Researchers also found that when looking at effects of food on our "microbiomes," considering the whole diet, not just individual ingredients, is critical.
In the study published in the American Chemical Society's Journal of Agricultural and Food Chemistry, researchers noted that the bacteria in our guts, or our microbiome, play an important role in our health.
When certain populations of bacteria drop, people become more prone to disease. One of the most effective ways to maintain a good balance of the microbes living in our guts is through our diets.
To figure out what dietary ingredients promote helpful bacteria, several studies have looked at the effects of individual fibres and probiotics.
But few researchers had investigated the role of polyphenols, which are common in much of what we consume - spices, teas, fruits and vegetables - or how polyphenols and fibres together help balance our gut microbes.
Researchers in the new study asked 38 healthy adults questions about their diets and figured out which bacteria were present in the participants' stool samples.
Their analysis revealed that pectin, a compound in citrus fruits, lowers the levels of some helpful bacteria.
This is contrary to previous research on pectin alone.
The researchers suggest that pectin interacts with other substances in oranges, leading to this unexpected effect.
Their most novel finding, they said, was that white bread boosted Lactobacillus, a group of beneficial bacteria.