The mode of delivery affects the diversity and colonization pattern of the gut microbiota during the first year of infants' life: a systematic review

The term microbiota refers to the sum of all microbial communities living in or on the human body. The human gut mainly the large intestine harbors the greatest numbers of microbiota in the body when compared to other human body niches such as the skin, vagina, mouth, and ears [1, 2]. The human gut contains 10¹⁴ bacteria which represent 10 times the total number of human cells. Particularly, after bacterial colonization in infant, intestinal microbial composition is unique for each individual, although more than 95 % can be assigned to four major phyla: Firmicutes, Bacteroidetes, Actinobacteria and Protecteobacteria [3]. The development of the intestinal microflora starts at birth, several reports highlighted that the early life development of the infant gut microbiota plays an important role in the maturation of the host immune system, protection from pathogens, and in providing nutrients [4, 5]. The main function of intestinal immune system is to control the exposure of bacteria to host tissues and prevent the potential for pathologic outcome. It has been suggested that innate and adaptive immune responses influence enteric bacteria composition and luminal alterations of decreased bacterial diversity and expansion of selected species during inflammation of various causes [6]. According to the review, the immune system on microbiota may evolve in immune deficiencies that alter microbial communities in ways that predispose the host to diseases [7]. Specifically, postnatal gut function and immune development are largely influenced by the intestinal microbiota, emerging evidence has shown that early microbiota colonization may influence the occurrence of later diseases [8]. In human, West et al. [6] observed that low microbial diversity in infancy precede onset of allergic disease. Specifically, Azad et al. [9] found more abundant enterobacteriaceae and less abundant bacteroidaceae in the gut microbiota of food sensitized infants at 3 months and 1 year. The diversity and colonization pattern of infants gut microbiota during first year of life are influenced by numerous factors, of which delivery mode is an important one. Furthermore, evidence is growing that an aberrant gut microbiota composition as a result of delivery mode affects the subsequent regulation of immune response [10], and the changes in the composition of the gut microbiota (dysbiosis) may be associated with several clinical conditions [11]. Recent studies reported increased risk of asthma [12], obesity [13], celiac disease [14], and type 1diabetes [14] in children born via CS compared with vaginally delivered. The possible explanation for this increased risk is that the lack of contact at birth with maternal vaginal and intestinal flora would expose these children to a number of diseases because of changes in the development of immune system [15]. Furthermore, independently to the mode of delivery, low total diversity of the gut microbiota during the first year of life was reported to be associated with allergic diseases [16]. Modulation of gut microbiota with probiotics, prebiotics, or fermented dairy products has been suggested as a treatment of, or prevention for, different disorders such as irritable bowel syndrome (IBS), infectious diarrhea, allergic disease, and necrotizing enterocolitis [8].

The gut microbiota colonization patterns of infants’ delivery by Caesarean Section (CS) differ from those who were delivered vaginally [17]. In the last two decades CS has been on the rise worldwide [18]. At the same time infants delivered by CS were found to have abnormal gut microbiota [19‐21]. Considering the pattern of infants gut microbiota, previous studies reported delay or absence of Bacteroides in the first year of life in infants delivered by CS [20, 22]. In contrast, infant gut bacterial dominated by clostridial was found not associated with delivery mode [23]. A study conducted in developing country reported early colonization of Bacteroides in infants delivered by CS; this was attributed to the fecal bacteria in surrounding environment. For instance phylum diversity within Actinobacteria was higher among vaginally delivered (VD) infants [24]. However, the relation between those patterns with delivery mode remains unclear. Conflicting results observed in several previous studies may not all be attributed to techniques used to detect fecal microbiota in early infancy, as anaerobic genera or facultative anaerobes could be detected by both culture-dependent methods and culture-independent techniques.

In addition to delivery mode, other factors such as place of birth, maternal vaginal or skin microbiota, type of infant feedings, birth weight, gestational age at birth, hospitalization after birth, prenatal administration of probiotics, and intrapartum antibiotics prophylaxis were found to influence the pattern of infant gut microbiota [25]. However, the implication of some factors on the abundance of some specific gut bacterial was refuted in some studies [19, 23, 26, 27]. In facts, detailed discussion on these factors is not in the scope of this systematic review. So far there is insufficient explanation regarding the pattern and diversity of infant gut microbiota in relation to delivery mode. To better elucidate this relation, the present systematic review intends to look whether the mode of delivery affect the diversity and microbial colonization pattern during the first year of infants' lives.

In this review we emphasized on the gut microbiota commonly detected by both culture based method, and culture-independent techniques and this gives us the broad view on the common gut microbiota that colonized infants during their first year of life with respect to the mode of delivery. From birth to 90 days of life, phyla diversity within Actinobacteria and Bacteriodetes such as Bifidobacterium, Bacteroides were significantly lower in the infants delivered by CS compared with those delivered vaginally. In fact, the mode of delivery affects the colonization pattern of infants’ gut microbiota within these periods but the constituent genera from Firmicutes phylum (dominated by Clostridium and Lactobacilli) are independently associated with the mode of delivery. The discrepancy within reviewed studies regarding the colonization pattern of the genera of Clostridia and Lactobacilli in relation to the mode of delivery may due to the microbiota isolation and analysis techniques [20, 36]. The findings of previous cultured-based studies, showed contradicted results, for example Mitsou et al. [34] found significantly lower colonization rates of the Bifidobacterium genus at the age of 4 and 30 days, the Lactobacillus genus at the age of 4 days in the CS delivered infants compared with vaginally delivered at the age of 30 days while Gronlund et al. [20] could not confirm these associations. In addition, Bezirtzoglou [37] reported the similar colonization of the Bifidobacterium genus in both infants delivered by CS and vaginally. However, the author’s conclusion was based on the studies which used culture-based method to detect infants gut microbiota. Contradicted results within these studies may due to other methodological aspects, not necessarily due to microbial isolation and detection techniques. Interestingly, the findings of Gronlund et al. [20] have been collaborated by several more recent culture-independent studies, which reported no significant association between the colonization by the Clostridium, and Lactobacillus genera and the mode of delivery at the age of one month [21, 36]. In contrast, a birth cohort study conducted in three European countries, confirmed high prevalence of Clostridia in CS delivered infants compared with vaginally delivered [38]. Another study conducted in India highlighted the high abundance of Clostridium difficile in CS infants and absence of those bacteria in VD infants [30].

Recent studies used modern technology to analyze the composition of the human gut microbiota over time. For instance, a cross-sectional study used polymerase chain reaction (PCR)-denaturing gradient gel electrophoresis in combination with 16r RNA gene sequencing to analyze profiles of the fecal microbiota have reported the total absence of the Bifidobacterium genus in infants delivered by CS at the age of 4 days [33]. Biasucci et al. [19] used PCR-denaturing gradient gel electrophoresis (DGGE) and PCR-temperature gradient gel electrophoresis (TGGE) to analyze infants gut microbiota found that total microbial diversity was influenced by the delivery mode, with significantly lower abundance of the Bifidobacterium genus at the age of 3 days of life. Indeed, low total diversity of the gut microbiota during the first 3 months of life is associated with Caesarean section. The beneficial health effects attributed to the bacteria communities from the genera Lactobacillus and Bifidobacterium included the fed as probiotics to promote health and effective in prevention of gastroenteritis in early infancy [39, 40]. Specifically, infants delivered by CS were colonized by high abundance of Enterococcus, Klebsieella, streptococcus, Haemophilius and veillonella from first week of life to one month [26, 27, 32, 33, 35]. Veillonellaceae and Enterobacteriaceae bacteria were more abundance in CS infants compared to VD infants [41]. These types of bacteria were not fully studied in relation to the mode of delivery, and explore their benefits to human health and diseases.

Lower abundance of the Bifidobacteria and Bacteroides, and higher abundance of Clostridia, and lactobacilli in the infants delivered by CS as observed in some studies, may explained by the antibiotics use. Mothers undergoes CS are more likely to take antibiotics before, during, and after delivery, which may affect the diversity of infants gut microbiota. Previous studies found antibiotic consumption as potential factor that influences the composition of the infant gut microbiota. Specifically, postnatal consumption of antibiotic was associated with higher relative abundance of the Clostridium leptum, and decreased numbers of Bifidobacterium and Bacteroides [32, 42, 43]. The lack of contact with maternal vaginal microbiota, may be a possible reason of higher abundance of genera from Firmicutes phylum and lower colonization pattern of the genera from the Bacteroidetes phylum among CS delivered infants. Previous studies suggested that the genus Bacteroides may be transmitted from the maternal gut to new born during delivery [38, 44], while higher abundance of the genus Clostridium among CS delivered infants was attributed to nosocomial infection [43].

Caesarean delivery reduces breastfeeding in the first hour of life, which may complicate the management of lactation in the first year of infant’s life. Bai et al. indicated that shorter duration of any breastfeeding was associated with CS delivery [45]. This may disrupt the diversity and colonization pattern of infants gut microbiota. In contrast, world literature meta-analysis on the association between CS and breastfeeding, reported that CS had no significant effect on any breastfeeding at the age of 6 months [46]. However, formula feeding has been associated with higher microbial diversity [47], high abundance of Clostridium difficile [48], and lower abundance of Bifidobacteria [49]. Indeed, higher abundance of the Bifidobacterium genus was observed in breastfeed infants [48]. The findings from a large cohort of Danish infants reported a significant changes in the gut microbiota occurred from age 9 to 18 months, when cessation of breastfeeding and introduction of a complementary feeding induce replacement of a microbiota dominated by Clostridium and Bacteroides species [50]. It was recently shown that human milk contains beneficial factors for the intestinal microbiota, such as human milk oligosaccharides (HMOs), this function as prebiotics by stimulating the growth of Bifidobacterium and Lactobacillus species, thereby selectively altering the microbial composition of the intestine [51]. Moreover, there is accumulating evidence that human milk is not sterile but contains maternal derived bacterial molecular motifs that are thought to influence the newborn’s immune system development [52]. It was suggested that host defenses can be improved by feeding breast milk, which helps the immature intestinal mucosal immune system to develop and respond appropriately to highly variable bacterial colonization and food antigen loads [8].

Given the evidence that infants delivered by CS lacked the early support of breast milk as stimulator for a physiological gut microbiota [15], and thus breast milk contains microbes such as Lactobacilli and Bifidobacteria [53] and this may be a direct source of higher colonization rates of these genera in vaginally delivered than in CS delivered infants. It is plausible that lower total microbial diversity observed from birth to the age of 90 days in CS delivered infants may contribute to weak immune system, poor health and infant well-being. As result of changes of early life gut microbiota, mounting evidences showed that infants delivered by CS had increased risk of developing immune related disorders in childhood, including atopic or allergic diseases [54], inflammatory bowel disease [55], asthma [56], and metabolic disorders [13, 57].

In subsequent days, from the age of 91 to 360 days the effects of the mode of delivery on the diversity and colonization pattern of infant gut microbiota decreased. Within mentioned periods, two studies reported significantly lower abundance of the Bifidobacterium and Bacteroides genera in CS delivered infants, whereas only one study observed significantly higher abundance of unclassified Enterobacteriaceae and Clostridiales in CS delivered infants (Table 2). However, no difference was observed between Bacteroides colonization and the mode of delivery at the age of 6 months [20], and at the age of 12 months [26]. Similarly, colonized by the genus Lactobacillus was not significantly associated to the mode of delivery at the age of 6 months [21]. In contrast, Yap et al. [32] found lower abundance of Lactobacilli-enterococci in vaginally delivered infants at the age of 12 months.

Following 6 months of age, in both culture-dependent and culture-independent studies, no difference observed between the vaginally delivered and CS delivered infants regarding the colonization by the Bifidobacterium, Bacteroides, Clostridium, and the Lactobacillus species [20, 21, 26, 36]. Some of these studies have also revealed that total microbiota diversity not differs between vaginally and CS delivered infants. In contrast, total microbial diversity was found significantly higher in vaginally delivered infants compared to CS delivered [27, 32]. Moreover, we could not attribute the observed differences to methodology used, as some reviewed studies reported almost the similar types of infant gut microbiota independently to bacterial detection techniques. Instead, some studies found small numbers of CS infants colonized by similar genera with their vaginally delivered counterparts. Specifically, the lower colonization of Bifidobacterium and Bacteroidetes, and high abundance of genera from the Firmicutes phylum after the age of 6 months of life may not attributed to Caesarean delivery rather than other environmental factors. The diversity of infants gut microbiota may be influenced by geographical variation such as latitude. We therefore suggested that the conflicting results reported in reviewed studies may due to the demographic factors and structure of infants stool microbiota during the first year of life. As previous reported that population living in different latitudes may differ from Firmicutes and Bacteroides colonization levels [58, 59]. The major limitation in the present systematic review is that few studies have reported on microbial diversity or colonization level of the gut microbiota in relation to the mode of delivery from 6 to 12 months of infants’ life. Furthermore, the effects of breastfeeding, antibiotic use during or after pregnancy were not mentioned in some reviewed studies.

CS delivery is associated with a lower abundance and diversity of the phyala Actinobacteria, Bacteroidetes, and higher abundance and diversity of the Firmicute phylum at the first 3 months of life but not in the following periods. At the colonization level, Bifidobacterium, and Bacteroides genera seems to be significantly more frequent in vaginally delivered infants compared with CS delivered, these infants are more colonized by the Clostridium, and Lactobacillus genera at the first 3 months of age, but not in the subsequent periods. From the reports, it is tempting to say that delivery mode has less effect on colonization of Bifidobacteria, and Bacteroides at six and 12 month of age. The high abundance of Bifidobacterium species in infants is considered to promote development and maturation of the immune system to sustain health and high abundance of Clostridium difficile is considered as one of the major nosocomial threats causing severe gastrointestinal infections during the infancy. Future studies should deeply investigate colonization pattern of infant gut microbiota in relation to delivery mode and its broad impact on infant’s health at each stage of life, special attention to the demographics factors should be considered. Also, increasing the sample size in both groups could be considered by future studies.

CS, Cesarean Section; PCR, Polymerase Chain Reaction; TGGE, Temperature gradient gel electrophoresis; VD, Vaginal Delivery