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GigaScience, ISSN 2047-217X, 2013, Volume 2, Issue 1, pp. 16 - 16
Background: As microbial ecologists take advantage of high-throughput sequencing technologies to describe microbial communities across ever-increasing numbers... 
Microbial ecology | Data visualization | QIIME | MULTIDISCIPLINARY SCIENCES
Journal Article
GigaScience, ISSN 2047-217X, 07/2012, Volume 464, Issue 1, pp. 7 - 7
Background: We present the Biological Observation Matrix (BIOM, pronounced "biome") format: a JSON-based file format for representing arbitrary observation by... 
Metagenomics | Comparative genomics | Microbial ecology | BIOM | MG-RAST | QIIME | VAMPS | PHYLOGENY | COMMUNITY | MULTIDISCIPLINARY SCIENCES | DIVERSITY | RARE BIOSPHERE
Journal Article
MICROBIOME, ISSN 2049-2618, 05/2015, Volume 3, Issue 1, p. 19
Background: The rapid expansion of 16S rRNA gene sequencing in challenging clinical contexts has resulted in a growing body of literature of variable quality.... 
16S rRNA | Pair-end reads | Otitis media | MICROBIOLOGY | Respiratory | COMMUNITIES | MiSeq | Contamination | QIIME | Bacteria | Information management | Microbiota (Symbiotic organisms) | RNA | Biotechnology industry
Journal Article
Current Protocols in Bioinformatics, ISSN 1934-3396, 2011, Volume Chapter 10, Issue 36, p. Unit 10.7.
QIIME (canonically pronounced "chime") is a software application that performs microbial community analysis. It is an acronym for Quantitative Insights Into... 
Microbial ecology | Software | SSU | Bioinformatics | 16S | QIIME | Sequence Analysis, RNA - methods | Bacteria - classification | RNA, Ribosomal, 16S - genetics | DNA, Bacterial - chemistry | Genes, rRNA | Phylogeny | Biodiversity | Bacteria - genetics
Journal Article
FRONTIERS IN MICROBIOLOGY, ISSN 1664-302X, 05/2019, Volume 10, p. 1084
Metataxonomic analysis represents a fast and cost-effective approach for acquiring informative insight into the composition of the microbiome of samples with... 
Ion Torrent | metataxonomics | bioinformatics | MICROBIOLOGY | DIVERSITY | Illumina | QIIME | PCR | wine | next-generation-sequencing
Journal Article
Data in Brief, ISSN 2352-3409, 10/2019, Volume 26, p. 104405
We present high-throughput amplicon sequence (HTS) datasets of the microbial metacommunity DNA of the gut tissue and the gut digesta of naturally occurring... 
Arcobacter | MiSeq | QIIME | Echinoderm | PhyloToAST
Journal Article
PeerJ, ISSN 2167-8359, 2015, Volume 2015, Issue 12, p. e1487
Background. 16S rRNA gene sequences are routinely assigned to operational taxonomic units (OTUs) that are then used to analyze complex microbial communities. A... 
16S rRNA gene sequences | Culture-independent | OTU | Mothur | Microbial ecology | Bioinformatics | Next generation sequencing | QIIME | Microbiome | mothur | RDNA | MULTIDISCIPLINARY SCIENCES | MICROBIAL DIVERSITY | SOIL | PYROSEQUENCES | RNA | Genes | Analysis | Methods | Studies | rRNA 16S | Algorithms | Taxonomy | Abundance | Ecology | Biodiversity
Journal Article
Frontiers in Microbiology, ISSN 1664-302X, 12/2018, Volume 9, p. 3010
Background: Microbiome studies need to analyze massive sequencing data, which requires the use of sophisticated bioinformatics pipelines. Up to date, several... 
Rumen microbiota | 16S rRNA | Bovine | Mothur | QIIME | mothur | EMISSIONS | rumen microbiota | MICROBIOLOGY | SUPPLEMENTATION | DAIRY-COWS | FEED-EFFICIENCY | FERMENTATION | bovine | DIETARY | DIVERSITY | TRAITS | Microbiota (Symbiotic organisms) | RNA | Rumen
Journal Article
Genes & Diseases, ISSN 2352-3042, 12/2019
Diversity analysis and taxonomic profiles can be generated from marker-gene sequence data with the help of many available computational tools. The Quantitative... 
Alpha diversity | Sample size calculation | ANOVA | Microbiome data | Beta diversity | Bioinformatics | QIIME | 16S rRNA gene
Journal Article