From what I understand, the two largest type of bacteria in the human gut are lactobacillus and bifidobacteria. You can get lactobacillus from fermented foods, but I believe that the only natural source of bifidobacteria is breastmilk.
For the past few months, I have been consuming only plant-based lactobacillus bacteria, trying to mimic the type of bacteria a person could consume in a natural (Paleo) environment. However, the more I look into bifidobacteria, the more important it seems.
For many newborns, the gut gets populated with bifidobacteria through breastmilk. Breastmilk contains a very high concentration of bifidobacteria. Some formulas now try to mimic this, but it is unclear as to how effective they are.
However, if a child isn't breastfed, then how would they ever get bifidobacteria in their gut? Adding lactobacillus won't help. Adding prebiotics may help, but usually this increases the amount of bifidobacteria already in the gut. If the bifidobacteria is not there in the first place, then I'm not sure how much the prebiotics can help.
There are a couple of studies that focus on the importance of bifidobacteria. This older study looks at the relationship between breatfeeding and obesity. It finds that breastfeeding for 3 to 6 months leads to a 35% reduction in the odds a child will be obese upon beginning school.
This study that was just published looks more at bifidobacteria and obesity. It found that by giving mice bifidobacteria, it reduced food intake, body weight, and lipids.
Most likely in Paleo times, bifidobacteria in the gut was stable throughout the lifetime. It was implanted through breastfeeding and then remained there over the years. Today, you have a variety of novel elements which can reduce bifidobacteria: antibiotics, oral contraceptives, food additives, pollution, etc.
Therefore, even though it may be "unnatural" to supplement with bifidobacteria since it doesn't naturally occur in food, it may in fact improve health in the modern world.