The Longevity Microbiome: What the Over-90s Can Teach Us About Diversity, Diet, and Ecological Resilience

There’s growing interest in what allows certain individuals to live into their 90s and beyond with relative vitality and a key emerging theme is microbial diversity. Recent studies of long-lived populations (such as centenarians in Sardinia and Japan, or nonagenarians in Italy) consistently find that gut microbiome diversity remains high well into old age, often more so than in younger adults from industrialised societies [1, 2].

But how do these individuals maintain such microbial richness? The answer appears to lie not in supplements or superfoods, but in something far more fundamental: dietary diversity, environmental exposure, and continuity with nature.

Rethinking Microbial Diversity: Beyond Probiotics

We often think of gut health in terms of adding in probiotics or fermented foods. While helpful, these are only one part of the picture. The microbiome thrives on continuous, dynamic input from the environment, including soil microbes, air, water, and the chemical complexity of whole foods.

Microbial richness is particularly influenced by:

• Plant diversity: More types of fibres and phytochemicals nourish more species of microbes.

• Seasonal variation: Eating in tune with the seasons exposes the gut to changing inputs- mimicking the natural cycles our bodies evolved with.

• Environmental contact: Gardening, walking barefoot, touching animals and soil all contribute to microbial exchange.

You’re Not Just Eating Food—You’re Eating 

Data

Food isn’t inert. Each plant, root, leaf, and fruit carries information: in its microbial fingerprint, its polyphenols, and its ecological history. When you eat food, you’re consuming the microbial ecosystem that food was exposed to and this communicates with your microbiome. This idea is gaining ground: we are not just what we eat, we are what our microbes make of what we eat, and that depends on the complexity of what we consume.

In contrast, most supermarket shelves today offer an illusion of variety. You might see 50 different types of crackers or cereals, but they are often built on the same monocropped base ingredients: wheat, corn, soy, sugar, and seed oils. These offer minimal microbial stimulation and contain additives and emulsifiers (e.g. polysorbates, carboxymethylcellulose) shown to disrupt gut barrier function and microbial balance [3].

The Modern Gut: A Biodiversity Desert?

Western microbiomes are now being called ecological collapse zones. Compared to traditional societies or long-lived rural populations, our guts are often depleted—lacking keystone species like Akkermansia, Faecalibacterium prausnitzii, or butyrate-producing bacteria that regulate immunity, inflammation, and brain health [4].

This isn’t just about gut symptoms, it’s about systemic resilience. Reduced microbial diversity has been linked to everything from depression to metabolic dysfunction, autoimmunity, and even cancer risk.

Restoring Diversity: Clinical Recommendations

To support microbial diversity in clients, especially peri- and post-menopausal women, or those experiencing metabolic or immune challenges consider the following strategies:

1. Rotate foods weekly – Encourage at least 30 different plant foods per week (even if you don’t believe fibre is essential, the diversity of polyphenols and compounds is critical for microbiome signalling).

2. Emphasise bitter and wild foods – These often carry more phytochemicals and microbial richness than cultivated produce.

3. Seasonal eating – Build plans around seasonal availability to mimic ancestral dietary rhythms and avoid repetitive input.

4. Soil exposure and ferments – Encourage time in nature and traditional ferments (if tolerated) to reseed microbial variety.

5. Avoid ultra-processed foods – These not only lack microbial data but often contain compounds that actively damage microbial balance.

Final Thoughts: We Are Not Separate from Nature

Our microbiome is a living record of our contact with the world. The healthiest, longest-lived people aren’t living in sterile bubbles or following perfect diets—they are part of their ecosystems. They eat food grown in real soil, they breathe unfiltered air, and they are not afraid of a little microbial mess.

To truly support healthspan and microbiome integrity, we must step outside the monocrop illusion and rejoin our ecological context - as active participants, not isolated observers.

References

1. Odamaki, T., et al. (2016). Age-related changes in gut microbiota composition from newborn to centenarian: a cross-sectional study. BMC Microbiology, 16:90.

2. Biagi, E., et al. (2016). Gut microbiota and extreme longevity. Current Biology, 26(11), 1480–1485.

3. Chassaing, B., et al. (2015). Dietary emulsifiers impact the mouse gut microbiota promoting colitis and metabolic syndrome. Nature, 519(7541), 92–96.

4. Sonnenburg, E.D., & Sonnenburg, J.L. (2019). The ancestral and industrialized gut microbiota and implications for human health. Nature Reviews Microbiology, 17, 383–390.