Microbial Bioactives
Microbial Bioactives | Online ISSN 2209-2161
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Volume 6 Number 1 2023
REVIEWS (Open Access)
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*
Microbial Bioactives 6 (1) 1-13 https://doi.org/10.25163/microbbioacts.6110673
Submitted: 17 March 2023 Revised: 14 May 2023 Accepted: 21 May 2023 Published: 23 May 2023
Abstract
The study of microbiomes and their associated pathogens has changed remarkably over the last decade, moving far beyond the limitations of traditional culture-based microbiology. Earlier approaches captured only a very small portion of microbial diversity, leaving much of the microbial world unexplored and, in many cases, misunderstood. This review synthesizes current advances in microbiome analysis, with particular emphasis on high-throughput sequencing, integrated meta-omics, and modern bioinformatic pipelines used for pathogen detection across marine, terrestrial, and extreme ecosystems. Evidence gathered from recent studies suggests that second- and third-generation sequencing technologies have substantially improved taxonomic resolution, functional prediction, and real-time microbial surveillance. Approaches such as metabarcoding, shotgun metagenomics, metatranscriptomics, proteomics, and metabolomics now provide a more dynamic understanding of microbial activity rather than simple presence–absence observations. The review also highlights the importance of high-fidelity sampling systems, including pressure-retaining and in situ fixation devices, which preserve native microbial structure and reduce post-sampling bias. Quantitative molecular tools such as qPCR, droplet digital PCR, and CARD-FISH further enhance detection sensitivity and ecological interpretation. Despite these advances, methodological heterogeneity, primer bias, incomplete reference databases, and variability in sequencing depth remain important challenges. Overall, this review demonstrates how integrated meta-omics and advanced sequencing technologies are reshaping pathogen monitoring, ecological prediction, and microbiome research across diverse environmental systems.
Keywords: Microbiome analysis; high-throughput sequencing; shotgun metagenomics; meta-omics; pathogen detection; marine microbiology; bioinformatics
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