Fig. 1

Gut microbiome dynamics with ageing, decreased Lactobacillus and increased Alistipes bacterial genera in the BAC-hSNCA (α-Syn) TG rats. a To understand the microbiome dynamics with ageing, heterozygous females and heterozygous males were used for breeding to keep the same gut microbiome from the mother to avoid maternal effect. When females were pregnant, the male was removed from the cage and pups were allowed to stay with the mothers for 3 weeks or until weaning. Three weeks old pups were genotyped and then separated into either WT or homozygous TG groups then fecal sample collections were started at the age of 1 M (4–5 weeks age 1 M; N = 7 WT (female) and N = 7 TG (female)) onwards [2 M; N = 8 WT (4 male and 4 female) and N = 7 TG (4 male and 4 female), 2.5 M; N = 10 WT (6 male and 4 female) and N = 10 TG (6 male and 4 female), 3 M; N = 5 WT (female) and N = 5 TG (female), 6 M; N = 10 WT (6 male and 4 female) and N = 10 TG (6 male and 4 female), > 12 M (12–14 M); N = 4 WT (male) and N = 4 TG (male)] for the microbiome analysis by either 16 s rRNA gene amplicon or shotgun sequencing methods. The animals were kept in 3–4 different cages to avoid the ‘cage affect’ bias in data analysis. Both male and females were used for the fecal sample collection depending on the breeding. b Representation of bacterial diversity (hollow pie chart) at phylum levels in WT and TG rats. c F/B ratio was calculated for WT and TG rat samples and significant difference was observed at 2.5 M and > 12 M age. F/B ratio was lower in TG rats at 2.5 M of age however, this ratio was reversed at > 12 M of age which was significantly higher in TG rats. Student’s t-test was performed for comparisons at a given age for WT and TG. Two-way ANOVA was performed to find the significance between different time points and genotypes. d The microbiome dynamics at genera level was estimated. Each bar chart represents the % relative abundance of bacterial genera of the total bacteria in each group at particular age. Significant change in bacterial phyla is shown in asterisk for particular phyla together with p value significance. e, f The dynamic representation of Lactobacillus and Alistipes with ageing in WT and TG respectively. A significant difference was observed with ageing in Lactobacillus and Alistipes. Two-way ANOVA was performed to find the significance between different time points and genotypes. The plots show the means ± SEM at each time point (age in months) with respective numbers shown in (a). P value significance represents *p ≤ 0.05, **p ≤ 0.01 and ***p ≤ 0.001