Comparative Study of Metagenomics and Metatranscriptomics to Reveal Microbiomes in Overwintering Pepper Fruits

Abstract

Red pepper (Capsicum annuum, L.), is one of the most important spice plants in Korea. Overwintering pepper fruits are a reservoir of various microbial pepper diseases. Here, we conducted metagenomics (DNA sequencing) and metatranscriptomics (RNA sequencing) using samples collected from three different fields. We compared two different library types and three different analytical methods for the identification of microbiomes in overwintering pepper fruits. Our results demonstrated that DNA sequencing might be useful for the identification of bacteria and DNA viruses such as bacteriophages, while mRNA sequencing might be beneficial for the identification of fungi and RNA viruses. Among three analytical methods, KRAKEN2 with raw data reads (KRAKEN2_R) might be superior for the identification of microbial species to other analytical methods. However, some microbial species with a low number of reads were wrongly assigned at the species level by KRAKEN2_R. Moreover, we found that the databases for bacteria and viruses were better established as compared to the fungal database with limited genome data. In summary, we carefully suggest that different library types and analytical methods with proper databases should be applied for the purpose of microbiome study.

Characterization of Microbial Diversity of Two Tomato Cultivars through Targeted Next-Generation Sequencing 16S rRNA and ITS Techniques

“…The prevalence of Gammaproteobacteria, particularly the order Enterobacteriales, the family Erwiniaceae , and the genus Pantoea , is conspicuous within the high abundance found in round tomato. Despite its versatility, Pantoea is known to manifest as either a commensal or a pathogenic organism [ 61 ], with reports of its isolation from plants and soil, as well as instances of infecting pepper fruits [ 62 ]. Hence, the notable presence of Pantoea in high abundance on days 6 and 12 in round tomato could potentially suggest a pathogenic role.…”

Metagenomics: An Effective Approach for Exploring Microbial Diversity and Functions

“…Although methods and bioinformatics tools have been developed for exploring microbiomes in fruits, a suitable strategy should be selected for the aims of study. Previously, Jo et al compared DNA and mRNA libraries and three analytical methods for microbial diversity in overwintering pepper fruits and demonstrated that library types, analytical methods, and proper databases contribute to the achievement of microbiome study [113].…”

Genomics: Infectious Disease and Host–Pathogen Interaction

“…Jo Y et al compared two distinct library types (DNA for metagenomics, RNA for metatranscriptomics) and three different analytical methods for the identification of microbiome in overwintering pepper fruits. Their results revealed that DNA sequencing is more useful for the identification of bacteria and DNA viruses, whereas mRNA sequencing is superior for identifying fungi and RNA viruses [ 15 ].…”

“…This Special Issue of the International Journal of Molecular Sciences entitled “Genomics: Infectious Disease and Host –Pathogen Interaction” contains twelve original articles and three reviews that provide new insights into infectious diseases with regard to biofilm formation [ 1 , 2 , 3 ], diagnostics [ 4 ], vaccine development [ 5 ], and host–pathogen interaction [ 6 , 7 ]; these insights are based on genomic [ 8 , 9 , 10 , 11 , 12 ], transcriptomic [ 13 , 14 ], and microbiomic [ 15 ] studies.…”