16S-Metagenomic data profiling of the bacterial community in ready-to-eat vegetable salads sold in Kampala, Uganda.

This article presents a dataset on bacterial community structure associated with Ready-to-eat (RTE) vegetable salads sold in Kampala City, Uganda. The Illumina Miseq sequencing of 16S rRNA gene amplicon unveiled the bacterial communities and generated a metagenomic library from RTE vegetable salads to understand the diversities and distribution. The metagenome contained a total of 23,805 sequences with 35,420 Taxonomic units (OTUs). Metagenome sequence information is obtainable at NCBI under the Bioproject assigned accession number PRJNA1064313. Taxonomic hits distribution from VSEARCH analysis at phylum level classification of NN-3 discovered predominantly Proteobacteria (65.34%) followed by Firmicutes (31.60%) and Bacteroidota (0.14%). Deinococcota (0.01%) and Planctomycetota (0.01%) were also detected. Also, VSEARCH-assisted analysis of NN-4 detected a higher prevalence of Firmicutes (65.68%) than Proteobacteria (33.25%), while Bacteroidota (0.04%) indicating the presence of contaminants of faecal sources.

Amplicon sequencing data profiling of bacterial community connected with the rhizospheric soil from sunflower plants.

This article presents dataset on the bacterial community structure associated with rhizospheric sunflower soils from Lichtenburg, South Africa. The Illumina Miseq sequencing of 16S rRNA gene amplicon unveiled the bacterial community diversities as well as generated metagenomic library from sunflower rhizospheric soils to understand the diversities and distribution. The metagenome contained a total of 41,471 sequences with 45,975 operational taxonomic units (OTUs). Metagenome sequence information is obtainable at NCBI under the Bioproject assigned accession number PRJNA782103. Taxonomic hits distribution from USEARCH analysis at phylum level classification of BN_E discovered predominantly Actinobacteria (33.89%), followed by Proteobacteria (35.45%), Firmicutes (6.45%), Planctomycetes (4.12%), Chloroflexi (4.28%) and Gemmatimonadetes (2.40%). Also, USEARCH assisted analysis of BN_F sample also detected the prevalence of Actinobacteria (45.92%), Proteobacteria (23.23%), Firmicutes (3.84%), Planctomycetes (6.46%), Chloroflexi (4.94%) and Gemmatimonadetes (1.99%), which take part in vital ecological functions and biogeochemical activities needed for plant growth and health.

Locus-Specific DNA Methylation Analysis by Targeted Deep Bisulfite Sequencing.

DNA methylation, i.e., the methylation of cytosine at carbon atom C5, has an important role in the regulation of gene expression. The methylation status of each cytosine in a specific genomic region can be determined by targeted deep bisulfite sequencing at single-molecule resolution. Here we describe the design of PCR primers that are used to amplify specific sequences from bisulfite-converted DNA, the preparation of sequencing libraries, the sequencing of these libraries on the MiSeq system, as well as the analysis of the sequence reads. Using appropriate software tools such as amplikyzer2, it is easy to analyze complex multiplexed samples with several regions of interest, to determine the mean methylation values of all CpG dinucleotides in a region or of each CpG dinucleotide across all or selected reads, and to compare these values between different samples and between different alleles within a sample.