A group of scientists in Israel claim foods that are packed with good bacteria - called probiotics - are almost useless.
Their study is among the most detailed analyses of what happens when we consume probiotics.
They are seen as healthy and good for the gut, but the results found they had little or no effect inside the body.
The researchers said probiotics of the future would need tailoring to the needs of each individual.
The team at the Weizmann Institute of Science made their own probiotic cocktail using 11 common good bacteria including strains of Lactobacillus and Bifidobacteria.
It was given to 25 healthy volunteers for a month.
They were then sedated and samples were surgically taken from multiple places in the stomach and small and large intestines.
The researchers were looking to see where bacteria successfully colonised and whether they led to any changes in the activity of the gut.
The results in the journal Cell, showed in half of cases the good bacteria went in the mouth and straight out the other end.
In the rest, they lingered briefly before being crowded out by our existing microbes.
- You're more microbe than human - if you count all the cells in your body, only 43% are human
- The rest is our microbiome and includes bacteria, viruses, fungi and single-celled archaea
- The human genome - the full set of genetic instructions for a human being - is made up of 20,000 instructions called genes
- But add all the genes in our microbiome together and the figure comes out at between two million and 20 million microbial genes
- It's known as the second genome and is linked to diseases including allergy, obesity, inflammatory bowel disease, Parkinson's, whether cancer drugs work and even depression and autism
Trillions of bacteria call the lining of our guts home and everyone has a different mix of microbial inhabitants.
Dr Eran Elinav said it was wrong to expect an off-the-shelf probiotic to work for everyone.
He says that in the future probiotics will need to be tailored to the needs of individual patients.
He told the BBC: "And in that sense just buying probiotics at the supermarket without any tailoring, without any adjustment to the host, at least in part of the population, is quite useless."
The research group also looked at the impact of probiotics after a course of antibiotics, which wipe out both good and bad bacteria.
Their trial on 46 people, also in the journal Cell, showed it led to delays in the normal healthy bacteria re-establishing themselves.
Dr Elinav added: "Contrary to the current dogma that probiotics are harmless and benefit everyone, these results reveal a new potential adverse side effect of probiotic use with antibiotics that might even bring long-term consequences."
There have been some proven benefits of probiotics, notably in protecting premature babies from necrotising enterocolitis.
And there remains great hope within science that understanding the complex relationship between the microbial and human parts of our body will lead to new treatments.
However, Dr Trevor Lawley, a microbiome researcher at the Sanger Institute, said he was not surprised by the findings.
He told the BBC: "Probiotics have been around for a long time and they're coming under more scrutiny.
"These are very innovative studies, but they are preliminary findings that need replicating.
"The gut has a natural property to stop colonisation, as it usually blocks pathogens, and that is something we have to outmanoeuvre."
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