Last week ibdcrohns.about.com cited a study showing that babies given antibiotics in their first year of life had a greater chance of developing ulcerative colitis and Crohn's disease in childhood.

A press release from Digestive Disease Week 2010 (Abstract #95) reads:

Researchers believe that antibiotic use in infants can cause irrevocable impact to developing bowel flora, or bacteria, in the human bowel. Changes or irregularities in bowel flora are thought to be a potential cause of IBD.

source: Antibiotic Prescriptions in the First Year of Life Increases the Risk of Pediatric Inflammatory Bowel Disease: A Population-Based Analysis

In other words:

Antibiotic Use¹ -> Intestinal Flora Changed -> Higher change of developing Crohn's/Ulcerative Colitis

The researchers note that this study, using a Canadian population, was relatively small.  The doctors matched medical and prescription records of 36 children with IBD to 360 children without IBD.  However, the data exists to conduct a larger study.

This is hardly new news.  The 1994 release of Breaking the Vicious Cycle describes this pattern:

       Antibiotic therapy¹ -> Wide ranging microbial changes in the stomach and small intestine -> Increased risk of diarrhea, Crohn's/Ulcerative Colitis, diverticulitis

Gottschall also cites studies, some done decades earlier than 1994.  It seems that interest/research in the intestinal flora waned for many decades but is making a comeback.  

Interestingly, other IBD studies with infants/children indicate that breastfeeding, which establishes normal intestinal flora, results in a lower chance of having IBD².

Breastfeeding* -> Healthy intestinal flora -> Decreased chance of IBD

It should be mentioned that anecodotal information from two clinics used to treating pediatric GI problems have found that the moms regularly have have out-of-balance flora themselves.  Therefore, breastfeeding alone doesn't guarantee good flora.  The good news is that the state of intestinal flora is quite dynamic.

¹Note: This does not mean that antibiotics should not be used--in many cases they are invaluable.  Also, intestinal flora is quite dynamic.  Several friends report that their pediatricians now recommend using Florastor, a well-studies probiotic), when taking antibiotics.  That said, antibiotics should not be over-used either--talk to your doctor.

²Breastfeeding and risk of inflammatory bowel disease: a systematic review with meta-analysis. American Journal of Clinical Nutrition, Vol. 80, No. 5, 1342-1352, November 2004