Recently, the gut microbiome has become a focal point in health science, captivating both scientists and the general public. This interest largely stems from its links to overall health and various diseases, such as type 2 diabetes and heart conditions. Plus, it’s something that can be influenced, which makes it even more appealing. Nevertheless, the science behind gut microbes is still evolving, and there’s a lot left to uncover.
A study recently published in Nature has provided significant insights into the human microbiome. The researchers examined gut microbiomes, diets, and health indicators from more than 34,500 participants in the US and the UK. They found connections between hundreds of specific gut microbe species and critical health and dietary markers. This data originated from the Zoe PREDICT program, managed by the microbiome testing firm, Zoe.
A new microbiome ranking system
The study employed machine learning to connect certain gut microbe species among the 34,694 participants to diet and recognized health risk factors like body mass index (BMI), triglycerides, blood sugar, and HbA1c levels, as well as various clinical markers that reflect cardiometabolic health. From the 661 microbial species analyzed, the researchers focused on 50 that showed the most positive associations with good health and 50 that had the least favorable associations.
This led to the creation of the “ZOE Microbiome Health Ranking 2025” and the “Diet Ranking 2025.” These rankings evaluate microbes on a scale from 0 to 1, where those nearer to zero are linked positively to health indicators, while those closer to one have negative correlations. The evaluation included all 661 microbes studied.
Linking gut bacteria to key health indicators
The ranking system identified many gut microbe species—referred to as species-level genome bins (SGBs)—that are significantly linked to health markers and dietary quality. Favorable microbes tended to be found more often in individuals with lower BMI and fewer health issues, whereas unfavorable microbes were more prevalent among those who were obese or had diseases. A specific part of the study gauging BMI categorized 5,348 healthy participants into three groups: healthy weight, overweight, and obese.
The research noted that “linear regression analyses showed that individuals with healthy weight carried, on average, 5.2 more of the 50 favorably ranked SGBs compared to those with obesity,” the authors mentioned.
Moreover, the study examined if the ZOE health-ranked SGBs were more abundant in those with certain diseases. They discovered that individuals in the control group possessed higher counts of positively ranked gut microbes than those with diseases, who in turn had a higher presence of negatively ranked microbes.
Linking gut bacteria to diet
Additionally, dietary changes were shown to improve the presence of beneficial microbes while reducing harmful ones. The researchers analyzed data from two studies known as ZOE METHOD and BIOME, where participants followed personalized dietary intervention programs aimed at enhancing their microbiomes or took prebiotic supplements. The microbiomes of these participants demonstrated notable changes by the studies’ end.
The authors explained, “Both clinical trials focusing on dietary improvement—through a prebiotic blend for BIOME and a personalized dietary plan for METHOD—showed a significant increase in favorable SGBs. Notably, we observed rises in Bifidobacterium animalis, commonly found in dairy products, as well as new Lachnospiraceae species associated with both vegan and vegetarian diets.”
In addition to linking known bacterial species to health markers and dietary habits, the study identified several key microbes that had not been previously characterized. Future research could potentially provide more detailed descriptions of these newly discovered species. While this is an observational study and can’t definitively establish causation between gut microbes, diet, and health, these new rankings offer a foundation for future investigations into these relationships, potentially including more diverse populations and direct interventions.
