Probiotics can evolve to be harmful? Experts slam reporting of new mouse study...but note opportunity in the science

By Nathan Gray contact

- Last updated on GMT

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Multiple experts have questioned news reports claiming probiotics can evolve to do more harm than good – warning that news reports have vastly over-simplified and sensationalised the findings.

Last week, multiple news outlets ran with headlines suggesting ‘bacteria in probiotics can evolve in your gut and turn nasty’​ – warning that “a new experiment on mice has shown how our microbial allies can evolve into traitorous backstabbers that risk causing damage to our guts.”

The mouse study behind the headlines, published in Cell Host & Microbiome, ​shows that the strain of strain of Escherichia coli (E. coli) used is able to evolve once inside the gut ecosystem of a mouse, while under experimental conditions – and has the potential to become less effective and sometimes even harmful.

The team reported that E. coli​ Nissle (EcN) accumulates genetic mutations that impact carbohydrate utilisation, stress response, and adhesion to gain competitive fitness, while previous exposure to antibiotics reveals an acquisition of resistance.

While the study behind the headlines does raise some interesting questions, experts have been quick to tell NutraIngredients that the methods involved in the study mean findings the suggestions of ‘harm’ cannot be generalised from mice into humans – and that the reporting of the study has been irresponsible in places.

Dr Jessica Terhaar, scientific diretor at the International Probiotics Association told us that the paper was ‘interesting’, but that “there are some questions as to the validity of the results.”

“Let’s not forget that studies in this area of biomedical and microbial engineering are limited thus far to only results of preclinical efficacy and this study only check for stability of their engineered gene over one week,”​ she said.

Meanwhile, Professor Gregor Reid of the Lawson Health Research Institute and Western University, Canada, noted added that the study “shows that just because a probiotic strain like E. coli Nissle 1907 has been safe and effective in humans for many years doesn’t mean it can help mice”

“The reporting of the paper shows that no matter how many times we tell people what probiotics are, the reporters find ways to get it wrong,"​ said Reid. "It would be hilarious if it wasn't so frustrating and a serious flaw in how scientific studies are communicated.”

What did the study find?

The two-part study started by exposing the EcN strain to mouse gastrointestinal tract over several weeks, and systematically altering diet and background microbiota complexity.

The researchers, led by senior author Gautam Dantas from Washington University School of Medicine in St. Louis, used mice that harboured four kinds of gut microbiomes: one with no pre-existing bacteria; another with a limited set of bacteria, characteristic of an unhealthy gut; a normal microbiome; and a normal microbiome after antibiotic treatment.

They gave the mice the EcN strain and then varied the food the mice ate – giving them either mouse chow, high-fibre pellets that mimic the natural mouse diet; high-fat, high-sugar, low-fibre pellets meant to model typical Western eating habits; and Western pellets plus fibre.

After five weeks, they then sampled the bacteria from the mice's guts and analysed the microbes' DNA.

Dantas and colleagues reported that EcN's DNA changed and they developed new capabilities after living in mice's intestines for a few weeks.

Under some conditions, the strains even turned on their hosts and acquired the ability to eat the protective coating on the intestine, noted the researchers – who noted that destruction of this layer has been linked to irritable bowel syndrome.

The mice's diets and the make-up of their gut bacterial community influenced how much the probiotic evolved and in what ways, they added.

"In a healthy, high-diversity background we didn't capture a lot of adaptation, maybe because this is the background that Nissle is used to,"​ said Aura Ferreiro, one of the first authors of the study.

"But you have to remember that quite often we wouldn't be using probiotics in people with a healthy microbiome. We'd be using them in sick people who have a low-diversity, unhealthy microbiome. And that seems to be the condition when the probiotic is most likely to evolve."

However in all cases mice were given an artificial gut from humans, noted experts commenting on the study.

“None of them had a native murine gut,”​ noted Terhaar of the IPA. So it remains to be seen if they are actually studying the effect of adding artificial microbes into a sterile mouse gut with a specific diet or the actually evolutionary trajectory of wild type and engineered EcN strains.”

“The results could just be an artifact of the experimental conditions.”

Dr Arthur Ouwehand of the IPA and DuPont Health and Nutrition also noted that while it may be understandable, it is ‘especially’ unfortunate that the authors generalise their findings from EcN to the whole probiotics category.

“Most commercial probiotics are Gram positive. E. coli Nissle is one of the few Gram negative probiotics,”​ he noted.

“I do not wish to single out Gram negatives, but they are of course very different in terms acceptance and transfer of genetic material and genetic stability compared to the usual Gram positive lactobacilli and bifidobacteria.”

Furthermore, he questioned whether any of the changes actually transformed a benign strain into a dangerous organism.

“That apparently did not happen as no unexpected deaths or abnormalities were reported in the paper,”​ he noted

PKU study

In the second part of the study Dantas and his colleagues applied the initial findings to designing a potential probiotic therapy for phenylketonuria (PKU).

People with PKU are unable to break down phenylalanine, a protein building block found in many foods. High phenylalanine levels cause brain damage, so people with PKU must strictly adhere to a low-protein diet.

The team inserted a gene into EcN that gave the bacteria the ability to degrade phenylalanine into a compound that is safely excreted in the urine. Then, they gave the bio-engineered bacteria to mice that lacked the capacity to metabolize phenylalanine.

The next day, phenylalanine levels in some of the mice had dropped by half.

Moreover, the researchers did not find significant changes to the DNA of the engineered strain after one week of treatment, suggesting the EcN strain could be safe to use as a chassis for probiotic therapies over short time scales.

Opportunity or problem?

Dantas added that ‘evolution is a given’ – adding that the study outlines important questions on how to monitor safety but also provides potential opportunities.  

Indeed, he suggested the finding that probiotics evolve and behave differently in individuals with disparate microbiomes and diets opens up avenues for personalising probiotic-based therapies.

"There is no microbe out there that is immune to evolution,”​ said Dantas.

This isn't a reason not to develop probiotic-based therapies, but it is a reason to make sure we understand how they change and under what conditions."

Ouwehand noted that the study does raise a point in that conventional safety testing may not be appropriate for living entities such as probiotics.  

“Hence testing for presence of transferable antibiotic resistance in probiotics and in Europe, Enterococcus is not on the QPS list as it may facilitate the transfer of genetic material,”​ he said.

Terhaar noted that the potential evolution of not just the EcN strain but all strains and commensal bacteria should be looked into further.

However, putting this in context: there are thousands of bacterial species in the human gut, so to track and identify whether or not a particular mutation / adaptation is significant in the mix of things would be very difficult to do I imagine,”​ she noted.

“Everything is going to evolve,"​ Dantas reiterated. "We don't need to be scared of it.We can use the principles of evolution to design a better therapeutic that is carefully tailored to the people who need it.”

“This is an opportunity, not a problem."

Source: Cell Host & Microbiome
Published online ahead of print, doi: 10.1016/j.chom.2019.02.005
“Adaptive Strategies of the Candidate Probiotic E. coli Nissle in the Mammalian Gut”
Authors: Nathan Crook, et al

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