Microbiome, the invisible world inside us shapes health, disease and medicine

Microbiome, the invisible world inside us shapes health, disease and medicine | Photo: National Cancer Institute

Published on 15 July 2026 at 04:03 GMT

By Editorial Team SDG3

The human body hosts trillions of microorganisms: bacteria, fungi, viruses and other microscopic life forms. Collectively known as the microbiome, these organisms are not passive passengers but active participants in fundamental biological processes. Research accumulated over the past two decades has established that the microbiome influences immune development, metabolic function, hormonal regulation, neurological signalling and the body’s response to disease, medication and stress.

The gut microbiome, the community of microorganisms residing in the gastrointestinal tract, is the most extensively studied. The Human Microbiome Project, coordinated by the National Institutes of Health, mapped the microbial communities across multiple body sites in healthy adults and demonstrated the extraordinary diversity and individual specificity of these communities. Each person carries a microbiome shaped by birth, feeding, geography, environment, diet, antibiotic exposure and genetics, making it as personal as a fingerprint.

The microbiome interacts with the immune system in ways that researchers are still mapping. During early development, the presence of diverse microorganisms appears to calibrate the immune system, teaching it to distinguish between harmless environmental substances and genuine threats. Disruption of this process through antibiotic use, caesarean delivery, formula feeding or limited environmental exposure during infancy has been associated with higher rates of allergic and autoimmune conditions in high-income countries.

Metabolic function provides another area of active investigation. The gut microbiome assists in extracting energy from food, synthesising certain vitamins and regulating signalling molecules involved in appetite and fat storage. Studies comparing the gut microbiomes of individuals across different metabolic conditions have found consistent differences in microbial composition, though interpreting causality from such associations remains a methodological challenge in the field.

The gut-brain axis has attracted particular scientific and public interest. The gut and the central nervous system communicate through neural pathways, hormones and immune signalling. Microorganisms produce neurotransmitters and their precursors, including serotonin, and can influence inflammation in ways that affect neurological function. Research in Nature Medicine and other journals has explored the relationship between gut microbiome composition and conditions including depression, anxiety, autism spectrum conditions and neurodegenerative diseases, though the mechanistic understanding of these connections remains incomplete.

Dysbiosis, a term used to describe imbalances in microbial community composition, has been associated in published research with inflammatory bowel disease, metabolic syndrome, obesity, type 2 diabetes, cardiovascular disease, liver disease and certain cancers. However, scientific caution is warranted. Associations between microbiome composition and disease states do not automatically establish that microbial changes are causal. Human microbiome research often involves complex confounding factors related to diet, lifestyle, geography and host genetics.

Research into how the microbiome affects the body’s response to medication is generating clinically significant findings. Gut bacteria can metabolise certain pharmaceutical compounds before absorption, altering their effectiveness or producing metabolites with different properties. Nature Reviews Microbiology and other publications have documented how differences in gut microbiome composition may help explain variability in patient responses to drugs, particularly immunotherapies used in cancer treatment.

The development of cancer immunotherapy provides a particularly striking example. Clinical studies have found that patients receiving certain immune checkpoint inhibitor therapies show different treatment responses depending on their gut microbiome composition. Researchers have identified specific bacterial species associated with better responses to immunotherapy, and clinical trials are now examining whether manipulating the microbiome through faecal microbiota transplantation or dietary change can improve treatment outcomes.

Faecal microbiota transplantation, sometimes called FMT, involves transferring gut microbiome material from a screened donor to a patient. It has been approved in several jurisdictions as a treatment for recurrent Clostridioides difficile infection, where antibiotic-resistant bacterial overgrowth causes severe gastrointestinal illness. Regulated FMT programmes have demonstrated substantial clinical effectiveness for this indication. The potential application of FMT to other conditions including inflammatory bowel disease, metabolic disorders and neurological conditions is being investigated in clinical trials, though evidence for broader use remains at earlier stages.

Probiotics and prebiotics have been the subject of extensive research and significant commercial marketing. Probiotics are defined preparations of live microorganisms intended to confer a health benefit when consumed in adequate amounts. The World Health Organization (WHO) and the Food and Agriculture Organization have published a joint framework for evaluating probiotic health claims, emphasising the need for evidence specific to particular strains and health outcomes. Many commercially available products do not meet the evidentiary standards required to substantiate specific health claims under regulatory frameworks in the European Union and other jurisdictions.

Diet is one of the most modifiable influences on microbiome composition. Fibre from plant sources, particularly diverse types of vegetables, legumes, fruits and whole grains, provides substrate for fermentation by gut bacteria and supports the production of short-chain fatty acids that are important for gut barrier integrity and immune function. Research consistently associates dietary patterns rich in diverse plant foods with more diverse and compositionally different microbiomes compared with diets high in processed foods, refined sugars and saturated fats.

Antibiotic treatment has well-documented effects on the gut microbiome. Broad-spectrum antibiotics can cause substantial reductions in microbial diversity, and recovery to baseline composition can take weeks to months, or may be incomplete. The clinical implications depend on the antibiotic used, the individual’s baseline microbiome and the duration of treatment. The relationship between antibiotic use and longer-term microbiome changes is particularly relevant in early life, when the microbiome is still developing.

The skin, oral cavity, respiratory tract and urogenital system each host distinct microbial communities with roles in local defence and tissue maintenance. Oral microbiome research has found associations between certain bacterial communities and cardiovascular disease, possibly through inflammatory pathways. The lung microbiome, previously assumed to be sterile, has been characterised in conditions including chronic obstructive pulmonary disease and asthma. The vaginal microbiome, dominated in many women by Lactobacillus species, plays a role in protecting against infection and has been studied in relation to preterm birth and sexually transmitted infections.

The environmental microbiome, the microbial communities present in soil, water, food and built environments, connects human health to ecological conditions. Urbanisation, reduced contact with natural environments, intensive agriculture, water treatment and changes in food production have all been hypothesised to affect the microbial diversity to which human populations are exposed across their lives. This ecological framing places microbiome science within broader questions about the relationship between biodiversity, environmental health and human disease.

Technological advances have transformed the field. Culture-independent sequencing methods allow researchers to characterise microbial communities without growing organisms in the laboratory. Metagenomic approaches can reconstruct the functional potential of microbial communities from their genetic material. Metabolomic studies can measure the small molecules produced by microbial activity. The integration of these methods with clinical data and longitudinal studies is enabling more sophisticated investigation of how microbiome changes relate to health outcomes over time.

Reproducibility and methodological variation remain challenges. Studies may differ in sample collection, storage, DNA extraction, sequencing platform, bioinformatic analysis and the reference databases used to classify microbial taxa. These differences can affect findings and complicate direct comparisons between studies. As the field matures, standardisation of methods and the development of larger, more representative datasets are priorities for improving the reliability and generalisability of research.

The clinical translation of microbiome research is advancing but uneven. FMT for recurrent C. difficile is an established clinical intervention. Live biotherapeutic products, a regulatory category for microbiome-based medicines distinct from conventional probiotics, are under evaluation by regulatory authorities in several countries. Microbiome diagnostics, profiling services and dietary guidance products have entered the consumer market with varying degrees of scientific support, and the regulation of health claims in this area varies across jurisdictions.

From a public-health perspective, the microbiome field raises questions relevant to SDG 3 (good health and well-being). Understanding how early microbial exposures influence immune development has implications for policies related to breastfeeding support, antibiotic stewardship, access to diverse environments and food systems. Research on the relationship between diet and microbiome function reinforces public-health messages about dietary diversity and plant food consumption. The potential for microbiome-based therapies to address treatment-resistant conditions has relevance for healthcare access and the burden of chronic disease.

Equity considerations will become increasingly important as the field develops. Microbiome research has historically concentrated on populations in high-income countries, and the microbial communities found in people across different geographies, diets and lifestyles vary substantially. Diagnostics and therapies developed primarily on the basis of data from specific populations may not perform equivalently across diverse groups. Ensuring that microbiome science benefits people across different settings will require inclusive research design, equitable access to interventions and investment in research capacity in lower-income contexts.

The microbiome represents one of the most significant areas of biological discovery of the early twenty-first century. It has changed how scientists and clinicians understand the human body, shifted perspectives on the relationship between environment and health, and opened new avenues for prevention, diagnosis and treatment. The pace of discovery continues to accelerate, and the implications for medicine, public health and the understanding of disease are still unfolding.

Further information:

* National Institutes of Health Human Microbiome Project, the original source and continuing resource for the scientific programme that defined the human microbiome across body sites. https://www.hmpdacc.org

* World Health Organization and Food and Agriculture Organization guidelines on probiotics, the official framework for evaluating evidence relating to probiotic health claims. https://www.who.int/publications/i/item/9241562382

* Nature Reviews Microbiology, a primary source for peer-reviewed research on the human microbiome, its clinical implications and pharmaceutical interactions. https://www.nature.com/nrmicro

* Nature Medicine, a leading clinical research journal that has published key studies on the gut-brain axis, immunotherapy and microbiome-related disease associations. https://www.nature.com/nm