High-resolution microbial community reconstruction by integrating short reads from multiple 16S rRNA regions
Amnon Amir,Amit Zeisel,Or Zuk,Michael Elgart,Shay Stern,Ohad Shamir,Peter J. Turnbaugh,Yoav Soen,Noam Shental +8 more
TLDR
In this article, a generic approach for integrating short reads from large genomic regions, thus enabling phylogenetic resolution far exceeding current methods, is presented, based on a mapping to a statistical model that is later solved as a constrained optimization problem.Abstract:
The emergence of massively parallel sequencing technology has revolutionized microbial profiling, allowing the unprecedented comparison of microbial diversity across time and space in a wide range of host-associated and environmental ecosystems. Although the high-throughput nature of such methods enables the detection of lowfrequency bacteria, these advances come at the cost of sequencing read length, limiting the phylogenetic resolution possible by current methods. Here, we present a generic approach for integrating short reads from large genomic regions, thus enabling phylogenetic resolution far exceeding current methods. The approach is based on a mapping to a statistical model that is later solved as a constrained optimization problem. We demonstrate the utility of this method by analyzing human saliva and Drosophila samples, using Illumina single-end sequencing of a 750bp amplicon of the 16S rRNA gene. Phylogenetic resolution is significantly extended while reducing the number of falsely detected bacteria, as compared with standard single-region Roche 454 Pyrosequencing. Our approach can be seamlessly applied to simultaneous sequencing of multiple genes providing a higher resolution view of the composition and activity of complex microbial communities.read more
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Journal ArticleDOI
Analyses of Intestinal Microbiota: Culture versus Sequencing.
TL;DR: In this review, differences and pitfalls in current experimental protocols are summarized, including all steps from nucleic acid extraction to bioinformatical analysis which may produce variation that outweighs subtle biological differences.
Journal ArticleDOI
Combining 16S rRNA gene variable regions enables high-resolution microbial community profiling.
TL;DR: Short MUltiple Regions Framework (SMURF), a method to combine sequencing results from different PCR-amplified regions to provide one coherent profiling approach that enables the identification of near full-length 16S rRNA gene sequences in microbial communities, having resolution superior compared to current techniques.
Journal ArticleDOI
Microbial community and fermentation characteristic of Italian ryegrass silage prepared with corn stover and lactic acid bacteria
Yanhong Yan,Li Xiaomei,Hao Guan,Linkai Huang,Xiao Ma,Yan Peng,Zhou Li,Gang Nie,Ji-Qiong Zhou,Wenyu Yang,Yimin Cai,Xinquan Zhang +11 more
TL;DR: It is demonstrated that addition of CS and LAB can change the microbial community and influence the silage fermentation of IR, and PacBio SMRT reveals more specific microbial information.
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Assessment of bacterial profiles in aged, home-made Sichuan paocai brine with varying titratable acidity by PacBio SMRT sequencing technology
Jialu Cao,Jixia Yang,Jixia Yang,Qiangchuan Hou,Haiyan Xu,Yi Zheng,Heping Zhang,Liebing Zhang +7 more
TL;DR: The results presented here report the comprehensive bacterial profiles of home-made Sichuan paocai for the first time via SMRT sequencing technology and the correlation between TA and bacterial compositions.
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Evaluation of bacterial contamination in raw milk, ultra-high temperature milk and infant formula using single molecule, real-time sequencing technology.
Qiangchuan Hou,Haiyan Xu,Yi Zheng,Xiaoxia Xi,Lai-Yu Kwok,Zhihong Sun,Heping Zhang,Wenyi Zhang +7 more
TL;DR: The data have demonstrated for the first time the feasibility of using the SMRT sequencing platform in detecting bacterial contamination in dairy samples and provide interesting reference information for future development of new precautionary strategies for controlling the dairy safety in large-scale industrialized production lines.
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Journal ArticleDOI
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TL;DR: The Human Microbiome Project Consortium reported the first results of their analysis of microbial communities from distinct, clinically relevant body habitats in a human cohort; the insights into the microbial communities of a healthy population lay foundations for future exploration of the epidemiology, ecology and translational applications of the human microbiome as discussed by the authors.
Journal ArticleDOI
Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample
J. Gregory Caporaso,Christian L. Lauber,William A. Walters,Donna Berg-Lyons,Catherine A. Lozupone,Peter J. Turnbaugh,Noah Fierer,Rob Knight +7 more
TL;DR: This work sequences a diverse array of 25 environmental samples and three known “mock communities” at a depth averaging 3.1 million reads per sample to demonstrate excellent consistency in taxonomic recovery and recapture diversity patterns that were previously reported on the basis of metaanalysis of many studies from the literature.
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