ArticlePeerJ2021
To culture or not to culture: a snapshot of culture-dependent and culture-independent bacterial diversity from peanut rhizosphere.
Article in PeerJ, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed.
- Comparative metagenomic analysis of microbial communities: unravelling microbial communities from the great Rann of Kachchh and coastal saltpans, Gujarat, India.Extremophiles : life under extreme conditions · 2026Article
- Microbial decomposer diversity and metabolic function during the decomposition of brine shrimp carcasses in a saline lake.Microbiome · 2026Article
- Habitat heterogeneity drives microbial community assembly and functional specialization in extremely arid ecosystems.Applied and environmental microbiology · 2026Article
- Metagenomic evaluation of peanut rhizosphere microbiome from the farms of Saurashtra regions of Gujarat, India.Scientific reports · 2024Article
- Yeast metagenomics: analytical challenges in the analysis of the eukaryotic microbiome.Microbiome research reports · 2024Review
- Metagenomic Study of Fungal Microbial Communities in Two PDO Somontano Vineyards (Huesca, Spain): Effects of Age, Plant Genotype, and Initial Phytosanitary Status on the Priming and Selection of their Associated Microorganisms.Plants (Basel, Switzerland) · 2023Article
- Microbial Profiling of Biltong Processing Using Culture-Dependent and Culture-Independent Microbiome Analysis.Foods (Basel, Switzerland) · 2023Article
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundSequencing driven metagenomics studies have been instrumental in various aspects of microbiology including identification of newer taxa. While this culture-independent approach has its own merits and demerits, several studies have focussed on comparing it with traditional culture-dependent (CD) approach. However, most of these comparative studies rely on Sanger sequencing of complete 16S rRNA gene from pure culture colonies to determine the culturable bacterial diversity. This approach undercounts culturable diversity as only fewer isolates are selected, sequenced, and identified.
methodsIn this study, we have used an Illumina based partial 16S sequencing to identify all the microbes growing on the media and directly comparing with its culture-independent (CI) counterpart. Eight different media were used to target different organisms from soil. Diversity on these media were compared with their CI counterpart. The NGS data was analysed using DADA2 to provide more resolution to the data.
resultsIn line with studies of similar nature, current study presented higher bacterial diversity in CI approach. However, the current study reflected that a greater number of sequence variants were missed out in CI approach as compared to number of sequence variants shared with CD approach. We observed around 322 (5.98%) ASVs (Amplicon Sequence Variants) exclusively present in CD samples while, 234 (4.35%) ASVs were shared between both approaches. Most of these 322 CD exclusive ASVs were classified as
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