Table 1.

Summary of important preclinical and clinical studies on the gut–microbiota–brain axis.

Target Sample	Evaluation Tools	Outcomes and Mechanism of Disease Modulation	Research
11 healthy subjects	Fecal sample analysis via 16S rRNA	Microbiota composition may change based on diet.	David et al. [23]
Wistar rats	Feeding patterns, food preference, locomotor activity, and body temperature	Olanzapine leads to increases in the levels of Firmicutes and decreases in the levels of Protobacteria and Actinobacteria.	Davey et al. [26]
Male Sprague Dawley rat pups	Endocrine and immune measurements, polymerase chain reaction of partial 16S ribosomal RNA gene fragments and analysis by denaturing gradient gel electrophoresis	The stress caused by separation from the mother reduces the levels of Bifidobacteria and Lactobacilli in newborn rat guts.	O’Mahony et al. [28]
Male CD-1 mice	Social disruption tests, real-time PCR, bacterial tag-encoded FLX amplicon pyrosequencing	Bacteroides species decrease and Clostridium species increase in the feces of mice that are exposed to chronic stress.	Bailey et al. [29]
Adult male Sprague-Dawley rats	Porsolt’s test, levels of components of the toll-like receptor 4 (TLR-4) signaling pathway, of lipopolysaccharide (LPS), and of different inflammatory, oxidative/nitrosative, and anti-inflammatory mediators were measured by RT-PCR, Western blot and/or ELISA in brain prefrontal cortex.	Plasma LPS, LPS-binding protein, brain LPS receptor and TLR4 levels were found to be high.	Garate et al. [30]
871 European mothers and their children	Maternal interview, The Strengths and Difficulties Questionnaire, Conners Rating Scales Revised, The Centre for Epidemiological Studies Depression Scale for Children, intelligence tests	Correlation between usage of antibiotics before the age of one year and adulthood depression.	Slykerman et al. [31]
NIH Swiss mice	Novel object recognition test, light/dark box test, acute restraint stress analysis, corticosterone immunoassay, DNA extraction, and high-throughput DNA sequencing	Long-term usage of broad-spectrum antibiotics change gut microbiota composition permanently.	Desbonnet et al. [32]
Ninety-two patients with early stage schizophrenia	Scale for the Assessment of Negative Symptoms (SANS), Positive and Negative Syndrome Scale (PANSS), Clinical Global Impression Scale (CGI), and cognitive tests.	Minocycline creates antipsychotic-like effect.	Liu et al. [33]
112 depressed patients and 28 normal controls	Hamilton Depression Rating Scale. Indirect ELISA method was employed to assay the immunoglobulin M (IgM) and IgA responses against the LPS of the commensal bacteria	Due to leaky gut, endotoxins originated from microorganisms join the systemic circulation.	Maes et al. [47]
Female Wistar rats	Partial restraint stress tests, oral administration of Lactobacillus farciminis	Lactobacillus farciminis suppressed stress-induced hyperpermeability, endotoxemia and prevented hypothalamic–pituitary–adrenal (HPA) axis stress response and neuroinflammation.	Ait-Belgnaoui et al. [48]
Specific pathogen-free mice	Open field test, real-time PCR analysis to assess neuroinflammation, HPLC for analysis of 5-HT and 5-HIAA in brain and intestine	In autistic mice, neuroinflammatory parameters increase.	de Theije et al. [50]
Pregnant C57BL/6N mice	Intestinal permeability assay, 16S rRNA gene sequence analysis, behavioral tests	Autistic behaviors can be eliminated by adding Bacteroides fragilis to the microbiota. Bacteroides fragilis can repair leaky gut.	Hsiao et al. [53]
Male Wistar rats, healthy subjects	Hopkins Symptom Checklist-90, Hospital Anxiety and Depression Scale, Perceived Stress Scale, Coping Checklist, urinary free cortisol levels	Lactobacillus helveticus and Bifidobacteria longum reduced the anxiety levels in rats and psychological distress in volunteers.	Messaoudi et al. [54]
Germ-free mice	Acute restraint test, maternal behavior observation	Brain-derived neurotrophic factor (BDNF), N-methyl D-aspartate (NMDA) 2a levels decreased in the hippocampus of germ-free mice.	Sudo et al. [63]
Healthy volunteers	Hospital Anxiety and Depression Scale, Hopkins Symptoms Checklist, urinary free cortisol levels	Anxiety levels recessed, and urine free cortisol levels decreased.	Messaoudi et al. [64]
37 depressed patients, and 18 non-depressed controls	Montgomery-Asberg Depression Rating Scale, Illumina deep sequencing of 16S rRNA gene amplicons	Bacteroides levels are high and Lachnospiraceae levels are low in the stool of depression patients.	Naseribafrouei et al. [72]
Specific pathogen–free BALB/c mice, germ-free BALB/c mice	Levels of serotonin, noradrenaline, dopamine, and brain-derived neurotropic factor were assessed by enzyme-linked immunosorbent assay	In germ-free mice BDNF levels and 5HT1A expression are low.	Bercik et al. [80]
Germ free mice, Specific pathogen-free mice	Elevated plus maze	In germ-free mice anxiety levels are low.	Neufeld et al. [90]
Germ free mice	Open field test, elevated plus maze, light–dark box test	Microbial colonization affects brain development and behavior.	Diaz Heijtz et al. [92]
Sprague–Dawley rat pups	Forced swim test, corticosterone enzyme immunoassay, brain monoamine analysis, plasma tryptophan pathway analysis	Bifidobacterium infantis led to decreases in anxiety and depression levels and increases in central norepinephrine levels.	Desbonnet et al. [94]
Healthy male participants	Self-report stress measures, cognitive assessments, resting electroencephalography, plasma interleukin 10 (IL10), IL1β, IL6, IL8, and TNFα levels, whole blood toll-like receptor-4 agonist-induced cytokines, salivary cortisol analysis.	Lactobacillus rhamnosus was not found to be superior to placebo.	Kelly et al. [108]
Patients with major depression and healthy subjects	Hamilton’s Depression Scale, Montgomery–Asberg Depression Rating Scale, Serum tumor necrosis factor-a, IL-1b, IL-6, brain-derived neurotrophic factor analysis, polymerase chain reaction and pyrosequencing	Increases in the levels of Alistipes, Enterobacteriaceae Bacteroides, Proteobacteria and Actinobacteria and decreases in the levels of Faecalibacterium and Firmicutes in the fecal samples of depression patients.	Jiang et al. [114]
Male germ-free Kunming mice and Specific pathogen-free Kunming mice	Open-field test, Y-maze, tail suspension test, forced swimming test	After stool transplantation from depression patients to germ-free mice started to show depression-like behaviors.	Zheng et al. [116]
Patients with major depression and healthy subjects, adult male Sprague-Dawley rats	Plasma C-reactive protein, panel of cytokines, salivary cortisol levels, plasma tryptophan and kynurenine, plasma lipopolysaccharide binding protein, 16sRNA metagenomic sequencing for fecal samples	After fecal microbiota transplantation from depressed persons to rats, depression- and anxiety-like behaviors were observed in the laboratory animals.	Kelly et al. [117]