Journal ArticleDOI
Accurate and universal delineation of prokaryotic species
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TLDR
The specI (species identification tool) as mentioned in this paper ) is a method to group organisms into species clusters based on 40 universal, single-copy phylogenetic marker genes, applied to 3,496 prokaryotic genomes, specI identified 1,753 species clusters.Abstract:
The exponentially increasing number of sequenced genomes necessitates fast, accurate, universally applicable and automated approaches for the delineation of prokaryotic species. We developed specI (species identification tool; http://www.bork.embl.de/software/specI/), a method to group organisms into species clusters based on 40 universal, single-copy phylogenetic marker genes. Applied to 3,496 prokaryotic genomes, specI identified 1,753 species clusters. Of 314 discrepancies with a widely used taxonomic classification, >62% were resolved by literature support.read more
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1,520 reference genomes from cultivated human gut bacteria enable functional microbiome analyses.
Yuanqiang Zou,Wenbin Xue,Guangwen Luo,Ziqing Deng,Panpan Qin,Ruijin Guo,Haipeng Sun,Yan Xia,Suisha Liang,Ying Dai,Daiwei Wan,Rongrong Jiang,Lili Su,Qiang Feng,Zhuye Jie,Tongkun Guo,Zhongkui Xia,Liu Chuan,Yu Jinghong,Yuxiang Lin,Shanmei Tang,Guicheng Huo,Xun Xu,Yong Hou,Xin Liu,Jian Wang,Huanming Yang,Karsten Kristiansen,Junhua Li,Huijue Jia,Liang Xiao +30 more
TL;DR: A collection of 1,520 nonredundant, high-quality draft genomes generated from >6,000 bacteria cultivated from fecal samples of healthy humans, chosen to cover all major bacterial phyla and genera in the human gut.
Journal ArticleDOI
Metagenome-wide association studies: fine-mining the microbiome
Jun Wang,Huijue Jia +1 more
TL;DR: The need to better characterize the biology of many of the bacteria that are found in the human microbiota as an essential step in understanding how bacterial strains that have been identified by MWAS are associated with disease is highlighted.
Journal ArticleDOI
Dietary Modulation of Gut Microbiota Contributes to Alleviation of Both Genetic and Simple Obesity in Children
Chenhong Zhang,Aihua Yin,Hongde Li,R.Z. Wang,Guojun Wu,Jian Shen,Menghui Zhang,Linghua Wang,Yaping Hou,Haimei Ouyang,Yan Zhang,Yi-Nan Zheng,Jicheng Wang,Xiaofei Lv,Yulan Wang,Feng Zhang,Benhua Zeng,Wenxia Li,Feiyan Yan,Yufeng Zhao,Xiaoyan Pang,Xiaojun Zhang,Huaqing Fu,Feng Chen,Naisi Zhao,Bruce R. Hamaker,Bruce R. Hamaker,Laura C. Bridgewater,Laura C. Bridgewater,David Weinkove,Karine Clément,Joël Doré,Elaine Holmes,Huasheng Xiao,Guoping Zhao,Shengli Yang,Peer Bork,Jeremy K. Nicholson,Hong Wei,Huiru Tang,Xiaozhuang Zhang,Liping Zhao +41 more
TL;DR: It is found that children genetically obese with Prader–Willi syndrome shared a similar dysbiosis in their gut microbiota with those having diet-related obesity, which contributes to the alleviation of metabolic deteriorations in obesity regardless of the primary driving forces.
Journal ArticleDOI
Microbial abundance, activity and population genomic profiling with mOTUs2
Alessio Milanese,Daniel R. Mende,Lucas Paoli,Guillem Salazar,Hans-Joachim Ruscheweyh,Miguelangel Cuenca,Pascal Hingamp,Renato J. Alves,Paul I. Costea,Luis Pedro Coelho,Thomas Schmidt,Alexandre Almeida,Alex L. Mitchell,Robert D. Finn,Jaime Huerta-Cepas,Peer Bork,Georg Zeller,Shinichi Sunagawa +17 more
TL;DR: mOTUs2, an updated and functionally extended profiling tool for microbial abundance, activity and population profiling, shows that mOTUs, which are based on essential housekeeping genes, are demonstrably well-suited for quantification of basal transcriptional activity of community members.
Journal ArticleDOI
Microbiome, Metagenomics, and High-Dimensional Compositional Data Analysis
TL;DR: Important issues include normalization and quantification of relative taxa, bacterial genes, and metabolic abundances; incorporation of phylogenetic information into analysis of metagenomics data; and multivariate analysis of high-dimensional compositional data.
References
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