Vinegar will not kill off beneficial gut flora, particularly if you are using unpasteurized vinegar with the mother intact. This will actually contribute towards healthy flora in the bowel and can help prevent disease. Mother vinegar contains the very probiotics that promote healthy intestinal flora. If you are using regular, pasteurized vinegar there is nothing in it that will "kill off" anything in the body either unless you are using it in high concentrations.
Mother vinegar has many beneficial bacteria types within it that can benefit our digestive systems and overall health. I've been using it in the water every day for my chickens for many years now and it shows in their health and production levels. I've never had illness or disease of any kind in my flocks and I have hens that still lay every day or every other day in peak season at the ripe old age of 6 and 7 years of age. I regularly keep flocks of 30 or more on free range of dual purpose breeds chosen for exceptional laying, hardy vigor and meaty builds.
I'm currently using it in the water for a batch of 50 CX chickens and have seen their feces go from the typical stinky, liquid stool that is the norm for this breed to normal, formed feces with little smell at all. This indicates a normal, well-cultured intestinal function and it happened as quickly as the first week after they arrived. As day old chicks, I placed it in their water immediately and I started to see changes in the fecal matter within three day's time.
Lactic acid bacteria refers to a large
group of beneficial bacteria that have
similar properties and all produce
lactic acid as an end product of the
fermentation process.
They are widespread in nature and are
also found in our digestive systems.
At least one beneficial bacteria found in unpasteurized vinegar, in particular, that might interest those who are fearful of cocci in new chicks and want to take steps to prevent it.
Pediococcus acidilactici
Pediococcus acidilactici can function as immune modulators. Animals fed with P. acidilactici have shown enhanced immune responses against infectious coccidioidal diseases.
Pediococcus acidilactici is also known to prevent colonization of the small intestine by pathogens like Shigella, Salmonella, Clostridium difficile and Escherichia coli among small animals.
Pediococcus acidilactici has not been stated in any literature to have toxic effects. Another potential benefit of using them as Probiotics is their use as alternative medicines against infectious parasitic pathogens like
Eimeria* in broiler-chicken [6].
*Eimeria, genus of parasitic protozoans of the spore-producing phylum Apicomplexa (previously Sporozoa). Eimeria, which causes coccidiosis in livestock and wild animals, infects mainly the cells of the digestive tract, although it also attacks cells of the liver and the bile duct. Symptoms of infection are diarrhea, weight loss, and general weakness. Eimeria is characterized by spore cases that contain four spores, each with two infective sporozoites. Among the common pathogenic species are E. necatrix and E. tenella (in poultry); E. stiedae (in
rabbits); and E. bovis, E. ellipsoidalis, and E. zuernii (in
cattle).
As for the feed, any unmedicated feed should be fine for your chicks...you don't have to give them starter feeds. I've fed new chicks on layer mash and general flock ration before and they all turn out the same...healthy and thriving, living to be a ripe old age.