Using Next-Generation Sequencing To Understand the Role of the Microbiome in Health and Disease
Discover how next-generation sequencing is uncovering the microbiome’s impact on health, disease and potential therapeutic breakthroughs.
The term "microbiome" was popularized by microbiologist and Nobel Laureate Joshua Lederberg in the early 2000s, emphasizing that microbial communities play a crucial role in human health and disease.1 However, the concept was already in use. In 1988, Whipps et al. defined the microbiome as “a characteristic microbial community occupying a reasonably well-defined habitat which has distinct physio-chemical properties,” encompassing the organisms and their environmental interactions.2 This definition of the microbiome is still used over 35 years after its initial description.
A significant turning point in microbiome research came with the advent of next-generation sequencing (NGS) technologies, particularly metagenomics, which allowed scientists to study entire microbial communities without needing cultivation. This shift significantly expanded researchers’ abilities to explore microbial ecosystems in various environments, from the human gut to soil, oceans and extreme habitats.
Unlocking the microbiome using next-generation sequencing
The impact of NGS on microbiome research cannot be overstated. Traditional microbiology relied on culture-based methods, which provided limited insights into microbial diversity, as several microorganisms are fastidious or unculturable in laboratory conditions.
The innovation of NGS technologies, particularly metagenomics, has revolutionized the field by enabling the high-throughput sequencing of microbial DNA directly from environmental or host-associated samples. This culture-independent approach allows researchers to analyze entire microbial communities comprehensively, identifying species or strains, functional genes and microbial interactions.
One of the most influential projects in modern microbiome research was the Human Microbiome Project (HMP), launched in 2007.3 By applying NGS, this large-scale initiative provided the first detailed catalog of microbial populations across different body sites, deepening our understanding of their role in human health and disease. Similar sequencing-based studies have since extended microbiome research into agriculture, marine ecosystems and extreme environments, further demonstrating the microbiome’s vast ecological significance.4,5,6
Leading experts emphasize how NGS has transformed our ability to study microbial communities. Professor Lindsay Hall, chair of microbiome research at the University of Birmingham, stated, “NGS has revolutionized microbiome research by enabling us to uncover the immense complexity of microbial communities. Metagenomics, one of the first applications of NGS in this field, allowed for culture-independent profiling of microbiomes, revealing the taxonomic and functional diversity within these ecosystems. This approach has shed light on not just ‘who is there’ but also ’what they might be doing’."
This was further supported by Professor Jack Gilbert, director of the Microbiome and Metagenomics Center at UC San Diego, who strengthened the argument for improvements in microbiome research using alternative NGS methods, “Similarly, single-cell RNA sequencing has revealed heterogeneity in bacterial transcription, such as within Bacillus subtilis, enhancing our ability to link microbial functions to specific health outcomes. These insights have revealed mechanisms by which the microbiome influences host health, provided metrics for disease prediction and diagnostics, and identified novel therapeutic opportunities to modify microbial communities for clinical benefit.”
As sequencing technologies evolve, third-generation sequencing methods, such as long-read metagenomic sequencing, further refine our ability to characterize the microbiome with greater accuracy and resolution.7 Integration of NGS with bioinformatics and machine learning has also expanded microbiome research, allowing scientists to uncover complex host-microbe interactions and predict microbial functions more effectively, which has successfully been demonstrated in several research studies.8,9,10
Exploiting the microbiome to understand human health and disease
Today, microbiome research is at the forefront of biomedicine, environmental science and biotechnology, with NGS playing a central role in unraveling the complexities of microbial communities. As technology advances, the future of microbiome research could see discoveries leading to innovative applications in health, disease prevention and ecosystem management.
The microbiome is crucial in maintaining human health and influencing disease development. Increasing evidence has shown that microbial communities interact with the human body. For example, microbial communities within the gut influence metabolic and immunological pathways. Furthermore, these host–microbe interactions can be impacted by diet, environmental exposures and genetics. As research advances, understanding the mechanisms through which the microbiome influences health and disease has created new opportunities for therapeutic interventions, particularly in areas such as diet-gut microbiota interactions, colorectal cancer (CRC) and mental health.
The relationship between diet and gut microbiota is dynamic, with dietary patterns influencing the composition and activity of the microbiome, which can be either beneficial or detrimental to health. Gilbert emphasized how utilizing metagenomics has been pivotal in understanding key bacterial taxa and their influence on human health.11 “NGS has provided transformative insights into the relationship between diet, gut microbiota and diseases like inflammatory bowel disease (IBD). In IBD, a reduction in microbial diversity and an increase in pro-inflammatory taxa such as Enterobacteriaceae are key features of the disease.
Metagenomic sequencing has further identified microbial metabolic disruptions, such as reduced short-chain fatty acid production and increased hydrogen sulfide synthesis, which exacerbate inflammation and epithelial barrier damage.” Hall further explained how the microbiome mediates dietary breakdown by identifying enzymatic clusters involved in key metabolic processes. She stated, “Metagenomic analyses have uncovered specific microbial genes and pathways responsible for fiber fermentation and short-chain fatty acid production, which may be disrupted in certain patient groups. Screening across vast numbers of microbes for these gene clusters has provided insights into how microbial metabolism contributes to gut health.”
Studies showcasing the success of microbial biomarkers highlight the potential of the microbiome as both a diagnostic tool and a therapeutic target in cancer prevention and treatment.12 Bacterial biomarkers such as Fusobacterium nucleatum have been identified as being associated with CRC, and can be used to facilitate early detection.13 Hall noted, "This organism's presence in tumors has been linked to its virulence pathways, such as immune evasion and pro-inflammatory signaling. NGS has also revealed functional pathways enriched in CRC-associated microbiomes, providing a framework for understanding microbial contributions to tumorigenesis. These findings are now driving efforts to use microbiome data for early detection and risk stratification in CRC.”
Mental health has also become an area of research gaining popularity over the last decade, with emerging evidence suggesting that the microbiome may influence brain function through the gut–brain axis, which has been explored using NGS methods such as metagenomics.14 Gilbert addressed the potential of developing probiotic therapeutics to support the treatment of mental health conditions. “Analyses have shown that diets rich in fiber promote the growth of bacteria that produce butyrate, which enhances gut barrier integrity and modulates neuroinflammation. Conversely, dysbiosis associated with high-fat diets has been linked to increased gut permeability, systemic inflammation and depressive symptoms. These insights highlight the potential for dietary modulation and microbiome-targeted therapies, such as probiotics or psychobiotics, to support mental health and treat related conditions.”
Future directions of microbiome research
The exploration of the microbiome has rapidly evolved from a foundational understanding of microbial diversity to its crucial role in human health and disease. Insights into diet-gut interactions, the microbiome’s role in colorectal cancer, and mental health have opened new avenues by demonstrating the benefits of understanding the microbiome for personalized medicine and therapeutic interventions.
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Looking ahead, experts predict that future microbiome research will increasingly rely on cutting-edge technologies such as artificial intelligence (AI) to overcome these challenges.15 Hall expressed that AI will be pivotal in analyzing the vast amounts of data produced using NGS technologies. “In the next 5–10 years, microbiome research will increasingly rely on larger, open-access datasets, enabling better cross-validation and integration of findings across studies. AI and machine learning will play a pivotal role in handling the vast and complex datasets generated, hopefully facilitating the discovery of new microbial biomarkers and therapeutic targets.” However, she also addressed the importance of not forgetting crucial lab-based experimental techniques required for validations, further stating, “Despite advances in computational methods, experimental validation will remain essential. The genotype-to-phenotype gap in NGS data will need to be bridged through functional experiments and in-depth characterizations.”
Current microbiome research is constrained by the collection methods used for samples. Ingestible sampling devices could unlock new ecological niches, enhancing microbiome research by enabling real-time, non-invasive monitoring of microbial populations across different gastrointestinal tract regions. Gilbert explained, "Ingestible devices for sampling different regions of the gastrointestinal tract and engineered bacterial strains for in vivo data collection promise to deepen our spatial and functional understanding of the microbiome. These technologies will complement efforts to overcome current limitations, such as the reliance on stool samples, by capturing the mucosal microbiome and its dynamic interactions.” This technology will allow for more targeted interventions and a better understanding of gut microbiota dynamics as microbes transverse through the gastrointestinal tract.
Hall also offered insights into the potential of live biotherapeutics, living microorganisms engineered to treat disease, which are expected to become a transformative tool in microbiome-based therapeutics.16 “The [microbiome] field will increasingly focus on microbiome-based interventions, building on the proof-of-concept success of fecal microbiota transplants. This could include live biotherapeutics, next-generation probiotics or targeted microbial consortia designed to modulate specific host pathways.” These therapies could offer more precise, individualized treatment options, which have the potential to be less invasive than treatments currently available.
Finally, as the microbiome becomes a more prominent target for therapeutic intervention, changes in regulatory frameworks will be crucial to ensuring the safe and effective use of microbiome-based therapies. “As the regulatory landscape matures and the costs of microbiome-based interventions decrease, the adoption of microbiome-based therapies and diagnostics in routine clinical practice is anticipated to accelerate. The integration of microbiome science into precision healthcare and personalized nutrition will likely redefine the boundaries of preventive medicine and treatment strategies,” Gilbert said. As we progress, these advancements are poised to address current challenges and open up new possibilities for microbiome-driven healthcare.
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