16S rRNA metagenomic profiling of red amaranth grown organically with different composts and soils

Appl Microbiol Biotechnol. 2024 Dec;108(1):129. doi: 10.1007/s00253-023-12982-7. Epub 2024 Jan 15.


In recent years organic food is gaining popularity as it is believed to promote better human health and improve soil sustainability, but there are apprehensions about pathogens in organic produces. This study was designed to understand the effect of different composts and soils on the status of the microbiome present in organically grown leafy vegetables. 16S rRNA metagenomic profiling of the leaves was done, and data were analyzed. It was found that by adding composts, the OTU of the microbiome in the organic produce was higher than in the conventional produce. The beneficial genera identified across the samples included plant growth promoters (Achromobacter, Paenibacillus, Pseudomonas, Sphingobacterium) and probiotics (Lactobacillus), which were higher in the organic produce. Some pathogenic genera, viz., plant pathogenic bacteria (Cellvibrio, Georgenia) and human pathogenic bacteria (Corynebacterium, Acinetobacter, Streptococcus, Streptomyces) were also found but with relatively low counts in the organic produce. Thus, the present study highlights that organic produce has lesser pathogen contamination than the conventional produce. KEY POINTS: • 16S rRNA metagenomics profiling done for organic red amaranth cultivar • Microbial richness varied with respect to the soil and compost type used • The ratio of beneficial to pathogenic genera improves with the addition of compost.

Keywords: 16S rRNA Metagenomics; Composts; Microbiome; Organic; Pathogens.

MeSH terms

  • Bacteria / genetics
  • Composting*
  • Humans
  • Metagenome
  • RNA, Ribosomal, 16S / genetics
  • Soil


  • RNA, Ribosomal, 16S
  • Soil