PyNAST: A flexible tool for aligning sequences to a template alignment
ABSTRACT The Nearest Alignment Space Termination (NAST) tool is commonly used in sequence-based microbial ecology community analysis, but due to the limited portability of the original implementation, it has not been as widely adopted as possible. Python Nearest Alignment Space Termination (PyNAST) is a complete reimplementation of NAST, which includes three convenient interfaces: a Mac OS X GUI, a command-line interface and a simple application programming interface (API).
The availability of PyNAST will make the popular NAST algorithm more portable and thereby applicable to datasets orders of magnitude larger by allowing users to install PyNAST on their own hardware. Additionally because users can align to arbitrary template alignments, a feature not available via the original NAST web interface, the NAST algorithm will be readily applicable to novel tasks outside of microbial community analysis.
PyNAST is available at http://pynast.sourceforge.net.
Full-textDOI: · Available from: Todd Z DeSantis, Sep 26, 2015
- SourceAvailable from: Wenjie Ren
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- "(http://qiime.sourceforge.net). The analysis process was as follows: (1) removal of low-quality or ambiguous sequencing reads (reads with lengths <150 bp, >0 ambiguous bases, >6 homopolymers, primer mismatches, or average quality scores <25); (2) assignment of the multiplexed reads to samples through examination of the 12-bp barcode; (3) removal of all putative chimeras, which can be detected by the Usearch tool using a chimera-free reference database according to the Uchime algorithm ; (4) assignment of similar sequences to operational taxonomic units (OTUs) via the clustering method at a 97% sequence similarity level ; (5) alignment of a representative sequence from each OTU with Python Nearest Alignment Space Termination (PyNAST)  "
ABSTRACT: The increased application of graphene raises concerns about its environmental impact, but little information is available on the effect of graphene on the soil microbial community. This study evaluated the impact of graphene on the structure, abundance and function of the soil bacterial community based on quantitative real-time polymerase chain reaction (qPCR), pyrosequencing and soil enzyme activities. The results show that the enzyme activities of dehydrogenase and fluorescein diacetate (FDA) esterase and the biomass of the bacterial populations were transiently promoted by the presence of graphene after 4 days of exposure, but these parameters recovered completely after 21 days. Pyrosequencing analysis suggested a significant shift in some bacterial populations after 4 days, and the shift became weaker or disappeared as the exposure time increased to 60 days. During the entire exposure process, the majority of bacterial phylotypes remained unaffected. Some bacterial populations involved in nitrogen biogeochemical cycles and the degradation of organic compounds can be affected by the presence of graphene. Copyright © 2015 Elsevier B.V. All rights reserved.Journal of hazardous materials 10/2015; 297. DOI:10.1016/j.jhazmat.2015.05.017 · 4.53 Impact Factor
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- "Operational Taxonomic Units (OTUs) were picked with 97% sequence similarity using uclust (Edgar, 2010). Most abundant sequences found in each OTU were picked as representative sequences and aligned against Greengenes core set (DeSantis et al., 2006) using PyNAST (Caporaso, Bittinger et al., 2010) with a minimum sequence identity of 75% and a minimum sequence length of 300 nt. Taxonomy was assigned to the representative sequences using Ribosomal Database Project (RDP) Classifier with minimum confidence score of 0.8 (Cole et al., 2007). "
ABSTRACT: Two probiotic products containing either live Lactobacillus plantarum strain DSM 15313 or bilberries fermented by the same bacterial strain were tested for their antihypertensive potentials and their impact on the oral and the faecal microbiota in hypertensive adults. The results showed that consumption of the tested products for three months did not reduce the blood pressure in adults with hypertension. Neither the diversity nor the composition of the oral and faecal microbiota was significantly affected by the tested probiotic products. Moreover, the oral and the faecal microbiota remained generally stable over the intervention period of 3 months. Keywords: Microbiota; Blood pressure; Lactobacillus plantarum DSM 15313; BilberryJournal of Functional Foods 10/2015; 18(Part A):275-288. DOI:10.1016/j.jff.2015.07.005. · 3.57 Impact Factor
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- "Filtered alignments were used to generate an uncorrected pairwise distance matrix, followed by binning the sequences into operational taxonomic units (OTUs) at 3, 6, 8, 10, and 15% cutoffs. For phylogenetic placement, representative OTUs defined at the 3% cutoff (OTU 0.03 ) were classified with Greengenes taxonomy scheme using the PyNAST pipeline (Caporaso et al., 2010). Phylum level affiliation of sequences were determined according to the classifier output, and sequences with less than 85% similarity to their closest relative in Greengenes database were considered unclassified. "
ABSTRACT: Within highly diverse ecosystems, the majority of bacterial taxa are present in low abundance as members of the rare biosphere. The rationale for the occurrence and maintenance of the rare biosphere, and the putative ecological role(s) and dynamics of its members within a specific ecosystem is currently debated. We hypothesized that in highly diverse ecosystems, a fraction of the rare biosphere acts as a backup system that readily responds to environmental disturbances. We tested this hypothesis by subjecting sediments from Zodletone spring, a sulfide- and sulfur-rich spring in Southwestern OK, to incremental levels of salinity (1, 2, 3, 4, and 10% NaCl), or temperature (28°, 30°, 32°, and 70 °C), and traced the trajectories of rare members of the community in response to these manipulations using 16S rRNA gene analysis. Our results indicate that multiple rare bacterial taxa are promoted from rare to abundant members of the community following such manipulations and that, in general, the magnitude of such recruitment is directly proportional to the severity of the applied manipulation. Rare members that are phylogenetically distinct from abundant taxa in the original sample (unique rare biosphere) played a more important role in the microbial community response to environmental disturbances, compared to rare members that are phylogenetically similar to abundant taxa in the original sample (non-unique rare biosphere). The results emphasize the dynamic nature of the rare biosphere, and highlight its complexity and non-monolithic nature.PeerJ 08/2015; 3:e1182. DOI:10.7717/peerj.1182 · 2.11 Impact Factor