Am J Gastroenterol Suppl (2012) 1:1–1; doi:10.1038/ajgsup.2012.1

Intestine Microbes in Gastroenterology: Health and Disease

Mark Pimentel MD, FRCP(C)1

1Cedars-Sinai Medical Center, Los Angeles, California, USA

Correspondence: Mark Pimentel, MD, FRCP(C), Cedars-Sinai Medical Center, 8730 Alden Drive, Suite 225E, Los Angeles, California 90048, USA. E-mail:



In the seventeenth century, Antonie van Leeuwehoek improved upon microscopic techniques, allowing him to discover bacteria, and labeling him the “father of microbiology.” In the 300 years since then, the field of microbiology has made advancements in environmental and human microbial ecosystems. Much of this incredible work has been to name and characterize the species in these systems and their potential for benefit and harm.

With modern molecular techniques, scientists have evolved to think of bacteria not as individuals but as collectives. Nowhere is this more relevant than the human digestive tract. The human digestive tract contains nearly 100 times more single-cell organisms than the sum total of all human cells in the body. As bacteria have existed long before humans, it is safe to assume that humans have evolved in a contaminated environment and the evolution was in ways mutualistic and symbiotic.

In the past 100 years, much attention has been in identifying pathogenic bacteria (e.g., Cholera, Salmonella, Campylobacter, and Yersinia among others). More recently, the focus of this work has been redirected toward events that happen after the pathogen has infected. Consequences of intestinal infection have included Guillain-Barré, seronegative spondyloarthropathies, and others. However, more common disorders such as irritable bowel syndrome, nonulcer dyspepsia, and even gastroesophageal reflux disease are being recognized as postinfectious events in a large proportion of subjects.

Advancing technologies now allow large-scale genomic evaluations of the intestinal microflora (qualitative and quantitative). These techniques are now recognizing that our host flora are beneficial in ways previously unexpected. Even more interesting is that categorical changes in flora (rather than a single organism) can have effects on human health as the gut flora have an enormous metabolic potential. This is now relevant to the study of obesity where increased firmicutes may be important. Additionally, curiosity component organisms such as the Archaea (e.g., Methanobrevibacter smithii) appear important in human obesity and constipation.

Although it is interesting to assume that we have the ability to change the composition of the flora populations in humans with probiotics and diet, the human intestinal flora are an intricate balance of 500–1,000 species. We would be naive to assume that a single-organism probiotic could correct the recognized imbalances. However, probiotics and directed antibiotics will be important tools in restoring the correct localization and composition of intestinal flora in certain disease states.

In this supplement, the importance of gut microflora in human health and disease is examined. Emphasis is placed on novel topics with recent discoveries that will guide the future of this area. Yet, it is important to remember that we have a symbiotic relationship with our gut colonists. For Charles Darwin once stated, “In the long history of humankind (and animal kind, too) those who learned to collaborate and improvise most effectively have prevailed.”