During the course of evolution, dogs and cats have been subjected to extensive domestication, becoming the principal companion animals for humans. For this reason, their health care, including their intestinal microbiota, is considered of considerable importance. However, the canine and feline gut microbiota still represent a largely unexplored research area. In the present work, we profiled the microbiota of 23 feline fecal samples by 16S rRNA gene and bifidobacterial internally transcribed spacer (ITS) approaches and compared this information with previously reported data from 138 canine fecal samples. The obtained data allowed the reconstruction of the core gut microbiota of the above-mentioned samples coupled with their classification into distinct community state types at both genus and species levels, identifying Bacteroides, Fusobacterium, and Prevotella 9 as the main bacterial components of the canine and feline gut microbiota. At the species level, the intestinal bifidobacterial gut communities of dogs and cats differed in terms of both species number and composition, as emphasized by a covariance analysis. Together, our findings show that the intestinal populations of cats and dogs are similar in terms of genus-level taxonomical composition, while at the bifidobacterial species level, clear differences were observed, indicative of host-specific colonization behavior by particular bifidobacterial taxa.

IMPORTANCE Currently, domesticated dogs and cats are the most cherished companion animals for humans, and concerns about their health and well-being are therefore important. In this context, the gut microbiota plays a crucial role in maintaining and promoting host health. However, despite the social relevance of domesticated dogs and cats, their intestinal microbial communities are still far from being completely understood. In this study, the taxonomical composition of canine and feline gut microbiota was explored at genus and bifidobacterial species levels, allowing classification of these microbial populations into distinct gut community state types at either of the two investigated taxonomic levels. Furthermore, the reconstruction of core gut microbiota coupled with covariance network analysis based on bifidobacterial internally transcribed spacer (ITS) profiling revealed differences in the bifidobacterial compositions of canine and feline gut microbiota, suggesting that particular bifidobacterial species have developed a selective ability to colonize a specific host.

在进化过程中，猫狗经历了广泛的驯化，成为人类的主要伴侣动物。由于这个原因，他们的医疗保健，包括肠道菌群，被认为是相当重要的。但是，犬和猫的肠道菌群仍然代表了一个尚未开发的研究领域。在本工作中，我们通过16S rRNA基因和双歧杆菌内部转录间隔区（ITS）方法分析了23种猫粪便样品的微生物群，并将此信息与138种犬粪便样品的先前报道数据进行了比较。获得的数据可以重建上述样品的核心肠道菌群，并在属和种水平上将它们分类为不同的群落状态类型，从而确定拟杆菌，梭菌和普氏杆菌9是犬和猫肠道菌群的主要细菌成分。在物种一级，如协方差分析所强调的，狗和猫的肠道双歧杆菌肠道群落在物种数量和组成方面都不同。在一起，我们的发现表明，在属水平分类学组成方面，猫和狗的肠道种群相似，而在双歧杆菌物种水平上，观察到明显的差异，表明特定双歧杆菌分类群的宿主特异性定殖行为。

重要性当前，家养的狗和猫是人类最珍惜的伴侣动物，因此，对它们的健康和福祉的关注非常重要。在这种情况下，肠道菌群在维持和促进宿主健康中起着至关重要的作用。然而，尽管家养的狗和猫具有社会意义，但它们的肠道微生物群落仍远未完全了解。在这项研究中，在属和双歧杆菌物种水平上探索了犬和猫肠道微生物群的分类学组成，从而在两个所研究的分类学水平中，将这些微生物种群分为不同的肠道群落状态类型。此外，