By George Ochoa

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Long understudied, the human microbiome—the microbes, with their genomes, that dwell in and on the human body—is now under intense scrutiny. It is increasingly clear that “the human indigenous microbial communities … play a larger role in human health and disease than previously recognized” (Nutr Rev 2012;70:S2-S9).

In August, two studies provided new evidence that antibiotics administered in early life can result in obesity, presumably by disturbing the gut microbiome. Conversely, disturbance of microbial communities in obese individuals can result in beneficial outcomes, as a third study, in October, showed with bariatric surgery.

“The important thing is that there are interesting theories and hypotheses about how the bacterial flora of the stool might contribute to the etiology of obesity,” Philip Schauer, MD, director, Bariatric and Metabolic Institute, Cleveland Clinic, in Ohio, told General Surgery News. “This is an interesting and early and somewhat speculative area of research. It may challenge the notion that obesity is just due to not eating the right things and not exercising enough.”

Ilseung Cho, MD, MS, assistant professor of medicine, associate program director, Division of Gastroenterology, NYU School of Medicine, New York City, wrote by email: “Many investigators who study the gut microbiome think that it plays a significant role in the obesity epidemic in concert with a variety of other risk factors, such as poor dietary habits or a sedentary lifestyle. The microbiome plays a key role in a variety of host functions, including immune response and metabolism.”

Antibiotics and the Mouse

Dr. Cho was the lead investigator on a study in mice that demonstrated that antibiotics altered the gut microbiome in such a way as to affect murine metabolism and cause increased adiposity (Nature 2012;488:621-626).

In their drinking water, young mice received subtherapeutic doses of penicillin, vancomycin, penicillin plus vancomycin, or chlortetracycline; a control group received no antibiotic. There were 10 mice per group. After an exposure of seven weeks, the mice did not differ significantly in weight gain, but all four antibiotic-exposed groups had significantly higher total fat mass (P<0.05) compared with controls, and most (with the exception of the vancomycin group) had higher percent body fat (P<0.05).

The antibiotic exposure caused taxonomic changes in the microbiome, with the ratio of the phylum firmicutes to the phylum Bacteroidetes elevated in the antibiotic-exposed mice. Additionally, there was evidence of metabolic changes. For example, glucose-dependent insulinotropic polypeptide was elevated in the antibiotic-exposed mice, and glucose tolerance tests showed a trend toward hyperglycemia.

“In our paper, we describe a model where, by exposing mice to low-dose antibiotics, we were able to alter their microbiome,” said Dr. Cho. “Altering their microbiome resulted in a metabolic change in the mice that led to increased adiposity. The paper demonstrates that we are able to affect host metabolism by altering the gut microbiome.”

Antibiotics in Infants

In the same month that Dr. Cho and his colleagues published their results about young mice, a related paper about infants exposed to antibiotics was released in advance online (Int J Obes 2012 Aug 21; doi:10.1038/ijo.2012.132).

“Knowledge of the importance of the microbiome in human development raises new issues about antibiotic use in children, as such exposures may disrupt the microbial ecology,” the authors wrote.

In the longitudinal birth cohort study, data were analyzed from 11,532 children. Exposure to antibiotics during three early-life time windows (ages <6 months, 6-14 months, 15-23 months) was assessed by questionnaires that had been administered to the parents near the measured time interval. Body mass indices (BMIs) were examined at five time points (six weeks, 10 months, 20 months, 38 months and seven years).

Exposure to antibiotics during the period before 6 months of age (and only during that period, of those studied) was found to be consistently associated with increases in BMI from 10 to 38 months. At 38 months, children who had been exposed to antibiotics before 6 months had significantly higher standardized BMI scores (P=0.009) and were 22% more likely to be overweight than children who had not been exposed (P=0.029). The researchers controlled for known social and behavioral risk factors for obesity.

Bariatric Surgery

Following the recent evidence that antibiotics can disrupt the microbiome comes new evidence that bariatric surgery can do the same. In this case, the disruption may be a source of health benefits.

“The things we do to the gut in gastric bypass could alter the gut flora in a positive way and could be a major factor in why patients lose weight,” said Dr. Schauer.

A study published in advance online on Oct. 2, 2012 (Pharmacogenomics J; doi:10.1038/tpj.2012.43) sought to ascertain exactly what happens to the human gut flora in Roux-en-Y gastric bypass (RYGB).

“Postoperative modification of gut microbial composition could be directly related to the metabolic status of the patients,” emailed lead author Juergen Graessler, MD, PhD, Prof. Dr. med., head of the Division of Pathological Biochemistry, and senior author Stefan R. Bornstein, MD, PhD, Prof. Dr. med., director and chair of medicine, both from the Department of Internal Medicine III, Carl Gustav Carus Medical School, Technical University Dresden, Germany.

The researchers aimed to characterize changes of gut microbial composition within an individual before and three months after RYGB. The six patients examined in this pilot study were morbidly obese (BMI >40 kg/m<00B2>) with type 2 diabetes. Through metagenomic sequencing, 1,061 microbial species were identified in the fecal DNA of these patients. Of these, 22 species (and 11 of 729 genera) were found to be significantly affected by RYGB and were possibly associated with postoperative metabolic changes. firmicutes and Bacteroidetes were reduced, and the phylum Proteobacteria was increased. The authors observed that the shift to Proteobacteria might bring potential risk for bowel inflammation and colorectal carcinomas.

Dr. Schauer commented: “Just the opposite has been seen. Everything so far suggests that bariatric surgery reduces cancer risk.”

Of the 22 affected species, 10 correlated with plasma total and low-density lipoprotein cholesterol levels, five with triglyceride level, and two with hemoglobin A1c level. These data suggest, the authors wrote, that metabolic changes may result not only from RYGB-induced malnutrition but modified gut microbiota composition. All six patients lost weight and showed an improved metabolic situation after three months, with type 2 diabetes alleviated and inflammatory activity reduced.

“This is the first clinical demonstration of a profound and specific intraindividual modification of gut microbial composition by full metagenomic sequencing,” said Drs. Graessler and Bornstein. “A clear correlation exists between microbiome composition and gene function with an improvement in metabolic and inflammatory parameters.”

“[The study by Graessler et al] is important and adds to the body of literature that shows microbial alterations postsurgery, ” Elaine Holmes, PhD, head of biomolecular medicine, Imperial College, London, who is not associated with the study, wrote by email. “It is important to try to identify how the microbiome may contribute to the mechanisms of weight loss or weight gain. If we can mimic this effect pharmacologically without necessity for surgery, then this would be a less invasive and safer option and could be critical in controlling the increasing diabetes epidemic.”

Dr. Holmes was a co-author of studies that reported alterations in the microbiome and metabolism of rats following RYGB (Gut 2011;60:1214-1223; Front Microbiol 2011 Sep 13; doi:10.3389; fmicb.2011.00183). About those studies, she commented: “Following gastric bypass surgery there is an increase in the Gammaproteobacteria and in Enterobacteria in particular. This was accompanied by alterations in metabolism including … energy metabolism, gut microbial metabolites such as cresols, and … amino acids and biogenic amines.”

Dr. Holmes is currently engaged in a similar study in humans. “We have compared the results from surgery with nonsurgically achieved weight loss,” she said. “We have looked at samples up to one year postsurgery and still find a substantially altered microbiome and metabolism. The microbiome is unquestionably altered following bariatric surgery. This has been shown in both rodent models and in man.”

On the study by Graessler et al, Dr. Schauer noted: “This is very early stuff, a small set of six patients, basically showing a correlation between surgery and changes in populations of bacteria after surgery. A lot more work needs to be done to show that changes in bacteria are a cause of the improvement.” He also pointed out the lack of a control group in the study.

Dr. Cho also commented on the Graessler study, calling it a “a good study that begins to demonstrate the associations between surgical interventions and the microbiome.” But, he pointed out a limitation of the study, saying that it, like most studies of its kind, only reported associations.

“We will eventually need long-term studies to evaluate whether changes are durable,” Dr. Cho said. “And perhaps more importantly, how those changes affect the host. Associations may exist but may not have any clinical impact, so all that information remains to be explored.”

The Future

Although research on the microbiome, obesity and bariatric surgery is still in its infancy, the general lines it will follow are beginning to be defined.

“The microbiome does bear careful examination in the setting of bariatic surgery (a radical ecological disturbance), and will require time series analyses (with dense sampling before and after the procedure) in a significant number of subjects, in such a manner that a number of confounding variables are controlled,” wrote David A. Relman, MD, in an email. Dr. Relman is the Thomas C. and Joan M. Merigan Professor, Departments of Medicine and of Microbiology & Immunology, Stanford University, and chief, Infectious Diseases Section, VA Palo Alto Health Care System, Palo Alto, Calif. “The measurement of functional attributes will be very important,” he said.

“We are just beginning to appreciate how integral the gut microbiome is to human health and disease,” said Dr. Cho. “I think that we will discover far-ranging effects of the microbiome on a wide variety of diseases, including cardiovascular disease, obesity, colorectal cancer and inflammatory bowel disease.”