Genomic insights into members of the candidate phylum Hyd24-12 common in mesophilic anaerobic digesters

The role of hydrogenotrophic methanogens in an acidogenic reactor

(2015) Wenhai Huang et al.   CHEMOSPHERE

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

Unusual biology across a group comprising more than 15% of domain Bacteria

(2015) Christopher T. Brown et al.   NATURE

Marine microbial community dynamics and their ecological interpretation

(2015) Jed A. Fuhrman et al.   NATURE REVIEWS MICROBIOLOGY

Back to Basics – The Influence of DNA Extraction and Primer Choice on Phylogenetic Analysis of Activated Sludge Communities

(2015) Mads Albertsen et al.   PLoS One

Ammonia and temperature determine potential clustering in the anaerobic digestion microbiome

(2015) Jo De Vrieze et al.   WATER RESEARCH

MiDAS: the field guide to the microbes of activated sludge

(2015) Simon Jon McIlroy et al.   Database-The Journal of Biological Databases and Curation

First genomic insights into members of a candidate bacterial phylum responsible for wastewater bulking

(2015) Yuji Sekiguchi et al.   PeerJ

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

The return of metabolism: biochemistry and physiology of the pentose phosphate pathway

(2014) Anna Stincone et al.   BIOLOGICAL REVIEWS

Microbial consumption of zero-valence sulfur in marine benthic habitats

(2014) Petra Pjevac et al.   ENVIRONMENTAL MICROBIOLOGY

Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes

(2014) M. Kim et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences

(2014) Pablo Yarza et al.   NATURE REVIEWS MICROBIOLOGY

The InterPro protein families database: the classification resource after 15 years

(2014) Alex Mitchell et al.   NUCLEIC ACIDS RESEARCH

Growth of nitrite-oxidizing bacteria by aerobic hydrogen oxidation

(2014) H. Koch et al.   SCIENCE

Proton-coupled sugar transport in the prototypical major facilitator superfamily protein XylE

(2014) Goragot Wisedchaisri et al.   Nature Communications

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

(2014) Rim Driss Limam et al.   MicrobiologyOpen

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

(2013) Carina Sundberg et al.   FEMS MICROBIOLOGY ECOLOGY

Insights into the phylogeny and coding potential of microbial dark matter

(2013) Christian Rinke et al.   NATURE

Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes

(2013) Mads Albertsen et al.   NATURE BIOTECHNOLOGY

Activities at the Universal Protein Resource (UniProt)

(2013)   NUCLEIC ACIDS RESEARCH

Data, information, knowledge and principle: back to metabolism in KEGG

(2013) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data

(2013) Paul J. McMurdie et al.   PLoS One

SINA: Accurate high-throughput multiple sequence alignment of ribosomal RNA genes

(2012) Elmar Pruesse et al.   BIOINFORMATICS

Phylogenetic stratigraphy in the Guerrero Negro hypersaline microbial mat

(2012) J Kirk Harris et al.   ISME Journal

Type IV Pilin Proteins: Versatile Molecular Modules

(2012) Carmen L. Giltner et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

MicroScope—an integrated microbial resource for the curation and comparative analysis of genomic and metabolic data

(2012) David Vallenet et al.   NUCLEIC ACIDS RESEARCH

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

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

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

(2011) T. Magoc et al.   BIOINFORMATICS

Flagella and Pili-Mediated Near-Surface Single-Cell Motility Mechanisms in P. aeruginosa

(2011) Jacinta C. Conrad et al.   BIOPHYSICAL JOURNAL

H2S gas biological removal efficiency and bacterial community diversity in biofilter treating wastewater odor

(2011) Ilhem Omri et al.   BIORESOURCE TECHNOLOGY

Bacterial sulfur cycling shapes microbial communities in surface sediments of an ultramafic hydrothermal vent field

(2011) Regina Schauer et al.   ENVIRONMENTAL MICROBIOLOGY

In Search of an Uncultured Human-Associated TM7 Bacterium in the Environment

(2011) Jorge M. Dinis et al.   PLoS One

Identification of Surprisingly Diverse Type IV Pili, across a Broad Range of Gram-Positive Bacteria

(2011) Saheed Imam et al.   PLoS One

Bacteria use type-IV pili to slingshot on surfaces

(2011) F. Jin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Bacterial community structures are unique and resilient in full-scale bioenergy systems

(2011) J. J. Werner et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

mathFISH, a Web Tool That Uses Thermodynamics-Based Mathematical Models forIn SilicoEvaluation of Oligonucleotide Probes for FluorescenceIn SituHybridization

(2010) L. Safak Yilmaz et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

Non-target sites with single nucleotide insertions or deletions are frequently found in 16S rRNA sequences and can lead to false positives in fluorescence in situ hybridization (FISH)

(2010) Simon J. McIlroy et al.   ENVIRONMENTAL MICROBIOLOGY

Double Labeling of Oligonucleotide Probes for Fluorescence In Situ Hybridization (DOPE-FISH) Improves Signal Intensity and Increases rRNA Accessibility

(2009) K. Stoecker et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Biogas production: current state and perspectives

(2009) Peter Weiland   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Genome sequence ofDesulfobacterium autotrophicumHRM2, a marine sulfate reducer oxidizing organic carbon completely to carbon dioxide

(2009) Axel W. Strittmatter et al.   ENVIRONMENTAL MICROBIOLOGY

FIGfams: yet another set of protein families

(2009) Folker Meyer et al.   NUCLEIC ACIDS RESEARCH

Shifting the genomic gold standard for the prokaryotic species definition

(2009) Michael Richter et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

MicroScope: a platform for microbial genome annotation and comparative genomics

(2009) D. Vallenet et al.   Database-The Journal of Biological Databases and Curation

Discovery and characterization of a new bacterial candidate division by an anaerobic sludge digester metagenomic approach

(2008) Sonda Guermazi et al.   ENVIRONMENTAL MICROBIOLOGY

"Candidatus Cloacamonas Acidaminovorans": Genome Sequence Reconstruction Provides a First Glimpse of a New Bacterial Division

(2008) E. Pelletier et al.   JOURNAL OF BACTERIOLOGY

The Ribosomal Database Project: improved alignments and new tools for rRNA analysis

(2008) J. R. Cole et al.   NUCLEIC ACIDS RESEARCH

Sec- and Tat-mediated protein secretion across the bacterial cytoplasmic membrane—Distinct translocases and mechanisms

(2007) Paolo Natale et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES