The gut microbiota consists of all the bacteria, yeasts, and archea found in the intestines, primarily the large intestine. Over the last several years we've begun to see the importance of the gut microbiome. We know it plays a crucial role in immunity, digestion, synthesizing certain vitamins and overall health. We also know that thin people and fat people have a very different collection of microbiota in their guts, and we also know that changing one's diet can also change the microbiota in the gut. A recent study published in the journal Molecular Nutrition and Food Research looked at the gut microbiota in rats who were fed a healthy diet, rats who were fed a junk food diet, and compared these to rats who were fed a healthy diet 4 days a week and fed a junk food diet 3 days a week. It turns out that eating junk food 3 days a week resulted in microbiota that resembled the microbiota of the junk food only rats. So in order to change the microbiota, it is important to be consistent with the healthy diet--at least for rats. There is no reason to think the same wouldn't apply to humans, but the studies haven't been done yet.
As a side note, we're also beginning to see that the gut microbiota influence our food cravings. Microbiota that thrive on junk food could perpetuate the junk food cravings. Food for thought!