One Microbiome, Many Outcomes: Understanding Responses To Probiotic Supplementation
Dr. Ratna SudhaNov 06, 2026
Research highlights how individual gut microbiomes, diet, medications and probiotic strains influence colonisation and health outcomes, paving the way for personalised supplementation
The average human body is home to about 38 trillion bacteria, almost as many as our 30 trillion human cells. Most live in the gut, forming a complex community known as the gut microbiome. The Human Microbiome Project revealed that even healthy individuals have different communities of microorganisms in their gut, skin, vagina, and other parts of the body
So, What Does This Mean For Probiotics?Probiotics are live microorganisms that provide health benefits when consumed in adequate amounts. However, they do not act in isolation; they interact with the trillions of microorganisms already present in our gut. As a result, the same probiotic may produce different results in different individuals
No Two Microbiomes Are AlikeWhile we may share many of the same gut bacteria, the types and amounts present vary from person to person.Our genes play only a small role in these differences. A study of over 1,000 healthy individuals found that genetics accounted for about 2 per cent of the differences in gut microbiomes, while more than 20 per cent was linked to factors such as diet, medications, and body weight. This may explain why even family members can have different gut microbiomes, while unrelated people living together may have more similar gut bacteria.
What May Influence Whether A Probiotic StaysProbiotics may therefore behave differently in each person. Researchers at Israel’s Weizmann Institute of Science studied this by sampling the gut directly, rather than relying only on stool samples. In some people, called “persisters”, the probiotic settled in the gut. In others, called “resisters”, the existing gut bacteria prevented it from settling. This process, known as colonisation, appeared to depend on the individual, the probiotic strain, and the region of the gut. The researchers could also predict who was more likely to allow probiotics to settle, based on existing gut bacteria and other individual traits.
Another study provided further insight. A strain of Bifidobacterium longum remained in the gut of about 30 per cent of participants for at least six months. These individuals initially had lower levels of this species and fewer of the genes it uses to break down carbohydrates. This suggests a probiotic may settle more easily where there is less competition from similar bacteria for space and nutrients, an opportunity known as a “niche”.
Responders And Non-responders: Why Results VaryClinical studies show that individuals respond differently to probiotics. Those who benefit are commonly referred to as “responders”, and those who do not as “non-responders”. Factors that may influence this include diet, existing gut microbiota, medications such as antibiotics, and the strain, dose, formulation, and manufacturing of the probiotic.
Among these, an individual’s existing gut microbiota is increasingly recognised as an important factor, suggesting it could serve as a biomarker to predict who is most likely to benefit. An expert workshop convened by the International Scientific Association for Probiotics and Prebiotics (ISAPP) recommended that clinical trials set clearly defined objectives, use standardised outcome measures, and specify in advance the criteria for identifying responders.
Personalised Probiotics: The Road AheadUnderstanding why individuals respond differently is paving the way for personalised probiotics, tailored to each person’s gut microbiota. In future, a simple test could group people by their gut bacteria before they take probiotics, guiding the choice of strain. The Bifidobacterium findings also point to the potential for replenishing beneficial bacteria that are underrepresented in an individual’s gut. The future of probiotics lies in understanding which probiotic works best, for whom, and under what conditions. As research advances, this understanding could help make supplementation more precise, personalised, and effective.
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