Runts who are not submissive but simply lack the ability to position themselves in the litter for proper nourishment are easier to deal with. In extreme cases, they are rejected by the mother and have to be bottle fed. In most cases, they make it to weaning, but will lag in size and ability to thrive during this most important growth period.
When I have a litter of newly weaned puppies, I 'group' feed them so they can learn NOT to be surprised of react negatively to being bumped and pushed by other dogs when they eat. This goes a long way towards desensitizing the pups while they eat so they don't snap at other dogs or children (now and when they get older) when intentionally or accidentally touched during feeding.
When I have a runt puppy, I often can't leave him/her with the others because the runt won't get enough food to stay optimally healthy. What I like to do is to separate the runt...sometimes feeding them separately in their crate (even if the crate is usually shared with siblings during sleep time). This way the runt gets enough nourishment and should rapidly improve in weight. It also reduces the stress the puppy feels during feeding, so it helps reduce anxiety for the runt puppy.
But I quickly found out that if you do this with some runt puppies, they start to feel "superior" to the other puppies. This can make them a little 'bolder' than they should be when they are around their siblings again. This artificial boldness can be detrimental as it can upset the puppy hierarchy. The puppies learn from each other the consequences of what they should or shouldn't do. If a puppy decides that it doesn't have to 'play well with others' you can develop a thorny socialization problem.
So, to counteract this issue, I start separately feeding another puppy as soon as the runt has recovered to a more 'normal' size and weight -- when he/she is beginning to thrive. I start rotating all the puppies (including the runt) between solo eating and group eating. By separating two out, the remaining 'gang' at the group food dish is smaller and more manageable for the runt. And, no puppy is consistently the 'special' puppy. I have had this work to correct this artificial boldness and after a short time, the runt is big enough and socialized enough to eat with its siblings with no outside help.
Even if you don't have an entire litter of puppies to deal with, if you take a runt puppy home and have other dogs that you feed in the same area, you may still feel a need to separate the puppy for awhile because of the pup's fearfulness or agitation at feeding time. I would suggest you might then want to feed the runt in a crate that is very near the other dogs so they can see the bigger dogs but can still feel protected. You have to remember that this puppy just came from a litter where it was pushed around and deprived of access to food. Once it learns that it has free access to its food and doesn't have to equate feeding time to a wrestling match, you can start opening the crate door during feeding -- and eventually feeding your puppy outside next to the bigger dogs.
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