A powerful new tool to reveal communication between gut microbes and the brain


Summary: Researchers develop a new tool that allows the study of microbe communication in the gastrointestinal tract and in the brain.

Source: Baylor College of Medicine

In the last decade, researchers have begun to appreciate the importance of a two-way communication that occurs between microbes in the gastrointestinal tract and the brain, known as the gut-brain axis.

These “conversations” can modify the way these organs function and involve a complex network of chemical signals derived from microbes and the brain that are challenging for scientists to uncouple in order to gain an understanding.

“Currently, it is difficult to determine which microbial species drive specific brain changes in a living organism,” said first author Dr. Thomas D. Horvath, instructor of pathology and immunology at Baylor College of Medicine and Texas Children’s Hospital.

“Here we present a valuable tool that allows investigations into the connections between gut microbes and the brain. Our laboratory protocol allows the identification and comprehensive evaluation of metabolites – compounds produced by microbes – at the cellular and whole animal levels.”

The gastrointestinal tract is home to a rich and diverse community of beneficial microorganisms known collectively as the gut microbiota. In addition to their roles in maintaining the gut environment, gut microbes are increasingly recognized for their influence on other distant organs, including the brain.

“Gut microbes can communicate with the brain in a variety of ways, for example producing metabolites such as short-chain fatty acids and peptidoglycans, neurotransmitters such as gamma-aminobutyric acid and histamine, and compounds that modulate the immune system, as well as other ,” said co-first author Dr. Melinda A. Engevik, assistant professor of cellular and regenerative medicine at the Medical University of South Carolina.

The role microbes play in central nervous system health is highlighted by links between the gut microbiome and anxiety, obesity, autism, schizophrenia, Parkinson’s disease and Alzheimer’s disease.

“Animal models have been instrumental in linking microbes to these fundamental neural processes,” said co-author Dr. Jennifer K. Spinler, assistant professor of pathology and immunology at Baylor and the Texas Children’s Hospital Microbiome Center.

“The current study protocol allows researchers to take steps to unravel the specific involvement of the gut-brain axis in these conditions, as well as its role in health.”

A roadmap to understanding the complex traffic system in the gut-brain axis

One strategy the researchers used to gain insight into how a single type of microbe might influence the gut and brain was to grow the microbes first in the lab, collect the metabolites they produced, and analyze them using mass spectrometry and metabolomics.

Mass spectrometry is a laboratory technique that can be used to identify unknown compounds by determining their molecular weight and quantify known compounds. Metabolomics is a technique for the large-scale study of metabolites.

This shows a diagram of the study
This protocol provides researchers with a roadmap for understanding the complex gut-brain traffic system and its effects on health and disease. Credit: Baylor College of Medicine

“The effect of the metabolites was then studied in the mini-gut, a laboratory model of human intestinal cells that retains the properties of the small intestine and is physiologically active,” said Engevik. “In addition, the microbe’s metabolites can be studied in live animals.”

“We can expand our study to a community of microbes,” Spinler said.

“In this way, we investigated how microbial communities work together, synergize and influence the host. This protocol provides researchers with a roadmap for understanding the complex gut-brain traffic system and its effects.”

“We were able to create this protocol thanks to great interdisciplinary collaborations involving clinicians, behavioral scientists, microbiologists, molecular biology scientists and metabolomics experts,” said Horvath.

“We hope that our approach will help create communities of beneficial microbe designers that can contribute to the maintenance of a healthy body. Our protocol also offers a way to identify potential solutions when miscommunication between the gut and the brain leads to disease.”

Read all the details of this work at Nature’s Protocols.

Other contributors to this work included Sigmund J. Haidacher, Berkley Luck, Wenly Ruan, Faith Ihekweazu, Meghna Bajaj, Kathleen M. Hoch, Numan Oezguen, James Versalovic, and Anthony M. Haag. The authors are affiliated with one or more of the following institutions: Baylor College of Medicine, Texas Children’s Hospital, and Alcorn State University.

Financing: This study was supported by an NIH grant K01 K12319501 and Global Probiotic Council 2019-19319 grants from the National Institute of Diabetes and Digestive and Kidney Diseases (Grant P30-DK-56338 to Texas Medical Center Digestive Disease Center, Gastrointestinal Experimental Model Systems) , NIH U01CA170930 and unrestricted research support from BioGaia AB (Stockholm, Sweden).

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About this gut-brain axis research news

Author: Homa Shalchi
Source: Baylor College of Medicine
Contact: Homa Shalchi – Baylor College of Medicine
Image: The image is credited to Baylor College of Medicine

Original search: Closed access.
“Interrogation of the mammalian gut-brain axis using LC-MS/MS-based targeted metabolomics with in vitro bacterial and organoid cultures and in vivo gnotobiotic mouse models” by Thomas D. Horvath et al. Nature’s Protocols


Interrogation of the mammalian gut-brain axis using LC-MS/MS-based targeted metabolomics with in vitro bacterial and organoid cultures and in vivo gnotobiotic mouse models

Interest in the communication between the gastrointestinal tract and the central nervous system, known as the gut-brain axis, has led to the development of quantitative analytical platforms to analyze signals derived from microbes and hosts.

This protocol allows investigations into the connections between microbial colonization and intestinal and brain neurotransmitters and contains strategies for the comprehensive evaluation of in vitro metabolites (organoids) and in vivo mouse model systems.

Here we present an optimized workflow that includes procedures for preparing these gut-brain axis model systems: (stage 1) growth of microbes in defined media; (stage 2) microinjection of intestinal organoids; and (stage 3) generation of animal models, including germ-free (no microbes), specific pathogen-free (complete intestinal microbiota) and conventionalized specific pathogen-free (germ-free mice associated with a complete intestinal microbiota of a mouse free of specific pathogens) and Bifidobacterium dentium and Bacteroides ovatus monoassociated mice (germ-free mice colonized with a single intestinal microbe).

We describe metabolomic methods based on tandem mass spectrometry-directed liquid chromatography to analyze microbially derived short-chain fatty acids and neurotransmitters from these samples.

Unlike other protocols that commonly examine only stool samples, this protocol includes bacterial cultures, organoid cultures, and in vivo samples, as well as monitoring the metabolite content of stool samples. The incorporation of three experimental models (microbes, organoids and animals) increases the impact of this protocol.

The protocol requires 3 weeks of murine colonization with microbes and ~1–2 weeks for instrumental and quantitative analysis based on tandem-liquid chromatography and quantitative analysis and sample post-processing and normalization.


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