Microbial Bioactives

Microbial Bioactives | Online ISSN 2209-2161
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Microbial Bioactives

Volume 6 Number 1 2023

Article Contents

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REVIEWS   (Open Access)
Contents Vol 6 (1)

Advancements in Microbiome Analysis of Pathogenic Microorganisms: From Culture-Dependent Methods to Integrated Meta-Omics Approaches

Jegathambigai Rameshwar Naidu 1, Mahfoudh A.M. Abdulghani 2*

+ Author Affiliations

Microbial Bioactives 6 (1) 1-8 https://doi.org/10.25163/microbbioacts.6110673

Submitted: 17 March 2023 Revised: 14 May 2023  Published: 23 May 2023 

Abstract

The study of microbiomes and their associated pathogens has evolved dramatically, transitioning from culture-dependent approaches to integrated high-throughput sequencing (HTS) and meta-omics analyses. Historically, only a small fraction of microbial diversity could be assessed due to the limitations of traditional cultivation methods, leaving the majority of microbial life unexplored. Modern technologies, including second- and third-generation sequencing platforms, have revolutionized this field by enabling comprehensive characterization of microbial communities in both terrestrial and marine ecosystems. Metabarcoding and shotgun metagenomics now allow for detailed taxonomic profiling, functional gene prediction, and identification of emerging pathogens at the species or strain level. High-fidelity in situ sampling tools, such as pressure-retaining samplers and microbial filtration devices, preserve native microbial physiology, providing a more accurate representation of environmental microbial activity. Complementary techniques including quantitative PCR, droplet digital PCR, and CARD-FISH enhance pathogen detection and quantification, while integrated meta-omics approaches—metatranscriptomics, proteomics, and metabolomics—allow researchers to distinguish active microbial populations from dormant or extracellular DNA, elucidating functional interactions within the microbiome. Bioinformatic pipelines, including QIIME2, DADA2, and CoMA, facilitate the analysis of complex datasets, providing high-resolution insights into microbial dynamics and host-pathogen interactions. This systematic review and meta-analysis highlight the advances, challenges, and opportunities in microbiome research, underscoring the critical role of technological innovations in monitoring microbial pathogens across diverse environmental contexts.

Keywords: microbiome, high-throughput sequencing, meta-omics, metabarcoding, shotgun metagenomics, microbial pathogens, in situ sampling, qPCR, droplet digital PCR

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