You are right to question that. I should correct myself.
"Oxidized bile creating dark flecks from normal gut bacteria" is not a well-supported, specific cause of black specks. I included it too casually and it was not accurate in the way I stated it. I should not have listed it as a distinct cause. I apologize for the imprecision.
Here is what the evidence actually shows for black specks in breastfed baby stool:
Actual Well-Supported Causes of Black Specks in Infant Stool
1. Iron in vitamin/supplement drops (most likely in your baby's case)
Iron supplements or iron-containing multivitamin drops are a well-known and leading cause of black/dark specks or dark-green-to-black discoloration in infant stool. Unabsorbed iron oxidizes in the gut and produces dark particles. Your baby is getting multivitamin drops - this is almost certainly the main explanation here.
2. Swallowed maternal blood
If a breastfeeding mother has cracked or bleeding nipples, the baby swallows small amounts of blood. Digested blood turns black and appears as dark specks - they can look like "poppy or sesame seeds," as
BabyCenter describes. Worth checking if your nipples are sore.
3. Upper GI bleeding (must rule out)
Black, tarry stool throughout (not just specks) - called melena - means blood digested from the upper digestive tract. This is a warning sign. But scattered tiny specks in an otherwise well baby on iron supplements is a very different picture from this.
What You Can Disregard
The "oxidized bile from gut bacteria" line I wrote - there is no strong, specific clinical evidence that this produces visible black specks as a distinct phenomenon in infants. Bile does get chemically modified by gut bacteria, but this does not produce distinct black flecks as a recognized clinical entity. I should not have listed it.
Bottom line: Given that your baby is on multivitamin drops containing iron, that is by far the most likely and straightforward explanation for the black specks you are seeing. The overall picture - yellow-green, loose, seedy stool with tiny dark specks in a healthy breastfed 5-month-old on vitamin drops - is reassuring. But if you notice the specks increasing, the stool turning uniformly dark/tarry, or your baby showing any signs of illness, have a pediatrician check.