A standardized, extensible framework for optimizing classification improves marker-gene taxonomic assignments

Bokulich, Nicholas A.; Rideout, Jai Ram; Kopylova, Evguenia; Bolyen, Evan; Patnode, Jessica; Ellett, Zach; McDonald, Daniel; Wolfe, Benjamin E.; Maurice, Corinne F.; Dutton, Rachel J.; Turnbaugh, Peter; Knight, Rob; Caporaso, J. Gregory

doi:10.7287/peerj.preprints.934v1

Cited by 8 publications

(5 citation statements)

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“…The UPARSE algorithm was then employed to determine the operational taxonomic units (OTUs) using the trimmed sequences on the basis of their sequence similarity at 97% . Taxonomic assignments were determined using USEARCH with the centroid sequence from each cluster against the NCBI database. , …”

Section: Methodsmentioning

confidence: 99%

Wastewater-Enhanced Microbial Corrosion of Concrete Sewers

Jiang

Zhou

Chiu

et al. 2016

Environ. Sci. Technol.

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Microbial corrosion of concrete in sewers is known to be caused by hydrogen sulfide, although the role of wastewater in regulating the corrosion processes is poorly understood. Flooding and splashing of wastewater in sewers periodically inoculates the concrete surface in sewer pipes. No study has systematically investigated the impacts of wastewater inoculation on the corrosion of concrete in sewers. This study investigated the development of the microbial community, sulfide uptake activity, and the change of the concrete properties for coupons subjected to periodic wastewater inoculation. The concrete coupons were exposed to different levels of hydrogen sulfide under well-controlled conditions in laboratory-scale corrosion chambers simulating real sewers. It was evident that the periodic inoculation induced higher corrosion losses of the concrete in comparison to noninoculated coupons. Instantaneous measurements such as surface pH did not reflect the cumulative corrosion losses caused by long-term microbial activity. Analysis of the long-term profiles of the sulfide uptake rate using a Gompertz model supported the enhanced corrosion activity and greater corrosion loss. The enhanced corrosion rate was due to the higher sulfide uptake rates induced by wastewater inoculation, although the increasing trend of sulfide uptake rates was slower with wastewater. Increased diversity in the corrosion-layer microbial communities was detected when the corrosion rates were higher. This coincided with the environmental conditions of increased levels of gaseous H2S and the concrete type.

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Section: Methodsmentioning

confidence: 99%

Wastewater-Enhanced Microbial Corrosion of Concrete Sewers

Jiang

Zhou

Chiu

et al. 2016

Environ. Sci. Technol.

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“…Then the UPARSE algorithm [ 39 ] was used to cluster the obtained sequences into operational taxonomic units (OTUs). The centroid sequence from each cluster was run against a database of sequences from the NCBI using the USEARCH global alignment algorithm [ 40 ] to obtain taxonomic information. The raw sequencing data have been deposited in the NCBI Sequence Read Archive (SRA) as BioProjectPRJNA777436.…”

Section: Methodsmentioning

confidence: 99%

Effect of Biochar on Metal Distribution and Microbiome Dynamic of a Phytostabilized Metalloid-Contaminated Soil Following Freeze–Thaw Cycles

et al. 2022

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In the present paper the effectiveness of biochar-aided phytostabilization of metal/metalloid-contaminated soil under freezing–thawing conditions and using the metal tolerating test plant Lolium perenne L. is comprehensively studied. The vegetative experiment consisted of plants cultivated for over 52 days with no exposure to freezing–thawing in a glass greenhouse, followed by 64 days under freezing-–thawing in a temperature-controlled apparatus and was carried out in initial soil derived from a post-industrial urban area, characterized by the higher total content of Zn, Pb, Cu, Cr, As and Hg than the limit values included in the classification provided by the Regulation of the Polish Ministry of Environment. According to the substance priority list published by the Toxic Substances and Disease Registry Agency, As, Pb, and Hg are also indicated as being among the top three most hazardous substances. The initial soil was modified by biochar obtained from willow chips. The freeze–thaw effect on the total content of metals/metalloids (metal(-loid)s) in plant materials (roots and above-ground parts) and in phytostabilized soils (non- and biochar-amended) as well as on metal(-loid) concentration distribution/redistribution between four BCR (community bureau of reference) fractions extracted from phytostabilized soils was determined. Based on metal(-loid)s redistribution in phytostabilized soils, their stability was evaluated using the reduced partition index (Ir). Special attention was paid to investigating soil microbial composition. In both cases, before and after freezing–thawing, biochar increased plant biomass, soil pH value, and metal(-loid)s accumulation in roots, and decreased metal(-loid)s accumulation in stems and total content in the soil, respectively, as compared to the corresponding non-amended series (before and after freezing–thawing, respectively). In particular, in the phytostabilized biochar-amended series after freezing–thawing, the recorded total content of Zn, Cu, Pb, and As in roots substantially increased as well as the Hg, Cu, Cr, and Zn in the soil was significantly reduced as compared to the corresponding non-amended series after freezing–thawing. Moreover, exposure to freezing–thawing itself caused redistribution of examined metal(-loid)s from mobile and/or potentially mobile into the most stable fraction, but this transformation was favored by biochar presence, especially for Cu, Pb, Cr, and Hg. While freezing–thawing greatly affected soil microbiome composition, biochar reduced the freeze–thaw adverse effect on bacterial diversity and helped preserve bacterial groups important for efficient soil nutrient conversion. In biochar-amended soil exposed to freezing–thawing, psychrotolerant and trace element-resistant genera such as Rhodococcus sp. or Williamsia sp. were most abundant.

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“…We examine three mock datasets, Extreme ( Callahan et al , 2016 ), Even1 and Stag1 from Mock5 ( Bokulich et al , 2015 , 2016 ) and one real vaginal microbiome dataset ( MacIntyre et al , 2015 ) ( Table 1 ). Most denoisers are part of a complete analysis pipeline, including both pre- and post-processing steps.…”

Section: Methodsmentioning

confidence: 99%

AmpliCI: a high-resolution model-based approach for denoising Illumina amplicon data

Peng

Dorman

2020

Bioinformatics

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Motivation Next-generation amplicon sequencing is a powerful tool for investigating microbial communities. A main challenge is to distinguish true biological variants from errors caused by amplification and sequencing. In traditional analyses, such errors are eliminated by clustering reads within a sequence similarity threshold, usually 97%, and constructing operational taxonomic units, but the arbitrary threshold leads to low resolution and high false positive rates. Recently developed “denoising” methods have proven able to resolve single-nucleotide amplicon variants, but they still miss low frequency sequences, especially those near more frequent sequences, because they ignore the sequencing quality information. Results We introduce AmpliCI, a reference-free, model-based method for rapidly resolving the number, abundance and identity of error-free sequences in massive Illumina amplicon datasets. AmpliCI takes into account quality information and allows the data, not an arbitrary threshold or an external database, to drive conclusions. AmpliCI estimates a finite mixture model, using a greedy strategy to gradually select error-free sequences and approximately maximize the likelihood. AmpliCI has better performance than three popular denoising methods, with acceptable computation time and memory usage. Availability Source code is available at https://github.com/DormanLab/AmpliCI. Supplementary information Supplementary material are available at Bioinformatics online.

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A standardized, extensible framework for optimizing classification improves marker-gene taxonomic assignments

Abstract: 36Background: Taxonomic classification of marker-gene (i.e., amplicon) sequences 37

Cited by 8 publications

References 0 publications

Wastewater-Enhanced Microbial Corrosion of Concrete Sewers

Wastewater-Enhanced Microbial Corrosion of Concrete Sewers

Effect of Biochar on Metal Distribution and Microbiome Dynamic of a Phytostabilized Metalloid-Contaminated Soil Following Freeze–Thaw Cycles

AmpliCI: a high-resolution model-based approach for denoising Illumina amplicon data

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