(Q28595871)

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Identification and genome reconstruction of abundant distinct taxa in microbiomes from one thermophilic and three mesophilic production-scale biogas plants

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Identification and genome reconstruction of abundant distinct taxa in microbiomes from one thermophilic and three mesophilic production-scale biogas plants (English)

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5

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6

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1

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Andreas Bremges

2

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Alexander Sczyrba

7

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Andreas Schlüter

object named as

Andreas Schlüter

8

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author name string

Madis Rumming

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Christian Henke

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language of work or name

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publication date

2016

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Biotechnology for Biofuels

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9

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1

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156

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Eubacteria and archaea communities in seven mesophile anaerobic digester plants in Germany

1 reference

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17 March 2017

Comparative metagenomics of biogas-producing microbial communities from production-scale biogas plants operating under wet or dry fermentation conditions

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17 March 2017

Biogas production from protein-rich biomass: fed-batch anaerobic fermentation of casein and of pig blood and associated changes in microbial community composition

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4960831

17 March 2017

Insights into the phylogeny and coding potential of microbial dark matter

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4960831

17 March 2017

A pyrosequencing-based metagenomic study of methane-producing microbial community in solid-state biogas reactor

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4960831

17 March 2017

Characterization of a biogas-producing microbial community by short-read next generation DNA sequencing

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4960831

17 March 2017

Fast gapped-read alignment with Bowtie 2

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4960831

17 March 2017

Integrative analysis of environmental sequences using MEGAN4

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4960831

17 March 2017

Comparative and joint analysis of two metagenomic datasets from a biogas fermenter obtained by 454-pyrosequencing

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4960831

17 March 2017

QIIME allows analysis of high-throughput community sequencing data

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17 March 2017

The Sequence Alignment/Map format and SAMtools

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17 March 2017

Genome sequence and analysis of the oral bacterium Fusobacterium nucleatum strain ATCC 25586

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17 March 2017

Fast and sensitive protein alignment using DIAMOND

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4960831

23 March 2017

Search and clustering orders of magnitude faster than BLAST

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7 April 2017

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

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7 April 2017

ARB: a software environment for sequence data

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7 April 2017

FLASH: fast length adjustment of short reads to improve genome assemblies

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4960831

7 April 2017

Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4960831

7 April 2017

PyNAST: a flexible tool for aligning sequences to a template alignment

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4960831

7 April 2017

EDGAR 2.0: an enhanced software platform for comparative gene content analyses

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4960831

29 September 2017

Metagenomic analysis and functional characterization of the biogas microbiome using high throughput shotgun sequencing and a novel binning strategy

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4960831

29 September 2017

MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4960831

29 September 2017

Deeply sequenced metagenome and metatranscriptome of a biogas-producing microbial community from an agricultural production-scale biogas plant

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4960831

29 September 2017

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

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29 September 2017

Complete genome sequence of the strain Defluviitoga tunisiensis L3, isolated from a thermophilic, production-scale biogas plant

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4960831

29 September 2017

New steady-state microbial community compositions and process performances in biogas reactors induced by temperature disturbances

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4960831

29 September 2017

Semi-continuous anaerobic digestion for biogas production: influence of ammonium acetate supplement and structure of the microbial community

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4960831

29 September 2017

Temperature and solids retention time control microbial population dynamics and volatile fatty acid production in replicated anaerobic digesters

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4960831

29 September 2017

Taxator-tk: precise taxonomic assignment of metagenomes by fast approximation of evolutionary neighborhoods.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4960831

29 September 2017

A metagenomic study of the microbial communities in four parallel biogas reactors

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4960831

29 September 2017

Diversity and variability of methanogens during the shift from mesophilic to thermohilic conditions while biogas production

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4960831

29 September 2017

Illuminating microbial dark matter in meromictic Sakinaw Lake

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4960831

29 September 2017

A mini review on renewable sources for biofuel

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4960831

29 September 2017

Microbial community composition and dynamics in high-temperature biogas reactors using industrial bioethanol waste as substrate

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4960831

29 September 2017

Process diagnosis using methanogenic Archaea in maize-fed, trace element depleted fermenters

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4960831

29 September 2017

CopyRighter: a rapid tool for improving the accuracy of microbial community profiles through lineage-specific gene copy number correction.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4960831

29 September 2017

Isolation and differentiation of methanogenic Archaea from mesophilic corn-fed on-farm biogas plants with special emphasis on the genus Methanobacterium

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4960831

29 September 2017

Multiple approaches to characterize the microbial community in a thermophilic anaerobic digester running on swine manure: a case study

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4960831

29 September 2017

Members of the uncultured bacterial candidate division WWE1 are implicated in anaerobic digestion of cellulose.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4960831

29 September 2017

Drivers of microbial community composition in mesophilic and thermophilic temperature-phased anaerobic digestion pre-treatment reactors

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4960831

29 September 2017

First case of Fusobacterium necrophorum endocarditis to have presented after the 2nd decade of life

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4960831

29 September 2017

454 pyrosequencing analyses of bacterial and archaeal richness in 21 full-scale biogas digesters

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4960831

29 September 2017

Microbial community structure and dynamics during anaerobic digestion of various agricultural waste materials.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4960831

29 September 2017

Detailed analysis of metagenome datasets obtained from biogas-producing microbial communities residing in biogas reactors does not indicate the presence of putative pathogenic microorganisms

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4960831

29 September 2017

Methanogenic Community Dynamics during Anaerobic Utilization of Agricultural Wastes.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4960831

29 September 2017

Ray Meta: scalable de novo metagenome assembly and profiling.

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4960831

29 September 2017

Gene and translation initiation site prediction in metagenomic sequences

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4960831

29 September 2017

Monitoring bacterial community structure and variability in time scale in full-scale anaerobic digesters

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4960831

29 September 2017

Profiling of the metabolically active community from a production-scale biogas plant by means of high-throughput metatranscriptome sequencing

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4960831

29 September 2017

Clostridia: the importance of their exceptional substrate and metabolite diversity for biofuel and biorefinery applications

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4960831

29 September 2017

Defluviitoga tunisiensis gen. nov., sp. nov., a thermophilic bacterium isolated from a mesothermic and anaerobic whey digester

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4960831

29 September 2017

Characteristic microbial community of a dry thermophilic methanogenic digester: its long-term stability and change with feeding

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4960831

29 September 2017

Phylogeny and molecular signatures for the phylum Thermotogae and its subgroups

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4960831

29 September 2017

Release LTPs104 of the All-Species Living Tree

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4960831

29 September 2017

Companion animals symposium: microbes and gastrointestinal health of dogs and cats

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4960831

29 September 2017

Multiple syntrophic interactions in a terephthalate-degrading methanogenic consortium

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4960831

29 September 2017

Biogas production: current state and perspectives

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4960831

29 September 2017

Phylogenetic characterization of a biogas plant microbial community integrating clone library 16S-rDNA sequences and metagenome sequence data obtained by 454-pyrosequencing

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4960831

29 September 2017

Towards the definition of a core of microorganisms involved in anaerobic digestion of sludge

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4960831

29 September 2017

The structure of the bacterial and archaeal community in a biogas digester as revealed by denaturing gradient gel electrophoresis and 16S rDNA sequencing analysis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4960831

29 September 2017

Diversity of the resident microbiota in a thermophilic municipal biogas plant

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4960831

29 September 2017

Metabolic, phylogenetic, and ecological diversity of the methanogenic archaea

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4960831

29 September 2017

Indigenous bacteria and bacterial metabolic products in the gastrointestinal tract of broiler chickens

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4960831

29 September 2017

Effect of process temperature on bacterial and archaeal communities in two methanogenic bioreactors treating organic household waste

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4960831

29 September 2017

Expression profiles of fhs (FTHFS) genes support the hypothesis that spirochaetes dominate reductive acetogenesis in the hindgut of lower termites

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4960831

29 September 2017

The Thermotoga maritima phenotype is impacted by syntrophic interaction with Methanococcus jannaschii in hyperthermophilic coculture

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4960831

29 September 2017

Novel major bacterial candidate division within a municipal anaerobic sludge digester

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4960831

29 September 2017

GenDB--an open source genome annotation system for prokaryote genomes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4960831

29 September 2017

Oral microbial communities: biofilms, interactions, and genetic systems

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4960831

29 September 2017

Treponema lecithinolyticum sp. nov., a small saccharolytic spirochaete with phospholipase A and C activities associated with periodontal diseases

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4960831

29 September 2017

Construction of environmental DNA libraries in Escherichia coli and screening for the presence of genes conferring utilization of 4-hydroxybutyrate

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4960831

29 September 2017

Treponema brennaborense sp. nov., a novel spirochaete isolated from a dairy cow suffering from digital dermatitis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4960831

29 September 2017

Sugar metabolism by fusobacteria: regulation of transport, phosphorylation, and polymer formation by Fusobacterium mortiferum ATCC 25557

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4960831

29 September 2017

Spirochete chemotaxis, motility, and the structure of the spirochetal periplasmic flagella

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4960831

29 September 2017

"Candidatus Cloacamonas acidaminovorans": genome sequence reconstruction provides a first glimpse of a new bacterial division

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4960831

3 June 2018

Evidence for existence of "mesotogas," members of the order Thermotogales adapted to low-temperature environments

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4960831

3 June 2018

Degradation efficiency of agricultural biogas plants--a full-scale study

1 reference

https://api.crossref.org/works/10.1186%2FS13068-016-0565-3

21 January 2018

Cutadapt removes adapter sequences from high-throughput sequencing reads

1 reference

https://api.crossref.org/works/10.1186%2FS13068-016-0565-3

21 January 2018

Biomethanation and its potential

1 reference

https://api.crossref.org/works/10.1186%2FS13068-016-0565-3

21 January 2018

Biogas production and methanogenic archaeal community in mesophilic and thermophilic anaerobic co-digestion processes.

1 reference

https://api.crossref.org/works/10.1186%2FS13068-016-0565-3

21 January 2018

Characterization of microbial biofilms in a thermophilic biogas system by high-throughput metagenome sequencing.

1 reference

https://api.crossref.org/works/10.1186%2FS13068-016-0565-3

21 January 2018

Taxonomic composition and gene content of a methane-producing microbial community isolated from a biogas reactor

1 reference

https://api.crossref.org/works/10.1186%2FS13068-016-0565-3

21 January 2018

Temperature-dependent transformation of biogas-producing microbial communities points to the increased importance of hydrogenotrophic methanogenesis under thermophilic operation

1 reference

https://api.crossref.org/works/10.1186%2FS13068-016-0565-3

21 January 2018

The metagenome of a biogas-producing microbial community of a production-scale biogas plant fermenter analysed by the 454-pyrosequencing technology

1 reference

https://api.crossref.org/works/10.1186%2FS13068-016-0565-3

21 January 2018

Reconstruction of ancestral 16S rRNA reveals mutation bias in the evolution of optimal growth temperature in the Thermotogae phylum

1 reference

https://api.crossref.org/works/10.1186%2FS13068-016-0565-3

21 January 2018

Spirochaetes as intestinal pathogens: lessons from a Brachyspira genome

1 reference

https://api.crossref.org/works/10.1186%2FS13068-016-0565-3

21 January 2018

Acetogenesis from H2 plus CO2 by spirochetes from termite guts

1 reference

https://api.crossref.org/works/10.1186%2FS13068-016-0565-3

21 January 2018

Genomic characterization of Defluviitoga tunisiensis L3, a key hydrolytic bacterium in a thermophilic biogas plant and its abundance as determined by metagenome fragment recruitment

1 reference

https://api.crossref.org/works/10.1186%2FS13068-016-0565-3

21 January 2018

Metabolism of sucrose and its five isomers by Fusobacterium mortiferum

1 reference

https://api.crossref.org/works/10.1186%2FS13068-016-0565-3

21 January 2018

Metabolic footprinting of the anaerobic bacterium Fusobacterium varium using 1H NMR spectroscopy

1 reference

https://pubmed.ncbi.nlm.nih.gov/27462367

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

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10.1186/S13068-016-0565-3

1 reference

Consolidated OpenCitations Corpus – April 2017

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0 references

OpenCitations bibliographic resource ID

1 reference

Consolidated OpenCitations Corpus – April 2017

OpenCitations bibliographic resource ID

PMC publication ID

1 reference

Consolidated OpenCitations Corpus – April 2017

OpenCitations bibliographic resource ID

PubMed publication ID

1 reference

Consolidated OpenCitations Corpus – April 2017

OpenCitations bibliographic resource ID

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