RESCRIPt: Reproducible sequence taxonomy reference database management

PLoS Computational Biology, Год журнала: 2021, Номер 17(11), С. e1009581 - e1009581

Опубликована: Ноя. 8, 2021

Nucleotide sequence and taxonomy reference databases are critical resources for widespread applications including marker-gene metagenome sequencing microbiome analysis, diet metabarcoding, environmental DNA (eDNA) surveys. Reproducibly generating, managing, using, evaluating nucleotide creates a significant bottleneck researchers aiming to generate custom databases. Furthermore, database composition drastically influences results, lack of standardization limits cross-study comparisons. To address these challenges, we developed RESCRIPt, Python 3 software package QIIME 2 plugin reproducible generation management databases, dedicated functions that streamline creating from popular sources, evaluating, comparing, interactively exploring qualitative quantitative characteristics across highlight the breadth capabilities provide several examples working with profiling (SILVA, Greengenes, NCBI-RefSeq, GTDB), eDNA metabarcoding surveys (BOLD, GenBank), as well genome comparison. We show bigger is not always better, standardized taxonomies those focus on type strains have advantages, though may be appropriate all use cases. Most appear benefit some curation (quality filtering), clustering appears detrimental quality. Finally, demonstrate extensibility RESCRIPt workflows comparison global hepatitis genomes. provides tools democratize process acquisition management, enabling reproducibly transparently create materials diverse research applications. released under permissive BSD-3 license at https://github.com/bokulich-lab/RESCRIPt .

Язык: Английский

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Reclassification of Clostridium difficile as Clostridioides difficile (Hall and O’Toole 1935) Prévot 1938

Anaerobe, Год журнала: 2016, Номер 40, С. 95 - 99

Опубликована: Июнь 28, 2016

Язык: Английский

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

Nature Microbiology, Год журнала: 2016, Номер 1(10)

Опубликована: Авг. 8, 2016

Abstract Intestinal bacteria influence mammalian physiology, but many types of are still uncharacterized. Moreover, reference strains mouse gut not easily available, although models extensively used in medical research. These major limitations for the investigation intestinal microbiomes and their interactions with diet host. It is thus important to study detail diversity functions microbiota members, including those colonizing intestine. To address these issues, we aimed at establishing Mouse Bacterial Collection (miBC), a public repository bacterial associated genomes from gut, studied host-specificity colonization sequence-based relevance resource. The collection includes several representing novel species, genera even one family. Genomic analyses showed that certain species specific intestine minimal consortium 18 covered 50–75% known functional potential metagenomes. present work will sustain future research on microbiota–host health disease, as it facilitate targeted molecular studies. resource available www.dsmz.de/miBC .

Язык: Английский

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A human gut bacterial genome and culture collection for improved metagenomic analyses

Nature Biotechnology, Год журнала: 2019, Номер 37(2), С. 186 - 192

Опубликована: Фев. 1, 2019

Understanding gut microbiome functions requires cultivated bacteria for experimental validation and reference bacterial genome sequences to interpret metagenome datasets guide functional analyses. We present the Human Gastrointestinal Bacteria Culture Collection (HBC), a comprehensive set of 737 whole-genome-sequenced isolates, representing 273 species (105 novel species) from 31 families found in human gastrointestinal microbiota. The HBC increases number genomes derived microbiota by 37%. resulting global Genome (HGG) classifies 83% genera abundance across 13,490 shotgun-sequenced metagenomic samples, improves taxonomic classification 61% compared Microbiome Project (HMP) collection achieves subspecies-level almost 50% sequences. improved resource circumvents dependence on de novo assembly metagenomes enables accurate cost-effective shotgun analyses A large strain will boost research.

Язык: Английский

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High taxonomic variability despite stable functional structure across microbial communities

Nature Ecology & Evolution, Год журнала: 2016, Номер 1(1)

Опубликована: Дек. 5, 2016

Язык: Английский

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