Diverse electron carriers drive syntrophic interactions in an enriched anaerobic acetate-oxidizing consortium

EMPress Enables Tree-Guided, Interactive, and Exploratory Analyses of Multi-omic Data Sets

(2021) Kalen Cantrell et al.   mSystems

Energy conservation under extreme energy limitation: the role of cytochromes and quinones in acetogenic bacteria

(2021) Florian P. Rosenbaum et al.   EXTREMOPHILES

Gradual development of ammonia-induced syntrophic acetate-oxidizing activities under mesophilic and thermophilic conditions quantitatively tracked using multiple isotopic approaches

(2021) Liping Hao et al.   WATER RESEARCH

A Shuttle-Vector System Allows Heterologous Gene Expression in the Thermophilic Methanogen Methanothermobacter thermautotrophicus ΔH

(2021) Christian Fink et al.   mBio

New insights from the biogas microbiome by comprehensive genome-resolved metagenomics of nearly 1600 species originating from multiple anaerobic digesters

(2020) Stefano Campanaro et al.   Biotechnology for Biofuels

MiDAS 3: An ecosystem-specific reference database, taxonomy and knowledge platform for activated sludge and anaerobic digesters reveals species-level microbiome composition of activated sludge

(2020) Marta Nierychlo et al.   WATER RESEARCH

The Beta Subunit of Non-bifurcating NADH-Dependent [FeFe]-Hydrogenases Differs From Those of Multimeric Electron-Bifurcating [FeFe]-Hydrogenases

(2020) Nathaniel A. Losey et al.   Frontiers in Microbiology

Syntrophic acetate oxidation replaces acetoclastic methanogenesis during thermophilic digestion of biowaste

(2020) Stefan Dyksma et al.   Microbiome

Catabolism and interactions of uncultured organisms shaped by eco-thermodynamics in methanogenic bioprocesses

(2020) Masaru K. Nobu et al.   Microbiome

Genome recovery and metatranscriptomic confirmation of functional acetate-oxidizing bacteria from enriched anaerobic biogas digesters

(2020) Yongjun Wei et al.   ENVIRONMENTAL POLLUTION

metaFlye: scalable long-read metagenome assembly using repeat graphs

(2020) Mikhail Kolmogorov et al.   NATURE METHODS

Integration of absolute multi-omics reveals dynamic protein-to-RNA ratios and metabolic interplay within mixed-domain microbiomes

(2020) F. Delogu et al.   Nature Communications

Diagnosing and Predicting Mixed-Culture Fermentations with Unicellular and Guild-Based Metabolic Models

(2020) Matthew J. Scarborough et al.   mSystems

Growth Characteristics and Thermodynamics of Syntrophic Acetate Oxidizers

(2019) Maria Westerholm et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Identification of novel potential acetate-oxidizing bacteria in thermophilic methanogenic chemostats by DNA stable isotope probing

(2019) Dan Zheng et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database

(2019) Pierre-Alain Chaumeil et al.   BIOINFORMATICS

Energy-Conserving Enzyme Systems Active During Syntrophic Acetate Oxidation in the Thermophilic Bacterium Thermacetogenium phaeum

(2019) Anja Keller et al.   Frontiers in Microbiology

Comment on “A compilation and bioenergetic evaluation of syntrophic microbial growth yields in anaerobic digestion” by Patón, M. and Rodríguez, J. [Water Research 162 (2019), 516–517]

(2019) Helena Junicke   WATER RESEARCH

Wet biowaste digestion: ADM1 model improvement by implementation of known genera and activity of propionate oxidizing bacteria

(2018) Frank Uhlenhut et al.   WATER RESEARCH

Performance and genome-centric metagenomics of thermophilic single and two-stage anaerobic digesters treating cheese wastes

(2018) Alessandra Fontana et al.   WATER RESEARCH

Microbial rRNA gene expression and co-occurrence profiles associate with biokinetics and elemental composition in full-scale anaerobic digesters

(2018) Ryan M. Ziels et al.   Microbial Biotechnology

A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life

(2018) Donovan H Parks et al.   NATURE BIOTECHNOLOGY

High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries

(2018) Chirag Jain et al.   Nature Communications

Metabolism and Occurrence of Methanogenic and Sulfate-Reducing Syntrophic Acetate Oxidizing Communities in Haloalkaline Environments

(2018) Peer H. A. Timmers et al.   Frontiers in Microbiology

metaSPAdes: a new versatile metagenomic assembler

(2017) Sergey Nurk et al.   GENOME RESEARCH

Fast and accurate de novo genome assembly from long uncorrected reads

(2017) Robert Vaser et al.   GENOME RESEARCH

dRep: a tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication

(2017) Matthew R Olm et al.   ISME Journal

Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea

(2017) Robert M Bowers et al.   NATURE BIOTECHNOLOGY

The Minimum Biological Energy Quantum

(2017) Volker Müller et al.   Frontiers in Microbiology

Bacteriophage–prokaryote dynamics and interaction within anaerobic digestion processes across time and space

(2017) Junyu Zhang et al.   Microbiome

Detection of novel syntrophic acetate-oxidizing bacteria from biogas processes by continuous acetate enrichment approaches

(2017) Maria Westerholm et al.   Microbial Biotechnology

BBMerge – Accurate paired shotgun read merging via overlap

(2017) Brian Bushnell et al.   PLoS One

Biogas production through syntrophic acetate oxidation and deliberate operating strategies for improved digester performance

(2016) Maria Westerholm et al.   APPLIED ENERGY

Bacterial community composition and fhs profiles of low- and high-ammonia biogas digesters reveal novel syntrophic acetate-oxidising bacteria

(2016) Bettina Müller et al.   Biotechnology for Biofuels

Untangling the Effect of Fatty Acid Addition at Species Level Revealed Different Transcriptional Responses of the Biogas Microbial Community Members

(2016) Laura Treu et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Identification of syntrophic acetate-oxidizing bacteria in anaerobic digesters by combined protein-based stable isotope probing and metagenomics

(2016) Freya Mosbæk et al.   ISME Journal

OpenMS: a flexible open-source software platform for mass spectrometry data analysis

(2016) Hannes L Röst et al.   NATURE METHODS

Genome-Guided Analysis and Whole Transcriptome Profiling of the Mesophilic Syntrophic Acetate Oxidising Bacterium Syntrophaceticus schinkii

(2016) Shahid Manzoor et al.   PLoS One

Microbial community adaptation influences long-chain fatty acid conversion during anaerobic codigestion of fats, oils, and grease with municipal sludge

(2016) Ryan M. Ziels et al.   WATER RESEARCH

HydDB: A web tool for hydrogenase classification and analysis

(2016) Dan Søndergaard et al.   Scientific Reports

A low phosphorylation potential in the acetogen Acetobacterium woodii reflects its lifestyle at the thermodynamic edge of life

(2015) Sebastian Spahn et al.   ARCHIVES OF MICROBIOLOGY

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

(2015) Donovan H. Parks et al.   GENOME RESEARCH

Microbial dark matter ecogenomics reveals complex synergistic networks in a methanogenic bioreactor

(2015) Masaru K Nobu et al.   ISME Journal

Modelling extracellular limitations for mediated versus direct interspecies electron transfer

(2015) Tomas Storck et al.   ISME Journal

Networks of energetic and metabolic interactions define dynamics in microbial communities

(2015) Mallory Embree et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Stable isotope probing of acetate fed anaerobic batch incubations shows a partial resistance of acetoclastic methanogenesis catalyzed by Methanosarcina to sudden increase of ammonia level

(2015) Liping Hao et al.   WATER RESEARCH

Ammonia and temperature determine potential clustering in the anaerobic digestion microbiome

(2015) Jo De Vrieze et al.   WATER RESEARCH

Anvi’o: an advanced analysis and visualization platform for ‘omics data

(2015) A. Murat Eren et al.   PeerJ

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

(2015) Dongwan D. Kang et al.   PeerJ

Microbial Community Dynamics and Stability during an Ammonia-Induced Shift to Syntrophic Acetate Oxidation

(2014) Jeffrey J. Werner et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

MetaProSIP: Automated Inference of Stable Isotope Incorporation Rates in Proteins for Functional Metaproteomics

(2014) Timo Sachsenberg et al.   JOURNAL OF PROTEOME RESEARCH

Multi-enzyme digestion FASP and the ‘Total Protein Approach’-based absolute quantification of the Escherichia coli proteome

(2014) Jacek R. Wiśniewski et al.   Journal of Proteomics

MS-GF+ makes progress towards a universal database search tool for proteomics

(2014) Sangtae Kim et al.   Nature Communications

Absolute Quantification of Individual Biomass Concentrations in a Methanogenic Coculture

(2014) Helena Junicke et al.   AMB Express

MetaPathways: a modular pipeline for constructing pathway/genome databases from environmental sequence information

(2013) Kishori M Konwar et al.   BMC BIOINFORMATICS

COBRApy: COnstraints-Based Reconstruction and Analysis for Python

(2013) Ali Ebrahim et al.   BMC Systems Biology

The dominant acetate degradation pathway/methanogenic composition in full-scale anaerobic digesters operating under different ammonia levels

(2013) I. A. Fotidis et al.   International Journal of Environmental Science and Technology

Syntrophic acetate oxidation in industrial CSTR biogas digesters

(2013) Li Sun et al.   JOURNAL OF BIOTECHNOLOGY

A Proteomic View at the Biochemistry of Syntrophic Butyrate Oxidation in Syntrophomonas wolfei

(2013) Alexander Schmidt et al.   PLoS One

Characterization and modelling of interspecies electron transfer mechanisms and microbial community dynamics of a syntrophic association

(2013) Harish Nagarajan et al.   Nature Communications

Genome-guided analysis of physiological and morphological traits of the fermentative acetate oxidizer Thermacetogenium phaeum

(2012) Dirk Oehler et al.   BMC GENOMICS

Methanothermobacter tenebrarum sp. nov., a hydrogenotrophic, thermophilic methanogen isolated from gas-associated formation water of a natural gas field

(2012) K. Nakamura et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

OptCom: A Multi-Level Optimization Framework for the Metabolic Modeling and Analysis of Microbial Communities

(2012) Ali R. Zomorrodi et al.   PLoS Computational Biology

Identification of a novel acetate-utilizing bacterium belonging to Synergistes group 4 in anaerobic digester sludge

(2011) Tsukasa Ito et al.   ISME Journal

Detection of active, potentially acetate-oxidizing syntrophs in an anaerobic digester by flux measurement and formyltetrahydrofolate synthetase (FTHFS) expression profiling

(2011) T. Hori et al.   MICROBIOLOGY-SGM

Tepidanaerobacter acetatoxydans sp. nov., an anaerobic, syntrophic acetate-oxidizing bacterium isolated from two ammonium-enriched mesophilic methanogenic processes

(2011) Maria Westerholm et al.   SYSTEMATIC AND APPLIED MICROBIOLOGY

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

Efficient Marginalization to Compute Protein Posterior Probabilities from Shotgun Mass Spectrometry Data

(2010) Oliver Serang et al.   JOURNAL OF PROTEOME RESEARCH

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

Monitoring the role of aceticlasts in anaerobic digestion: Activity and capacity

(2008) A CONKLIN et al.   WATER RESEARCH

Ammonia, a selective agent for methane production by syntrophic acetate oxidation at mesophilic temperature

(2008) A. Schnürer et al.   WATER SCIENCE AND TECHNOLOGY