The Microbiome: Clinical Insights from Oral, Gut, and Vaginal Ecosystems
The human microbiome has rapidly evolved from a niche research interest into one of the most transformative areas of modern clinical science. Trillions of microorganisms - bacteria, fungi, viruses, and archaea - colonise virtually every surface of the body, creating dynamic ecosystems that shape health and disease. While we often think of microbes as pathogens, the vast majority are either harmless or beneficial, engaging in complex symbiotic relationships with their human host. Only a subset of microbes is distinctly pathogenic, capable of disrupting host tissues, evading immune responses, and driving both local infections and systemic disease. Yet it is important to recognise that health depends on balance: even generally beneficial or harmless microbes can become opportunistic or disruptive if they grow disproportionately, upsetting the finely tuned ecological equilibrium that underpins host-microbe symbiosis.
Among the most clinically significant niches are the oral cavity, the gastrointestinal tract, and the vaginal environment. Each of these ecosystems is distinct in composition, function, and its impact on systemic health.
Understanding these microbial communities offers profound insights into preventive strategies, risk stratification, and targeted therapeutic interventions. With the advent of shotgun metagenomic sequencing, clinicians can now access highly detailed microbial profiles that illuminate both species composition and functional potential. This blog explores the oral, gut, and vaginal microbiomes, focusing on dominant microbial species, mechanisms by which they maintain health, and the systemic implications of dysbiosis.
The Oral Microbiome: A Gateway to Systemic Health
The oral cavity harbours one of the most diverse microbial communities in the body, with over 700 species identified. These microbes colonise the teeth, tongue, gingival crevices, and mucosal surfaces, forming structured biofilms. Dominant commensal taxa include Streptococcus mitis, Streptococcus sanguinis, Haemophilus parainfluenzae, and Rothia mucilaginosa. These organisms play key roles in maintaining ecological balance, preventing pathogen colonisation, and modulating local immune responses.
However, when oral ecology shifts toward pathogenic dominance, significant disease can occur. Porphyromonas gingivalis, Tannerella forsythia, and Treponema denticola - collectively known as the “red complex”- are strongly associated with periodontitis, a chronic inflammatory condition leading to gum destruction and tooth loss. These pathogens possess virulence factors such as proteolytic enzymes and biofilm-forming capacity, allowing them to persist despite host immune defences.
What makes oral dysbiosis particularly compelling for clinicians is its systemic impact. P. gingivalis has been linked to rheumatoid arthritis through its unique ability to citrullinate proteins, a process that can trigger autoimmune responses and the production of anti-citrullinated protein antibodies (ACPAs). Similarly, periodontal pathogens have been detected in atherosclerotic plaques, implicating oral infection in cardiovascular disease progression. Emerging evidence also suggests that P. gingivalis may play a role in neurodegenerative disease, particularly Alzheimer’s. Studies have identified P. gingivalis DNA and its virulence factors (gingipains) in the brains of patients with Alzheimer’s disease. These gingipains are neurotoxic, contribute to neuroinflammation, and may accelerate amyloid plaque formation. Possible pathways of entry include haematogenous spread during gum bleeding as well as neuronal routes such as the trigeminal and olfactory nerves. Chronic periodontal inflammation can also raise systemic cytokine levels, creating an inflammatory environment that may exacerbate neurodegeneration. The presence of these microbes in systemic circulation may promote chronic inflammation, endothelial dysfunction, and plaque instability. For practitioners, oral microbiome health is no longer just about dentistry - it is a window into health or broader inflammatory and cardiovascular risk.
The Gut Microbiome: The Second Genome
The gut microbiome is the largest and most metabolically active microbial community in the human body, and it is increasingly viewed not only as a digestive aid but as a central organ in its own right. Estimates suggest that over 1,000 species colonise the gastrointestinal tract, with a collective genome far larger than our own. The dominant phyla are Firmicutes and Bacteroidetes, but what excites researchers today is not simply which species are present, but how they interact with each other and with the host.
Among the most influential organisms are Faecalibacterium prausnitzii, a prolific producer of butyrate with powerful anti-inflammatory effects, and Akkermansia muciniphila, a mucin-degrading bacterium now being trialled as a live biotherapeutic for metabolic disease. These keystone species help maintain the intestinal barrier and metabolic balance, and their depletion has been linked to obesity, type 2 diabetes, and inflammatory bowel disease.
One of the most compelling directions in gut microbiome research is its role in regulating the intestinal barrier. When this barrier is disrupted, also referred to as hyperpermeability or “leaky gut,” microbial products such as lipopolysaccharides escape into systemic circulation, where they act as inflammatory triggers. This mechanism is being connected not only to autoimmune conditions, but also to psychiatric and neurodegenerative disorders, including depression and Alzheimer’s disease. The fact that microscopic breaches in the gut lining can drive inflammation in the brain and joints is a striking example of how local microbial changes echo systemically.
Adding to this, recent studies highlight how gut microbes generate bioactive molecules, sometimes called postbiotics, which act as chemical messengers. These include neurotransmitter-like compounds such as gammaaminobutyric acid (GABA) and serotonin precursors, which can influence mood and cognition through the gut–brain axis. Experimental work has shown that transplanting gut microbiota from patients with depression or autism into germ-free mice can transfer behavioural traits, underlining just how powerful this microbial community is in shaping brain function.
Clinically, this opens up provocative new avenues. Engineered probiotics are being developed to secrete therapeutic molecules directly in the gut. Microbiome-based drugs, built from carefully designed groups of microbes, are under investigation for conditions ranging from ulcerative colitis to cancer immunotherapy. Even more exciting is the concept of manipulating microbial signalling networks to modulate host metabolism, immunity, or brain activity.
For clinicians, the gut microbiome is no longer just about digestion - it is about inflammation, immunity, and even identity. The possibility that diet today could influence not only a patient’s risk of colon cancer but also their mood or dementia risk tomorrow demands a broader, more integrative approach to healthcare.
The Vaginal Microbiome: A Unique Low-Diversity Ecosystem
Unlike the gut, where diversity is generally synonymous with health, the vaginal microbiome thrives on low diversity dominated by Lactobacillus species. Lactobacillus crispatus, Lactobacillus jensenii, Lactobacillus gasseri, and Lactobacillus iners are the most common species in healthy women. These organisms maintain vaginal health by producing lactic acid, which keeps the vaginal pH low (typically around 3.5–4.5). This acidic environment prevents overgrowth of pathogenic organisms, reduces the risk of bacterial vaginosis (BV), and provides protection against other types of infections such as sexually transmitted infections.
When this balance is disrupted, BV-associated species such as Gardnerella vaginalis, Fannyhessea vaginae and Prevotella bivia can dominate. Dysbiosis is associated with increased risk of pelvic inflammatory disease, infertility, and adverse pregnancy outcomes such as preterm birth. Interestingly, recent studies have highlighted the role of vaginal microbiota in modulating susceptibility to human papillomavirus (HPV) persistence, with implications for cervical cancer risk. Other emerging research has linked vaginal dysbiosis to poorer outcomes in assisted reproductive technologies, underscoring its importance in fertility medicine.
The vaginal microbiome is also dynamic, influenced by hormonal changes across the menstrual cycle, pregnancy, and menopause. Declines in oestrogen can reduce Lactobacillus abundance, increasing susceptibility to infection and discomfort. Newer studies suggest that distinct microbiome profiles may help predict risk for preterm birth, gestational complications, or even the effectiveness of certain contraceptives. There is also evidence that microbial metabolites influence local immune tolerance, which may play a role in recurrent miscarriage or implantation failure. These advances highlight the vaginal microbiome not only as a guardian of local health but as a potential lever in reproductive medicine and oncology.
Microbiome Health and Clinical Practice
Across oral, gut, and vaginal niches – the microbiome represents an organ system - one that is dynamic, adaptable, and profoundly influential. The clinical relevance of these ecosystems is no longer speculative. Associations between Porphyromonas gingivalis and rheumatoid arthritis/cardiovascular disease, between gut dysbiosis and neurodegeneration, and between vaginal imbalance and adverse pregnancy outcomes illustrate how central microbes are to human health. As shotgun metagenomic sequencing and other tools become more accessible, the integration of microbiome assessment into everyday practice will allow clinicians to move from reactive to truly preventive care engaging in risk assessment and personalised interventions.
Testing with Colab Services
With the rapid development of sequencing technologies, shotgun metagenomic testing is now available to clinicians through Colab Services. These tests provide an unprecedented level of detail, capturing the entire microbial ecosystem while also identifying functional genes such as those related to antimicrobial resistance and metabolic pathways.
For clinicians, this means moving beyond assumptions and partial data to a more precise and actionable picture of client health. Testing can reveal early microbial imbalances in the oral cavity before gum disease progresses, detect gut profiles associated with inflammatory risk even in asymptomatic patients, and highlight vaginal dysbiosis that could compromise fertility or pregnancy outcomes. Armed with this information, clinicians can make more informed decisions, whether recommending preventive interventions, tailoring dietary and lifestyle strategies, or selecting targeted antimicrobial or probiotic therapies:
SA105 – Oral microbiome: The Salient Oral Microbiome Test provides an in-depth analysis of the microbial communities present in the mouth. It identifies both beneficial and potentially harmful bacteria, fungi, and other microbes that influence oral and systemic health. By assessing microbial balance and diversity, this test can reveal factors contributing to gum disease, tooth decay, bad breath, and chronic inflammation. Since oral health is closely linked to cardiovascular, metabolic, and immune health, this test can also provide valuable insights into broader systemic conditions influenced by oral dysbiosis.
SA104 – Vaginal microbiome: The Salient Vaginal Microbiome Test provides a comprehensive analysis of the vaginal microbiota, identifying both beneficial and potentially pathogenic microorganisms. It evaluates the balance of Lactobacillus species, which are key to maintaining a healthy vaginal environment, alongside the detection of bacteria, fungi, and other microbes associated with dysbiosis, recurrent infections, or altered reproductive health. This test can be a valuable tool in understanding drivers of symptoms such as chronic vaginal irritation, recurrent bacterial vaginosis or yeast infections, and in assessing overall reproductive and urogenital health.
Coming soon - the new shotgun stool test