We may finally know what a healthy gut microbiome looks like (Dec 2025, n=34,694) Gut micro-organisms associated with health, nutrition and dietary interventions Testing

[Michael Harrop]

https://www.newscientist.com/article/2508109-we-may-finally-know-what-a-healthy-gut-microbiome-looks-like/
https://www.nature.com/articles/s41586-025-09854-7

Previous measures mainly looked at species diversity, with a greater array of bacteria being better. But it is difficult to identify particular communities of interacting organisms that are implicated in a specific aspect of our health, because microbiomes vary so much from person to person.

“There is a very intricate relationship between the food we eat, the composition of our gut microbiome and the effects the gut microbiome has on our health. The only way to try to map these connections is having large enough sample sizes,” says Nicola Segata at the University of Trento in Italy.

To create such a map, Segata and his colleagues have assessed a dataset from more than 34,500 people who took part in the PREDICT programme in the UK and US, run by microbiome testing firm Zoe, and validated the results against data from 25 other cohorts from Western countries.

Of the thousands of species that reside in the human gut, the researchers focused on 661 bacterial species that were found in more than 20 per cent of the Zoe participants. They used this to determine the 50 bacteria most associated with markers of good health – assessed via markers such as body mass index and blood glucose levels – and the 50 most linked to poor health.

The 50 “good bug” species – 22 of which are new to science – seem to influence four key areas: cholesterol levels; inflammation and immune health; body fat distribution; and blood sugar control.

As to the specific species that were present, most microbes in both the “good” and “bad” rankings belong to the Clostridia class. Within this class, species in the Lachnospiraceae family featured 40 times, with 13 seemingly having favourable effects and 27 unfavourable.

The link between these microbes and diet was assessed via food questionnaires and data logged on the Zoe app, where users are advised to aim for at least 30 different plants a week and at least three portions a day of fermented foods, with an emphasis on fibre and not too many ultra-processed options.

This doesn’t mean the ideal healthy gut microbiome has been pinned down, though.

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Ended with a big caveat there.

Abstract​

The incidence of cardiometabolic diseases is increasing globally, and both poor diet and the human gut microbiome have been implicated1. However, the field lacks large-scale, comprehensive studies exploring these links in diverse populations2.

Here, in over 34,000 US and UK participants with metagenomic, diet, anthropometric and host health data, we identified known and yet-to-be-cultured gut microbiome species associated significantly with different diets and risk factors. We developed a ranking of species most favourably and unfavourably associated with human health markers, called the ‘ZOE Microbiome Health Ranking 2025’.

This system showed strong and reproducible associations between the ranking of microbial species and both body mass index and host disease conditions on more than 7,800 additional public samples. In an additional 746 people from two dietary interventional clinical trials, favourably ranked species increased in abundance and prevalence, and unfavourably ranked species reduced over time.

In conclusion, these analyses provide strong support for the association of both diet and microbiome with health markers, and the summary system can be used to inform the basis for future causal and mechanistic studies. It should be emphasized, however, that causal inference is not possible without prospective cohort studies and interventional clinical trials.

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