A dog’s gut microbiome is transformed within a week of changing its food, according to a study published in Animal Microbiome.
]. In the present study, both 16S rRNA gene and shotgun sequencing were used to identify how different the results were between methods. While some taxonomic differences were noted, the overall shifts were generally in agreement between shotgun and 16S formats.In this study, we demonstrate that an abrupt dietary change results in a rapid change to and stabilization of fecal characteristics, metabolites, and microbial diversity, taxa, and gene content of dogs.
A crossover design was conducted. Each 28-d experimental period consisted of an adaptation phase and a diet transition phase . Diets that met all Association of American Feed Control Officials nutrient recommendations for adult dogs at maintenance were fed, including a baseline control diet ; a commercial CD ; and a HFD that was composed of the experimental diet plus 22.5 g/d of soluble corn fiber that was top-dressed on the diet just prior to feeding.
An aliquot of fresh feces was dried at 105 °C for 2 d for DM determination. Aliquots for analysis of phenols and indoles were frozen at -20 °C immediately after collection. One aliquot was collected and placed in approximately 2 mL of 2 N hydrochloric acid for ammonia, SCFA, and BCFA analyses. Fresh fecal samples for microbiome analysis were collected into 2.0 mL cryogenic vials, immediately snap-frozen in liquid nitrogen, and stored at − 80 °C until analysis.
16S rRNA gene sequencing data were processed using QIIME 2 . Trimmomatic was used to remove sequencing adaptors and then imported into the QIIME2 environment. DADA2 was used to remove low-quality reads, denoise, and filter chimeras. Amplicon sequence variants were generated using DADA2 and then taxonomically assigned using scikit-learn classifier against the Greengenes 13_8 reference database . An even sampling depth of 24,423 sequences was used for assessing alpha- and beta-diversity measures.
]. Libraries were sequenced on an Illumina NovaSeq 6000 using single-end 1 × 100 reads . Library controls included a no template control and DNA from a characterized homogenized stool.
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