Internal Pathogens:
For simplicity's sake, there are four basic possibilities when it comes to an intestinal problem in marine fish:
- Intestinal worms - Symptoms: White stringy feces, pinched stomach, loss of color, fish eats voraciously but still seems to be losing weight. Treatment of choice: Praziquantel. Alternative treatments: Fenbendazole, Levamisole.
- Internal parasites/flagellates - Symptoms: White stringy feces, pinched stomach, loss of color, fish eats voraciously but still seems to be losing weight. Treatment of choice: Metronidazole.
- Internal infections (bacteria) - Symptoms: Bloating, and lumps or swollen areas on the body. Also, poor water quality can cause/aggravate an internal infection. Treatment of choice: Metronidazole combined with Neomycin Sulfate in a medicated fish food slurry can be a very good full spectrum internal/gut infection treatment, treating both aerobic and anaerobic bacterium.
- Fish constipation (non-disease) - Symptoms: Bloating in stomach area, obvious anal obstruction, rectal prolapse, erratic swimming behavior. Treatments: Feed the fish a peeled boiled pea (high in fiber), dose Epsom salt @ 1 tablespoon per 5 gallons (laxative), dose Kanamycin (Seachem Kanaplex) into a QT (diarrhea is a side effect of kanamycin). ** Constipation is sometimes mistaken for a gas bubble in a fish's swim bladder (or vice versa.) More info on swim bladder disorders here: https://www.reef2reef.com/threads/venting-a-swim-bladder-black-cap-basslet.219954/ **
Does the color of the poop matter? Yes! It has to be
white;
brown stringy poop, for example, can just mean intestinal irritation which requires no treatment.
Internal parasites vs. intestinal worms Since these can be difficult to distinguish, it is best to treat with praziquantel + metronidazole so both pathogens are covered. You can combine different medications (e.g.
Prazipro +
Seachem Metroplex), or
API General Cure contains both.
Food soaking vs. dosing the water Sometimes dosing the water with the above medications can help clear an internal pathogen. After all, fish do drink the water and their skin will absorb medications. However, I feel soaking fish food with medication(s) is the best way to treat intestinal problems for obvious reasons. Food soaking delivers meds directly into the gut where the pathogens live. In order to food soak, you should also use a binder (ex.
Seachem Focus) to prevent the medication from leaching out. Binding also makes the treatment
reef safe.
Endgame Due to the resilience of these critters, it is recommended to treat (or food soak) for a
minimum of 10 days. However, it is not uncommon for symptoms to last for up to 3 weeks.

And just like with any other disease, you will sooner or later run up against a strain which seems resistant to one of the standard treatments. In which case, you should seek out an alternative medication e.g. Using fenbendazole or levamisole in lieu of praziquantel to treat stubborn intestinal worms.