Our study showed that the development of gut microbiota from weaning to adulthood in rats was characterized by increased α-diversity and reduced dissimilarity in β-diversity; changes that rapidly occurred after weaning onto solid food. These results are consistent with studies in people showing that the cessation of breast milk triggered infant gut microbiota development (27, 28), indicating a similar shift in the development of infant gut microbiota to adult-like gut microbiota across different species. Furthermore, we showed that maternal and postnatal consumption of a Caf diet comprised of palatable, processed foods eaten by people, reduced α diversity and altered β-diversity compared with maternal consumption of chow. On the other hand, a maternal Caf diet did not appear to prevent the age-associated increase in α diversity and reduction in β-diversity dissimilarity associated with the shift of offspring gut microbiota towards an adult-like profile.
At weaning, the gut microbial communities of offspring of Chow and Caf dams showed dramatically reduced α-diversity and altered β-diversity relative to their mothers and older offspring (7 and 14 weeks). At 7 weeks of age, α-diversity was suppressed in the CafCaf group compared with the ChowChow, ChowCaf and CafChow groups, suggesting an additive effect of maternal and postweaning exposure to Caf diet. The overall gut microbial composition (β-diversity) of 7 week-old ChowChow and CafCaf offspring clustered close to, but were nonetheless significantly different from, their respective mothers. In contrast, by 14 weeks of age, there was no difference in species richness, evenness and Shannon’s index across the four offspring groups. This may suggest adaptation of offspring gut microbiota to different types of diet, however, there are complex interactions between maternal diet and postnatal diet over time. It is also possible that development of the gastrointestinal tract in offspring (29) might have contributed to the absence of group differences in later life, hence further investigation is warranted.
Β-diversity of offspring gut microbiota exhibited greater similarity to the adult-like gut microbiota over time, both for groups whose postweaning diet was consistent with that of the mother (ChowChow and CafCaf) and for those whose postweaning diet differed from their mother (ChowCaf and CafChow groups). The trend of offspring gut microbiota maturation in this study, an increase in α-diversity and a decrease in dissimilarity of β-diversity is consistent with work by Bäckhed et al. (2015) examining the human gut microbiota in mother and infant dyads. In addition, we show for first time that the developmental trajectory of infant gut microbiota was not affected by the type of maternal and postnatal diets.
Nonetheless, DESeq2 and LEfSe analyses identified multiple OTUs that were reliably altered in the CafCaf relative to the ChowChow group across development. At 7 weeks, the largest number of OTUs were altered in CafCaf group; in total 48; 31 OTUs were depleted and 17 OTUs were enriched. By 14 weeks, the number of altered OTUs in CafCaf group compared with ChowChow group was 9 OTUs in total, of which 1 taxon was depleted and 8 taxa were enriched. Thus fewer OTUs differed between groups over time, underlining an increasing similarity of α-diversity and β-diversity of offspring gut microbiota. On the other hand, the relative abundance of Ruminococcus_Otu00086 was consistently depleted in Caf weaners and in group CafCaf at 7 and 14 weeks, compared with Chow groups. BLAST search with FASTA sequence of Otu_00086 did not identify any similarity to Ruminococcus species. Depletion of Otu_00086 was also observed in Caf dams (relative abundance 6.3%) compared with chow dams (42.2%). Together, this may indicate Ruminococcus is a potential biomarker for unhealthy dietary intake. Here offspring of Caf dams mirrored the effect of Caf diet on suppressing Ruminococcus, the effect that was consistent over time, since the depletion of the genus was observed in offspring gut microbiota from weaning to 14 weeks. In support, the relative abundance of Ruminococcus_Otu86 recovered after switching to chow diet. Ruminococcus are commensal bacteria and play key roles in plant fiber degradation (resistant starch) and butyrate production (30, 31). Continuous Caf diet consumption suppressed the abundance of this beneficial bacteria, which has been shown previously to be depleted (32) in Caf fed rats compared with purified high fat diet and ‘western style’ diet fed animals. Our finding is consistent with findings of Sonnenberg et al. (33) describing extinction of taxa mice consuming a western style diet lacking dietary fibre over multiple generations (33). Hence, this may suggest that the Ruminococcus genera might be affected by highly processed foods containing food additives and insufficient dietary fibre, rather than an effect of the energy density of the food per se (34, 35).
SourceTracker analysis indicated a greater overall contribution of Caf mothers’ microbial community (up to 20%) to that of their offspring than the contribution of Chow mothers’ (up to 8%) of the offspring community. The greater contribution of Caf mothers may be due to higher energy efficiency of representative taxa, however, this needs to be interpreted with caution. Another intriguing finding was the greater contribution of Caf mothers’ microbial community to the gut microbial community at weaning (PND19), regardless of maternal diet (Chow or Caf). Caf mothers’ contribution was characterized by higher relative abundance of Bacteroides_Otu00001 (98% similarity to Bacteoides vulgatus) and Bacteroides_Otu00002 (98% similarity to Bacteroides acidifaciens). On the other hand, Chow mothers’ contribution was characterized by higher relative abundance of Lachnospiraceae_unclassified_Otu00006, Prevotella_Otu00007, Lactobacillus_Otu00008 (98% similarity to Lactobacillus murinus) and Alloprevotella_Otu00009 (88% similarity to Alloprevotella rava). Increased relative abundance of Bacteroides vulgatus was in line with a higher abundance of this species in high fat diet fed rats in our previous study (36).
Finally, we did not find any evidence that sex interacted with α-diversity and β-diversity measures on the development of offspring gut microbiota in this cohort.
The study has some limitations. As the Caf style diet used mirrors the western diet eaten by people (16), by design, it includes foods containing various additives, preservatives, emulsifiers and colorants which can affect gut microbial diversity, in addition to being low in fibre. Future studies using purified diets could delineate the differential impacts of individual diet components on development of gut microbiota. As offspring gut microbial diversity rapidly changes on introduction of solid foods at weaning, it would be interesting to sample soon after the introduction of solid foods to provide additional insight into microbiota development in early life. This study assessed maternal microbial community based on feces collected from the mother at weaning. Recent evidence indicates that maternal microbial communities fluctuate during gestation (37). Hence, maternal gut microbiota at weaning might differ from that found pre-mating, during gestation and lactation.