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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Resistant starch can improve insulin sensitivity independently of the gut microbiota
Laure B. Bindels,Rafael R. Segura Munoz,João Carlos Gomes-Neto,Valentin Mutemberezi,Inés Martínez,Nuria Salazar,Elizabeth A. Cody,Maria I. Quintero-Villegas,Hatem Kittana,Clara G. de los Reyes-Gavilán,Robert Schmaltz,Giulio G. Muccioli,Jens Walter,Amanda E. Ramer-Tait +13 more
TL;DR: In this article, the role of the gut microbiota in mediating the metabolic benefits of resistant starches (RS) was examined in mice with and without a microbial community, and it was shown that some metabolic benefits exerted by dietary RS, especially improvements in insulin levels, occur independently of the microbiota and could involve alterations in the bile acid cycle and adipose tissue immune modulation.
Journal ArticleDOI
Advanced glycation end products dietary restriction effects on bacterial gut microbiota in peritoneal dialysis patients; a randomized open label controlled trial.
Rabi Yacoub,Melinda M. Nugent,Weijin Cai,Girish N. Nadkarni,Lee D. Chaves,Sham Abyad,Amanda M. Honan,Shruthi A. Thomas,Wei Zheng,Sujith A. Valiyaparambil,Mark A. Bryniarski,Yijun Sun,Michael J. Buck,Robert J. Genco,Richard J. Quigg,John Cijiang He,Jaime Uribarri +16 more
TL;DR: Significant microbiota differences in peritoneal dialysis patients’ population are shown, as well as the effects of dietary AGEs on gut microbiota, which might play a role in the increased cardiovascular events in this population and warrants further studies.
Journal ArticleDOI
Bacterial associations reveal spatial population dynamics in Anopheles gambiae mosquitoes.
Moritz Buck,Louise K. J. Nilsson,Carl Brunius,Roch K. Dabiré,Richard J. Hopkins,Richard J. Hopkins,Olle Terenius +6 more
TL;DR: Analysis of the whole-body bacterial flora of An.
Journal ArticleDOI
The Potential of Class II Bacteriocins to Modify Gut Microbiota to Improve Host Health
Özgün Candan Onarman Umu,Christine Bäuerl,Marije Oostindjer,Phillip B. Pope,Pablo E. Hernández,Gaspar Pérez-Martínez,Dzung B. Diep +6 more
TL;DR: Several bacteriocin-producing strains of LAB and their isogenic non-producing mutants have potential probiotic properties at diverse levels as they promote favorable changes in the host without major disturbance in gut microbiota, which is important for normal gut functioning.
References
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QIIME allows analysis of high-throughput community sequencing data.
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Search and clustering orders of magnitude faster than BLAST
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UCHIME improves sensitivity and speed of chimera detection
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Journal ArticleDOI
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Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB
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