FIG 7 .

A model of gut microbial succession after cholera. Our analyses suggest three groups of bacteria colonize the gut after cholera: an Early-Stage, a Mid-Stage, and a Late-Stage group. Initially, diarrheal infection and antibiotic treatment clear bacteria from the gut, allowing host-secreted oxygen and carbohydrates to accumulate (boxes around variables indicate elevated levels) (step 1). Early-Stage facultative anaerobes tolerate the elevated oxygen levels and are the first bacteria to recolonize; these bacteria are also likely to be introduced by ingested foods (step 2). Aerobic respiration by the Early-Stage microbes lowers oxygen tensions to the point where Mid- and Late-Stage obligate anaerobes can begin recolonizing the gut and better exploit built-up levels of carbohydrates. Phages targeting Early-Stage bacteria may hasten decreases in these bacteria (step 3). After several weeks, resource competition between Mid- and Late-Stage microbes for resources returns carbohydrates to normal levels and leads to the decline of the Mid-Stage group (step 4).