Microbes in the gut and their byproducts may uncover a better understanding of human health.

A new study from researchers in Australia and England, urges clinicians to look not just at the bacteria present in fecal samples, but also at metabolites—like amino acids— that the bacteria produces.

Typical DNA-based studies of the human microbiome or bacterial makeup are limited, because they do not report the metabolic output of a microbial community, according to senior study author Geraint Rogers, Ph.D., an associate professor of microbiology and infectious diseases at Flinders University in Adelaide, South Australia, and a member of the South Australia Health and Medical Research Institute.

Rogers said studying the microbiome and its metabolites should go hand in hand because a lot of microbes perform the same role and some microbes exploit metabolites from others, predicting what the metabolome might look like.

“Characterizing the metabolic products of the intestinal microbiota is essential in understanding how they influence a person's health,” Rogers said in a statement. “These compounds can modulate a person's immune regulation, central nervous system function and metabolism.”

“Analyzing antibiotic-induced disturbances in the gut microbiota and its corresponding metabolome can therefore provide insight into both the acute and chronic effects of antibiotics and may give a functional understanding of the development of any associated health conditions,” he added.

Rogers and colleagues used a combination of laboratory techniques, including next-generation sequencing and nuclear magnetic resonance metabolomics, to measure the effect of antibiotic treatment with the drugs ciprofloxacin or vancomycin-imipenem on the microbiome and metabolome of female mice.

The researchers took fecal samples from the mice immediately prior to antibiotic treatment, after 14 days of treatment and nine days after stopping antibiotic treatment, with one group of mice not given any antibiotics to serve as the control.

The ciprofloxacin treatment results in a significant reduction in the number of different types of bacteria within the samples (taxa richness) but had no effect on microbiota diversity or evenness, while the vancomycin-imipenem treatment resulted in a significant decrease in taxa richness, evenness and diversity.

The antibiotic treatment resulted in significant shifts of microbial composition and structure within 14 days of treatments, and ciprofloxacin resulted in a significant decrease in several types of bacteria including streptococcus, lactobacillus and clostridium.

Some of the bacteria families were completely destroyed by the treatment, and the vancomycin-imipenem treatment resulted in significant differences, including reductions in members of the bacteroides and firmicutes phyla, and increases in the relative abundance of proteobacteria.

Rogers explained how bacteria impacts human health.

“For example, the Ruminococcaceae family, which was substantially reduced, produces important short-chain fatty acids by fermenting carbohydrates that humans cannot absorb themselves,” Rogers said. “These acids contribute to many aspects of our health, including epithelial cell turnover, which reduces the risk of colon cancer; gut barrier function, which prevents bacteria from getting into the bloodstream; and regulation of immune and metabolic controls. Antibiotic exposure also increased levels of the Enterobacter genus of bacteria, many species of which cause disease."

The team led another investigation into which fecal microbial community had recovered by nine days after antibiotic treatment. In that study, the ciprofloxacin group had taxa richness levels unchanged, but microbiota evenness and diversity were significantly reduced compared to the levels measured before and at the end of the treatment.

In the vancomycin-imipenem group, levels of microbial richness, evenness and diversity significantly increased nine days after stopping antibiotics compared to levels measured at the end of treatment, but did not reach levels seen before antibiotic treatment began.

Rogers and the research team are now assessing whether comparable effects are seen in humans and whether prebiotics or fecal microbiota auto-transplant could be used as therapies to limit those effects.