BLAST-based validation of metagenomic sequence assignments

Bazinet, Adam L.; Ondov, Brian D.; Sommer, Daniel; Ratnayake, Shashikala

doi:10.7717/peerj.4892

Cited by 19 publications

(14 citation statements)

References 38 publications

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“…Therefore, there is a trade-off between sensitivity, accuracy, performance, speed, and computational requirements. Although these types of programs are useful in performing “first-pass” taxonomic analyses it is crucial that their assignments are validated using BLAST-based procedures [ 83 ]. The absolute majority of the transcripts were of plant origin, most hitting legume sequences as identified by DIAMOND-NCBI(NR) analysis.…”

Section: Discussionmentioning

confidence: 99%

Transcriptomics of the Rooibos (Aspalathus linearis) Species Complex

Stander

Williams

Mgwatyu

et al. 2020

BioTech

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Rooibos (Aspalathus linearis), widely known as a herbal tea, is endemic to the Cape Floristic Region of South Africa (SA). It produces a wide range of phenolic compounds that have been associated with diverse health promoting properties of the plant. The species comprises several growth forms that differ in their morphology and biochemical composition, only one of which is cultivated and used commercially. Here, we established methodologies for non-invasive transcriptome research of wild-growing South African plant species, including (1) harvesting and transport of plant material suitable for RNA sequencing; (2) inexpensive, high-throughput biochemical sample screening; (3) extraction of high-quality RNA from recalcitrant, polysaccharide- and polyphenol rich plant material; and (4) biocomputational analysis of Illumina sequencing data, together with the evaluation of programs for transcriptome assembly (Trinity, IDBA-Trans, SOAPdenovo-Trans, CLC), protein prediction, as well as functional and taxonomic transcript annotation. In the process, we established a biochemically characterized sample pool from 44 distinct rooibos ecotypes (1–5 harvests) and generated four in-depth annotated transcriptomes (each comprising on average ≈86,000 transcripts) from rooibos plants that represent distinct growth forms and differ in their biochemical profiles. These resources will serve future rooibos research and plant breeding endeavours.

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Section: Discussionmentioning

confidence: 99%

Transcriptomics of the Rooibos (Aspalathus linearis) Species Complex

Stander

Williams

Mgwatyu

et al. 2020

BioTech

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“…Remaining reads were mapped on viral RefSeq database (downloaded in March 2015) to determine the relative abundance of anelloviruses within the plasma virome. As recommended, a BLAST-based validation of metagenomic sequence assignments was performed for anelloviruses [ 11 ]. Thus, nonhuman NGS reads were aligned using BLAST on a manually curated database composed of the 56 reference sequences of human anelloviruse species as established by the International Committee on Taxonomy of Viruses (ICTV, TTV-1 to TTV-29, TTMV-1 to TTMV-12, TTMDV-1 and TTMDV-15).…”

Section: Methodsmentioning

confidence: 99%

Metagenomic Next-Generation Sequencing Reveals Individual Composition and Dynamics of Anelloviruses during Autologous Stem Cell Transplant Recipient Management

Bal

Sarkozy

Josset

et al. 2018

Viruses

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Over recent years, there has been increasing interest in the use of the anelloviruses, the major component of the human virome, for the prediction of post-transplant complications such as severe infections. Due to an important diversity, the comprehensive characterization of this viral family over time has been poorly studied. To overcome this challenge, we used a metagenomic next-generation sequencing (mNGS) approach with the aim of determining the individual anellovirus profile of autologous stem cell transplant (ASCT) patients. We conducted a prospective pilot study on a homogeneous patient cohort regarding the chemotherapy regimens that included 10 ASCT recipients. A validated viral mNGS workflow was used on 108 plasma samples collected at 11 time points from diagnosis to 90 days post-transplantation. A complex interindividual variability in terms of abundance and composition was noticed. In particular, a strong sex effect was found and confirmed using quantitative PCR targeting torque teno virus, the most abundant anellovirus. Interestingly, an important turnover in the anellovirus composition was observed during the course of the disease revealing a strong intra-individual variability. Although more studies are needed to better understand anellovirus dynamics, these findings are of prime importance for their future use as biomarkers of immune competence.

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“…Seventy-five percent of ASV yielded firstpass satisfactory taxonomic assignment with > 95% homology with their first-hit assigned sequence. The remaining 25% of ASV were blasted again against the next hit proposed by Kraken2 until a higher homology score was reached in a method inspired by [94]. After these iterative steps, we assigned up to 85% of all ASV with a homology score above 95%.…”

Section: Richness and Diversitymentioning

confidence: 99%

The microbial metabolite p-Cresol induces autistic-like behaviors in mice by remodeling the gut microbiota

et al. 2021

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Background Autism spectrum disorders (ASD) are associated with dysregulation of the microbiota-gut-brain axis, changes in microbiota composition as well as in the fecal, serum, and urine levels of microbial metabolites. Yet a causal relationship between dysregulation of the microbiota-gut-brain axis and ASD remains to be demonstrated. Here, we hypothesized that the microbial metabolite p-Cresol, which is more abundant in ASD patients compared to neurotypical individuals, could induce ASD-like behavior in mice. Results Mice exposed to p-Cresol for 4 weeks in drinking water presented social behavior deficits, stereotypies, and perseverative behaviors, but no changes in anxiety, locomotion, or cognition. Abnormal social behavior induced by p-Cresol was associated with decreased activity of central dopamine neurons involved in the social reward circuit. Further, p-Cresol induced changes in microbiota composition and social behavior deficits could be transferred from p-Cresol-treated mice to control mice by fecal microbiota transplantation (FMT). We also showed that mice transplanted with the microbiota of p-Cresol-treated mice exhibited increased fecal p-Cresol excretion, compared to mice transplanted with the microbiota of control mice. In addition, we identified possible p-Cresol bacterial producers. Lastly, the microbiota of control mice rescued social interactions, dopamine neurons excitability, and fecal p-Cresol levels when transplanted to p-Cresol-treated mice. Conclusions The microbial metabolite p-Cresol induces selectively ASD core behavioral symptoms in mice. Social behavior deficits induced by p-Cresol are dependant on changes in microbiota composition. Our study paves the way for therapeutic interventions targeting the microbiota and p-Cresol production to treat patients with ASD.

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BLAST-based validation of metagenomic sequence assignments

Cited by 19 publications

References 38 publications

Transcriptomics of the Rooibos (Aspalathus linearis) Species Complex

Transcriptomics of the Rooibos (Aspalathus linearis) Species Complex

Metagenomic Next-Generation Sequencing Reveals Individual Composition and Dynamics of Anelloviruses during Autologous Stem Cell Transplant Recipient Management

The microbial metabolite p-Cresol induces autistic-like behaviors in mice by remodeling the gut microbiota

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