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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Journal ArticleDOI
Estimating diversity via frequency ratios.
Amy D. Willis,John Bunge +1 more
TL;DR: In this paper, a nonlinear regression model for the ratios of consecutive frequency counts is proposed to estimate the total number of classes in a population based on sample counts, especially in the presence of high latent diversity.
Journal ArticleDOI
Inulin-type fructan improves diabetic phenotype and gut microbiota profiles in rats.
TL;DR: It is found that inulin treatment reduced fasting blood glucose levels and alleviated glucose intolerance and blood lipid panels in diabetic rats and can alleviate gut microbiota dysbiosis in T2D model rats.
Journal ArticleDOI
Differentiation strategies of soil rare and abundant microbial taxa in response to changing climatic regimes.
Yuting Liang,Xian Xiao,Erin E. Nuccio,Mengting Yuan,Na Zhang,Kai Xue,Kai Xue,Frederick M. Cohan,Jizhong Zhou,Jizhong Zhou,Bo Sun +10 more
TL;DR: The study indicates that the taxonomically and functionally diverse rare biosphere has the potential to increase functional redundancy and enhance the ability of soil communities to counteract environmental disturbances.
Journal ArticleDOI
Disentangling the mechanisms shaping the surface ocean microbiota
Ramiro Logares,Ramiro Logares,Ina M. Deutschmann,Pedro C. Junger,Caterina R. Giner,Caterina R. Giner,Anders K. Krabberød,Thomas Schmidt,Laura Rubinat-Ripoll,Mireia Mestre,Mireia Mestre,Mireia Mestre,Guillem Salazar,Guillem Salazar,Clara Ruiz-González,Marta Sebastián,Marta Sebastián,Colomban de Vargas,Silvia G. Acinas,Carlos M. Duarte,Josep M. Gasol,Josep M. Gasol,Ramon Massana +22 more
TL;DR: The differential action of ecological mechanisms seems to cause contrasting biogeography, in the tropical and subtropical ocean, among the smallest surface plankton, prokaryotes and picoeukaryotes, suggesting that the idiosyncrasy of the main constituents of the ocean microbiota should be considered in order to understand its current and future configuration.
Journal ArticleDOI
Population-level analysis of Blastocystis subtype prevalence and variation in the human gut microbiota.
Raul Y. Tito,Samuel Chaffron,Clara Caenepeel,Gipsi Lima-Mendez,Jun Wang,Sara Vieira-Silva,Gwen Falony,Falk Hildebrand,Youssef Darzi,Leen Rymenans,Chloë Verspecht,Peer Bork,Severine Vermeire,Marie Joossens,Jeroen Raes +14 more
TL;DR: It is shown its prevalence is reduced in patients with active IBD and demonstrated that subtype characterisation is essential for assessing the relationship between Blastocystis, microbiota profile and host health, which have direct clinical applications, especially in donor selection for faecal transplantation.
References
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QIIME allows analysis of high-throughput community sequencing data.
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