Recent studies have focused on the gut microbiota that exhibit probiotic or health promoting effects on the host [1–3]. These studies revealed that the gut microbiota are associated with some physiological effects on the host by modulation of the immune system, metabolic and hormonal regulation, competitive exclusion of pathogens, breakdown of nondigestable dietary carbohydrates for provision of nutrients [4–7]. In addition, alters in the gut microbiota have been associated with number of diseases such as colorectal cancer, allergic diseases, fatty liver disease, obesity and diabetes and many other metabolic, non-metabolic and inflammatory diseases [7–12]. Particular interest of studies have focused on the genus Bifidobacterium, which are included as probiotic bacteria [13].
Bifidobacteriaceae family is belonged to Actinobacteria class and includes nine genera including 55 species of the genus Bifidobacterium [14], and members of the genera Scardovia, Pseudiscardovia, Parascardovia, Neoscardovia, Gardnerella, Bombiscardovia, Alloscardobia and Aeriscardovia [14, 15]. This family are Gram-positive, anaerobic and facultative anaerobic, non-motile and non-spore forming bacteria, which are isolated from various ecological niches such as the gastrointestinal tract of human and various mammals, the insect gut, the oral cavity, sewage and water kefir [16, 17]. Several studies suggested that gut microbiota are quantitative and qualitative altered in patients with chronic kidney disease (CKD) and end-stage renal disease (ESRD) [18, 19]. In addition, in patients with CKD and ESRD, counts of both anaerobic and aerobic bacteria are greatly increased in the intestinal microbial population compared to healthy persons [19]. Notably, both Prevotellaceae and Lactobacillaceae families are decreased in patients with CKD [19]. As well as, higher numbers of Clostridium perfringens and lower Bifidobacteriaceae family are significantly revealed in hemodialysis patients [18]. The gastrointestinal tract is a major source of chronic inflammation, which could be one of the factors that play a role in cardiovascular pathology of CKD [20, 21]. Recent studies demonstrated that probiotics such as Streptococcus spp., Lactobacillus spp., and Bifidobacterium spp. could affect inflammatory state via alterations of gut microbiota [22, 23]. As well as, treatment of hemodialysis patients with Lactobacillus acidophilus could decrease serum dimethylamine, as a potential uremic toxins [24]. Identification and classification of bacteria with the development methods are facilitated by the sequencing of 16srRNA genes that are amplified DNA extracted from fecal samples [25], which next generation sequencing (NGS) is one of these developed methods.
As noted above, gut microbiota could affect inflammation, uremic toxicity, cardiovascular and other complications in patients with CKD. Therefore, the present study was aimed to assess the members of Bifidobacteriaceae family in fecal samples of patients with CKD and ESRD in compared to non-CKD/ESRD patients to find any changes of their counts in these patients.