Modern approaches to gut microbiome investigation: Sequencing, culturomics, metabolomics, and beyond.

Integrating multi-omics technologies to decipher microbiome functions

Multi-omics approaches have revolutionized our understanding of microbial communities by enabling simultaneous interrogation of genomic, transcriptomic, proteomic, and metabolomic data. The systematic integration and analysis of these deep datasets help decipher the functional roles of microbiomes, providing critical insights into microbial activities, interactions, and dynamics across diverse environments. Biological complexity makes multi-omics analysis of a single, isolated organism demanding but highly informative, yet this complexity increases further when samples comprise hundreds to thousands of individual species. As microbiome research continues to expand into clinical, environmental, and engineered systems, standardized workflows, benchmarked datasets, and community-driven initiatives are essential to ensure reproducibility, standardization and interpretability. Establishing and disseminating best practices for experimental design, data processing, and integrative analyses will be critical for maximizing comparability and scientific rigor across studies. This perspective highlights recent advances in multi-omics microbiome research, outlines key obstacles in data integration and metadata harmonization, and proposes a collaborative roadmap for scalable, FAIR-compliant multi-omics investigations and potentially disruptive Artificial Intelligence (AI) advances comparable to those of AlphaFold in the field of microbiome science. In this Perspective, the authors discuss recent advances in multi-omics microbiome research, outlining key obstacles in data integration and metadata harmonization, and proposing a roadmap for scalable, FAIR-compliant multi-omics investigations and potentially disruptive Artificial Intelligence advances.

Integrating human microbiome profiling into precision medicine for disease prevention

The human microbiome is a diverse and dynamic microbial community composed of trillions of microorganisms that inhabiting various body sites, such as the gut, skin, oral cavity, respiratory tract, and urogenital system. These microbial communities sustain the host’s physiological functions and health through interactions with immune, metabolic, and neurobiological processes. The microbiome has been extensively studied due to recent advancements in high-throughput genome sequencing and multi-omics technologies, which also demonstrated associations between microbial dysbiosis and a variety of metabolic, neurological, immune-mediated, cardiovascular, and infectious disorders. Simultaneously, precision medicine incorporates routine, environmental, and genetic variables to provide personalized solutions to disease prevention and treatment. The integration of microbiome research and precision medicine provide potential opportunities in early detection of diseases, risk stratification, and personalized therapeutic interventions. This narrative review identifies relevant literature from PubMed, Web of Science, and Scopus using terms like “human microbiome,” “precision medicine,” “microbiome profiling,” “artificial intelligence,” and “disease biomarkers,” with emphasis on current English-language publications. The review study the diversity, structure, and functional roles of the human microbiome, and the current profiling technologies and their potential clinical uses. It also examines microbiome-directed approaches, including personalized nutrition, probiotics, and fecal microbiota transplantation. Moreover, the document addresses ethical considerations, clinical challenges, artificial intelligence, and multi-omics integration. While microbiome profiling has significant potential in precision and preventive medicine, most applications are still investigational and need more validation before being implemented in clinical practice.

Gut-on-Chip Models for Host–Microbiome Studies: A Systematic Review

As a central regulator of nutrient absorption, immune homeostasis and overall health, the gastrointestinal tract has become a major focus of biomedical research. However, developing in vitro models that accurately reproduce human gastrointestinal architecture and physiological conditions remains a major challenge. Gut-on-chip (GoC) systems, which integrate microfluidics with cell cultures, have emerged as a promising solution in the past decade. By recreating dynamic microenvironments that incorporate fluid flow, peristalsis-like mechanical stimulation and co-culture with microorganisms, GoC systems enable more physiologically relevant investigation of host–microbe and host–microbiome interactions. This systematic review provides a comprehensive overview of available GoC technology used in host–microbe research, including their structural and cellular components. A systematic search of PubMed, Embase and Google Scholar databases up to May 2026 identified forty-eight studies evaluating interactions between the host and probiotic strains, postbiotics, commensal microorganisms, pathogenic bacteria, fungi, viruses, or faecal-derived microbiota using GoCs. Common features, distinctive characteristics and application for modelling host–microbiome interactions and pathogenic infections are summarized. The available literature is characterized by heterogeneous study designs, variable microbiome compositions and analytical approaches, and limited cross-platform standardization, which should be considered when interpreting findings. Lastly, current limitations and future perspectives are discussed, highlighting the potential of GoC models to support biotic characterization and preclinical evaluation while underscoring the need for further validation and standardization.

Metagenomics: Tools To Unpack the Total Genomes of Microorganisms: Methods, Applications, and Emerging Frontiers- A Narrative Review

Applications across healthcare, environmental science, agriculture, biotechnology, and industry are reviewed with particular emphasis on clinical metagenomic next-generation sequencing (mNGS) for infectious disease diagnostics, antimicrobial resistance (AMR) surveillance, gut microbiome research, and precision medicine.

From Scat to Sequencing: Non-Invasive Methods for Wildlife Microbiome Research and Conservation

The gut microbiome, a complex community of microorganisms in the gastrointestinal tract, plays a vital role in host health, nutrition and adaptability. Advances in next-generation sequencing and metagenomics have deepened our understanding of how diet and environmental factors shape microbial diversity. In wild animals, microbiome analysis enables rapid and comprehensive profiling of microbial communities, identifying diverse taxa and exploring their phylogeny and functional potential. Direct genetic examination of environmental samples reveals the collective genome of the microbiota, offering insights into disease susceptibility and supporting wildlife conservation. However, invasive sampling methods pose risks to wild animals, highlighting the need for reliable non-invasive sampling approaches. Scat analysis provides an effective alternative, allowing detection of microbial DNA, metabolites and biomarkers to assess microbiome composition and its implications for survival. Non-invasive techniques are cost-effective, time-efficient, suitable for large cohorts and reduce harms associated with traditional sampling. This review discusses current non-invasive sampling methods and advanced molecular tools for microbial profiling, emphasizing the integration of microbiome research into conservation strategies to strengthen biodiversity preservation amid ongoing environmental challenges.

: the impact of human microbiome variations on systems