(Q35225266)

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Comparative genomics highlights the unique biology of Methanomassiliicoccales, a Thermoplasmatales-related seventh order of methanogenic archaea that encodes pyrrolysine

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7 August 2017

Comparative genomics highlights the unique biology of Methanomassiliicoccales, a Thermoplasmatales-related seventh order of methanogenic archaea that encodes pyrrolysine (English)

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7 August 2017

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comparative genomics

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based on heuristic

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Nicolas Parisot

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Jean-François Brugère

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Eric Peyretaillade

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Guillaume Borrel

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Hugh M B Harris

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William Tottey

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13 August 2014

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7 August 2017

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3 June 2020

https://scigraph.springernature.com/pub.10.1186/1471-2164-15-679

0 references

Unique characteristics of the pyrrolysine system in the 7th order of methanogens: implications for the evolution of a genetic code expansion cassette

1 reference

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13 July 2018

Global phylogenomic analysis disentangles the complex evolutionary history of DNA replication in archaea

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Archaebiotics: proposed therapeutic use of archaea to prevent trimethylaminuria and cardiovascular disease

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CRISPRmap: an automated classification of repeat conservation in prokaryotic adaptive immune systems

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Pyrophosphate-fueled Na+ and H+ transport in prokaryotes.

1 reference

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Intestinal microbiota metabolism of L-carnitine, a nutrient in red meat, promotes atherosclerosis

1 reference

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Ribosomal intergenic spacer analysis as a tool for monitoring methanogenic Archaea changes in an anaerobic digester

1 reference

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13 July 2018

Candidatus Methanogranum caenicola: a novel methanogen from the anaerobic digested sludge, and proposal of Methanomassiliicoccaceae fam. nov. and Methanomassiliicoccales ord. nov., for a methanogenic lineage of the class Thermoplasmata

1 reference

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

1 reference

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13 July 2018

Evolution of Na(+) and H(+) bioenergetics in methanogenic archaea

1 reference

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Carbon source-dependent expansion of the genetic code in bacteria

1 reference

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Comparison of methanogen diversity of yak (Bos grunniens) and cattle (Bos taurus) from the Qinghai-Tibetan plateau, China

1 reference

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13 July 2018

"Methanoplasmatales," Thermoplasmatales-related archaea in termite guts and other environments, are the seventh order of methanogens

1 reference

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13 July 2018

Complete genome sequence of Methanomassiliicoccus luminyensis, the largest genome of a human-associated Archaea species

1 reference

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13 July 2018

Methanomassiliicoccus luminyensis gen. nov., sp. nov., a methanogenic archaeon isolated from human faeces

1 reference

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An archaeal immune system can detect multiple protospacer adjacent motifs (PAMs) to target invader DNA.

1 reference

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13 July 2018

Distribution of nitrogen fixation and nitrogenase-like sequences amongst microbial genomes

1 reference

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MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space

1 reference

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Purine biosynthesis in archaea: variations on a theme

1 reference

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13 July 2018

Genome sequence of a mesophilic hydrogenotrophic methanogen Methanocella paludicola, the first cultivated representative of the order Methanocellales

1 reference

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PHAST: a fast phage search tool

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Phylogeny and evolution of the Archaea: one hundred genomes later

1 reference

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The evolution of respiratory chain complex I from a smaller last common ancestor consisting of 11 protein subunits

1 reference

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13 July 2018

More than 200 genes required for methane formation from H₂ and CO₂ and energy conservation are present in Methanothermobacter marburgensis and Methanothermobacter thermautotrophicus

1 reference

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13 July 2018

Evolution and classification of the CRISPR-Cas systems

1 reference

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13 July 2018

Functional context, biosynthesis, and genetic encoding of pyrrolysine

1 reference

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13 July 2018

Enterotypes of the human gut microbiome

1 reference

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13 July 2018

Membrane-bound electron transport in Methanosaeta thermophila

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4153887

13 July 2018

Gut flora metabolism of phosphatidylcholine promotes cardiovascular disease

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4153887

13 July 2018

Trimethylaminuria: causes and diagnosis of a socially distressing condition

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4153887

13 July 2018

UniProt Knowledgebase: a hub of integrated protein data

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13 July 2018

Coupling of ferredoxin and heterodisulfide reduction via electron bifurcation in hydrogenotrophic methanogenic archaea

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4153887

13 July 2018

Hidden Markov model speed heuristic and iterative HMM search procedure

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4153887

13 July 2018

BMGE (Block Mapping and Gathering with Entropy): a new software for selection of phylogenetic informative regions from multiple sequence alignments

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13 July 2018

TransportTP: a two-phase classification approach for membrane transporter prediction and characterization

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13 July 2018

The appearance of pyrrolysine in tRNAHis guanylyltransferase by neutral evolution.

1 reference

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13 July 2018

Convergent evolution of coenzyme M biosynthesis in the Methanosarcinales: cysteate synthase evolved from an ancestral threonine synthase.

1 reference

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13 July 2018

Genomic characterization of methanomicrobiales reveals three classes of methanogens

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13 July 2018

Rfam: updates to the RNA families database

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13 July 2018

Methanogenic archaea: ecologically relevant differences in energy conservation

1 reference

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13 July 2018

High-throughput functional annotation and data mining with the Blast2GO suite

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13 July 2018

CRISPRcompar: a website to compare clustered regularly interspaced short palindromic repeats.

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13 July 2018

Structure of the archaeal community of the rumen

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13 July 2018

The CGView Server: a comparative genomics tool for circular genomes

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13 July 2018

Preliminary structural studies on the MtxX protein from Methanococcus jannaschii

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13 July 2018

The RAST Server: rapid annotations using subsystems technology

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13 July 2018

From one amino acid to another: tRNA-dependent amino acid biosynthesis

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13 July 2018

CRISPR--a widespread system that provides acquired resistance against phages in bacteria and archaea

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4153887

13 July 2018

Clusters of orthologous genes for 41 archaeal genomes and implications for evolutionary genomics of archaea

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13 July 2018

TFAM 1.0: an online tRNA function classifier

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Genomic and metabolic adaptations of Methanobrevibacter smithii to the human gut

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13 July 2018

CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats

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KAAS: an automatic genome annotation and pathway reconstruction server

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

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Origin and evolution of DNA topoisomerases

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13 July 2018

In vivo contextual requirements for UAG translation as pyrrolysine

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13 July 2018

TransportDB: a comprehensive database resource for cytoplasmic membrane transport systems and outer membrane channels

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Viruses of the Archaea: a unifying view

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13 July 2018

RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models

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13 July 2018

Sel1-like repeat proteins in signal transduction

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Genome of Rice Cluster I Archaea--the Key Methane Producers in the Rice Rhizosphere

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13 July 2018

Molecular identification of methanogenic archaea from sheep in Queensland, Australia reveal more uncultured novel archaea

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Evolutionary genomics of archaeal viruses: unique viral genomes in the third domain of life

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13 July 2018

The genome sequence of Methanosphaera stadtmanae reveals why this human intestinal archaeon is restricted to methanol and H2 for methane formation and ATP synthesis

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Methanol promotes atmospheric methane oxidation by methanotrophic cultures and soils.

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13 July 2018

Effects of nitrogen and carbon sources on transcription of soluble methyltransferases in Methanosarcina mazei strain Go1.

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13 July 2018

The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs

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13 July 2018

Identification and analysis of proton-translocating pyrophosphatases in the methanogenic archaeon Methansarcina mazei

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13 July 2018

Accelerated evolution associated with genome reduction in a free-living prokaryote

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13 July 2018

Function of genetically encoded pyrrolysine in corrinoid-dependent methylamine methyltransferases

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13 July 2018

MUSCLE: multiple sequence alignment with high accuracy and high throughput

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13 July 2018

Molecular diversity of rumen methanogens from sheep in Western Australia.

1 reference

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13 July 2018

ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences

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13 July 2018

The natural history of nitrogen fixation

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13 July 2018

The genome of Nanoarchaeum equitans: insights into early archaeal evolution and derived parasitism

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13 July 2018

Vienna RNA secondary structure server

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13 July 2018

Holding it together: chromatin in the Archaea

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4153887

13 July 2018

Pyrrolysine encoded by UAG in Archaea: charging of a UAG-decoding specialized tRNA.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4153887

13 July 2018

Identification of a salt-induced primary transporter for glycine betaine in the methanogen Methanosarcina mazei Gö1.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4153887

13 July 2018

Identification of genes that are associated with DNA repeats in prokaryotes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4153887

13 July 2018

Genetic analysis of the archaeon Methanosarcina barkeri Fusaro reveals a central role for Ech hydrogenase and ferredoxin in methanogenesis and carbon fixation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4153887

13 July 2018

Identification of coenzyme M biosynthetic phosphosulfolactate synthase: a new family of sulfonate-biosynthesizing enzymes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4153887

13 July 2018

Identification of coenzyme M biosynthetic 2-phosphosulfolactate phosphatase. A member of a new class of Mg(2+)-dependent acid phosphatases

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4153887

13 July 2018

Phylogenetic analysis of archaeal 16S rRNA libraries from the rumen suggests the existence of a novel group of archaea not associated with known methanogens

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4153887

13 July 2018

The MtsA subunit of the methylthiol:coenzyme M methyltransferase of Methanosarcina barkeri catalyses both half-reactions of corrinoid-dependent dimethylsulfide: coenzyme M methyl transfer

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4153887

13 July 2018

Genome sequence of the endocellular bacterial symbiont of aphids Buchnera sp. APS

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4153887

13 July 2018

Glycine betaine transport in the obligate halophilic archaeon Methanohalophilus portucalensis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4153887

13 July 2018

Identification of an archaeal 2-hydroxy acid dehydrogenase catalyzing reactions involved in coenzyme biosynthesis in methanoarchaea

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4153887

13 July 2018

The F420H2 dehydrogenase from Methanosarcina mazei is a Redox-driven proton pump closely related to NADH dehydrogenases

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4153887

13 July 2018

Variation and evolution of the citric-acid cycle: a genomic perspective.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4153887

13 July 2018

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4153887

13 July 2018

MUST, a computer package of Management Utilities for Sequences and Trees

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4153887

13 July 2018

The Minimal Gene Complement of Mycoplasma genitalium

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4153887

13 July 2018

Component A2 of the methylcoenzyme M methylreductase system from Methanobacterium thermoautotrophicum.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4153887

13 July 2018

The SWISS-PROT protein sequence data bank

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4153887

13 July 2018

Organization and expression of the 16S, 23S and 5S ribosomal RNA genes from the archaebacterium Thermoplasma acidophilum

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4153887

13 July 2018

Conversion of choline methyl groups through trimethylamine into methane in the rumen

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4153887

13 July 2018

List of new names and new combinations previously effectively, but not validly, published

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4153887

26 September 2018

Mapping of active replication origins in vivo in thaum- and euryarchaeal replicons.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4153887

26 September 2018

Phylogenomic data support a seventh order of Methylotrophic methanogens and provide insights into the evolution of Methanogenesis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4153887

26 September 2018

Genome Sequence of "Candidatus Methanomassiliicoccus intestinalis" Issoire-Mx1, a Third Thermoplasmatales-Related Methanogenic Archaeon from Human Feces.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4153887

26 September 2018

Genome sequence of "Candidatus Methanomethylophilus alvus" Mx1201, a methanogenic archaeon from the human gut belonging to a seventh order of methanogens

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4153887

26 September 2018

Involvement of Ech hydrogenase in energy conservation of Methanosarcina mazei

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4153887

26 September 2018

A putative new order of methanogenic Archaea inhabiting the human gut, as revealed by molecular analyses of the mcrA gene

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4153887

26 September 2018

Dominance of Prevotella and low abundance of classical ruminal bacterial species in the bovine rumen revealed by relative quantification real-time PCR.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4153887

26 September 2018

Production of amines in equine cecal contents in an in vitro model of carbohydrate overload

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4153887

26 September 2018

Molecular evaluation of the human gut methanogenic archaeal microbiota reveals an age-associated increase of the diversity

1 reference

https://pubmed.ncbi.nlm.nih.gov/25124552

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

List of new names and new combinations previously effectively, but not validly, published: Validation List no. 166.

1 reference

https://pubmed.ncbi.nlm.nih.gov/25124552

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Metabolism of Betaine in the Ruminant

1 reference

https://pubmed.ncbi.nlm.nih.gov/25124552

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Requirement for the proton-pumping NADH dehydrogenase I of Escherichia coli in respiration of NADH to fumarate and its bioenergetic implications

1 reference

https://pubmed.ncbi.nlm.nih.gov/25124552

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

10.1186/1471-2164-15-679

1 reference

Europe PubMed Central

PMC publication ID

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25124552%20AND%20SRC:MED&resulttype=core&format=json

3 June 2020

Dimensions Publication ID

0 references

PMC publication ID

1 reference

Europe PubMed Central

PMC publication ID

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25124552%20AND%20SRC:MED&resulttype=core&format=json

3 June 2020

PubMed publication ID

1 reference

Europe PubMed Central

PMC publication ID

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25124552%20AND%20SRC:MED&resulttype=core&format=json

3 June 2020

ResearchGate publication ID

0 references

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