Table 3.

Summary of recent research literature on the microbial community.

Region	Year	Published research themes	Process, tools and techniques	Key research outcomes	References
Saudi Arabia	2020	Metagenomics-based evaluation of microbial profiles	Shotgun metagenomic tools; CosmosID metagenomic software; high performance k-mer algorithm databases	Metagenomics revealed a lower alpha diversity for both bacteria and virus	[85]
United States of America	2019	Whole metagenomic sequencing for microbial community	Whole metagenome sequencing; Descriptive analyses using SAS® 9.4	whole metagenomics approach to characterize sediment microbial biodiversity	[63]
China	2019	Metagenomic sequencing for microbial gene catalog	Metagenomic sequencing using an Illumina Hiseq 2000 sequencing system; MetaGene predicted an open reading frames (ORFs); Gene taxonomic classification using BLASTP search	Metagenomic sequencing is conducted to investigate the microbial gene catalog	[62]
Singapore	2019	Bioinformatics analysis of metagenomics data of biogas-producing microbial communities	Next-generation sequencing (NGS) technologies used for qualitative and quantitative analysis of the microbial communities	Described the procedure of processing metagenomics data of microbial communities for revealing metagenomics characterization using bioinformatics approaches	[86]
China	2019	Metatranscriptomics for rhizosphere microbiomes	Random-primed cDNA libraries using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina; The cDNA libraries using the Experion DNA 12 K Analysis Kit (Bio-Rad) and quantified using the Qubit dsDNA HS Assay kit	Metatranscriptomics revealed significant eCO2 effects on the composition and activity of the grassland microbiomes	[87]
China	2020	Metagenomic insights for microbial community and antimicrobial resistance genes	Shotgun metagenomics sequences processed using Trimmomatic 0.36 and Bowtie2 via the KneadData wrapper software; MEGAHIT v1.1.3 used for de novo metagenomic assembly analyses; The draft genomes annotated using Prokka software and eggNOG-mapper (based on eggNOG 4.5 orthology	The results give first metagenomic insights into the salt-mediated changes in microbial community composition and a broad view of associated antibiotic resistance genes in the process of food fermentation.	[134]
Canada	2018	Mining metagenomic and metatranscriptomic data for microbial metabolic functions	Metagenomics and metatranscriptomics, including nucleic acid extraction, sequencing platform selection, library construction, quality control of sequencing outputs, compositional analysis, assembly-based functional analysis, assembly-free functional analysis, and comparative analysis.	Metagenomics and metatranscriptomics can arrest the whole genome and transcriptome range of microorganisms through sequencing entire DNA/RNA, providing both taxonomic and functional information with high resolution	[69]
Switzerland and Israel		Microbial Metagenomics Mock Scenario-based Sample Simulation (M3S3)	Microbial Metagenomics Mock Scenario-based Sample Simulation (M3S3) workflow generate virtual samples from raw reads or assemblies	The M3S3 tool is support the progress and authentication of identical metagenomics applications	[88]