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
Direct comparison of culture-dependent and culture-independent molecular approaches reveal the diversity of fungal endophytic communities in stems of grapevine (Vitis vinifera)
Asha J. Dissanayake,Witoon Purahong,Tesfaye Wubet,Kevin D. Hyde,Wei Zhang,Haiying Xu,Guojun Zhang,Chunyuan Fu,Mei Liu,Xing Qikai,Xinghong Li,Jiye Yan +11 more
TL;DR: The importance of applying both culture-dependent and culture-independent approaches to study the fungal endophytic community composition in Vitis vinifera is marked, as the results related to stem are consistent for fungal community composition and richness.
Journal ArticleDOI
Epidermal lipid composition, barrier integrity, and eczematous inflammation are associated with skin microbiome configuration.
Hansjörg Baurecht,Malte C. Rühlemann,Elke Rodriguez,Frederieke Thielking,I. Harder,Anna-Sophie Erkens,Dora Stölzl,Eva Ellinghaus,Melanie Hotze,Wolfgang Lieb,Sheng Wang,Femke-Anouska Heinsen-Groth,Andre Franke,Stephan Weidinger +13 more
TL;DR: Epidermal barrier integrity and function affect the skin microbiome composition, which is most pronounced at sites of predilection and AD, and Eczematous affection appears to be a more important determinant than body site.
Journal ArticleDOI
Gut Microbiota Community and Its Assembly Associated with Age and Diet in Chinese Centenarians.
Fang Wang,Ting Yu,Guo Hong Huang,Da Cai,Xiaolin Liang,Hai Yan Su,Zhenjun Zhu,Danlei Li,Yang Yang,Pei Hong Shen,Rui Feng Mao,Lian Yu,Mou Ming Zhao,Quan Yang Li +13 more
TL;DR: The age and high-fiber diet were concomitant with changes in the gut microbiota of centenarians, suggesting that age and High Fiber Diet can establish a new structurally balanced architecture of gut microbiota that may benefit the health of 100enarians.
Journal ArticleDOI
Altered gut microbiota and mucosal immunity in patients with schizophrenia.
Ruihuan Xu,Bingbing Wu,Jingwen Liang,Fusheng He,Wen Gu,Kang Li,Yi Luo,Jianxia Chen,Yongbo Gao,Ze Wu,Yongqiang Wang,Wenhao Zhou,Mingbang Wang +12 more
TL;DR: Glutamate synthase was more active in the guts of patients with schizophrenia than in those of healthy controls, and high GOGAT activity was associated with altered gut microbiota taxonomies associated with gut IgA levels, which may imply a role of the microbiome in the etiology of schizophrenia and contribute to the development of microbiome targeted interventions for schizophrenia.
Journal ArticleDOI
Composition, diversity and function of intestinal microbiota in pacific white shrimp (Litopenaeus vannamei) at different culture stages
TL;DR: Investigation of the intestinal microbiota at different culture stages of pacific white shrimp indicated that shrimp intestinal microbiota depended on culture stages, providing new evidence on intestinal microorganism microecology and greatly enhanced the understanding of stage-specific community in the shrimp intestinal ecosystem.
References
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QIIME allows analysis of high-throughput community sequencing data.
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QIIME allows analysis of high-throughput community sequencing data.
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