Evaluation of 16S rRNA Gene Primer Pairs for Monitoring Microbial Community Structures Showed High Reproducibility within and Low Comparability between Datasets Generated with Multiple Archaeal and Bacterial Primer Pairs

Deep metagenome and metatranscriptome analyses of microbial communities affiliated with an industrial biogas fermenter, a cow rumen, and elephant feces reveal major differences in carbohydrate hydrolysis strategies

(2016) Simon Güllert et al.   Biotechnology for Biofuels

Multicenter quality assessment of 16S ribosomal DNA-sequencing for microbiome analyses reveals high inter-center variability

(2016) Andreas Hiergeist et al.   INTERNATIONAL JOURNAL OF MEDICAL MICROBIOLOGY

Mode of action uncovered for the specific reduction of methane emissions from ruminants by the small molecule 3-nitrooxypropanol

(2016) Evert C. Duin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Restructuring of Epibacterial Communities on Fucus vesiculosus forma mytili in Response to Elevated pCO2 and Increased Temperature Levels

(2016) Birte Mensch et al.   Frontiers in Microbiology

Microbial metagenomics in the Baltic Sea: Recent advancements and prospects for environmental monitoring

(2015) Karolina Ininbergs et al.   AMBIO

Composition of Bacterial Communities Associated with Aurelia aurita Changes with Compartment, Life Stage, and Population

(2015) Nancy Weiland-Bräuer et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Reconstructing 16S rRNA genes in metagenomic data

(2015) Cheng Yuan et al.   BIOINFORMATICS

Microbial diversity and dynamicity of biogas reactors due to radical changes of feedstock composition

(2015) Davide De Francisci et al.   BIORESOURCE TECHNOLOGY

Microbial community dynamics in replicate anaerobic digesters exposed sequentially to increasing organic loading rate, acidosis, and process recovery

(2015) Xavier Goux et al.   Biotechnology for Biofuels

The truth about metagenomics: quantifying and counteracting bias in 16S rRNA studies

(2015) J Paul Brooks et al.   BMC MICROBIOLOGY

Ecophysiology of an uncultivated lineage of Aigarchaeota from an oxic, hot spring filamentous ‘streamer’ community

(2015) Jacob P Beam et al.   ISME Journal

Analysis of intestinal microbiota in hybrid house mice reveals evolutionary divergence in a vertebrate hologenome

(2015) Jun Wang et al.   Nature Communications

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

(2015) Gemma Henderson et al.   Scientific Reports

Seasonal dynamics of bacterial and archaeal methanogenic communities in flooded rice fields and effect of drainage

(2015) Björn Breidenbach et al.   Frontiers in Microbiology

Primer and platform effects on 16S rRNA tag sequencing

(2015) Julien Tremblay et al.   Frontiers in Microbiology

Microbiota of the indoor environment: a meta-analysis

(2015) Rachel I. Adams et al.   Microbiome

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

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

(2014) Linn Solli et al.   Biotechnology for Biofuels

Synthetic microbial communities

(2014) Tobias Großkopf et al.   CURRENT OPINION IN MICROBIOLOGY

Methane yield phenotypes linked to differential gene expression in the sheep rumen microbiome

(2014) Weibing Shi et al.   GENOME RESEARCH

Biogeography and individuality shape function in the human skin metagenome

(2014) Julia Oh et al.   NATURE

Dynamics and associations of microbial community types across the human body

(2014) Tao Ding et al.   NATURE

Composition of Microbial Oral Biofilms during Maturation in Young Healthy Adults

(2014) Daniela Langfeldt et al.   PLoS One

Biogeochemical Typing of Paddy Field by a Data-Driven Approach Revealing Sub-Systems within a Complex Environment - A Pipeline to Filtrate, Organize and Frame Massive Dataset from Multi-Omics Analyses

(2014) Diogo M. O. Ogawa et al.   PLoS One

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

(2014) Rim Driss Limam et al.   MicrobiologyOpen

Archaea in Biogeochemical Cycles

(2013) Pierre Offre et al.   Annual Review of Microbiology

Development of a Dual-Index Sequencing Strategy and Curation Pipeline for Analyzing Amplicon Sequence Data on the MiSeq Illumina Sequencing Platform

(2013) James J. Kozich et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

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

(2013) Felix G Eikmeyer et al.   Biotechnology for Biofuels

Fecal microbiota diversity in survivors of adolescent/young adult Hodgkin lymphoma: a study of twins

(2013) W Cozen et al.   BRITISH JOURNAL OF CANCER

Linking microbial community structure, interactions and function in anaerobic digesters using new molecular techniques

(2013) Inka Vanwonterghem et al.   CURRENT OPINION IN BIOTECHNOLOGY

Comparative metagenomic and rRNA microbial diversity characterization using archaeal and bacterial synthetic communities

(2013) Migun Shakya et al.   ENVIRONMENTAL MICROBIOLOGY

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

(2013) Ramiro Logares et al.   ENVIRONMENTAL MICROBIOLOGY

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

(2013) Carina Sundberg et al.   FEMS MICROBIOLOGY ECOLOGY

Simultaneous Amplicon Sequencing to Explore Co-Occurrence Patterns of Bacterial, Archaeal and Eukaryotic Microorganisms in Rumen Microbial Communities

(2013) Sandra Kittelmann et al.   PLoS One

Biased Diversity Metrics Revealed by Bacterial 16S Pyrotags Derived from Different Primer Sets

(2013) Lin Cai et al.   PLoS One

Archaea on Human Skin

(2013) Alexander J. Probst et al.   PLoS One

Ruminants, climate change and climate policy

(2013) William J. Ripple et al.   Nature Climate Change

Physiology and Diversity of Ammonia-Oxidizing Archaea

(2012) David A. Stahl et al.   Annual Review of Microbiology

Community Structure Analysis of Methanogens Associated with Rumen Protozoa Reveals Bias in Universal Archaeal Primers

(2012) Lisa D. Tymensen et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

“Methanoplasmatales,” Thermoplasmatales-Related Archaea in Termite Guts and Other Environments, Are the Seventh Order of Methanogens

(2012) Kristina Paul et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

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

(2012) Roland Wirth et al.   Biotechnology for Biofuels

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

(2012) J Gregory Caporaso et al.   ISME Journal

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies

(2012) Anna Klindworth et al.   NUCLEIC ACIDS RESEARCH

Direct Comparisons of Illumina vs. Roche 454 Sequencing Technologies on the Same Microbial Community DNA Sample

(2012) Chengwei Luo et al.   PLoS One

Methane emission by sectors: A comprehensive review of emission sources and mitigation methods

(2012) Rafiu O. Yusuf et al.   RENEWABLE & SUSTAINABLE ENERGY REVIEWS

Archaeal diversity and community development in deep-sea hydrothermal vents

(2011) Ken Takai et al.   CURRENT OPINION IN MICROBIOLOGY

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

(2011) Jeyamalar Jeyanathan et al.   FEMS MICROBIOLOGY ECOLOGY

Transitions in bacterial communities along the 2000 km salinity gradient of the Baltic Sea

(2011) Daniel PR Herlemann et al.   ISME Journal

Impact of training sets on classification of high-throughput bacterial 16s rRNA gene surveys

(2011) Jeffrey J Werner et al.   ISME Journal

Reducing the Effects of PCR Amplification and Sequencing Artifacts on 16S rRNA-Based Studies

(2011) Patrick D. Schloss et al.   PLoS One

Colonic mucosa-associated microbiota is influenced by an interaction of Crohn disease and FUT2 (Secretor) genotype

(2011) P. Rausch et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Methanogen diversity in the rumen of Indian Surti buffalo (Bubalus bubalis), assessed by 16S rDNA analysis

(2011) K.M. Singh et al.   RESEARCH IN VETERINARY SCIENCE

Methane mitigation from ruminants using tannins and saponins

(2011) Gunjan Goel et al.   TROPICAL ANIMAL HEALTH AND PRODUCTION

The Earth Microbiome Project: Meeting report of the “1st EMP meeting on sample selection and acquisition” at Argonne National Laboratory October 6th 2010.

(2011) Jack A. Gilbert et al.   Standards in Genomic Sciences

Novel primers for 16S rRNA-based archaeal community analyses in environmental samples

(2010) Stephan Gantner et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Evaluation of different partial 16S rRNA gene sequence regions for phylogenetic analysis of microbiomes

(2010) Minseok Kim et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Comparison of two next-generation sequencing technologies for resolving highly complex microbiota composition using tandem variable 16S rRNA gene regions

(2010) Marcus J. Claesson et al.   NUCLEIC ACIDS RESEARCH

Empirical Testing of 16S rRNA Gene PCR Primer Pairs Reveals Variance in Target Specificity and Efficacy Not Suggested by In Silico Analysis

(2009) S. E. Morales et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities

(2009) P. D. Schloss et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Partitioning diversity for conservation analyses

(2009) Lou Jost et al.   DIVERSITY AND DISTRIBUTIONS

Associations between species and groups of sites: indices and statistical inference

(2009) Miquel De Cáceres et al.   ECOLOGY

Microbial community profiling for human microbiome projects: Tools, techniques, and challenges

(2009) M. Hamady et al.   GENOME RESEARCH

The NIH Human Microbiome Project

(2009) et al.   GENOME RESEARCH

Structure of the Archaeal Community of the Rumen

(2008) P. H. Janssen et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Critical Evaluation of Two Primers Commonly Used for Amplification of Bacterial 16S rRNA Genes

(2008) J. A. Frank et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Comparative analysis of archaeal 16S rRNA and amoA genes to estimate the abundance and diversity of ammonia-oxidizing archaea in marine sediments

(2008) Soo-Je Park et al.   EXTREMOPHILES

Monitoring bacterial and archaeal community shifts in a mesophilic anaerobic batch reactor treating a high-strength organic wastewater

(2008) Changsoo Lee et al.   FEMS MICROBIOLOGY ECOLOGY

Archaea diversity within a commercial biogas plant utilizing herbal biomass determined by 16S rDNA andmcrA analysis

(2008) E. Nettmann et al.   JOURNAL OF APPLIED MICROBIOLOGY

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

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

Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex

(2008) Micah Hamady et al.   NATURE METHODS

Molecular eco-systems biology: towards an understanding of community function

(2008) Jeroen Raes et al.   NATURE REVIEWS MICROBIOLOGY

The influence of sex, handedness, and washing on the diversity of hand surface bacteria

(2008) N. Fierer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA