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We adopted a 2.5 year old possible dalmation/hound/pit terrier mix from the shelter about 2 weeks ago. She stays in a kennel inside the house when we're at work. She does have some separation anxiety issues. When we're home, she always has to be in close proximity to someone and she doesn't like to be outside unless there's someone with her. We have a camera on the kennel so I know that she barks and whines when we leave for a little while but tends to settle down fairly quickly.

Well this week, it rained one day and she hates water so she barely spent anytime on the grass. I let her outside three different times that morning before leaving for work to try to get her to do something. I put her in her kennel and 10 minutes after I had left, she pooped in it.

The next morning, the grass was a little wet from dew and she did not like being on it so I walked around on it with her for about 10 minutes. After I left for work, it took her even less time to poop in her kennel, she also peed this day. At this point I was concerned she might be sick so I took her to the vet that day. She tested negative for worms and everything. The vet said she had a very low bacterial count in her stool so she gave us some prebiotic powder but said that normally wouldn't result in issues like this.

Yesterday morning I walked with her outside again and she didn't do anything. I took her to the front yard on a leash to see if that could change anything but she was too distracted to go. It look about 5 minutes after I left for her to poop and pee again.

This morning I'm off from work so she's not in her kennel and she has yet to use the bathroom today. She also has no interest in eating her breakfast which isn't normal.

I've tried feeding her earlier in the morning to give her more time and removing bedding from the kennel. Any ideas of how I can get this dog to poop outside again? She hasn't had any issues up to this point. She's not clean about using the bathroom in the kennel either. She has no problem rolling around in it. I can't keep spending my lunch break giving her a bath which is a fight since she hates water so much. Please help me!
 

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I wonder if she has been scolded or punished for accidents, which makes dogs reluctant to toilet where their people are - they wait until the people are elsewhere.

I'd treat her like a pup. Take her out - stay out if you can. Or, come back in but go out again 5 minutes later. When she toilets outside (as she eventually must) go overboard with praise and reward. Immediately so that it's clear that it's for toileting and not for anything else. When it clicks that outside toilets earn fabulous rewards, and indoor toilets earn zero, that's when she will try to hold her toilet.
 

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If she's not overly anxious being outside when accompanied by a person, I'd probably start by taking her for long walks on a consistent schedule. Moving the dog also moves their bowels, so if you give her a long enough walk at the right time there's a pretty high chance she'll do her business outside - which you can then reward.
 

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It sounds like you have several things contributing to the messy outcome
1) I agree with JoanneF's thought that she might be nervous about toileting within view of someone
2) It's possible she had previously been kept kenneled so much, with so little opportunity to potty outside, that she now thinks it's normal to foul her bed
3) Her fear of water could certainly be discouraging her from wanting to toilet outdoors
4) Separation anxiety can trigger potty accidents

I wonder if she would be more likely to poop if you got up half an hour earlier in the morning and took her for a longer walk, especially if you could get her to an area big enough to let her wander on a longer leash. Sometimes physical exercise stimulates the need to pee and poop. The longer leash might make her less nervous about toileting in your vicinity.

Since you and your husband both work, it sounds like there isn't really a good choice other than to leave her kenneled during the day. You don't want her soiling other parts of the house or chewing the woodwork in her distress. However, I wonder if you could at least reduce the amount of mess created if and when she does toilet in her kennel. Normally you would put the dog into a just big enough for the dog to lie down, as most dogs don't want to soil their bed. Theoretically by giving the dog nothing but bed, you stop the dog from soiling the kennel. In her case, though, it's pretty clear that she has already learned to soil her bed.

I wonder if it might be better to do the exact opposite: give her a 48 inch kennel or even lash two kennels together. I'd put her bed on a raised platform on one end to reduce the chances of the bedding getting soaked if she does pee.
Put a pee pad (if she can be trusted not to chew it) at the opposite end of the kennel. A pee pad inside a dog sized litter pan would be even better if you have enough room. By giving her a bedroom suite with attached bathroom, she might begin to relearn the idea of not fouling where she sleeps.

I don't normally advocate pee pads, but getting her used to the idea of using one might help. For the next few weeks she could avoid rain and wet grass entirely if she is wiling to use one. Later you could use the soiled pad to help retrain her to pee outside. Take one of the soiled pads to her toilet spot outside and let her sniff it. Thinking she has already peed in that spot will help reassure her it's an ok spot to use.
 
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