Longitudinal Characterization of the Gut Bacterial and Fungal Communities in Yaks

Abstract

Development phases are important in maturing immune systems, intestinal functions, and metabolism for the construction, structure, and diversity of microbiome in the intestine during the entire life. Characterizing the gut microbiota colonization and succession based on age-dependent effects might be crucial if a microbiota-based therapeutic or disease prevention strategy is adopted. The purpose of this study was to reveal the dynamic distribution of intestinal bacterial and fungal communities across all development stages in yaks. Dynamic changes (a substantial difference) in the structure and composition ratio of the microbial community were observed in yaks that matched the natural aging process from juvenile to natural aging. This study included a significant shift in the abundance and proportion of bacterial phyla (Planctomycetes, Firmicutes, Bacteroidetes, Spirochaetes, Tenericutes, Proteobacteria, and Cyanobacteria) and fungal phyla (Chytridiomycota, Mortierellomycota, Neocallimastigomycota, Ascomycota, and Basidiomycota) across all development stages in yaks. As yaks grew older, variation reduced, and diversity increased as compared to young yaks. In addition, the intestine was colonized by a succession of microbiomes that coalesced into a more mature adult, including Ruminococcaceae_UCG-005, Romboutsia, Prevotellaceae_UCG-004, Blautia, Clostridium_sensu_stricto_1, Ruminococcus_1, Ruminiclostridium_5, Rikenellaceae_RC9_gut_group, Alloprevotella, Acetitomaculum, Lachnospiraceae_NK3A20_group, Bacteroides, Treponema_2, Olsenella, Escherichia-Shigella, Candidatus_Saccharimonas, and fungal communities Mortierella, Lomentospora, Orpinomyces, and Saccharomyces. In addition, microorganisms that threaten health, such as Escherichia-Shigella, Mortierella, Lomentospora and Hydrogenoanaerobacterium, Corynebacterium_1, Trichosporon, and Coprinellus, were enriched in young and old yaks, respectively, although all yaks were healthy. The significant shifts in microflora composition and structure might reflect adaptation of gut microbiome, which is associated with physicochemical conditions changes and substrate availability in the gut across all development periods of yaks.

Keywords: bacterial microbiota; fungal communities; high-throughput sequencing; natural aging; yaks.

Figure 1

The diversity indices of bacterial and fungal communities in all groups. (A–E) Represents bacterial ACE, Chao1, Simpson, Shannon, and Coverage indices, respectively. (F–J) Represents fungal ACE, Chao1, Simpson, Shannon, and Good’s Coverage indices, respectively. * p < 0.05; ** p < 0.01.

Figure 2

Venn diagram is showing OTUs compositions. (A) OTUs of bacterial compositions in all groups; (B–D) represents the compositions of bacterial OTUs within Y, A, and O groups, respectively. (E) OTUs of fungal compositions in all groups; (F–H) represents the compositions of fungal OTUs within Y, A, and O groups, respectively.

Figure 3

Analysis of bacterial and fungal communities’ structures in all groups. (A,B) Represents the bacterial similarity between individuals or groups by using PCA and UPGMA, respectively. (C,D) Represents the fungal similarity between individuals or groups by using PCA and UPGMA, respectively.

Figure 4

Histogram of the distribution of the top 10 species in abundance. (A,B) Showed bacterial abundance at the taxonomic level in phyla and genera, respectively; (C,D) showed fungal abundance at the taxonomic level in phyla and genera.

Figure 5

The differences in the relative abundance of bacteria and fungi between three development stages at the phylum level. * p < 0.05; ** p < 0.01.

Figure 6

The differences in the relative abundance of bacteria and fungi between three development stages at the genus level. * p < 0.05; ** p < 0.01.

Figure 7

LEfSe analysis for remarking the significantly abundant bacterial and fungal microbes across development periods in yaks. (A,B) Represents bacterial analysis; (C,D) represents fungal analysis.