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
Biogeographic patterns of soil diazotrophic communities across six forests in the North America
Qichao Tu,Qichao Tu,Ye Deng,Qingyun Yan,Lina Shen,Lu Lin,Zhili He,Liyou Wu,Joy D. Van Nostrand,Vanessa Buzzard,Sean T. Michaletz,Sean T. Michaletz,Brian J. Enquist,Brian J. Enquist,Michael D. Weiser,Michael Kaspari,Michael Kaspari,Robert B. Waide,James H. Brown,Jizhong Zhou,Jizhong Zhou,Jizhong Zhou +21 more
TL;DR: The results showed that each forest harboured markedly different soil diazotrophic communities and that these communities followed traditional biogeographic patterns similar to plant and animal communities, including the taxa–area relationship (TAR) and latitudinal diversity gradient.
Journal ArticleDOI
Non-cyanobacterial diazotrophs mediate dinitrogen fixation in biological soil crusts during early crust formation.
Charles Pepe-Ranney,Chantal Koechli,Ruth M. Potrafka,Cheryl P. Andam,Erin M. Eggleston,Ferran Garcia-Pichel,Daniel H. Buckley +6 more
TL;DR: DNA stable isotope probing with15N2 revealed that Clostridiaceae and Proteobacteria are the most common microorganisms that assimilate 15N2 in early successional crusts and this suggests that microorganisms other than cyanobacteria mediate N2-fixation during the critical early stages of BSC development.
Journal ArticleDOI
Effects of brewer's yeast hydrolysate on the growth performance and the intestinal bacterial diversity of largemouth bass (Micropterus salmoides)
Meng Zhou,Risheng Liang,Jinfeng Mo,Sen Yang,Na Gu,Zaohe Wu,V. Sarath Babu,Jun Li,Yunmao Huang,Li Lin +9 more
TL;DR: The overall intestinal bacterial diversity was decreased in fish fed with BYH which might promote the growth of some probiotics and inhibit some pathogenic bacteria, suggesting that BYH may serve as feed additive in modulation of the gut bacterial community of largemouth bass to decrease the potential pathogens.
Journal ArticleDOI
Alterations of the Human Gut Microbiome in Chronic Kidney Disease.
Zhigang Ren,Yajuan Fan,Ang Li,Quanquan Shen,Jian Wu,Lingyan Ren,Haifeng Lu,Suying Ding,Hongyan Ren,Chao Liu,Wenli Liu,Dan Gao,Zhongwen Wu,Shiyuan Guo,Ge Wu,Zhangsuo Liu,Zujiang Yu,Lanjuan Li +17 more
TL;DR: This study comprehensively characterizes gut microbiome in non‐dialysis CKD and demonstrates the potential of microbial markers as non‐invasive diagnostic tools for CKD in different regions of China.
Journal ArticleDOI
Fertilizer N application rate impacts plant-soil feedback in a sanqi production system
Wei Wei,Min Yang,Liu Yixiang,Huichuan Huang,Chen Ye,Zheng Jianfen,Cunwu Guo,Minwen Hao,Xiahong He,Shusheng Zhu +9 more
TL;DR: Over-application of nitrogen is not beneficial for disease management or the reduction of fungicide application in agricultural production, and it is suggested that over-application in the form of a high rate of N at 450kgNha-1 (450N) aggravated the NPSF.
References
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QIIME allows analysis of high-throughput community sequencing data.
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Journal ArticleDOI
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QIIME allows analysis of high-throughput community sequencing data.
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