Poor ability to gain or maintain weight can be secondary to heavy parasites infestation, but that is less likely in an adult dog. It can also be due to bacterial overgrowth, an inability due to digest and absorb food due to metabolic organ disease, (especially liver disease), pancreatic disease or endocrine disease (Addison's disease), or primary intestinal disease.
Does he have relatively loose stools as well?
Or does he seem to pass more stool than usual?
Is his appetite very good?
Dogs that have long term intestinal disease have abnormal gut motility, and thus may have some reverse gut motility or stasis and that can lead to vomiting and nausea, thus a loss of appetite. The cramping that comes along with loose stools also affects appetite.
If he has loose stools it is important to describe what sort of loose stools he has to try and localize the problem. Loose, small stools with mucous or bright red blood and straining or urgency to pass stools more frequently point more towards large bowel diarrhea or colitis, whereas watery stools with no mucous, no increased urgency or frequency to go, along with weight loss point more toward small bowel disease.
Chronic intestinal disease can also lead to bacterial overgrowth in the gut. Probiotics such as Fortiflora or Benebac can help replace appropriate bacteria.
I see that he has had stool samples checked to make sure that parasites aren't part of his problem. Have any other diagnostic tests on his stools been checked, such as fecal cultures or smears to look for bacteria or unusual parasites that may be hard to pick up of a regular fecal?
If not I recommend a fecal culture and direct smear to check for abnormal bacteria such as clostridia ect. be done. I would also submit a few fresh stool samples to the laboratory rather than running typical in clinic testing as laboratories have more comprehensive testing ability.
Has he had any blood tests done to look for liver and kidney disease and check for low blood proteins? If not that should be done. Low blood proteins point toward liver disease (lack of production), kidney disease (loss of blood protein through poor kidney filtering ability) or intestinal inflammation and an inability to digest or absorb nutrients from food or loss of proteins through a damaged intestinal wall.
It is quite possible that he has a food allergy/sensitivity or inflammatory bowel disease and that he needs a different low residue, easy to digest food or a hypoallergenic food to be able to properly digest and absorb his food and maintain his weight. I highly recommend a trial of either Hills i/d or Purina Veterinary Diets EN. No treats, table food or edible chewies while he is on his food trial. If he does well he can eat these foods for life as they are balanced. Having had 2 dogs with inflammatory bowel disease I have a personal preference for Purina Veterinary Diets EN. Dogs with food allergies can benefit from Hills z/d or Purina Veterinary Diets HA.
Dogs with inflammatory bowel disease will worsen with stressful situations. There may be times when he will need medications too, such as metronidazole or even steroids if that is his problem, but I have found that a consistent, easy to digest diet is very helpful for long term control.
There are other possibilities too as I mentioned.
Addison's disease, which is a poorly functioning adrenal gland, can lead to chronic diarrhea and vomiting. These dogs cannot handle stress at all because their adrenal gland doesn't produce cortisone when stressed and their electrolytes can be off too if their adrenal gland isn't controlling that normally either. We see vomiting, diarrhea and sometimes physical collapse in severely affected dogs. Testing is an ACTH response test to check adrenal gland function and checking electrolyte levels. Treatment is steroid replacement therapy and electrolyte replacement.
Pancreatic insufficiency is another possibility. These dogs have a pancreas that is unable to produce a normal amount of digestive enzymes, and the amount produced can wax and wane in some cases, especially early in the disease process. Testing is by running a blood test called a TLI which checks for digestive enzymes. Treatment is replacement of digestive enzymes at each meal. An easier to digest food would be expected to create less problems with digestion and as such less diarrhea and better ability to maintain his weight.
In short more diagnostics need to be done. They can be as simple as more fecal checks and cultures, as well as checking pancreatic and/or adrenal gland function. An abdominal ultrasound could be very helpful. Or more invasive testing such as biopsies of his gastrointestinal tract to look for inflammatory bowel disease or infiltrative cancers such as lymphoma an be done.
In the meantime a diet change may help.
Please let me know if you have any further questions.