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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Soil microbial communities in cucumber monoculture and rotation systems and their feedback effects on cucumber seedling growth
Xingang Zhou,Jie Liu,Fengzhi Wu +2 more
TL;DR: Increasing temporal plant diversity can change soil microbial communities and enhance crop productivity through positive plant-soil feedbacks mediated by soil biota.
Journal ArticleDOI
Soil pH determines the alpha diversity but not beta diversity of soil fungal community along altitude in a typical Tibetan forest ecosystem
TL;DR: In this article, high-throughput barcoded pyrosequencing and quantitative PCR approaches were employed to measure the community composition, diversity, and abundance patterns of soil fungal 18S ribosomal RNA (rRNA) gene in 20 samples collected along the altitudinal gradient of Mt. Shegyla.
Journal ArticleDOI
Exogenous addition of H2 for an in situ biogas upgrading through biological reduction of carbon dioxide into methane
Daniel Girma Mulat,Freya Mosbæk,Alastair James Ward,Daniela Polag,Markus Greule,Frank Keppler,Jeppe Lund Nielsen,Anders Feilberg +7 more
TL;DR: This inhibition mechanism underlines the importance of carefully regulating the H2 addition rate and gas retention time to the CO2 production rate, H2-uptake rate and growth of hydrogenotrophic methanogens in order to achieve higher CH4 content without the accumulation of acetate and other VFA.
Journal ArticleDOI
Altered Gut Microbiota in Chinese Children With Autism Spectrum Disorders.
TL;DR: Wang et al. as mentioned in this paper found that children with ASD had a lower relative abundance of Acidaminococcaceae than the healthy controls, and a decrease in the relative abundances of genera Lachnoclostridium, Tyzzerella subgroup 4, Flavonifractor, and unidentified Lchnospiraceae.
Journal ArticleDOI
Geographical Patterns of nirS Gene Abundance and nirS-Type Denitrifying Bacterial Community Associated with Activated Sludge from Different Wastewater Treatment Plants.
Haihan Zhang,Ji Feng,Shengnan Chen,Zhenfang Zhao,Baoqin Li,Yue Wang,Jingyu Jia,Sulin Li,Yan Wang,Miaomiao Yan,Kuanyu Lu,Huiyan Hao +11 more
TL;DR: In this paper, quantitative PCR and next-generation sequencing of the nirS gene were applied to characterize the abundance and denitrifying bacterial communities from 18 geographically distributed WWTPs.
References
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QIIME allows analysis of high-throughput community sequencing data.
J. Gregory Caporaso,Justin Kuczynski,Jesse Stombaugh,Kyle Bittinger,Frederic D. Bushman,Elizabeth K. Costello,Noah Fierer,Antonio Gonzalez Peña,Julia K. Goodrich,Jeffrey I. Gordon,Gavin A. Huttley,Scott T. Kelley,Dan Knights,Jeremy E. Koenig,Ruth E. Ley,Catherine A. Lozupone,Daniel McDonald,Brian D. Muegge,Meg Pirrung,Jens Reeder,Joel Sevinsky,Peter J. Turnbaugh,William A. Walters,Jeremy Widmann,Tanya Yatsunenko,Jesse R. Zaneveld,Rob Knight,Rob Knight +27 more
TL;DR: An overview of the analysis pipeline and links to raw data and processed output from the runs with and without denoising are provided.
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Search and clustering orders of magnitude faster than BLAST
TL;DR: UCLUST is a new clustering method that exploits USEARCH to assign sequences to clusters and offers several advantages over the widely used program CD-HIT, including higher speed, lower memory use, improved sensitivity, clustering at lower identities and classification of much larger datasets.
Journal ArticleDOI
UCHIME improves sensitivity and speed of chimera detection
TL;DR: UCHIME has better sensitivity than ChimeraSlayer (previously the most sensitive database method), especially with short, noisy sequences, and in testing on artificial bacterial communities with known composition, UCHIME de novo sensitivity is shown to be comparable to Perseus.
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Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB
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