Comparative Study of Gut Microbiota in Wild and Captive Giant Pandas (Ailuropoda melanoleuca)

Effects of the captive and wild environment on diversity of the gut microbiome of deer mice (Peromyscus maniculatus)

(2019) Elliott Schmidt et al.   ISME Journal

Population genetics reveals high connectivity of giant panda populations across human disturbance features in key nature reserve

(2019) Maiju Qiao et al.   Ecology and Evolution

Comparison of the Gut Microbiota Composition between the Wild and Captive Tibetan Wild Ass (Equus kiang )

(2019) Hongmei Gao et al.   JOURNAL OF APPLIED MICROBIOLOGY

The “wildness” of the giant panda gut microbiome and its relevance to effective translocation

(2019) Ran Yao et al.   Global Ecology and Conservation

Comparison of gut microbiota diversity between wild and captive bharals (Pseudois nayaur)

(2019) Xiangwen Chi et al.   BMC Veterinary Research

Gut microbiome differences between wild and captive black rhinoceros – implications for rhino health

(2019) Keylie M. Gibson et al.   Scientific Reports

Structural and compositional mismatch between captive and wild Atlantic salmon (Salmo salar ) parrs’ gut microbiota highlights the relevance of integrating molecular ecology for management and conservation methods

(2018) Camille Lavoie et al.   Evolutionary Applications

Age-associated microbiome shows the giant panda lives on hemicelluloses, not on cellulose

(2018) Wenping Zhang et al.   ISME Journal

Metagenomic Study Suggests That the Gut Microbiota of the Giant Panda (Ailuropoda melanoleuca) May Not Be Specialized for Fiber Fermentation

(2018) Wei Guo et al.   Frontiers in Microbiology

Correction to: Comparison of the gut microbiota composition between wild and captive sika deer (Cervus nippon hortulorum) from feces by high-throughput sequencing

(2018) Yu Guan et al.   AMB Express

Conservation metagenomics: a new branch of conservation biology

(2018) Fuwen Wei et al.   Science China-Life Sciences

The Effects of Captivity on the Mammalian Gut Microbiome

(2017) Valerie J. McKenzie et al.   INTEGRATIVE AND COMPARATIVE BIOLOGY

Captivity Shapes the Gut Microbiota of Andean Bears: Insights into Health Surveillance

(2017) Andrea Borbón-García et al.   Frontiers in Microbiology

You Are What You Eat: A Genomic Analysis of the Gut Microbiome of Captive and Wild Octopus vulgaris Paralarvae and Their Zooplankton Prey

(2017) Álvaro Roura et al.   Frontiers in Physiology

Catalogue of antibiotic resistome and host-tracking in drinking water deciphered by a large scale survey

(2017) Liping Ma et al.   Microbiome

Evaluating the impact of domestication and captivity on the horse gut microbiome

(2017) Jessica L. Metcalf et al.   Scientific Reports

The Bacterial Mobile Resistome Transfer Network Connecting the Animal and Human Microbiomes

(2016) Yongfei Hu et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Captive pandas are at risk from environmental toxins

(2016) Yi-ping Chen et al.   FRONTIERS IN ECOLOGY AND THE ENVIRONMENT

Co-occurrence of antibiotic and metal resistance genes revealed in complete genome collection

(2016) Li-Guan Li et al.   ISME Journal

Gut microbial ecology of lizards: insights into diversity in the wild, effects of captivity, variation across gut regions and transmission

(2016) Kevin D. Kohl et al.   MOLECULAR ECOLOGY

Diet-induced extinctions in the gut microbiota compound over generations

(2016) Erica D. Sonnenburg et al.   NATURE

Captivity humanizes the primate microbiome

(2016) Jonathan B. Clayton et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The healthy human microbiome

(2016) Jason Lloyd-Price et al.   Genome Medicine

Dietary Shifts May Trigger Dysbiosis and Mucous Stools in Giant Pandas (Ailuropoda melanoleuca)

(2016) Candace L. Williams et al.   Frontiers in Microbiology

The Microbiome of Animals: Implications for Conservation Biology

(2016) Simon Bahrndorff et al.   International Journal of Genomics

The structure and diversity of human, animal and environmental resistomes

(2016) Chandan Pal et al.   Microbiome

Effects of captivity and artificial breeding on microbiota in feces of the red-crowned crane (Grus japonensis)

(2016) Yuwei Xie et al.   Scientific Reports

Metagenome Sequencing of the Hadza Hunter-Gatherer Gut Microbiota

(2015) Simone Rampelli et al.   CURRENT BIOLOGY

VFDB 2016: hierarchical and refined dataset for big data analysis—10 years on

(2015) Lihong Chen et al.   NUCLEIC ACIDS RESEARCH

The Bamboo-Eating Giant Panda Harbors a Carnivore-Like Gut Microbiota, with Excessive Seasonal Variations

(2015) Zhengsheng Xue et al.   mBio

Investigation into the annotation of protocol sequencing steps in the sequence read archive

(2015) Jamie Alnasir et al.   GigaScience

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Characterization of the Gut Microbiota in the Red Panda (Ailurus fulgens)

(2014) Fanli Kong et al.   PLoS One

Dissemination of Cephalosporin Resistance Genes between Escherichia coli Strains from Farm Animals and Humans by Specific Plasmid Lineages

(2014) Mark de Been et al.   PLoS Genetics

Development of a Dual-Index Sequencing Strategy and Curation Pipeline for Analyzing Amplicon Sequence Data on the MiSeq Illumina Sequencing Platform

(2013) James J. Kozich et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Habitat degradation impacts black howler monkey (Alouatta pigra) gastrointestinal microbiomes

(2013) Katherine R Amato et al.   ISME Journal

Convergence of gut microbiomes in myrmecophagous mammals

(2013) Frédéric Delsuc et al.   MOLECULAR ECOLOGY

The draft genome of the fast-growing non-timber forest species moso bamboo (Phyllostachys heterocycla)

(2013) Zhenhua Peng et al.   NATURE GENETICS

BacMet: antibacterial biocide and metal resistance genes database

(2013) Chandan Pal et al.   NUCLEIC ACIDS RESEARCH

CD-HIT: accelerated for clustering the next-generation sequencing data

(2012) Limin Fu et al.   BIOINFORMATICS

IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth

(2012) Y. Peng et al.   BIOINFORMATICS

UCHIME improves sensitivity and speed of chimera detection

(2011) Robert C. Edgar et al.   BIOINFORMATICS

HMMER web server: interactive sequence similarity searching

(2011) R. D. Finn et al.   NUCLEIC ACIDS RESEARCH

Evidence of cellulose metabolism by the giant panda gut microbiome

(2011) L. Zhu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Diet Drives Convergence in Gut Microbiome Functions Across Mammalian Phylogeny and Within Humans

(2011) B. D. Muegge et al.   SCIENCE

Acquired Antibiotic Resistance Genes: An Overview

(2011) Angela H. A. M. van Hoek et al.   Frontiers in Microbiology

Metagenomic biomarker discovery and explanation

(2011) Nicola Segata et al.   GENOME BIOLOGY

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

Adaptation to herbivory by the Tammar wallaby includes bacterial and glycoside hydrolase profiles different from other herbivores

(2010) P. B. Pope et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Environmentally-acquired bacteria influence microbial diversity and natural innate immune responses at gut surfaces

(2009) Imke E Mulder et al.   BMC BIOLOGY

The sequence and de novo assembly of the giant panda genome

(2009) Ruiqiang Li et al.   NATURE

ACLAME: A CLAssification of Mobile genetic Elements, update 2010

(2009) Raphaël Leplae et al.   NUCLEIC ACIDS RESEARCH

The metagenomics RAST server – a public resource for the automatic phylogenetic and functional analysis of metagenomes

(2008) F Meyer et al.   BMC BIOINFORMATICS

The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics

(2008) B. L. Cantarel et al.   NUCLEIC ACIDS RESEARCH

ARDB--Antibiotic Resistance Genes Database

(2008) B. Liu et al.   NUCLEIC ACIDS RESEARCH

Evolution of Mammals and Their Gut Microbes

(2008) R. E. Ley et al.   SCIENCE