Survey of rumen microbiota of domestic grazing yak during different growth stages revealed novel maturation patterns of four key microbial groups and their dynamic interactions

Abstract

Background: The development and maturation of rumen microbiota across the lifetime of grazing yaks remain unexplored due to the varied lifestyles and feed types of yaks as well as the challenges of obtaining samples. In addition, the interactions among four different rumen microbial groups (bacteria, archaea, fungi and protozoa) in the rumen of yak are not well defined. In this study, the rumen microbiota of full-grazing yaks aged 7 days to 12 years old was assessed to determine the maturation patterns of these four microbial groups and the dynamic interactions among them during different growth stages. Results: The rumen microbial groups (bacteria, archaea, protozoa and fungi) varied through the growth of yaks from neonatal (7 days) to adult (12 years), and the bacterial and archaeal groups were more sensitive to changes in growth stages compared to the two eukaryotic microbial groups. The age-discriminatory taxa within each microbial group were identified with the random forest model. Among them, Olsenella (bacteria), Group 10 sp., belonging to the family Methanomassiliicoccaceae (archaea), Orpinomyces (fungi), and Dasytricha (protozoa) contributed the most to discriminating the age of the rumen microbiota. Moreover, we found that the rumen archaea reached full maturation at 5 approximately years of age, and the other microbial groups matured between 5 and 8 years of age. The intra-interactions patterns and keystone species within each microbial group were identified by network analysis, and the inter-interactions among the four microbial groups changed with growth stage. Regarding the inter-interactions among the four microbial groups, taxa from bacteria and protozoa, including Christensenellaceae R-7 group, Prevotella 1, Trichostomatia, Ruminococcaceae UCG-014 and Lachnospiraceae, were the keystone species in the network based on betweenness centrality scores.

Seasonal dynamics of diet–gut microbiota interaction in adaptation of yaks to life at high altitude

“…Furthermore, convergent evolution was reported for yaks and their rumen microbiota. The rumen microbiota follow unique maturation strategies 19 and differ in composition from microbiota of lowland ruminants 4 .…”

Microbial interaction-driven community differences as revealed by network analysis

“…The traditional and commonly used approach to identify microbial interactions is the construction of microbial co-occurrence networks using a correlation-based method (Pearson’s or Spearman’s correlation coefficient) [2] , [3] , [5] , [6] . This method is prone to detecting spurious correlations among low abundance taxa [7] and can lead to an ill-defined understanding of microbial interactions.…”

Metagenomic analysis reveals rumen microbiota alteration of the yak at different stages of growth

“…While, Firmicutes, Fibrobacteres, Bacteroidetes, Euryarchaeota, and Proteobacteria were the predominant phyla in the cattle-yak rumen microbial community [10]. The rumen microbial groups varied through the growth of yaks from neonatal to adult and compared with the protozoan and fungal groups, the bacterial and archaeal groups were more sensitive to changes in growth stages [32]. A total of 7200 operational taxonomic units (OTUs) were gained from the yak rumen using 16S rRNA gene sequencing, and 23 phyla within 159 families were identi ed by taxonomic summarization [18].…”