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Structural and functional neuroimaging of the effects of the gut microbiome


Interactions between intestinal microbiota and the central nervous system profoundly influence brain structure and function. Over the past 15 years, intense research efforts have uncovered the significant association between gut microbial dysbiosis and neurologic, neurodegenerative, and psychiatric disorders; however, our understanding of the effect of gut microbiota on quantitative neuroimaging measures of brain microstructure and function remains limited. Many current gut microbiome studies specifically focus on discovering correlations between specific microbes and neurologic disease states that, while important, leave critical mechanistic questions unanswered. To address this significant gap in knowledge, quantitative structural and functional brain imaging has emerged as a vital bridge and as the next step in understanding how the gut microbiome influences the brain. In this review, we examine the current state-of-the-art, raise awareness of this important topic, and aim to highlight immense new opportunities—in both research and clinical imaging—for the imaging community in this emerging field of study. Our review also highlights the potential for preclinical imaging of germ-free and gnotobiotic models to significantly advance our understanding of the causal mechanisms by which the gut microbiome alters neural microstructure and function.

Key Points

Alterations to the gut microbiome can significantly influence brain structure and function in health and disease.

Quantitative neuroimaging can help elucidate the effect of gut microbiota on the brain and with future translational advances, neuroimaging will be critical for both diagnostic assessment and therapeutic monitoring.

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Fig. 1



Autism-spectrum disorder


Central nervous system


Functional MRI


Gut-brain axis




Gut microbiome


Irritable bowel syndrome


Mean diffusivity


Positron emission tomography


Voxel-based morphometry


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Correspondence to John-Paul J. Yu.

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Montoro, R.A., Singh, A.P. & Yu, JP.J. Structural and functional neuroimaging of the effects of the gut microbiome. Eur Radiol 32, 3683–3692 (2022).

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  • Gut microbiome
  • Gut-brain axis
  • Magnetic resonance imaging
  • fMRI
  • Diffusion tensor imaging