IN ECOLOGY AND EVOLUTION (2012)

Article Biochemical Research Methods

Microbial Co-occurrence Relationships in the Human Microbiome

Karoline Faust et al.

PLOS COMPUTATIONAL BIOLOGY (2012)

Article Biochemistry & Molecular Biology

Evolutionary Relationships of Wild Hominids Recapitulated by Gut Microbial Communities

Howard Ochman et al.

PLOS BIOLOGY (2010)

Article Ecology

The rational exploration of microbial diversity

Christopher Quince et al.

ISME JOURNAL (2008)

Review Microbiology

Worlds within worlds: evolution of the vertebrate gut microbiota

Ruth E. Ley et al.

NATURE REVIEWS MICROBIOLOGY (2008)

Article Evolutionary Biology

Phylogenetic Signal, Evolutionary Process, and Rate

Liam J. Revell et al.

SYSTEMATIC BIOLOGY (2008)