Coprophagy is the eating of excrement and is a normal nutritional behavior for rats. It is essential for the maintenance of healthy gut flora and for the recovery of nutrients.

Rats have a simple stomach as opposed to ruminants (which have compartmentalized stomachs) such as cows, goats, and sheep. Without the multiple digestive compartments to aid in breaking down food, essential nutrients are not digested and are passed in the feces.

In a simple stomach digestive system the ingested food moves more rapidly than in the ruminant system. Microbial fermentation of the food occurs in the caecum, which is a pouch located at the beginning of the colon (also known as hind-gut fermentation). Cellulose (plant) fibers are not effectively broken down during this process.

Eating of the feces allows the recovery of nutrients that were not utilized during the first pass through the digestive system.

Rats excrete two types of feces, similar to those observed in rabbits. One type, hydrous feces, is not found in the cages of free-moving rats. It differs in smell and texture from the usual more firm feces obtained after conventional feeding.
Hydrous or soft feces (caecotrophes) are held within the anus and usually eaten directly from the anal orifice. Termed caecotrophy, this behavior has been described as being specific to rabbits. Sukemori, Kurosawa, et al. (2006) suggest that this behavior may also take place in rats, as hydrous feces are not found on the floor of their cages. However, the behavior is not specifically described.
It is believed that the soft or hydrous feces is covered with a mucus membrane that, once entering the stomach, slows down the digestive process of the feces and promotes fermentation; thus, allowing a more effective breakdown of nutrients.

Rats are typically known as being coprophagic, ingesting their fecal pellets or those of their cage mates from the floor of the cage.
A nutritional study has noted that rats prefer to ingest their feces produced during the last half of their diurnal defecation period. The study also shows it appears to have a higher nutrient content than that which is excreted during the first half of the period. While the rat is not recognized as a caecotrophe producer (or engaging in caecotrophy), differentiation of excreta on the basis of nutrient or moisture content implies nutritional benefit from coprophagy is not unlike that observed in rabbits¹.

Rats will regulate the amount of feces eaten according to their nutritional needs, and will eat between 0-11 percent of their own feces when fed a nutritionally complete diet. Thiamin and pantothenic acid deficiencies will cause a marked increase in coprophagy. Pregnancy increases nutritional needs and will also result in a normal increase in coprophagic behavior.
Preventing rats from eating their feces can lead to deficiencies of vitamin K, complex B vitamins, and biotin and can cause other vitamin deficiencies to develop. Rats, when not permitted to ingest their fresh feces show a stunted growth rate. Even if allowed to eat only the dry feces the benefits of coprophagy are still not fully attained.

References

1. Cree, T., Wadley, D., & Marlett, J. (1986). Effect of Preventing Coprophagy in the Rat on Neutral Detergent Fiber Digestibility and Apparent Calcium Absorption. J. Nutr., 116(7), 1204-8.
2. Donnelly, T., & Brown, C. (2007, February 8). Rodent Husbandry and Care. VeterinaryPartner.com. Retrieved January 28, 2012, from http://www.veterinarypartner.com/Content.plx?P=A&A=2497
3. Besselsen, D. (n.d.). Biology of Laboratory Rodents. Retrieved December 18, 2008, from https://uac.arizona.edu/VSC443/rodentbio/rodentbio.html.
4. Fajardo, G., & Hörnicke, H. (1989). Problems in estimating the extent of coprophagy in the rat. Br J Nutr, 62(3), 551-61. Retrieved December 18, 2008, from the Medline database.
5. Franz, R, M Kreuzer, et al. (2011). Intake, selection, digesta retention, digestion and gut fill of two coprophageous species, rabbits (oryctolagus cuniculus) and guinea pigs (cavia porcellus), on a hay-only diet. J Anim Physiol Anim Nutr (Berl) 95(5): 564-570.
6. Sukemori, S, A Kurosawa, et al. (2006). Relationships between coprophagy and nutrients intake of rats. Vitamins (Kyoto) 80(9): 457-464.