(Q39572479)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27446027%20AND%20SRC:MED&resulttype=core&format=json

19 March 2020

title

Taxonomic Assessment of Rumen Microbiota Using Total RNA and Targeted Amplicon Sequencing Approaches (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27446027%20AND%20SRC:MED&resulttype=core&format=json

19 March 2020

1 reference

1 reference

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27446027%20AND%20SRC:MED&resulttype=core&format=json

19 March 2020

Peter H. Janssen

5

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27446027%20AND%20SRC:MED&resulttype=core&format=json

19 March 2020

author name string

Fuyong Li

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27446027%20AND%20SRC:MED&resulttype=core&format=json

19 March 2020

Xu Sun

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27446027%20AND%20SRC:MED&resulttype=core&format=json

19 March 2020

Faith Cox

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27446027%20AND%20SRC:MED&resulttype=core&format=json

19 March 2020

Le Luo Guan

6

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27446027%20AND%20SRC:MED&resulttype=core&format=json

19 March 2020

publication date

22 June 2016

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27446027%20AND%20SRC:MED&resulttype=core&format=json

Frontiers in Microbiology

19 March 2020

published in

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27446027%20AND%20SRC:MED&resulttype=core&format=json

19 March 2020

volume

7

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27446027%20AND%20SRC:MED&resulttype=core&format=json

19 March 2020

page(s)

987

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27446027%20AND%20SRC:MED&resulttype=core&format=json

describes a project that uses

19 March 2020

Cytoscape

object named as

Cytoscape

2 references

9 June 2022

https://europepmc.org/search?query=(METHODS:'Cytoscape')

inferred from PubMed Central ID database lookup

CZ Software Mentions: A large dataset of software mentions in the biomedical literature

cites work

Intestinal microbiome is related to lifetime antibiotic use in Finnish pre-school children

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4916217

Rumen microbial community composition varies with diet and host, but a core microbiome is found across a wide geographical range

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4916217

Modulation of Chemical Composition and Other Parameters of the Cell at Different Exponential Growth Rates

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4916217

Nutritional modulation of gut microbiota - the impact on metabolic disease pathophysiology

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4916217

The gut microbiota and host health: a new clinical frontier

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4916217

Vertical Distribution of Functional Potential and Active Microbial Communities in Meromictic Lake Kivu

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4916217

Archaea and the human gut: new beginning of an old story.

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4916217

Gastrointestinal tract microbiota and probiotics in production animals

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4916217

Diversity and community composition of methanogenic archaea in the rumen of Scottish upland sheep assessed by different methods

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4916217

Metatranscriptomic analysis of arctic peat soil microbiota

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4916217

Relating the metatranscriptome and metagenome of the human gut.

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4916217

Variations in 16S rRNA-based microbiome profiling between pyrosequencing runs and between pyrosequencing facilities.

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4916217

Analysis, optimization and verification of Illumina-generated 16S rRNA gene amplicon surveys

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4916217

Trimmomatic: a flexible trimmer for Illumina sequence data

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4916217

Gut microbiome composition and function in experimental colitis during active disease and treatment-induced remission

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4916217

Metagenomics reveals sediment microbial community response to Deepwater Horizon oil spill

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4916217

Longitudinal study of murine microbiota activity and interactions with the host during acute inflammation and recovery

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4916217

Characterization of the core rumen microbiome in cattle during transition from forage to concentrate as well as during and after an acidotic challenge

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4916217

Diet alters both the structure and taxonomy of the ovine gut microbial ecosystem

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4916217

Efficiency of RNA extraction from selected bacteria in the context of biogas production and metatranscriptomics

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4916217

Effect of DNA extraction methods and sampling techniques on the apparent structure of cow and sheep rumen microbial communities

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4916217

Evaluating rRNA as an indicator of microbial activity in environmental communities: limitations and uses.

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4916217

Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq Illumina sequencing platform.

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4916217

Identification of metabolically active proteobacterial and archaeal communities in the rumen by DNA- and RNA-derived 16S rRNA gene.

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4916217

Influence of sire breed on the interplay among rumen microbial populations inhabiting the rumen liquid of the progeny in beef cattle

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4916217

Gut bacterial microbiota and obesity

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4916217

Simultaneous amplicon sequencing to explore co-occurrence patterns of bacterial, archaeal and eukaryotic microorganisms in rumen microbial communities

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4916217

Methylotrophic methanogenic Thermoplasmata implicated in reduced methane emissions from bovine rumen.

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4916217

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

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4916217

Gut microbiota composition and activity in relation to host metabolic phenotype and disease risk

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4916217

Rfam 11.0: 10 years of RNA families

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4916217

SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data.

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4916217

Nitrogen metabolism and rumen microbial enumeration in lactating cows with divergent residual feed intake fed high-digestibility pasture

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4916217

Comparison of next-generation sequencing systems

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4916217

Microbial co-occurrence relationships in the human microbiome

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4916217

High throughput whole rumen metagenome profiling using untargeted massively parallel sequencing

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4916217

Phylotype-level 16S rRNA analysis reveals new bacterial indicators of health state in acute murine colitis

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4916217

Composition and similarity of bovine rumen microbiota across individual animals

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4916217

Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4916217

Impact of feed efficiency and diet on adaptive variations in the bacterial community in the rumen fluid of cattle

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4916217

Using network analysis to explore co-occurrence patterns in soil microbial communities

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4916217

UCHIME improves sensitivity and speed of chimera detection

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4916217

Exploring the composition and diversity of microbial communities at the Jan Mayen hydrothermal vent field using RNA and DNA.

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4916217

Methanogen community structure in the rumens of farmed sheep, cattle and red deer fed different diets

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4916217

Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4916217

Ribosomal tag pyrosequencing of DNA and RNA from benthic coral reef microbiota: community spatial structure, rare members and nitrogen-cycling guilds.

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4916217

Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4916217

Polymerase chain reaction primers miss half of rRNA microbial diversity

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4916217

Effects of sampling location and time, and host animal on assessment of bacterial diversity and fermentation parameters in the bovine rumen

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4916217

Effect of PCR amplicon size on assessments of clone library microbial diversity and community structure

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4916217

A vaccine against rumen methanogens can alter the composition of archaeal populations

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4916217

Simultaneous assessment of soil microbial community structure and function through analysis of the meta-transcriptome

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4916217

Structure of the archaeal community of the rumen

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4916217

Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4916217

Postinoculation protozoan establishment and association patterns of methanogenic archaea in the ovine rumen

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4916217

Molecular diversity of methanogens in feedlot cattle from Ontario and Prince Edward Island, Canada

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4916217

The role of ecological theory in microbial ecology.

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4916217

A detailed analysis of 16S ribosomal RNA gene segments for the diagnosis of pathogenic bacteria

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4916217

Archaea predominate among ammonia-oxidizing prokaryotes in soils

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4916217

Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4916217

16S rDNA library-based analysis of ruminal bacterial diversity

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4916217

Cytoscape: a software environment for integrated models of biomolecular interaction networks

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4916217

Rapid method for coextraction of DNA and RNA from natural environments for analysis of ribosomal DNA- and rRNA-based microbial community composition

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4916217

Use of rRNA fluorescence in situ hybridization for measuring the activity of single cells in young and established biofilms.

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4916217

Single-Step Method of RNA Isolation by Acid Guanidinium Thiocyanate–Phenol–Chloroform Extraction

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4916217

Metagenomic 16S rDNA Illumina tags are a powerful alternative to amplicon sequencing to explore diversity and structure of microbial communities

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4916217

Development of a RT-qPCR method for the quantification of Fibrobacter succinogenes S85 glycoside hydrolase transcripts in the rumen content of gnotobiotic and conventional sheep.

21 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4916217

Partitioning diversity into independent alpha and beta components.

21 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4916217

Relative abundance of Archaea and Bacteria along a thermal gradient of a shallow-water hydrothermal vent quantified by rRNA slot-blot hybridization

21 August 2018

1 reference

Crossref

https://api.crossref.org/works/10.3389%2FFMICB.2016.00987

In situ identification and quantification of starch-hydrolyzing bacteria attached to barley and corn grain in the rumen of cows fed barley-based diets

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/27446027

12 December 2020

inferred from PubMed ID database lookup

An efficient RNA extraction method for estimating gut microbial diversity by polymerase chain reaction

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/27446027

12 December 2020

inferred from PubMed ID database lookup

Comparative metatranscriptomics reveals widespread community responses during phenanthrene degradation in soil

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/27446027

12 December 2020

inferred from PubMed ID database lookup

Identifiers

DOI

10.3389/FMICB.2016.00987

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27446027%20AND%20SRC:MED&resulttype=core&format=json

release_5qz4tpplcrdvxdkrfiyi4nbddm

19 March 2020

Fatcat ID

1 reference

Fatcat

https://api.fatcat.wiki/v0/release/5qz4tpplcrdvxdkrfiyi4nbddm

24 November 2022

mapped directly with Wikidata item

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27446027%20AND%20SRC:MED&resulttype=core&format=json

19 March 2020

PubMed publication ID

27446027

1 reference