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Phosphorus-mineralizing Communities Reflect Nutrient-Rich Characteristics in Japanese Arable Andisols

(2018) Kazumori Mise et al.   MICROBES AND ENVIRONMENTS

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

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Determinants of Reduced Genetic Capacity for Butyrate Synthesis by the Gut Microbiome in Crohn’s Disease and Ulcerative Colitis

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Microbiota studies in the bile duct strongly suggest a role for Helicobacter pylori in extrahepatic cholangiocarcinoma

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DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

KEGG: new perspectives on genomes, pathways, diseases and drugs

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Deriving accurate microbiota profiles from human samples with low bacterial content through post-sequencing processing of Illumina MiSeq data

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Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

Changes in Abundance of Oral Microbiota Associated with Oral Cancer

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Kraken: ultrafast metagenomic sequence classification using exact alignments

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Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences

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UPARSE: highly accurate OTU sequences from microbial amplicon reads

(2013) Robert C Edgar   NATURE METHODS

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases

(2013) Ron Caspi et al.   NUCLEIC ACIDS RESEARCH

SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data

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Phylogenetic stratigraphy in the Guerrero Negro hypersaline microbial mat

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Fast gapped-read alignment with Bowtie 2

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

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Induction of Intestinal Th17 Cells by Segmented Filamentous Bacteria

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Millimeter-scale genetic gradients and community-level molecular convergence in a hypersaline microbial mat

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A core gut microbiome in obese and lean twins

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