GABA Production by Human Intestinal Bacteroides spp.: Prevalence, Regulation, and Role in Acid Stress Tolerance.

Denisa Mujezinovic,Christian Braegger,Tomas de Wouters,Nize Otaru,Benoit Pugin,Christophe Lacroix,Florentin Constancias,Adam Krzystek,Laura Berchtold,Kun Ye,Fabián A. Cornejo

doi:10.3389/fmicb.2021.656895

Abstract

The high neuroactive potential of metabolites produced by gut microbes has gained traction over the last few years, with metagenomic-based studies suggesting an important role of microbiota-derived γ-aminobutyric acid (GABA) in modulating mental health. Emerging evidence has revealed the presence of the glutamate decarboxylase (GAD)-encoding gene, a key enzyme to produce GABA, in the prominent human intestinal genus Bacteroides. Here, we investigated GABA production by Bacteroides in culture and metabolic assays combined with comparative genomics and phylogenetics. A total of 961 Bacteroides genomes were analyzed in silico and 17 metabolically and genetically diverse human intestinal isolates representing 11 species were screened in vitro. Using the model organism Bacteroides thetaiotaomicron DSM 2079, we determined GABA production kinetics, its impact on milieu pH, and we assessed its role in mitigating acid-induced cellular damage. We showed that the GAD-system consists of at least four highly conserved genes encoding a GAD, a glutaminase, a glutamate/GABA antiporter, and a potassium channel. We demonstrated a high prevalence of the GAD-system among Bacteroides with 90% of all Bacteroides genomes (96% in human gut isolates only) harboring all genes of the GAD-system and 16 intestinal Bacteroides strains producing GABA in vitro (ranging from 0.09 to 60.84 mM). We identified glutamate and glutamine as precursors of GABA production, showed that the production is regulated by pH, and that the GAD-system acts as a protective mechanism against acid stress in Bacteroides, mitigating cell death and preserving metabolic activity. Our data also indicate that the GAD-system might represent the only amino acid-dependent acid tolerance system in Bacteroides. Altogether, our results suggest an important contribution of Bacteroides in the regulation of the GABAergic system in the human gut.

Highlights

The gut microbiota has emerged as a key player in the development and maintenance of human health
We show that GABA production is a common trait in human Bacteroides strains owing to a highly conserved glutamate decarboxylase (GAD)-system composed of a GAD, a glutaminase, a glutamate/GABA antiporter, and a potassium channel
As previous genetic studies suggested the presence of gadB orthologs in Bacteroides (Pokusaeva et al, 2017; Strandwitz et al, 2019), the strains were tested in mYCFA supplemented with glutamate

Summary

Introduction

The gut microbiota has emerged as a key player in the development and maintenance of human health. Accumulating evidence has suggested that gut microbes can produce metabolites with high neuroactive potential (neurotransmitters), including norepinephrine, tryptamine, serotonin, dopamine, and γ-aminobutyric acid (GABA; Strandwitz, 2018; Valles-Colomer et al, 2019) These microbiota-derived neurotransmitters can modulate host homeostasis within the gastrointestinal tract (GIT), and at distant body sites such as the brain via complex neuronal, immunological, and humoral signaling cascades, i.e., the gut-brain axis (Fischbach and Segre, 2016; Cryan et al, 2019). For most of these neurotransmitters, the exact function and benefits for the bacterial cells, the mechanisms regulating their production within the gut ecosystem, or their precise interaction with intestinal and peripheral tissues remain largely unexplored

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Conclusion