ANCHOR: a 16S rRNA gene amplicon pipeline for microbial analysis of multiple environmental samples

Best practices for analysing microbiomes

(2018) Rob Knight et al.   NATURE REVIEWS MICROBIOLOGY

Variation in the microbiome of the urogenital tract of Chlamydia-free female koalas (Phascolarctos cinereus) with and without ‘wet bottom’

(2018) Alistair R. Legione et al.   PLoS One

The Response of a 16S Ribosomal RNA Gene Fragment Amplified Community to Lead, Zinc, and Copper Pollution in a Shanghai Field Trial

(2018) Shumeng Kou et al.   Frontiers in Microbiology

Taxonomy annotation and guide tree errors in 16S rRNA databases

(2018) Robert Edgar   PeerJ

Trees, fungi and bacteria: tripartite metatranscriptomics of a root microbiome responding to soil contamination

(2018) E. Gonzalez et al.   Microbiome

Phylogenetic Placement of Exact Amplicon Sequences Improves Associations with Clinical Information

(2018) Stefan Janssen et al.   mSystems

Roseburia spp.: a marker of health?

(2017) Zohreh Tamanai-Shacoori et al.   Future Microbiology

Noviherbaspirillum denitrificans sp. nov., a denitrifying bacterium isolated from rice paddy soil and Noviherbaspirillum autotrophicum sp. nov., a denitrifying, facultatively autotrophic bacterium isolated from rice paddy soil and proposal to reclassify Herbaspirillum massiliense as Noviherbaspirillum massiliense comb. nov.

(2017) Satoshi Ishii et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Exact sequence variants should replace operational taxonomic units in marker-gene data analysis

(2017) Benjamin J Callahan et al.   ISME Journal

Assessing species biomass contributions in microbial communities via metaproteomics

(2017) Manuel Kleiner et al.   Nature Communications

Fast and Simple Analysis of MiSeq Amplicon Sequencing Data with MetaAmp

(2017) Xiaoli Dong et al.   Frontiers in Microbiology

How conserved are the conserved 16S-rRNA regions?

(2017) Marcel Martinez-Porchas et al.   PeerJ

A microbial survey of the International Space Station (ISS)

(2017) Jenna M. Lang et al.   PeerJ

Preparing for the crewed Mars journey: microbiota dynamics in the confined Mars500 habitat during simulated Mars flight and landing

(2017) Petra Schwendner et al.   Microbiome

Normalization and microbial differential abundance strategies depend upon data characteristics

(2017) Sophie Weiss et al.   Microbiome

The adaptation of Escherichia coli cells grown in simulated microgravity for an extended period is both phenotypic and genomic

(2017) Madhan R. Tirumalai et al.   NPJ Microgravity

NovelacsFGene Primers Revealed a Diverse Phototrophic Bacterial Population, Including Gemmatimonadetes, in Lake Taihu (China)

(2016) Yili Huang et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Haemophilus parainfluenzae as a marker of the upper respiratory tract microbiota changes under the influence of preoperative prophylaxis with or without postoperative treatment in patients with lung cancer

(2016) Urszula Kosikowska et al.   BMC MICROBIOLOGY

Lawsonella clevelandensis gen. nov., sp. nov., a new member of the suborder Corynebacterineae isolated from human abscesses

(2016) Melissa E. Bell et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Agathobaculum butyriciproducens gen. nov.  sp. nov., a strict anaerobic, butyrate-producing gut bacterium isolated from human faeces and reclassification of Eubacterium desmolans as Agathobaculum desmolans comb. nov.

(2016) Sharon Ahn et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Reclassification of four Polynucleobacter necessarius strains as representatives of Polynucleobacter asymbioticus comb. nov., Polynucleobacter duraquae sp. nov., Polynucleobacter yangtzensis sp. nov. and Polynucleobacter sinensis sp. nov., and emended description of Polynucleobacter necessarius

(2016) Martin W. Hahn et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Reclassification of Eubacterium desmolans as Butyricicoccus desmolans comb. nov., and description of Butyricicoccus faecihominis sp. nov., a butyrate-producing bacterium from human faeces

(2016)   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

Comparative Transcriptomic Approaches Exploring Contamination Stress Tolerance inSalixsp. Reveal the Importance for a Metaorganismal de Novo Assembly Approach for Nonmodel Plants

(2016) Nicholas J. B. Brereton et al.   PLANT PHYSIOLOGY

Riverine Bacterial Communities Reveal Environmental Disturbance Signatures within the Betaproteobacteria and Verrucomicrobia

(2016) John Paul Balmonte et al.   Frontiers in Microbiology

Microorganisms in Confined Habitats: Microbial Monitoring and Control of Intensive Care Units, Operating Rooms, Cleanrooms and the International Space Station

(2016) Maximilian Mora et al.   Frontiers in Microbiology

The Mouse Intestinal Bacterial Collection (miBC) provides host-specific insight into cultured diversity and functional potential of the gut microbiota

(2016) Ilias Lagkouvardos et al.   Nature Microbiology

Open-Source Sequence Clustering Methods Improve the State Of the Art

(2016) Evguenia Kopylova et al.   mSystems

A perspective on 16S rRNA operational taxonomic unit clustering using sequence similarity

(2016) Nam-Phuong Nguyen et al.   npj Biofilms and Microbiomes

Four-year bacterial monitoring in the International Space Station—Japanese Experiment Module “Kibo” with culture-independent approach

(2016) Tomoaki Ichijo et al.   NPJ Microgravity

Preliminary analysis of salivary microbiome and their potential roles in oral lichen planus

(2016) Kun Wang et al.   Scientific Reports

Meta-transcriptomics indicates biotic cross-tolerance in willow trees cultivated on petroleum hydrocarbon contaminated soil

(2015) Emmanuel Gonzalez et al.   BMC PLANT BIOLOGY

Fusobacterium nucleatum: a commensal-turned pathogen

(2015) Yiping W Han   CURRENT OPINION IN MICROBIOLOGY

Intrinsic challenges in ancient microbiome reconstruction using 16S rRNA gene amplification

(2015) Kirsten A. Ziesemer et al.   Scientific Reports

Variation in secondary structure of the 16S rRNA molecule in cyanobacteria with implications for phylogenetic analysis.

(2015) Klara Rehakova et al.   Fottea

Rhodoferax saidenbachensis sp. nov., a psychrotolerant, very slowly growing bacterium within the family Comamonadaceae, proposal of appropriate taxonomic position of Albidiferax ferrireducens strain T118T in the genus Rhodoferax and emended description of the genus Rhodoferax

(2014) R. Kaden et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Microbial Monitoring of Crewed Habitats in Space—Current Status and Future Perspectives

(2014) Nobuyasu Yamaguchi et al.   MICROBES AND ENVIRONMENTS

Exercise Prevents Weight Gain and Alters the Gut Microbiota in a Mouse Model of High Fat Diet-Induced Obesity

(2014) Christian C. Evans et al.   PLoS One

Comparison of Widely Used Listeria monocytogenes Strains EGD, 10403S, and EGD-e Highlights Genomic Differences Underlying Variations in Pathogenicity

(2014) C. Becavin et al.   mBio

Non-contiguous finished genome sequence and description of Fenollaria massiliensis gen. nov., sp. nov., a new genus of anaerobic bacterium

(2014) Isabelle Pagnier et al.   Standards in Genomic Sciences

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

PEAR: a fast and accurate Illumina Paired-End reAd mergeR

(2013) J. Zhang et al.   BIOINFORMATICS

Clostridium leptum group bacteria abundance and diversity in the fecal microbiota of patients with inflammatory bowel disease: a case–control study in India

(2013) Jayakanthan Kabeerdoss et al.   BMC GASTROENTEROLOGY

Lactobacillus faecis sp. nov., isolated from animal faeces

(2013) A. Endo et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Novel Fastidious, Partially Acid-Fast, Anaerobic Gram-Positive Bacillus Associated with Abscess Formation and Recovered from Multiple Medical Centers

(2013) S. M. Harrington et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Count-based differential expression analysis of RNA sequencing data using R and Bioconductor

(2013) Simon Anders et al.   Nature Protocols

The Variability of the 16S rRNA Gene in Bacterial Genomes and Its Consequences for Bacterial Community Analyses

(2013) Tomáš Větrovský et al.   PLoS One

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

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

Roseobacter clade bacteria are abundant in coastal sediments and encode a novel combination of sulfur oxidation genes

(2012) Sabine Lenk et al.   ISME Journal

Corynebacterium tuberculostearicum: a Potentially Misidentified and Multiresistant Corynebacterium Species Isolated from Clinical Specimens

(2012) V. Hinic et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Finegoldia magna (formerly Peptostreptococcus magnus): An overlooked etiology for toxic shock syndrome?

(2012) Marnie E. Rosenthal et al.   MEDICAL HYPOTHESES

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

Burden of emerging anaerobes in the MALDI-TOF and 16S rRNA gene sequencing era

(2011) Bernard La Scola et al.   ANAEROBE

Generation of Multimillion-Sequence 16S rRNA Gene Libraries from Complex Microbial Communities by Assembling Paired-End Illumina Reads

(2011) Andrea K. Bartram et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

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

(2011) T. Magoc et al.   BIOINFORMATICS

High-throughput single-cell sequencing identifies photoheterotrophs and chemoautotrophs in freshwater bacterioplankton

(2011) Manuel Martinez-Garcia et al.   ISME Journal

Promiscuity in mice is associated with increased vaginal bacterial diversity

(2011) Matthew David MacManes   NATURWISSENSCHAFTEN

Pan-genome of the dominant human gut-associated archaeon, Methanobrevibacter smithii, studied in twins

(2011) E. E. Hansen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Diversity and composition of the bacterial community of Poyang Lake (China) as determined by 16S rRNA gene sequence analysis

(2011) Lan Wu et al.   WORLD JOURNAL OF MICROBIOLOGY & BIOTECHNOLOGY

Diversity of 16S rRNA Genes within Individual Prokaryotic Genomes

(2010) A. Y. Pei et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Clinical relevance of surgical site infection as defined by the criteria of the Centers for Disease Control and Prevention

(2010) N.A. Henriksen et al.   JOURNAL OF HOSPITAL INFECTION

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

Nitrosopumilus maritimus genome reveals unique mechanisms for nitrification and autotrophy in globally distributed marine crenarchaea

(2010) C. B. Walker et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Temporal and spatial variability in nearshore bacterioplankton communities of Lake Michigan

(2009) Sabrina R. Mueller-Spitz et al.   FEMS MICROBIOLOGY ECOLOGY

Diversity, metabolism and microbial ecology of butyrate-producing bacteria from the human large intestine

(2009) Petra Louis et al.   FEMS MICROBIOLOGY LETTERS

Acinetobacter beijerinckii sp. nov. and Acinetobacter gyllenbergii sp. nov., haemolytic organisms isolated from humans

(2009) A. Nemec et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Isolation and characterization of fructophilic lactic acid bacteria from fructose-rich niches

(2009) Akihito Endo et al.   SYSTEMATIC AND APPLIED MICROBIOLOGY

Relative Abundance of Bacteroides spp. in Stools and Wastewaters as Determined by Hierarchical Oligonucleotide Primer Extension

(2008) P.-Y. Hong et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

It's all relative: ranking the diversity of aquatic bacterial communities

(2008) Allison K. Shaw et al.   ENVIRONMENTAL MICROBIOLOGY

Diversity of Capnocytophaga species in children and description of Capnocytophaga leadbetteri sp. nov. and Capnocytophaga genospecies AHN8471

(2008) E. V. G. Frandsen et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY