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      Metagenomic Survey of Tomato Rhizosphere Microbiome Using the Shotgun Approach

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      Author(s): a , , a , a
      Editor(s):
      Publication date (Electronic, pub):
      Publication date (Electronic, collection):
      Journal: Microbiology Resource Announcements
      Publisher: American Society for Microbiology

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          ABSTRACT

          Food sustainability, e.g., fruit and vegetables, is a major agricultural problem that requires monitoring. Rhizosphere microbiomes’ abundance and functionality are essential in promoting tomato plants’ growth and health. We selected farms in South Africa’s North West Province and present the metagenomes of their tomato rhizospheres and associated functional potentials.

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          The metagenomics RAST server – a public resource for the automatic phylogenetic and functional analysis of metagenomes

          Georg Meyer, D Paarmann, M J D'Souza … (2008)
          Background Random community genomes (metagenomes) are now commonly used to study microbes in different environments. Over the past few years, the major challenge associated with metagenomics shifted from generating to analyzing sequences. High-throughput, low-cost next-generation sequencing has provided access to metagenomics to a wide range of researchers. Results A high-throughput pipeline has been constructed to provide high-performance computing to all researchers interested in using metagenomics. The pipeline produces automated functional assignments of sequences in the metagenome by comparing both protein and nucleotide databases. Phylogenetic and functional summaries of the metagenomes are generated, and tools for comparative metagenomics are incorporated into the standard views. User access is controlled to ensure data privacy, but the collaborative environment underpinning the service provides a framework for sharing datasets between multiple users. In the metagenomics RAST, all users retain full control of their data, and everything is available for download in a variety of formats. Conclusion The open-source metagenomics RAST service provides a new paradigm for the annotation and analysis of metagenomes. With built-in support for multiple data sources and a back end that houses abstract data types, the metagenomics RAST is stable, extensible, and freely available to all researchers. This service has removed one of the primary bottlenecks in metagenome sequence analysis – the availability of high-performance computing for annotating the data.
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            SolexaQA: At-a-glance quality assessment of Illumina second-generation sequencing data

            Murray P Cox, Daniel A Peterson, Patrick J. Biggs (2010)
            Background Illumina's second-generation sequencing platform is playing an increasingly prominent role in modern DNA and RNA sequencing efforts. However, rapid, simple, standardized and independent measures of run quality are currently lacking, as are tools to process sequences for use in downstream applications based on read-level quality data. Results We present SolexaQA, a user-friendly software package designed to generate detailed statistics and at-a-glance graphics of sequence data quality both quickly and in an automated fashion. This package contains associated software to trim sequences dynamically using the quality scores of bases within individual reads. Conclusion The SolexaQA package produces standardized outputs within minutes, thus facilitating ready comparison between flow cell lanes and machine runs, as well as providing immediate diagnostic information to guide the manipulation of sequence data for downstream analyses.
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              High-throughput amplicon sequencing of the full-length 16S rRNA gene with single-nucleotide resolution

              Benjamin J. Callahan, Joan Wong, Cheryl Heiner … (2019)
              Abstract Targeted PCR amplification and high-throughput sequencing (amplicon sequencing) of 16S rRNA gene fragments is widely used to profile microbial communities. New long-read sequencing technologies can sequence the entire 16S rRNA gene, but higher error rates have limited their attractiveness when accuracy is important. Here we present a high-throughput amplicon sequencing methodology based on PacBio circular consensus sequencing and the DADA2 sample inference method that measures the full-length 16S rRNA gene with single-nucleotide resolution and a near-zero error rate. In two artificial communities of known composition, our method recovered the full complement of full-length 16S sequence variants from expected community members without residual errors. The measured abundances of intra-genomic sequence variants were in the integral ratios expected from the genuine allelic variants within a genome. The full-length 16S gene sequences recovered by our approach allowed Escherichia coli strains to be correctly classified to the O157:H7 and K12 sub-species clades. In human fecal samples, our method showed strong technical replication and was able to recover the full complement of 16S rRNA alleles in several E. coli strains. There are likely many applications beyond microbial profiling for which high-throughput amplicon sequencing of complete genes with single-nucleotide resolution will be of use.
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                Author and article information

                Contributors
                Olubukola Oluranti Babalola:
                ORCID: https://orcid.org/0000-0003-4344-1909
                John J. Dennehy: Role: Editor
                Journal
                Journal ID (nlm-ta): Microbiol Resour Announc
                Journal ID (iso-abbrev): Microbiol Resour Announc
                Journal ID (publisher-id): mra
                Title: Microbiology Resource Announcements
                Publisher: American Society for Microbiology (1752 N St., N.W., Washington, DC )
                ISSN (Electronic): 2576-098X
                Publication date (Electronic, pub): 3 February 2022
                Publication date (Electronic, collection): February 2022
                Publication date PMC-release: 3 February 2022
                Volume: 11
                Issue: 2
                Electronic Location Identifier: e01131-21
                Affiliations
                [a ] Food Security and Safety Niche, Faculty of Natural and Agricultural Sciences, North-West University, Mmabatho, South Africa
                Queens College CUNY
                Author notes

                Olubukola Oluranti Babalola is the main investigator. Afeez Adesina Adedayo and Ayomide Emmanuel Fadiji are co-investigators. All authors contributed equally to this work.

                The authors declare no conflict of interest.

                Author information
                https://orcid.org/0000-0003-4344-1909
                Article
                Publisher ID: MRA01131-21 Publisher ID: mra.01131-21
                DOI: 10.1128/mra.01131-21
                PMC ID: 8812306
                PubMed ID: 35112900
                SO-VID: 00f60b00-a4fd-4786-9578-f33ec3c6d88f
                Copyright © Copyright © 2022 Babalola et al.
                License:

                This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.

                History
                Date received : 22 November 2021
                Date accepted : 23 December 2021
                Page count
                Figures: 1, Tables: 1, Equations: 0, References: 10, Pages: 4, Words: 1445
                Funding
                Funded by: National Research Foundation (NRF), FundRef https://doi.org/10.13039/501100001321;
                Award ID: UID123634
                Award ID: UID132595
                Award Recipient :
                Categories
                Subject: Omics Data Sets
                Compound subject: food-microbiology, Food Microbiology
                Custom metadata
                cover-date February 2022

                Data availability:

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