Do Probiotics Permanently Colonise the Gut?

Do probiotics permanently colonise the gut?

Do probiotics permanently colonise the gut?

Check out this answer from Consensus:

While certain probiotic strains have the potential to colonize the gut, the colonization is often not permanent and is influenced by individual host and microbiome features, dietary components, and the interaction with resident gut microbiota. Continuous intake and personalized probiotic strategies may be necessary to achieve desired health outcomes. Further research incorporating clinical parameters is essential to understand the long-term implications of probiotic use on gut health.


The human gut microbiota is a complex and dynamic ecosystem, playing a crucial role in host health. Probiotics, defined as live microorganisms that confer health benefits to the host, have been extensively studied for their potential to modulate the gut microbiota. However, the permanence of probiotic colonization in the gut remains a subject of scientific inquiry.

Probiotic Colonization Potential

Probiotics, particularly strains of Lactobacillus and Bifidobacterium, have varying fates upon oral administration. Some strains are transient visitors, while others have the potential to colonize the gut more permanently1. The ability of probiotics to engraft in the gut is associated with beneficial effects such as enhanced metabolic activity and durable modulation of the indigenous microbiota1. However, identifying strains that can stably colonize the gut has been challenging.

Dietary Influence on Microbiota

Diet plays a significant role in shaping the gut microbiota. Prebiotics, which are nondigestible food ingredients, selectively stimulate the growth of beneficial bacteria like Bifidobacterium and Lactobacillus already present in the colon2. The concept of synbiotics, which combines probiotics and prebiotics, aims to enhance the colonization and activity of health-promoting bacteria2.

Survival and Growth of Probiotics in the Gut

The survival of probiotics such as Bifidobacteria and lactobacilli in the gut is influenced by several factors, including gastric acidity and bile salts. Studies suggest that probiotics do not typically adhere to mucosal cells but are passed in feces, indicating the need for continual ingestion for sustained effects3. Prebiotics and human milk components can enhance the survival and activity of probiotics3.

Individualized Colonization Patterns

Empiric probiotics show person-, region-, and strain-specific colonization patterns in the human gut. Baseline host and microbiome features can predict these patterns, but the presence of probiotics in stool does not guarantee mucosal colonization4. This suggests that the impact of probiotics on the gut mucosa is transient and individualized, highlighting the need for personalized probiotic approaches4.

Probiotics in Early Life

Administering probiotics early in life can influence bacterial colonization and reduce the susceptibility to gut dysfunction and diseases like necrotizing enterocolitis in preterm neonates5. Probiotics can promote the colonization of beneficial commensal microbiota, which in turn can limit pathogen load and mucosal atrophy5.

Interaction with Resident Gut Microbiota

Probiotics can impact the resident gut microbiota and host. For example, Bifidobacterium longum can induce changes in the polysaccharide utilization of Bacteroides thetaiotaomicron and affect host immune gene expression6. This interaction demonstrates the adaptability of both resident and probiotic species in response to each other6.

Probiotic Effects on Gut Epithelial Cell Proliferation

Probiotics like Lactobacillus casei can stimulate gut epithelial cell proliferation, which is beneficial for intestinal health7. This effect is observed across different sections of the gut and is not significantly influenced by the composition of the cecal bacteria7.

Challenges in Altering Gut Flora

The gut flora acquired during early infancy remains relatively constant throughout life, making it difficult to permanently change the gastrointestinal flora later on8. Probiotics often only transiently colonize the gut due to various gastrointestinal defenses8.

Prebiotics Metabolism by Probiotics

The metabolism of prebiotics by gut-isolated probiotics involves specific substrate-dependent gene expressions and enzymatic activities. These metabolic pathways are crucial for the fermentation of prebiotics and the production of beneficial metabolites like organic acids9.

Clinical Implications and Risk Assessment

The colonization of the gut by probiotics is selective and can delay the reconstitution of the microbiome after antibiotic treatment10. However, without clinical parameters, it is difficult to assess the health consequences of probiotic use10.


Do probiotics permanently colonise the gut?

Tine Licht has answered Unlikely

An expert from Technical University of Denmark in Microbiology, Microbiome

The answer to this depends on several things; including (i) what is meant by ‘probiotics’, (ii) what is meant by ‘colonise’, and (iii) which kind of gut (e.g. child or adult, healthy or diseased) are we talking about?

If the question is whether the typical commercially available probiotics, often containing strains of Lactobacillus and/or Bifidobacterium will permanently establish and proliferate in the gut of healthy adults after consumption, the answer is that this is highly unlikely.

Actually, it is quite difficult to get new strains to establish in a healthy bacterial gut community – Which is a good thing because it means that the healthy community is robust and difficult to alter. Several studies show that after consumption of probiotics, one can (not surprisingly) measure that they they come out again with faeces, but they are eliminated from the gut after a short period.

That being said, permanent colonisation is not necessarily a prerequisite for the probiotics to have a relevant effect. Even dead bacteria may induce specific responses in a host.

Next generation probiotics, based on other groups of bacteria than the currently applied lactic acid bacteria, are currently being developed and might be able to colonise more efficiently. Also, in a gut with an incomplete bacterial community, for example that of a newborn child, or of a patient treated with antibiotics, probitic strains are more likely to establish for a longer period.


Do probiotics permanently colonise the gut?

Arthur C Ouwehand has answered Unlikely

An expert from DuPont Nutrition and Health in Microbiology

While there are some odd cases where a certain probiotic strain has been identified in one or two subjects of a large number of people consuming the strain. This is the rare exception that confirms the rule. It is difficult for a an incoming microbe to establish itself in a fully inhabited environment. Let’s be grateful for that; it also makes it difficult for pathogens to establish themselves.


Do probiotics permanently colonise the gut?

Hannah Wardill has answered Unlikely

An expert from University of Adelaide in Gastroenterology, Microbiome

Like the other experts have commented here, assuming you mean commercially available probiotic formulations in a fairly ‘normal’ clinical scenario, the answer is no. Probiotics usually colonise the gut transiently, meaning if you want the “benefits” to stick around, you need to keep taking the capsules. Importantly, the term “benefits” must be approached with caution, as there is limited evidence to support any benefits of probiotic use in healthy people, and varied data to support them across other clinical scenarios e.g. inflammatory bowel disease. A balanced diet full of fibre is the best to support the long term health of your gut microbes 🙂


Do probiotics permanently colonise the gut?

Anders Abildgaard has answered Unlikely

An expert from Aarhus University in Microbiome

In most cases with commercially available probiotics: no. But it depends on the probiotic strains and the cohabiting microbiota.


Do probiotics permanently colonise the gut?

Dan Waitzberg has answered Likely

An expert from University of Sao Paulo in Nutrition

This will depend on the Probiotic type. Some will stay for months after interruption others will stay for about a week.


Do probiotics permanently colonise the gut?

Toni Gabaldon has answered Unlikely

An expert from Institute for Research in Biomedicine in Microbiome, Genomics, Microbiology, Bioinformatics

In any ecological niche, the arrival of a new species, even in massive amounts, does not guarantees long-term colonization. This is also true for microbial ecosystems, particularly when they are diverse and in an established equilibrium. Research, analyzing the gut of persons taking probiotics have shown that strains in probiotics are usually not persisting colonizers of the gut microbiota. In some persons this can happen, and this may be related to the existence of an already low diversity or unbalanced ecosystem, given the probiotic a change to colonize the niche. This situation can often happen after taking antibiotics. In such sircumstances probiotics may establish themselves more easily, although this may also retard the re-colonization of the normal microbiota.


Do probiotics permanently colonise the gut?

Juan Arques has answered Uncertain

An expert from INIA Spain in Microbiology, Food Science, Gastroenterology

The question is too generalist. Can all fishes permanently live in the Loch Ness? The variety of potential probiotic species is huge, moreover is strain dependent. So, it is imposible to answer this question.


Do probiotics permanently colonise the gut?

Dr. Ashok Kumar Pattanaik has answered Unlikely

An expert from Indian Veterinary Research Institute in Animal Production, Nutrition, Health

My experience while working on allochthonous probiotics (a probiotic bacteria, derived from one species and fed to a different species; for example, a diary-origin bacteria used in the diet of human or dog or pig) was that the probiotic-effects disappears within a fortnight of its withdrawal from the diet, indirectly proving that it does not colonize permanently.

However, I cannot say the same about the autochthonous probiotics (a probiotic bacteria, derived and used in the same species; for example, a human-origin bacteria used in the diet of dogs or fish).


Do probiotics permanently colonise the gut?

Bernhard Paetzold has answered Near Certain

An expert from S-Biomedic in Microbiome

The difficulty of this question is around what is a Probiotic. There is clearly science that applied bacterial strains can colonize long term the gut. However at the same time we see that not every strain that we swallow (including gut bacterial species) will colonize. See this publication for another interesting view on this.

If the question is will a random pill containing some Lacto or bifido bacteria colonize my gut. The answer is “Uncertain”

If the question if a bacteria in yoguhrt with Probiotics will colonise the gut the answer is: Unlikely

In Summary: It will depend on the exact strain of probiotic, its way of application/ingestion and the existing microbiome of the host whether a bacterial strain will permanently colonise the gut.


Do probiotics permanently colonise the gut?

Bruno Pot has answered Unlikely

An expert from Vrije Universiteit Brussel in Microbiology

Colonization time will indeed depend on the strain and the age of the consumer. Permanent colonization (life-time long) is extremely unlikely and is also not wanted for probiotics (for safety reasons, explained in the paper below). You are likely to find other answers in this paper as well:


Do probiotics permanently colonise the gut?

Philippe Langella has answered Unlikely

An expert from Institut National de la Recherche Agronomique in Microbiology

My feeling is that by definition, the traditional probiotics as lactobacilli or bifidobacteria will not colonize the gut of an healthy volunteer in which they will only transit. Such probiotics could persist in the gut between 2-3 days for lactobacilli and 5-7 days for bifidobacteria but they won’t colonize the gut. That’s why the probiotics should be taken daily as they won’t persist.

Since 10 years, the probiotics domain has been enlarged to next generation probiotics (NGps) which are commensal bacteria identified on the basis of human clinical data. Such NGPs have more chance to colonize that the traditional probiotics but event in this case, this possible colonization willl depend on the quality of the gut environment: a good healthy gut environment won’t facilitate a possible colonization whereas a more dysbiotic one will facilitate such event.

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