Rat Lactiplantibacillus plantarum 299v study of microbial diversity on rat stool samples

At 21-days of age, DRlyp/lyp littermates were randomly weaned onto ND, containing both plant and animal protein sources (LabDiet 5L0D, Purina, St. Louis, MO, USA), or a gluten-free hydrolyzed casein diet (HCD, Modified AIN-93G diet, Dyets Inc., Bethlehem, PA, USA). These compositionally similar diets differ in protein source and gluten content 8. Subgroups of DRlyp/lyp rats receiving these diets were supplemented with 50X106 CFU/gram body weight/day Lactiplantibacillus plantarum 299v (Lp299v, NextFoods, Boulder, CO, USA) by oral gavage from weaning. The composition of the probiotic was confirmed to be >99.999% Lp299v through metagenomic sequencing using MetaPhlAn v.3.0 (20x106 reads per sample; Diversigen, Waco, TX, USA). Flyp/lyp rats were weaned at 21 days onto ND without Lp299v. Stool, collected from 40-day old pups, was immediately homogenized in PBS. DNA was extracted using the DNeasy PowerLyzer PowerSoil Kit (QIAGEN, Germantown, MD, USA). The V4 region of the 16S rDNA gene was amplified by PCR and sequenced (Diversigen) on the MiSeq platform (Illumina, San Diego, CA, USA) using the 2x250-bp protocol 25. Paired-end 16S rRNA gene sequencing reads were analyzed with QIIME2 (v. 2020.8) 26.