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Somethings cross into the milk but probiotics generally help the dogs gastrointestinal health and digestion which in turn help her produce healthy milk with the proper good bacteria the pups need. THey usually get their immunity from the dam's milk in the first 24 hours. You will be starting to wean the pups at about 3 weeks of age. You could add a little probiotics to their food at that time if you wanted. That will be a more important period in their lives as they transition onto solid food. Generally feeding a good high quality puppy food is enough for a mother to provide the proper nutritional requirements for her pup. Now the fecal matter of puppies is generally a soft yellowish color to begin with. You usually don't notice it earlier because mom is keeping it cleaned up. So the color alone I wouldn't be too worried about. In addition, the foods you feed can affect the taste of the milke and might lead to some changes in the stool as well. While it may help keep her having a variety, you might want to stick to one diet until they are weaned.
What you do want to look for though is the possibility of herpes. Herpes can be a problem in pups younger than 3 weeks aga. Pups infected with the herpes virus often display a yellow green feces but also tend to cry persistently, have weakness, not much of an appetite, possible bruising on the stomach or pain in the abdomen and even a nasal discharge. If you are not seeing any of those signs, I wouldn't worry too much about the color of the fecal matter.
You do want to start deworming around 2 weeks of age. Your vet can give you their choice of dewormer. You will be deworming mom and pups at the same time. I recommend deworming every 2 weeks until all worms are gone or the pups go to new homes. This allows you to catch any hatching worms before they mature into adults and reproduce.
I'd be ready to deworm and for weaning the pups in the next week or so and monitor the pups for additional symptoms. Here is a site that discusses weaning. I do want to mention that it can take a couple of hours for puppy food to puff up and be suitable to feed to pups.
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