Castañeda Sergio, Ariza Gineth, Rincón-Riveros Andres, Muñoz Marina, Ramírez Juan David
Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia.
Grupo de Investigación REMA, Facultad de Ciencias de la Salud, Universidad Colegio Mayor de Cundinamarca, Bogotá, Colombia.
Comp Immunol Microbiol Infect Dis. 2023 Jul;98:102007. doi: 10.1016/j.cimid.2023.102007. Epub 2023 Jun 15.
Diet is known to strongly modulate the composition of the gut microbiota, thereby affecting health conditions and disease. Natural BARF-type and commercial diets have been used for feeding pets (e.g. dogs and cats) promoting changes in the canine microbiota in terms of abundance, richness, and diversity that may favor certain metabolic processes and resistance to certain infectious agents. Therefore, the present study sought to identify microbiota changes in dogs fed with a BARF-type diet versus dogs fed with a commercial diet by sequencing the V4 region of the 16S rRNA gene.
The microbiota of dogs fed with the BARF-diet (n = 20) and commercial-diet (n = 26) was studied using fecal samples. A metabarcoding strategy was employed by sequencing the V4 hypervariable region of the 16S rRNA gene using the Illumina HiSeq platform. DADA2 was used to assess the quality profile of the reads and to determine the core sample inference algorithm of the reads to infer amplicon sequence variants (ASVs). The taxonomic assignment was performed using sequences from the Silva v138 formatted reference database. The microbial diversity analysis was performed using the R package Phyloseq, which was used to calculate diversity and abundance indices and construct the respective graphs. Linear discriminant analysis (LDA) effect size analysis (LEfSe) was used to identify the differentially abundant taxa in the BARF group versus the commercial-diet group.
The diet causes changes in fecal microbiota composition and diversity, with richness and diversity being higher in BARF-fed dogs. Beta diversity analyses confirmed that diet is directly related to microbiota composition regardless of breed or sex. Differentially enriched taxa were identified in each of the diets as Fusobacterium, Bacteroides, and Clostridium perfringens in BARF-fed dogs and Prevotella, Turicibacter, Faecalibacterium, and Peptacetobacter (Clostridium) hiranonis, mostly relevant in carbohydrate metabolism, in commercial-fed dogs.
This study is the first one carried out in dogs from Colombia that seeks to identify changes in the intestinal microbiota concerning natural BARF type diet and commercial diet using a metabarcoding approach. Important differences were identified in terms of richness, diversity, and differentially enriched bacteria in each of the diets. The microbiota of dogs fed the BARF diet was characterized by higher richness and diversity compared to the commercial diet. However, it was identified that BARF-fed dogs can potentially acquire more opportunistic infections by pathogens of importance such as C. perfringens. Most of the taxa enriched in commercial diet-fed dogs are linked to carbohydrate metabolism, which may be directly related to diet composition.
已知饮食会强烈调节肠道微生物群的组成，从而影响健康状况和疾病。天然生食（BARF）型饮食和商业宠物食品已被用于喂养宠物（如狗和猫），促进犬类微生物群在丰度、丰富度和多样性方面的变化，这可能有利于某些代谢过程和对某些传染原的抵抗力。因此，本研究旨在通过对16S rRNA基因的V4区域进行测序，确定喂食BARF型饮食的狗与喂食商业宠物食品的狗的微生物群变化。
使用粪便样本研究喂食BARF饮食（n = 20）和商业饮食（n = 26）的狗的微生物群。采用元条形码策略，使用Illumina HiSeq平台对16S rRNA基因的V4高变区进行测序。DADA2用于评估读数的质量概况，并确定读数的核心样本推断算法以推断扩增子序列变体（ASV）。分类学归属使用来自Silva v138格式参考数据库的序列进行。微生物多样性分析使用R包Phyloseq进行，该包用于计算多样性和丰度指数并构建相应的图表。线性判别分析（LDA）效应大小分析（LEfSe）用于识别BARF组与商业饮食组中差异丰富的分类群。
饮食导致粪便微生物群组成和多样性发生变化，喂食BARF的狗的丰富度和多样性更高。β多样性分析证实，无论品种或性别如何，饮食都与微生物群组成直接相关。在每种饮食中都鉴定出差异富集的分类群，喂食BARF的狗中为梭杆菌属、拟杆菌属和产气荚膜梭菌，而在喂食商业宠物食品的狗中为普雷沃氏菌属、Turicibacter、粪杆菌属和hiranonis肽乙酸杆菌（梭菌属），这些大多与碳水化合物代谢相关。
本研究是在哥伦比亚的狗中进行的首次研究，旨在使用元条形码方法确定与天然BARF型饮食和商业饮食相关的肠道微生物群变化。在每种饮食的丰富度、多样性和差异富集细菌方面发现了重要差异。与商业饮食相比，喂食BARF饮食的狗的微生物群具有更高的丰富度和多样性。然而，已确定喂食BARF的狗可能更容易受到诸如产气荚膜梭菌等重要病原体的机会性感染。在喂食商业饮食的狗中富集的大多数分类群与碳水化合物代谢有关，这可能与饮食组成直接相关。
