Advancing Gut Microbiome Research: The Shift from Metagenomics to Multi-Omics and Future Perspectives

Abstract

Advancements in NGS technologies have significantly expanded the scope and efficiency of metagenomics, surpassing traditional culture-based methods (Fig. 2).These innovations enable multi-domain microbial analysis through advanced bioinformatics tools, long-read sequencing, single-cell omics, and enhanced culture-based techniques, facilitating deeper insights into microbial diversity, function, and host interactions.The integration of cutting-edge computational tools and experimental methodologies has enhanced microbiome research, enabling the discovery of novel microbes, metabolic pathways, and therapeutic targets. Multi-domain microbial analysis and advanced bioinformatics tools.Recent metagenomic research has expanded beyond bacterial communities to encompass archaea, fungi, and viruses, fostering a more holistic understanding of the microbiome.Specialized databases such as IMG/VR for viruses [64] and fungiDB for fungal communities [65] facilitate comprehensive taxonomic and functional analyses.Advanced bioinformatics tools further enhance the ability to predict microbial functions and uncover disease-associated elements.For taxonomic classification, 16S rRNA reference databases, such as SILVA, Greengenes2 (GG2), and the Ribosomal Database Project (RDP) improve the accuracy of amplicon sequencing annotations [66][67][68].Functional prediction tools, including PICRUSt/PICRUSt2, Tax4Fun, and FARPROTAX, provide expanded insights into microbial functions by leveraging enhanced genome reference databases [69][70][71][72].Metagenomic shotgun sequencing tools such as MetaPhlAn 3, Kraken2, and HUMAnN 3 allow for high-resolution taxonomic

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