There is no single list of bacteria that defines a healthy gut microbiome.
Two healthy people can have quite different microbial communities.
What may matter just as much as which microorganisms live in the gut is what those microorganisms actually do.
They help process food
Some components of our diet cannot be fully digested by human enzymes alone.
Gut microorganisms help break down these substances, particularly dietary fiber, producing compounds that can be used by both the gut and the rest of the body.
Among the most important are short-chain fatty acids, including butyrate.
These microbial products are one of the major ways in which the microbiome communicates with human cells.
They help support the intestinal barrier
The intestinal lining creates an important boundary between the contents of the gut and the rest of the body.
Microbial metabolites such as butyrate can provide energy for cells lining the colon and contribute to normal intestinal barrier function.
This matters because the gut barrier and the microbiome are closely connected with the immune system.
They interact with immunity and inflammation
The microbiome is in constant communication with our immune system.
A balanced relationship can help maintain appropriate immune responses. Disturbances in the microbial ecosystem, on the other hand, have been associated with chronic low-grade inflammation.
Recent research illustrates this connection.
In a large population study, different gut microbiome profiles were associated with substantial differences in systemic inflammatory markers. A high-diversity profile was associated with lower inflammation, while another microbiome pattern was associated with higher levels of markers including CRP, IL-6 and TNF-α.
They are connected with metabolism
Gut microorganisms and the compounds they produce also interact with metabolic processes.
Different microbiome profiles have been associated with differences in body weight, triglycerides, HDL cholesterol and cardiorespiratory fitness.
This does not mean that gut bacteria alone determine metabolic health. Diet, physical activity, medications, genetics and many other factors remain important.
But it shows why scientists increasingly view the microbiome as part of a larger biological system connecting the gut, metabolism and immune function.
So what makes a microbiome healthy?
We cannot yet define one ideal microbiome that everyone should have.
But we know more than simply “nothing.”
A healthier microbial ecosystem appears to combine diversity with useful biological functions — processing components of food, producing beneficial metabolites, supporting the intestinal environment and interacting appropriately with metabolism and immunity.
Based on Research
Eriksen C, Chatzigiannidou I, Dehli RK, et al. Gut microbiota composition outperforms chronological age in predicting systemic inflammation and incident disease risk. Nature Communications. 2026.
