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 insulinsensitivity independently of the gutmicrobiota
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: It is demonstrated 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
Community dynamics of free-living and particle-attached bacteria following a reservoir Microcystis bloom
TL;DR: The analyses showed that PA bacterial communities were generally more diverse and appeared to be more responsive to routinely measured environmental variables than FL bacteria, suggesting that Microcystis blooms had a facilitative influence on specific bacteria by mediating the transitions from free-living to particle-attached lifestyles.
Journal ArticleDOI
Vertical distribution of microbial communities in soils contaminated by chromium and perfluoroalkyl substances.
TL;DR: Soil bacterial communities were mainly composed of Proteobacteria, Chloroflexi, Actinobacteria and Firmicutes, and archaeal communities were dominated by Thaumarchaeota and unclassified Archaea, and microbial abundance and richness increased with increasing perfluorohexane sulfonate (PFHxS) content.
Journal ArticleDOI
Stair-Step Pattern of Soil Bacterial Diversity Mainly Driven by pH and Vegetation Types Along the Elevational Gradients of Gongga Mountain, China.
TL;DR: The null model analysis suggested that environmental filtering played an overwhelming role in the assembly of bacterial communities in this region, and variation partition analysis indicated that, at lower elevations, environmental attributes explained much larger fraction of the β-deviation than spatial attributes, while spatial attributes increased their contributions at higher elevations.
Journal ArticleDOI
Insights into Feast-Famine polyhydroxyalkanoate (PHA)-producer selection: Microbial community succession, relationships with system function and underlying driving forces.
TL;DR: Deterministic processes dominated the entire FF system, resulting in the inevitable microbial community succession in the acclimation phase and maintenance of the stable PHA-accumulating function in the maturation phase, however, neutral processes also occurred, which led to the unpredictable temporal dynamics of the top competitors.
References
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