Table 3:

Effects of microbiome manipulations in animal models for NDs

Parkinson’s disease: Microbial effects on pathology and behavior in animal models
Subject	Perturbation	Sample	Test	Result	Reference
Pink1−/− mice	Oral administration of Citrobacter rodentium	n=5-72 males and females	Grip strength test Pole test Open field test Flow cytometry for brain infiltrated immune subsets Histology for dopaminergic neurons in the striatum	Impaired motor ability shown in Citrobacter rodentium treated Pink1−/− mice Decreased density of dopaminergic axonal varicosities and enhanced CD8+ T cells in the brain of Citrobacter rodentium treated Pink1−/− mice	(Matheoud et al., 2019)
Thyl-αSyn mice	Administration of microbiota from PD patients	n=3-6 males	Beam traversal test Pole descent test Nasal adhesive removal test Hindlimb clasping reflexes Beam traversal test Pole descent test Nasal adhesive removal test Hindlimb clasping reflex	PD-derived gut microbiota promotes motor impairments	(Sampson et al., 2016)
Thyl-αSyn mice	GF vs SPF	n=4-6 males	Western blot and immunofluorescence staining for α-Syn aggregation Representative 3D reconstructions of Iba1-stained microglia in the caudoputamen	Reduced locomotor deficits, α-syn accumulation and decreased activation of microglia in GF Thy1-αSyn mice	(Sampson et al., 2016)
Thyl-αSyn mice	Monocolonization of curli-sufficient vs curli-deficient E. coli	n=7-9 males	ELISA and immunofluorescence staining for α-Syn aggregation in the brain and gut Immunofluorescence staining for TH neurons, microglia activation in the brain Beam traversal Pole descent test Nasal adhesive removal test Hindlimb clasping reflex Wire hang test	Increased locomotor deficits, α-syn accumulation and enhanced activation of microglia in Thy1-αSyn mice colonized with curli-sufficient Ecoli	(Sampson et al., 2020)
Aged Fischer 344 rats	Oral administration of curli-sufficient E. coli vs curli-deficient E. coli	n=9-13 males	Histology for astrocytes, α-syn aggregation Serum cytokine profiling	Increased a-syn accumulation and enhanced activation of astrocytes in rats with curli-sufficient E. coli	(Chen et al., 2016)
C. elegans expressing human α-syn	Curli-sufficient vs curli-deficient E. coli feeding	n=15 Sex unknown	Immunofluorescence staining for α-syn aggregation	Increased α-syn accumulation in C. elegans feed with curli-sufficient E. coli	(Chen et al., 2016)
Thyl-αSyn mice	Drinking water containing 10 μg/ml LPS 12 consecutive days treatment	n is unknown males and females	Hindlimb clasping reflex	Mildly exacerbated motor impairments in LPS treated Thy1-αSyn mice	(Gorecki et al., 2019)
MPTP mouse model Rotenone mouse model	Probiotic cocktail containing Lactobacillus rhamnosus GG, Bifidobacterium animalis lactis and Lactobacillus acidophilus 4 weeks treatment before animal model establishment	n=3-4 males	Cylinder test Beam traversal test Challenge beam test Stride length test Histology for dopaminergic neurons and glial activation in the striatum and substantial nigra	Mitigated behavioral impairments, ameliorated dopaminergic neuronal loss and gliosis in probiotics treated MPTP and rotenone mouse model	(Srivastav et al., 2019)
6-OHDA rat model	Antibiotic (neomycin, 2 mg/mL; vancomycin 0.2 mg/mL; bacitracin, 0.5 mg/mL; pimaricin 1.2 μg/mL) treatment for 14 days before animal model establishment	n=4-12 males	Cylinder test Forepaw adjusted steps test Amphetamine-induced rotation Histology for TH neuron loss in striatum and substantial nigra Q-PCR for expression of proinflammatory cytokines in striatum	Attenuated motor deficits, decreased dopaminergic neuron loss and lower expression of proinflammatory cytokines in antibiotic treated 6-OHDA rat model	(Koutzoumis et al., 2020)
MPTP mouse model	Fecal microbiota of transplantation after animal model establishment	n=15 males	Pole test Traction test Histology for dopaminergic neuron loss and glial activation in the substantial nigra Western blot for striatal TH expression	Attenuated motor deficits, decreased dopaminergic neuron loss and glial activation in the MPTP mouse model transplanted fecal microbiota from wildtype littermates	(Sun et al., 2018)
C. elegans model of synucleinop athy	Bacillus subtilis probiotic strain PXN21 feeding	n=25 sex unknown	Histology for αSyn aggregation	reduced αSyn aggregation in the C. elegans feed with Bacillus subtilis	(Goya et al., 2020)
MPTP mouse model	Oral administration of Proteus mirabilis	n=9-12 males	Rotarod test Open field test Histology for dopaminergic neuron loss and glial activation in the substantial nigra Histology for TH positive axons loss in the striatum	Exacerbated motor deficits, loss of dopaminergic neurons and glial activation in MPTP mouse model received Proteus mirabilis	(Choi et al., 2018)
MPTP mouse model	antibiotic (ampicillin 1 g/L, neomycin sulfate 1 g/L, metronidazole 1 g/L) treatment before animal model establishment	n=10 males	Histology for dopaminergic neuron loss in the substantial nigra	Attenuated dopaminergic neuron loss in the antibiotic treated MPTP mouse model	(Pu et al., 2019)
Alzheimer’s disease: Microbial effects on pathology and behavior in mice
Subject	Perturbation	Sample	Test	Result	Reference
APP/PS1 mice	GF vs CONV	n=5-8 males and females	Histopathology for Aβ in brain Immunostaining for microglia Western blot for Aβ ELISA for Aβ38, Aβ40, Aβ42, and cytokines	For GF-APP/PS1 mice: lower Aβ deposition in cortex and hippocampus, Aβ levels in western blot and Aβ42 levels in ELISA reduction in Iba-1 positive microglial leading to reduction in cortical neuroinflammation For CONV-APP/PS1 mice: increase in IL-1β, INF-χ, IL-2, IL-5	(Harach et al., 2017)
APP/PS1 mice	Antibiotics (gentamycin 1mg/mL, vancomycin 0.5mg/mL, metronidazole 2mg/mL, neomycin 0.5mg/mL, ampicillin 1mg/mL, kanamycin 3mg/mL, colistin 6000U/mL, cefaperazone 1mg/mL) for 1 week	n=5-14 males	Flow cytometry for immune cells Immunohistochemistry for Aβ, Iba-1, GFAP ELISA for Aβ Cytokine/chemokine array	For ABX treated mice: reduced Aβ deposition in cortex and hippocampus reduction in Aβ plaque localized microglial and astrocytes leading to reduction in neuroinflammation elevation in FOXP3+ Tregs upregulation of CCL11, IL-1β, IL-2, IL-3, SCF and downregulation of IL-6	(Minter et al., 2017)
ADLP mice	Fecal microbiota transplant daily for 4 months	n=14-16 sex unknown	Behavioral tests: Y-maze, contextual fear conditioning, open field ELISA for Aβ Immunohistochemistry for Aβ, tau, GFAP	For FMT treated mice: better performance on behavioral tests reduction in Aβ deposition in frontal cortex and hippocampus reduction in cortex Aβ40 levels reduction in tau aggregates in hippocampus reduction in activated microglia and astrocytes in frontal cortex	(Kim et al., 2020)
APP/PS1 mice	Fecal microbiota transplant daily for 4 weeks	n=4-6 males	Behavioral tests: Morris Water Maze, object recognition test ELISA for Aβ40 and Aβ42 Western blot for tau Immunostaining for PSD-95, CD11b and COX-2 NMR for SCFAs	For FMT treated mice: better performance on behavioral tests compared to controls reduction in Aβ deposition in cortex and hippocampus and in Aβ40/Aβ42 levels reduction in tau phosphorylation increase in PSD-95 staining reduction in COX-2 and CD11b levels increase in butyrate levels	(Sun, J. et al., 2019)
APP/PS1 mice	Oral administration of Clostridium butyricum for 4 weeks	n=20 sex unknown	Behavioral tests: Morris Water Maze, object recognition test Histology for Aβ and CD11b ELISA for Aβ42 Butyrate assay	Treated mice performed better on behavioral tests compared to controls Decrease of Aβ levels in the brain for treated mice Reduction of activated microglial in treated mice Reduction of IL-1β and TNF-α in treated mice Higher levels of butyrate in treated mice	(Sun et al., 2020)
3xTg mice	SLAB51 probiotic treatment	n=48-64 males	Behavioral test: open field, novel object recognition and elevated maze GC for SCFAs ELISA for cytokines Histology and immunostaining for Aβ Western blot for tau	For SLAB51 treated mice: better performance on behavioral tests Reduction in Aβ deposition in hippocampus Reduction in tau phosphorylation Reduction in oxidative stress	(Bonfili et al., 2017; Bonfili et al., 2018; Bonfili et al., 2019)
APPPS1-21 mice	Antibiotics (kanamycin 4 mg/ml, gentamicin 0.35 mg/ml, colistin 8,500 U/ml, metronidazole 2.15 mg/ml, vancomycin 0.45 mg/ml) from P14-P21	n=6-10 males and females	Immunofluorescence for Ab and microglia activation	Antibiotics treatment reduce Aβ pathology and activation of microglia only in the male brain but not female	(Dodiya et al., 2019)
Amyotrophic lateral sclerosis: Microbial effects on pathology and behavior in mice
Subject	Perturbation	Sample	Test	Result	Reference
SOD1G93A mice	2% sodium butyrate in water	n=5-10 sex unknown	ALS progression (body weight loss, lifespan) Intestinal tight junction (western blot and immunofluorescence staining for ZO-1)	Delayed ALS progression Increased the intestinal tight junction	(Zhang, Y.G. et al., 2017)
SOD1G93A mice	Repeated oral administration of Akkermansia muciniphila into antibiotic pre-treated Sod1 mice at 6-day intervals for a total of 15 treatments.	n= 5-61 males and females	lifespan analysis rotarod locomotor test Hanging-wire grip test Histological staining for spinal cord T2 relaxation time	Extended lifespan Ameliorated locomotor deficits Increased number of motor neurons in spinal cord Reduced brain atrophy	(Blacher et al., 2019)
Huntington’s disease: Microbial effects on pathology and behavior in mice
Subject	Perturbation	Sample	Test	Result	Reference
BACHD mice	GF vs SPF	n=4-12 males and females	Transmission electron microscopy for myelination Q-PCR and western blot for myelin based protein	Reduced levels of myelin-related proteins and decreased numbers of mature oligodendrocytes in the prefrontal cortex of BACHD mice reared in GF condition	(Radulescu et al., 2019)