Journal ArticleDOI
UPARSE: highly accurate OTU sequences from microbial amplicon reads
TLDR
The UPARSE pipeline reports operational taxonomic unit (OTU) sequences with ≤1% incorrect bases in artificial microbial community tests, compared with >3% correct bases commonly reported by other methods.Abstract:
Amplified marker-gene sequences can be used to understand microbial community structure, but they suffer from a high level of sequencing and amplification artifacts. The UPARSE pipeline reports operational taxonomic unit (OTU) sequences with ≤1% incorrect bases in artificial microbial community tests, compared with >3% incorrect bases commonly reported by other methods. The improved accuracy results in far fewer OTUs, consistently closer to the expected number of species in a community.read more
Citations
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Lactobacillus reuteri induces gut intraepithelial CD4+CD8αα+ T cells.
Luisa Cervantes-Barragan,Jiani N. Chai,Ma. Diarey B. Tianero,Blanda Di Luccia,Philip P. Ahern,Joseph A. Merriman,Victor S. Cortez,Michael G. Caparon,Mohamed S. Donia,Susan Gilfillan,Marina Cella,Jeffrey I. Gordon,Chyi-Song Hsieh,Marco Colonna +13 more
TL;DR: It is found that DP IEL numbers in mice varied in different vivaria, correlating with the presence of Lactobacillus reuteri, a particular species of probiotic bacteria that can reprogram intraepithelial CD4+ T cells into immunoregulatory T cells.
Journal ArticleDOI
Sequence depth, not PCR replication, improves ecological inference from next generation DNA sequencing.
Dylan P. Smith,Kabir G. Peay +1 more
TL;DR: The results suggest that molecular ecology studies will benefit more from investing in robust sequencing technologies than from replicating PCRs, and the potential for continuous integration of older datasets with newer technology is demonstrated.
Journal ArticleDOI
Identification of an Intestinal Microbiota Signature Associated With Severity of Irritable Bowel Syndrome
Julien Tap,Muriel Derrien,Hans Törnblom,Rémi Brazeilles,Stéphanie Cools-Portier,Joël Doré,Stine Störsrud,Boris Le Nevé,Lena Öhman,Lena Öhman,Magnus Simren,Magnus Simren +11 more
TL;DR: IBS symptom severity is found to be associated negatively with microbial richness, exhaled CH4, presence of methanogens, and enterotypes enriched with Clostridiales or Prevotella species.
Journal ArticleDOI
Updating the 97% identity threshold for 16S ribosomal RNA OTUs.
TL;DR: Using a large set of high‐quality 16S rRNA sequences from finished genomes, the correspondence of OTUs to species is assessed for five representative clustering algorithms using four accuracy metrics and all algorithms had comparable accuracy when tuned to a given metric.
Journal ArticleDOI
Durable coexistence of donor and recipient strains after fecal microbiota transplantation.
Simone S. Li,Ana Zhu,Vladimir Benes,Paul I. Costea,Rajna Hercog,Falk Hildebrand,Jaime Huerta-Cepas,Max Nieuwdorp,Max Nieuwdorp,Jarkko Salojärvi,Anita Y. Voigt,Georg Zeller,Shinichi Sunagawa,Willem M. de Vos,Willem M. de Vos,Peer Bork +15 more
TL;DR: The authors found extensive coexistence of donor and recipient strains, persisting 3 months after treatment, and same-donor recipients displayed varying degrees of microbiota transfer, indicating individual patterns of microbiome resistance and donor-recipient compatibilities.
References
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