Multiple Microbiomes In Health & Disease
Humphrey Bacchus
Humphrey Bacchus joined Invivo as Director of Clinical Services in 2014 after a decade of working as a physical therapist and clinical nutritionist in hospitals and clinics both in the USA and the UK. His vision for microbiome-centered medicine and responsible business practice has led Invivo's development of clinical microbiome diagnostics and therapeutics, as well as B Corp certification and a carbon-neutral company commitment.
There is a bi-directional communication constantly at play between a human host species and the environmental microbiome that lives both in us and around us. The gut microbiome is important, but what about the importance of the emerging microbiomes that have a huge impact on health, performance, and disease. Advances in research and testing are exposing the importance of multiple microbiomes like those in the oral cavity and its impact on systemic health. Modulating the oral microbiome can profoundly influence neurological, cardiovascular and systemic health.
We need to look at our bodies more like gardens rather than battlefields. Most people think about bugs as being good or bad, but for the bacteria, viruses and yeast within the human body, pathogenicity is a contextual state.
Summary
- Microbes are not simply good or bad but are part of a contextual ecosystem that should be viewed like a garden rather than a battlefield to be fought with antibiotics.
- While most research focuses on the gastrointestinal tract, the human body contains multiple microbiomes, including the oral, nasal, vaginal, and urinary tracts.
- The oral microbiome is a key area of research linked to neurodegenerative conditions like Alzheimer's disease, as well as mental health issues like anxiety and depression.
- Effective treatment requires specific, targeted diagnostics and products rather than general probiotics to address the complex ecosystems within different body sites.
- Diagnostic and screening services for multiple microbiomes are currently used by 4,000 clinicians across Europe, with plans for expansion to Australia and the United States.
Article
Multiple Microbiomes In Health & Disease: Beyond The Gut And Towards Personalized Medicine
At Biohacker Summit 2019 Helsinki, Humphrey Bacchus Argued That The Future Of Medicine Lay In Treating The Body As An Ecosystem, Not A Battlefield
For years, the microbiome conversation had been dominated by the gut. It was the colon, the stool sample, the familiar language of probiotics and digestion that captured the public imagination. But at **Biohacker Summit 2019 Helsinki**, held in **Helsinki, Finland**, **Humphrey Bacchus** urged his audience to look up, outward and inward all at once.
In his presentation, **“Multiple Microbiomes In Health & Disease,”** delivered on **Friday, 1 November 2019**, Bacchus made the case that modern medicine had been asking the right question too narrowly. The microbiome, he said, was not a single organ system story. It was a networked human story, spread across the **oral, nasal, vaginal and urinary tracts**, with each microbial niche shaping health in ways medicine was only beginning to understand.
“The microbiome is every single thing in and around us,” Bacchus said. “There are multitudes of other microbiomes that exist within us, from the oral and nasal cavities to the vaginal and urinary tract microbiomes.”
A Radical Shift In Perspective
Bacchus, who joined **Invivo** in 2014 as Director of Clinical Services after a decade working as a physical therapist and clinical nutritionist in hospitals and clinics in the **USA and the UK**, spoke with the urgency of someone who had watched a field mature in real time. His central argument was deceptively simple: microbes could not be sorted neatly into saints and villains.
That binary, he suggested, belonged to an older medical imagination.
Instead, he described a living ecology in which bacteria, fungi, viruses and yeast became harmful or helpful according to context. The body, in this framing, was less a site of perpetual microbial war than a delicately managed landscape.
Drawing on a line associated with microbiome scholar Martin Blaser, Bacchus said the human body should be viewed “more like gardens rather than battlefields”. It was an image that did more than decorate the science. It challenged an era shaped by antibiotic overreach and by the instinct to eliminate first, understand later.
Dysbiosis And The Conditions Of Disease
What mattered, Bacchus argued, was not merely which organisms were present but **the state of the ecosystem** in which they lived. Sleep, stress, diet and lifestyle all had profound effects on microbial balance. When that balance tipped, opportunistic organisms could gain a foothold.
“Lifestyle, sleep patterns, diet, and stress all impact hugely on the human microbiome,” he said. “When we have a dysbiotic state within the body, it allows specific bacteria, fungi, or yeast to take hold and become more pathogenic.”
This was not microbiome science as wellness cliché, nor as vague self-optimization. It was a direct argument for precision. Dysbiosis, in Bacchus’s telling, was not an abstract state but a biological opening, one through which inflammatory, metabolic and neurological disorders might emerge or worsen.
Beyond The Gut, Toward The Mouth
The most striking turn in Bacchus’s talk came when he moved the conversation decisively beyond the gastrointestinal tract. Gut research had been essential, he acknowledged, but it had also overshadowed other crucial microbial habitats.
“When we are assessing human health, it is really important that we look beyond the gastrointestinal tract,” he said. “The oral cavity is an incredibly important microbiome in a wide array of diseases, from neurodegeneration to autoimmunity.”
The oral microbiome, in particular, stood at the center of a growing body of research linking microbial imbalance to **Alzheimer’s disease**, **anxiety**, **depression**, **obesity**, **metabolic syndrome** and **autoimmune conditions**. Bacchus pointed to interest around **Porphyromonas gingivalis**, a pathogen associated with the oral cavity and increasingly studied in relation to Alzheimer’s.
Yet even here, he warned against simplistic narratives. Targeting one species might prove useful, but it risked obscuring the deeper complexity of the ecosystem from which disease emerged.
“One of the misconceptions is that there is a general way to improve health,” Bacchus said. “Actually, we are finding that we have to be targeted and specific, looking at the microbiome as a complex ecosystem rather than just individual species.”
Personalized Medicine, But Truly Personalized
The promise of microbiome science has often been sold as universal: take this probiotic, follow this protocol, restore balance. Bacchus pushed back on that formula. In its place, he outlined a more exacting and more demanding vision of **personalized medicine**.
Different body sites, he explained, required different diagnostics, different interventions and different therapeutic logic. A vaginal microbiome associated with recurrent infections or IVF outcomes could not be approached in the same way as an oral microbiome implicated in neuroinflammation. Nor could a generalized gut-health product plausibly solve problems rooted elsewhere.
This was where diagnostics entered the frame. Bacchus described services designed to assess not only the gut but also multiple microbiomes across the body, allowing clinicians to identify specific imbalances and tailor treatment accordingly. In human probiotic studies aimed at modulating the gut-brain axis, he noted, meaningful outcomes often appeared only after **daily use over two to three months**, a reminder that microbial intervention was neither instantaneous nor one-size-fits-all.
From Clinic To Market
If the science carried philosophical weight, the business surrounding it was already moving at speed. Bacchus said the diagnostic and screening services he discussed were being used by **around 4,000 clinicians across Europe**, spanning private doctors, dentists, periodontal specialists, gastroenterologists and clinical nutritionists.
Licensed in the UK by the **Care Quality Commission**, the service had begun opening not only to clinicians but also to patients directly. At the time of the summit, Bacchus said the company could ship globally except to the United States, with **Australia** emerging as the next major target market, alongside a broader European expansion.
The commercial details mattered because they underscored a larger shift: microbiome medicine was no longer confined to research labs and speculative headlines. It was becoming infrastructure, with tests, regulatory frameworks, clinical pathways and international ambition.
The New Frontier Of Mental And Neurological Health
Perhaps the most arresting implication of Bacchus’s presentation was the possibility that microbiome modulation, especially in the mouth, might help reshape how medicine approached some of its most devastating disorders.
“We are now starting to tease out how modulating the oral microbiome can help stave off not only neurodegeneration but also conditions like anxiety and depression,” he said.
It was a careful claim, not a miracle cure. But it hinted at an extraordinary convergence: dentistry, neurology, psychiatry and immunology speaking to one another through the shared language of microbial ecology. In that sense, Bacchus was not merely broadening the microbiome map. He was redrawing the borders between medical disciplines.
A More Humble Medicine
What remained after the talk was not hype but a kind of scientific humility. The microbiome, as Bacchus presented it at **Biohacker Summit 2019 Helsinki**, resisted reduction. It asked clinicians and patients alike to give up the comforting fiction that health could be repaired by generic solutions or by naming a single microbial culprit.
The deeper lesson was harder, and richer. Human beings were hosts to layered ecologies. Health depended on stewardship, not conquest.
In the years since microbiome science first entered mainstream conversation, it had often been framed as a revolution. Bacchus’s presentation suggested something more subtle and perhaps more lasting: an education in complexity. The body was not one microbiome but many. And if medicine hoped to become genuinely personalized, it would have to learn to listen to all of them.
Part of Biohacker Summit 2019 Helsinki