GRAPHIC: KELLIE HOLOSKI/SCIENCE938 27 MAY 2022 • VOL 376 ISSUE 6596 science.org SCIENCEBy J ohn F. Cryan^1 and Sarkis K. Mazmanian^2T
he gut microbiota is associated with
brain development and function,
as well as altered emotional, motor,
and cognitive behaviors in animals.
However, there remains a pressing
need to unravel the mechanisms and
pathways of communication that underpin
microbiota-brain connections. Reductionist
animal models have revealed profound con-
tributions by gut bacteria to brain activity
and behavior, although the extent to which
these findings translate to humans
is largely unclear. Associations be-
tween fecal microbiome profiles
and human behavior and neurologi-
cal diseases are prevalent. Longitu-
dinal studies that integrate genetic,
environmental, and experiential
factors in shaping and responding
to gut microbial functions, as well
as interventions that modify micro-
biota-brain interactions at the cel-
lular and molecular level, will help
resolve contexts in which microbes
may influence the human brain and
its health. Accordingly, prospects
for targeting the gut, rather than
the brain, to improve altered be-
haviors or brain pathologies appear
both feasible and timely.
Exposure to microbes at birth
and in early life blossoms into di-
verse microbial ecosystems that
inhabit the skin, oral cavity, vaginal
cavity, and lungs, with most human-
associated bacteria harbored in the
lower gastrointestinal (GI) tract.
The human microbiome has been
profiled in individuals from numer-
ous geographies and with diverse
conditions. Metagenomic surveys allow
for reconstruction of bacterial biosynthetic
pathways and provide insights into poten-
tial microbiome functions. Coupling DNA
sequencing to metatranscriptomics, metab-
olomics, lipidomics, and proteomics offers
exciting opportunities to uncover molecular
mediators of the gut microbiota–brain axis.
Studies using germ-free (GF) mice, which
are devoid of all microorganisms, have pro-vided compelling and converging evidence
that the microbiota is crucial for brain de-
velopment ( 1 ). GF mice display changes in
brain expression of neurotransmitters and
their receptors as well as neurotrophic fac-
tors, show region-specific gene expression,
and have an impaired blood-brain barrier.
Even hippocampal neurogenesis and neu-
roplasticity in mice are affected by the ab-
sence of a gut microbiota. Oligodendrocyte
maturation is restrained by specific gut
microbial metabolites that alter myelina-
tion patterns within the limbic system ofmice, which promotes anxiety-like behav-
iors ( 2 ). Furthermore, GF or antibiotic-
treated mice have increased risk-taking,
hyperactivity, and feeding behaviors and
display learning and memory deficits ( 3 ).
Across a variety of animal species—includ-
ing flies, worms, and fish—there is grow-
ing evidence for a link between complex
behaviors and gut microbiota composition
( 3 , 4 ). Moreover, altered bacterial commu-
nities, antibiotic treatment, and fecal mi-
crobiota transplants (FMTs) affect symp-
toms and pathology in mouse models of
anxiety, depression, autism spectrum dis-order (ASD), epilepsy, Parkinson’s disease
(PD), amyotrophic lateral sclerosis (ALS),
and Alzheimer’s disease ( 5 ).
Animal studies offer valuable platforms
and opportunities for hypothesis genera-
tion and testing. Preclinical models con-
tinue to evolve and improve in their trans-
lational value; for example, the immune
system, liver, and microbiota of mice can
be “humanized.” However, it remains chal-
lenging to capture human genetic diversity
and varied environmental influences in ani-
mal models, and correlating functional and
structural similarities between the
mouse brain and human brain has
limitations. Similarly, cross-species
behavioral repertoires vary con-
siderably, hampering truly transla-
tional interpretations. Animal re-
search has, however, convincingly
demonstrated that the gut micro-
biota can be a consequence of the
disease state, a contributor along
with genetic or environmental risk,
or a cause of changes to brain func-
tion, behavior, brain pathology, and
disease-related symptoms. Indeed,
dietary interventions or probiotic
treatments that target the micro-
biota can ameliorate symptoms in
some animal models of neurodevel-
opmental and neurodegenerative
diseases ( 5 – 7 ).
Despite these breakthroughs,
human studies have lagged behind
animal research. A small number of
brain imaging studies in infants or
adults comparing gut microbiome
profiles to brain activity scans and
naturalistic behaviors have yielded
intriguing associations ( 1 ). Cross-
sectional studies have shown dra-
matic differences in the gut microbiomes
and metabolomes of patients with major
depression, ASD, and PD compared with
matched controls. Although concordance
between individual studies at the bacterial
species level are often limited, larger meta-
analyses that aggregate several datasets
are revealing previously unrealized trends
within specific disease indications. In some
cases, microbiome profiles can define dis-
ease subtypes and correlate with use of
medications. The quality of human micro-
biome research is improving, and sample
sizes are increasing, with important con-PERSPECTIVE
Microbiota–brain axis: Context and causality
Gut bacteria influence the brain and behavior, b ut causation in humans remains unclear
(^1) APC Microbiome Ireland, University College Cork, Cork,
Ireland.^2 Division of Biology and Biological Engineering,
California Institute of Technology, Pasadena, CA, USA.
Email: [email protected]; [email protected]
Document a complete inventory of human-associated microbiota
Define “normal” and
“healthy” gut microbiota
Define directionality
between cause and e ect
Understand the contribution
of gene-environment impacts
Perform large-scale
translational and
longitudinal studies
Use more
accurate
controls
Understand the e ect
of lifestyle
What is needed
to inform
causality in
humans?
SPECIAL SECTION THE SYSTEMIC MICROBIOME
Advancing human microbiota research
Most evidence linking the gut microbiota to brain phenotypes
and behaviors is from animal models. These preclinical studies have
informed strategies for further analyses and interventions in humans,
but more rigorous human studies are needed to distinguish
causality from association.