Hello, my name is***** and I have over 20 years of experience as a veterinarian. I am sorry to hear that your fellow Cooper is leaving behind a bloody discharge from his bottom in his bed for the past couple of months, and has a distinctive odor associated with the discharge.
From your description it appears that this improves with antibiotic use, but always returns.
That history would make me suspicious of an infection that we are somewhat suppressing with antibiotic use, but not addressing completely.
Although colitis could cause blood in the stools and a foul odor I would expect that we would also see loose stools and mucous in the stools throughout the day too. Since this discharge only seems to occur when he is relaxed and sleeping and his stools otherwise are normal then the infection would most likely be in his anal glands.
The infection can be a primary problem that we haven't addressed properly, or it can be related to autoimmune conditions such as perianal fistulas, or a mass in his anal gland or colon.
At this point I highly recommend that your fellow be rechecked by his veterinarian and his anal glands be palpated for any signs of a mass, emptied completely and infused with an antibiotic/anti-inflammatory ointment to treat the gland directly. Many times that is the best way of clearing the infection. In cases like his where the problem has been long standing I have the pup return in 10-14 days and reinfuse the glands a second time as a precaution.
If he has lesions on the outside of his anus too then we may need to consider that he has a perianal fistula too. While treating the anal glands is a good start he may need the fistulas treated too long term to prevent reoccurrence. If the problem returns even with treating the anal gland that should be done. Perianal fistulas are addressed with antibiotics to treat secondary infections, steroids like prednisone and/or cyclosporine to quiet the inflammation and then a topical immune suppressant, either cyclosporine or Tacrolimus.
We will often put these pups on a hypoallergenic diet too.
Please let me know if you have any further questions.