The liver, as well as gut bacteria, in humans can alter molecules in food to influence signaling pathways that can activate or deactivate an array of genes, according to a new study led by researchers at Penn State.
The study, which took place in both humans and mice, was published in the Nature journal Communications Biology. When gut bacteria break down the dietary amino acid tryptophan - a protein building block found in common foods, including nuts, cheese and chicken - it produces a molecule, or metabolite, called indole-3-acetic acid (IAA).
The researchers found that the gut bacteria and the liver can chemically attach glycine, an amino acid produced by the body and found in beans and meats, to IAA. Typically, this process, called conjugation, helps make the metabolite water-soluble so the body can safely eliminate it. IAA-glycine, however, may have special characteristics, the researchers said.
IAA is a molecule that can bind to and activate the aryl hydrocarbon (Ah) receptor, a protein that can activate or deactivate other genes. Previous research has shown that the activation of the Ah receptor enhances gut immune function and intestinal barrier integrity, according to Gary H. Perdew, Thomas and Dorothy Willits Hallowell Emeritus Chair in Agricultural Sciences in the College of Agricultural Sciences and lead author of the paper.
"Surprisingly, we found that IAA-glycine also activates the Ah receptor, thereby contributing to its physiological activity," he said. "In contrast, previous work has demonstrated has that conjugation reactions can with some Ah receptor ligands can lead to blocking receptor activation potential. This unexpected finding raises the possibility that other microbial metabolites generated through conjugation reactions may also function as Ah receptor agonists, a hypothesis that is currently under investigation."
Andrew Patterson, H. Thomas and Dorothy Willits Hallowell Chair in Agricultural Sciences and co-author on the paper, said the study not only reveals a new way gut microbes can produce molecules that may interact with human signaling pathways, but also serves as an example of how research can be made possible through collaboration.
"Research like this requires microbiologists, chemists, toxicologists and computational scientists to work together," he said. "The interdisciplinary environment fostered by the Huck Institutes of the Life Sciences and Penn State's Institute of Energy and the Environment helps bring those perspectives together and enables discoveries that would be difficult to achieve within a single field."
The study was born from research from both Perdew's and Patterson's labs. While Perdew's lab is interested in molecules that can bind to and activate the Ah receptor, Patterson's group conducts research on metabolites produced by bacteria in the microbiome and what effect, if any, they have on human physiology.
"Part of this work is discovering which bile acids are conjugated with different amino acids," Perdew said. "This made me curious about whether any of the metabolites we work with could be conjugated this way."
For the study, the researchers used an advanced characterization approach called targeted liquid chromatography-mass spectrometry to analyze multiple biological samples - including 40 human serum samples and 29 human fecal samples, as well as fecal samples from both conventional and germ-free mice - for IAA and its glycine conjugate at the Huck Metabolomics Core Facility.
They found that IAA-glycine was present in human serum at concentrations comparable to those of IAA. However, in human feces, IAA-glycine concentrations were about twice as high as IAA levels.
Perdew said these observations raised two important questions: Why is IAA-glycine produced at such high concentrations, and does it trigger biological activity in humans?
"In plants, conjugation of IAA with amino acids serves as a mechanism for storage and regulation of hormone activity," he said. "In contrast, the evidence presented in this report suggests that in humans, IAA-glycine is produced to help the kidneys flush it from the body. The reason certain gut microbes produce IAA-glycine remains unclear and will require further investigation. One possibility is that glycine conjugation reduces IAA toxicity."
The findings are a springboard for questions that could be explored in future studies, the researchers said. For example, some people's microbiome seemed better at making this conjugate than others, suggesting more research could clarify which bacteria are more capable of catalyzing these reactions.
"It's an interesting question: What would that mean from a health standpoint, if your microbiome can make a lot more of it than mine?" he said. "And now that we've identified that this conjugate is present, there's also the question of whether there are any other targets for this compound. Do they exhibit biological activity through other pathways?"
In addition to Perdew and Patterson, other collaborators from Penn State include Ethan Morgan, graduate student in biochemistry and molecular biology; Denise Coslo, research technologist; Krishne Gowda, associate professor of molecular and precision medicine; Dhimant Desai, professor of molecular and precision medicine; Iain Murray, assistant research professor; Fuhua Hao, assistant research professor of veterinary and biomedical sciences; Imhoi Koo, associate research professor; Kristina Petersen, associate professor of nutritional sciences; Penny Kris-Etherton, Evan Pugh University Professor of Nutritional Sciences Emeritus; Jordan Bisanz, assistant professor of biochemistry and molecular biology; and Shantu Amin, professor of pharmacology. Other contributors include Ethan Davis, Thermo Fisher Corporation; Fangcong Dong, Harvard Medical School; Trenton Wolfe, Montana State University; Andrew Annalora and Craig Marcus, Oregon State University; and Reece Erickson and Seth Walk, Montana State University.
This research was supported by the National Institutes of Health under the National Institutes of Environmental Health Sciences grants ES028244 and ES028288, and the National Institute of Diabetes and Digestive and Kidney Diseases grant T32DK120509; and by the U.S. Department of Agriculture's National Institute of Food and Federal Appropriations under project PEN04916 and accession number 7006396. This content is solely the responsibility of the authors and does not necessarily represent the official views of the funders.
