‘Mining’ the Gut: The Microbiome ‘Lassonde curve’

Initial exploration: The compass and its scalability

Similarly, while high-throughput sequencing is the technological engine of the current microbiome revolution, the compelling revolutionary concept was laid down by Carl Woese in 1977.² His fundamental and game-changing contribution was the establishment of the Three-Domain System of life, which was based on the phylogenetic analysis of 16S ribosomal RNA (rRNA) gene sequences. The true conceptual breakthrough was his pioneering use of the 16S rRNA gene as a ‘molecular chronometer’ to determine evolutionary relationships. Woese’s work, which is often overshadowed by subsequent technological advances, laid the vital foundation upon which all modern molecular microbiology—and thus, the entire microbiome field—is built. In essence, Woese provided the map and the compass (the 16S rRNA taxonomy), which high-throughput sequencing later made it possible to read at scale and speed.

Microbiome discovery phase: Basic concepts

With the introduction of DNA sequencing technologies, commonly referred to as next-generation sequencing (NGS), microbiological advances have been in focus. From culturing and isolating single microbes, we have progressed to sequencing entire microbial genomes and identifying and characterizing unculturable microbes. This has led to the identification of distinct microbiomes in the oral cavity, respiratory tract, skin and the gastrointestinal (GI) tract, often collectively termed the ‘second human genome.’ These microbial cells in our bodies are estimated to outnumber our own human cells by 30% and contain 100 times more genes than the human genome, thus making us ‘more microbial than human’.^3–5 Around 95% of these microbial cells reside in our gut, thus making the gut microbiome a key organ of the body.⁶

The gut microbiome in healthy adults is characterized by high diversity and richness, comprising an estimated 500 to 1000 bacterial species, predominantly of the phyla Firmicutes (60%), Bacteroidetes (20%), Actinobacteria (10%), Proteobacteria (5%) and Verrucomicrobia (<1%).⁷ Additionally, methanogenic archaea (primarily Methanobrevibacter smithii), fungi (Candida, Saccharomyces, Aspergillus) and viruses (bacteriophages, Adenoviruses, Noroviruses) are also present, though constituting only a minor fraction (<2%) by mass of the gut microbiota (Fig. 1). Factors affecting the gut microbiome composition include age, sex, genetics, lifestyle factors such as stress, exercise and sleep, diet, antibiotics and drug exposures, environmental factors and geographical location.^8–10

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FIG 1.

Alterations in gut microbiota and metabolites across various stages of human life cycle SCFA short chain fatty acids

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The gut microbiome of the Indian population shows considerable differences from the western population. While Prevotella and Megasphaera have been found predominant in the Indian population, the gut microbiome of the western population is dominated by Blautia and Fecalibacterium.^10–13 These differences are largely attributable to dietary patterns; Indian diets are high in carbohydrates and fibres, whereas western diets contain higher amounts of animal proteins and fats.¹⁴ Functionally, the Indian gut microbiome shows enrichment in pathways related to glycan biosynthesis, xenobiotic metabolism and branched-chain amino acid biosynthesis. In contrast, the western microbiomes are more associated with short-chain fatty acids (SCFAs) production and other metabolic pathways.^15,16 Similarly, differences in the composition of gut microbiota have also been found between individuals residing in rural and urban areas at sea level and high altitude in India.¹⁰

The gut microbiome is involved in various physiological processes, including nutrient metabolism, maintaining gut barrier integrity, immunomodulation, and the gut–brain axis. The gut microbes metabolize dietary fibres, proteins and bile acids into SCFA, trimethylamine-N-oxide (TMAO) and secondary bile acids, respectively, which are involved in the regulation of metabolism, inflammation, cardiovascular and hepatic functions. SCFAs are also involved in the regulation of gut epithelial barrier integrity. The gut microbiome modulates the immune system via several mechanisms, including promotion of immune tolerance via microbial-associated molecular patterns (MAMPs); promoting regulatory T-cell (Treg) differentiation and maintaining Th17/Treg balance; production of immunomodulatory metabolites, including SCFAs; and exerting colonization resistance by stimulating production of antimicrobial peptides and secretory IgA.¹⁷

The gut-organ axes refer to the bidirectional communication networks between the gastrointestinal tract and other organs, including the brain, liver, lung, kidney and others (Fig. 2). The gut microbiome plays a central role in the functioning of these axes. These axes are mediated by microbial metabolites (e.g. SCFAs, bile acids, neurotransmitters), immune signalling, neural pathways (including the vagus nerve) and endocrine factors. The gut microbiota regulate host metabolism, immune responses and gut barrier integrity, thereby influencing the functions and disease susceptibility of extra-intestinal organs.¹⁸

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FIG 2.

Various gut-organ axes and diseases associated with gut microbiome dysbiosis

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During the first three years of life, the gut microbiome undergoes structured changes that parallel and influence the development of metabolism, immunity and cognition.¹⁹ By 3 years of age, the gut microbiome achieves diversity and functional capacity resembling that of healthy adults.

Perturbation of the gut microbiome in disease

In adults, the microbiome is relatively stable and resilient, meaning it can return to its baseline state after perturbations like dietary changes or a short course of antibiotics.²⁰ However, prolonged use of antibiotics and other drugs, immune dysfunction, environmental exposures and other factors lead to long-term alterations in the microbiome, referred to as dysbiosis. Dysbiosis has been associated with multiple diseases, including gastrointestinal disorders such as Clostridioides difficile infection (CDI), inflammatory bowel disease (IBD), and irritable bowel syndrome, as well as extra-intestinal conditions like metabolic syndrome, obesity, atherosclerosis, lung cancer, asthma, Parkinson’s disease and chronic kidney disease.^21–23 However, despite extensive data linking dysbiosis to various clinical diseases, a causal relationship is yet to be established in human studies. Dysbiosis can disrupt the gut-organ axes, contributing to the pathogenesis of conditions such as metabolic dysfunction-associated steatotic liver disease, neuropsychiatric disorders and dysfunction of other organs. For example, altered gut microbial metabolites and bile acid metabolism contribute to hepatic inflammation and steatosis; altered gut metabolites, endocrine signalling, and immune dysregulation can influence neuroinflammation and central nervous system homeostasis; and disruption of gut barrier integrity leads to increased exposure of microbial products to the pancreas, contributing to metabolic dysregulation and islet dysfunction.

The promise of microbiome manipulation therapies

In light of the microbiome–disease associations, even in the absence of causality, it appears reasonable to consider microbiome manipulation as a therapeutic strategy against these diseases.²⁴ These microbiome manipulation strategies include diet, antibiotics, prebiotics, probiotics and faecal microbiota transplantation. Amongst these, the intervention having the most robust data supporting its efficacy and safety is faecal microbiota transplantation (FMT).

FMT, which involves the infusion of a faecal suspension from a healthy individual into the gastrointestinal tract of an individual with GI disease, has been evaluated in randomized controlled trials and cohort studies, demonstrating clear benefits for the management of recurrent CDI and, to a lesser extent, ulcerative colitis (UC). Additionally, studies suggest FMT may offer therapeutic potential in a variety of other conditions, including Crohn’s disease, irritable bowel syndrome, hepatic encephalopathy, metabolic syndrome and in the eradication of multidrug-resistant organisms from the gut.²⁵ Response to FMT is also affected by donor factors, recipient factors and procedural variables. Certain donors, sometimes termed ‘super-donors,’ have microbiota profiles associated with higher rates of clinical response, particularly those enriched with butyrate-producing taxa (e.g. Lachnospiraceae, Oscillospiraceae) and higher overall microbial diversity. Baseline recipient microbiome composition, immune status, genetics, age and underlying disease state also impact microbiota engraftment and clinical efficacy. The route of administration (colonoscopy versus upper GI endoscopy and oral capsules), frequency and number of infusions, the amount infused and use of antibiotics before FMT can all affect engraftment and efficacy.²⁶

IBD, which includes ulcerative colitis and Crohn’s disease, has an unknown aetiology and a multifactorial pathogenesis. IBD arises from a complex interplay of genetic susceptibility, environmental exposures, immune dysregulation and alterations in gut microbiome. Manipulation of the gut microbiome targets the pathophysiology of IBD at a stage upstream of the dysregulated immune response by addressing the microbial dysbiosis that contributes to immune activation and barrier dysfunction.^27,28 Alteration of the microbiome with a combination of FMT as well as dietary changes has been explored in this disease. A novel study combining both these approaches showed that FMT with an anti-inflammatory diet (AID) in mild-to-moderate UC not only led to induction of remission rates as high as 50%, but also AID was able to maintain clinical remission in 50% of patients at 48 weeks.²⁹ Furthermore, FMT was found to refurbish the crypt-associated microbiota (CAM), and FMT-restored CAM taxa correlated negatively with disease activity.³⁰ Despite successful trials of FMT in IBD, it has not gained mainstream acceptance as an established therapeutic modality, and this leads us to analyze the possible reasons for the lack of confidence in microbiome manipulation therapies.

Microbiome manipulation therapy: Struggle to meet broader transformative expectations The field has delivered on a narrow, high-impact application (treatment of recurrent CDI) but is still struggling to meet the broader, transformative expectations for chronic disease treatment. The main hurdles preventing widespread success are the immense inter-individual variability of the microbiome, the complexity of microbial interactions, and the ‘chicken-or-egg’ dilemma (unclear if dysbiosis causes or is merely a result in most diseases). The challenge starts with defining a ‘healthy’ human gut microbiome due to individual and geographical variability. To address this, various indices have been developed. The HACK index (Health-Associated Core Keystone index) is a ranked metric for gut microbiome taxa that quantifies their association with host health and microbiome resilience. It was developed by analysing the prevalence and health associations of 201 gut microbial taxa across 45 000 adult gut microbiome samples from 42 countries and 28 disease categories. It provides a reproducible, standardized way to compare microbiomes, regardless of profiling strategy.³¹ Other indices similar to the HACK index have also been developed, including Gut Microbiome Health Index (GMHI), Gut Microbiome Index (GMI), Metagenomic Aerotolerant Predominance Index (MAPI) and Keystone Species Score.^32–36 Longitudinal microbiome studies have shown that intra-individual variability in gut microbiome is generally lower than inter-individual variability, with the majority of microbial community structure and genetic profiles remaining stable over extended periods of time (months to years). The individual-specific microbial signatures enable ‘microbial fingerprinting’ to accurately group samples from the same person over many years. One study reported an accuracy of 95% at 1 year and 85% at 4 years in detecting samples from the same individual.³⁷

Translation of microbiome sciences into routine clinical practice is not without obstacles. Regulatory barriers stem from methodological heterogeneity in the studies and the absence of clear regulatory pathways for microbiome-based diagnostics and therapeutics. Ethical issues involve concerns about data sharing and privacy, informed consent and responsible communication of results. Variability in sample collection, sequencing platforms, bioinformatic pipelines and interpretation of results leads to difficulty in reproducing the findings. Table 1 lists the remaining knowledge gaps in microbiome therapeutics.

Microbiome ‘Lassonde curve’

The Lassonde curve describes the lifecycle of value creation in the mining industry. It is a speculative model for junior mining companies, detailing the rise and fall of stock value as they move from exploration to production.³⁸ The Lassonde curve provides an appropriate, if metaphorical, framework to understand the hype and consolidation phases. The core concept of a hype cycle with distinct stages can be used as an analogy to explain the journey of microbiome-related technologies from discovery to practical application. Gut microbiome researchers are “mining the metagenome” to extract the genetic and functional gold that can be leveraged for health, and hence, possibly the example of the Lassonde curve can be used, where investigators in this field are shifting from surface-level enthusiasm to the difficult, deep-digging work required to reach sustained productivity. The key stages are: Initial exploration, Discovery, Orphan period (speculative interest wanes), and Production (Table 2).

The success precedent is strong

The unmet expectation is not that the science is flawed, but that it has not yet been successfully translated to more complex, chronic diseases like IBD, diabetes or other diseases. The treatment of CDI with FMT is an undeniable success story. Reinforcing this success are seminal studies that have shown that the gut microbiome may not only be a marker of current health but also a potential predictor of future health and overall longevity. People with advanced age display higher gut microbial diversity and enrichment of beneficial taxa, including Akkermansia and Lactobacillus, which are associated with increased SCFA production, improved amino-acid metabolism and reduced systemic inflammation— factors that contribute to healthy aging. Conversely, age-related dysbiosis, characterized by reduced diversity and increased proinflammatory taxa, has been linked to frailty, chronic inflammation and age-related diseases.³⁹

The field of microbiota sciences has made major strides in the past 20 years. Looking ahead, the next 20 years are expected to bring in the development of novel biotics (including engineered probiotics, prebiotics and synthetic communities), which will allow targeted or personalized modulation of the microbiome. Discovery of microbiome-derived novel antibiotics and anti-inflammatory compounds is expected to accelerate. Precision gene-editing tools (e.g. CRISPR-Cas9) may enable modification of specific organisms in the gut, unlocking new ways to treat disease or maintain health. Microbiome composition may serve as both a diagnostic marker and a predictor of future disease risk, improving early detection and preventive healthcare. Machine learning and advanced computational tools will interpret complex microbiome data, improve diagnostics, and facilitate large-scale, multidisciplinary research collaborations. Research focus will expand from broad taxonomic surveys to detailed strain-level characterization and integrated “multi-omics” (combining genomics, metabolomics, proteomics) to offer a comprehensive view of the human microbiome. Collectively, these advances will drive the field towards precision medicine and a mechanistic understanding of microbiome-related health and disease.