In this general population cohort of 746 Canadian infants, we observed higher overall species richness and changes to taxon abundance in gut microbiota of infants exposed to furry pets during pregnancy or continuing to the postnatal period. These findings are in agreement with our previous report [17] of postnatal pet exposure on 3-month gut microbiota but not with studies in later infancy [26]. Moreover, elevations in microbial species richness in this study were evident with prenatal pet exposure. Since several studies including our own within the same cohort have reported low microbiota richness in early life to be associated with food sensitization and other atopic diseases [20, 27, 28], higher microbial richness with prenatal pet exposure may confer protection against the development of atopy.

Our study revealed that pet exposure significantly increased species richness in the phylum Firmicutes, composed of families like the Clostridiaceae, Lachnospiraceae and Ruminococcaceae. These families of the Firmicutes are obligate anaerobes which reduce the oxidative state of the gut [29]; they are common constituents of the gut microbiota of healthy infants and severely depleted in malnourished infants [30]. In particular, we found Ruminococcus, or Oscillospira, belonging to the Ruminococcaceae, to be more abundant (median levels and levels above the median) among infants exposed to pets pre- and postnatally across all birth scenarios. Associations with ruminococcal abundance above the median were independent of all covariates, but attenuated after adjustment for breastfeeding status and maternal race. Prenatal pet exposure alone was sufficient to produce associations with Ruminococcus or Oscillospira, even under conditions of undisturbed gut microbiota following vaginal birth and no IAP. Of note, enrichment in faecal Oscillospira was among the few changes observed for pet ownership within infants delivered by scheduled CS.

Oscillospira is an enigmatic bacterium which has never been isolated in culture, but has been detected by 16S rRNA gene surveys of the human microbiome in association with leanness or lower body mass index in both infants and adults [31–35]. Members of the genus Oscillospira are highly heritable, predominate in the lean host and are positively associated with the leanness-promoting bacterium, Christensenella minuta [32]. Escober et al. [34] also reported decreasing abundance of Oscillospira with obesity in three different geographical regions, despite substantial differences in gut microbial composition. As confirmed by meta-analysis [33], the abundance of Oscillospira has also been found to be negatively associated with paediatric inflammatory bowel disease [36]. The health-promoting effects of Oscillospira are not fully understood. Unlike Ruminococcus, they are not fibre degraders but rather, produce butyrate by relying on fermentation products secreted by other bacterial species or on sugars liberated from host mucins [37]. This is supported by an elegant animal study comparing the microbiota response to fasting across different vertebrates [38]. In this study, Oscillospira were observed to be the only genus whose levels increased during fasting, indicating their ability to degrade host glycans such as fucose, sialic acids and glucuronic acid.

Members of Ruminococcus have also been detected in the stool of neonates and infants [39] but are reportedly absent in some infants delivered vaginally or by CS [40]. Like the Oscillospira, they are also present in dogs and cats [41]. The role of ruminococci in infant health is also poorly understood. Among their noticeable functions, these microbes stimulate the production and degradation of mucin [42], vital to the maintenance of an intact microbiota-mucin barrier. They are also fibre degraders [43] and predominant in formula-fed infants [44, 45]. Yet, ruminococci are still found in breastfed infants and interestingly, their colonization depends on the oligosaccharide content of breast milk [46]. Lastly, they produce ruminococcin A, a bacteriocin which can inhibit various pathogenic species of Clostridium [47]. In our previous study within the same cohort, we observed a strong link between low levels of Ruminococcaceae and food sensitization at age 1, even after adjustment for major microbiota-disrupting events [20].

Our current study also suggests the potential for pet ownership to assist in reducing the burden of group B Streptococcus (GBS) in infants by lowering the abundance of its family, Streptococcaceae. According to a recent paper from McCloskey et al. [48], antenatal pet exposure has been linked to reduced cardiovascular risk of infants born to mothers colonized with GBS during pregnancy. In Canada and elsewhere, the major indication for providing IAP is to prevent GBS infection in newborns [49]. Within vaginally born infants with IAP, we found that prenatal pet exposure reduced the abundance of faecal Streptococcaceae; this association could not be explained by siblingship, breastfeeding status or other covariates. With mechanisms for microbe interactions to be elucidated, it is conceivable that bacteriocin produced from Ruminococcus, a microbe which was more abundant in study infants when Streptococcaceae were depleted, inhibits growth of streptococci. However, others have found lowered abundance of Oscillospira but elevated levels of Ruminococcus to co-occur with a greater abundance of Streptococcaceae at 6 months following vaginal GBS colonization in primarily formula-fed infants [50].

Under birth scenarios involving vaginal delivery, Proteobacteria became less abundant in infants with postnatal pet exposure which commenced prenatally. After emergency CS, the following changes with pet exposure were observed for Proteobacteria: reduced species richness, and abundance of Enterobacteriaceae and of Citrobacter. Pet exposure was also significantly associated with reduced Enterobacteriaceae among infants born vaginally without IAP but not exclusively breastfed afterwards. While our findings appear to contradict reports of greater Escherichia coli colonization in the vaginal microbiome of pregnant women who own pets [51], the timing of microbial changes in the developmental trajectory of infant microbiota is important to consider. Following vaginal delivery, Proteobacteria (especially Enterobacteriaceae) are dominant within 3 months after birth, while Bacteroidetes and Firmicutes become more prevalent as the gut microbiota matures towards an adult-like profile [52]. A bloom of Proteobacteria in the gut can indicate instability in the microbial community [53]; greater abundance (along with a higher abundance of streptococci) in 6-month-old infants has predicted future adiposity [54]. Using the E/B ratio as an indicator for gut microbiota maturity, we previously reported that a higher ratio predicted food sensitization at age 1 [20]; in the current study, pet exposure lowered the E/B ratio in vaginally born infants exposed to IAP. Using another ratio to represent gut microbiota maturity in the current study, pet exposure was linked to a higher F/P ratio following vaginal birth in the absence of maternal IAP. Of note, Ruminococcus and Oscillospira were also elevated under these circumstances.

Additional discussion of the differential impact of pet exposure on scheduled versus emergency CS is warranted. When compared to scheduled CS, our previous study also reported a distinct microbiota profile in infants born via emergency CS, posited to be a function of the multiplicity of exposures, such as repeated antibiotic treatment and prolonged hospitalization [21]. Here, we also found a greater number of pet-associated microbial changes in infants born by emergency CS. Recurrent antibiotic exposure or hospitalization may render gut microbiota more sensitive to colonization by other microbes [55]. It is also conceivable that pet-induced changes of the maternal microbiome are transmitted to a greater extent during labour prior to an emergency CS than in the absence of labour with scheduled CS.

Our current study has several strengths, including the application of high-throughput deep sequencing to profile gut microbiota in a longitudinal population cohort, with a representative and large sample size. Predominance of Proteobacteria in gut microbiota at 3 months and its higher prevalence in CS-delivered infants were consistent with observations in other birth cohorts. Unlike other studies, our study tested the differential impact of pet exposure according to various birth modes, with the aim of providing more translational information for practitioners. Finally, we implemented statistical modelling and sensitivity analyses to explore whether observed associations were attributable to confounding covariates. On the other hand, the use of 16S rRNA sequencing in our study may have resulted in under-representation of organisms such as bifidobacteria. The sensitivity of this technique also did not allow identification at the species level, which is possible with high-throughput microbial culturomics [56], as well as targeted PCR or phenotypic culturing [57]. Metagenomic sequencing was not conducted, which would enable characterization of the functional properties of microbial changes with pet exposure. Since the majority of households in our study owned at least one dog, a larger sample is required to differentiate the effects of different pet species (e.g. dog and or cat) in future studies.