Forest will initially pay $70m for joint development and commercialisation rights to linaclotide, a guanylate cyclase type-C (GC-C) receptor agonist.
Profits from the US will be shared, with Forest getting exclusive rights in Canada and Mexico, and Microbia retaining everywhere else.
The deal could eventually be worth up to $330m plus royalties.
As well as treating constipation-predominant IBS (IBS-C), the oral drug is also being tested as a therapy for chronic constipation (CC).
As many as 26 million Americans suffer from CC, and the discomfort of CC significantly affects patients' quality of life by impairing their ability to work and participate in typical daily activities.
One out of six adults in developed countries suffers from IBS and the condition accounts for 12 pre cent of adult visits to primary care physicians in the US. GC-C is an enzyme found in the lining of the intestine.
It is the key receptor for enterotoxin proteins, which kill cells in the intestine wall.
Normally, this causes fluid to leak into the intestinal tract and causes diarrhoea.
Linaclotide is currently being tested for these indications in a pair of Phase IIb trials, which together will enrol 700 patients.
In trials so far, the drug has been shown to improve bowel function and in preclinical testing it increases fluid secretion into the intestine, accelerates intestinal transit, and decreases visceral pain.
The companies intend to begin Phase III trials in the second half of 2008.
"Linaclotide offers the possibility of genuine relief for the millions of patients suffering from chronic constipation and IBS-C, for which there are currently few treatment options," said Howard Solomon, CEO of Forest.
"Joining forces with Forest is the best way to maximize linaclotide's value for patients and investors," said Peter Hecht, Microbia's CEO.
The deal seems to have come about, at least in part, due to Forest's established connections between its sales force and primary care physicians, with both CEOs mentioning this area.