What exactly is the microbiome?

The entire community of micro-organisms — mostly bacteria — that lives in and on your body, together with their genes and environment.

What is the difference between microbiome and microbiota?

Microbiota refers to the micro-organisms themselves; strictly speaking, microbiome also includes their genes and their environment. In practice the two terms are often used interchangeably.

Can I change my microbiome?

Yes. Diet — especially fibre and polyphenols — lifestyle, sleep and exercise all influence its composition. Major changes take time and consistency.

Is a diverse microbiome always better?

Higher diversity often goes hand in hand with resilience and health, but context matters: it is about the right functions, not diversity as a goal in itself.

CosmoLexicon › Microbiome

Microbiome

EN: microbiome · related terms: holobiont, dysbiosis, co-metabolism

Definition The microbiome is the entire community of micro-organisms — bacteria, archaea, viruses and fungi — that lives in and on your body, with the greatest density in the large intestine. Strictly speaking, the term also includes their genes and their environment. This ecosystem supports digestion, immunity and the production of countless biologically active molecules.

In plain language

Your gut is home to a lively city of trillions of micro-organisms: the microbiome. Most are bacteria, but there are also viruses, fungi and archaea. Together they weigh an estimated few hundred grams, and yet they play a surprisingly large role. They break down fibres that you cannot digest yourself, produce vitamins, keep unwanted intruders in check and are in constant conversation with your immune system and your brain. No two people have exactly the same microbiome — it is as personal as a fingerprint, shaped by your birth, diet, lifestyle and environment. A varied, resilient microbiome is generally associated with good health. The good news: unlike your genes, you can help shape your microbiome, above all through what you eat.

The science behind

The human microbiome is a complex ecosystem, of which the gut community is the most densely populated and best studied. Modern sequencing (16S rRNA and shotgun metagenomics) has made clear that what counts is not so much the presence of individual species, but the functional capacity and the diversity of the community.

• Diversity & resilience. Higher alpha diversity often goes hand in hand with stability and the ability to recover after disturbance (for example after antibiotics).
• Functional redundancy. Different species can perform the same metabolic task, which makes the system robust.
• Core functions. Fermentation of fibre into short-chain fatty acids, synthesis of B vitamins and vitamin K2, conversion of bile acids and polyphenols, and training of the immune system.
• Enterotypes and gradients. Composition shifts along dietary and lifestyle gradients (for example fibre-rich versus protein-/fat-rich).

The microbiome is central to co-metabolism: many health-relevant molecules only arise through the cooperation between host and microbes. A disturbed balance (dysbiosis) is linked to a wide range of conditions, although cause and effect often remain to be clarified. My InnerSelfie reads microbiome data as one layer alongside DNA and metabolome. This reading is supportive and observational — not a medical diagnosis.

Related concepts

Holobiont Dysbiosis Co-metabolism Prebiotics Probiotics Metabolomics

Where appropriate — support: a varied microbiome is nourished above all by fibre and polyphenols; targeted supplementation can help where diet falls short. Discover the My Key Nutrients range.

Scientific references

• Lee et al. (2024), The human gut microbiome in health and disease.
• Nature, Signal Transduction & Targeted Therapy — microbiota review (s41392-022-00974-4).
• Emily Leeming, Genius Gut.
• Heidi Moretti, The Whole-Body Guide to Gut Health.

Frequently asked questions

What exactly is the microbiome?: The entire community of micro-organisms — mostly bacteria — that lives in and on your body, together with their genes and environment.
What is the difference between microbiome and microbiota?: Microbiota refers to the micro-organisms themselves; strictly speaking, microbiome also includes their genes and their environment. In practice the two terms are often used interchangeably.
Can I change my microbiome?: Yes. Diet — especially fibre and polyphenols — lifestyle, sleep and exercise all influence its composition. Major changes take time and consistency.
Is a diverse microbiome always better?: Higher diversity often goes hand in hand with resilience and health, but context matters: it is about the right functions, not diversity as a goal in itself.