Exploring microbial worlds: a review of whole genome sequencing and its application in characterizing the microbial communities

Abstract

The classical microbiology techniques have inherent limitations in unraveling the complexity of microbial communities, necessitating the pivotal role of sequencing in studying the diversity of microbial communities. Whole genome sequencing (WGS) enables researchers to uncover the metabolic capabilities of the microbial community, providing valuable insights into the microbiome. Herein, we present an overview of the rapid advancements achieved thus far in the use of WGS in microbiome research. There was an upsurge in publications, particularly in 2021 and 2022 with the United States, China, and India leading the metagenomics research landscape. The Illumina platform has emerged as the widely adopted sequencing technology, whereas a significant focus of metagenomics has been on understanding the relationship between the gut microbiome and human health where distinct bacterial species have been linked to various diseases. Additionally, studies have explored the impact of human activities on microbial communities, including the potential spread of pathogenic bacteria and antimicrobial resistance genes in different ecosystems. Furthermore, WGS is used in investigating the microbiome of various animal species and plant tissues such as the rhizosphere microbiome. Overall, this review reflects the importance of WGS in metagenomics studies and underscores its remarkable power in illuminating the variety and intricacy of the microbiome in different environments.

Keywords:

• Illumina sequencing
• microbiome
• whole genome sequencing
• antimicrobial resistance genes
• rhizosphere microbiome
• 16s rRNA sequencing

Acknowledgments

We acknowledge the University Mohammed VI Polytechnic (UM6P), Morocco for giving us the enabling environment to conduct this critical review of metagenomics studies employing whole genome sequencing approaches.

Authors contributions

RD, AEA, and SA designed the study; the initial draft of the article was done by SA; Formal analysis and editing of the initial draft were done by all authors. Supervision was done by RD. All authors read and approved the submission of the article.

Disclosure statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Additional information

Funding

The author(s) reported there is no funding associated with the work featured in this article.