Stability and volatility shape the gut bacteriome and mycobiome dynamics in a pig model

Authors: FREEHAN, BRANDI - Kansas State University; RAN, QINGHONG - Kansas State University; DORMAN, VICTORIA - Kansas State University; RUMBACK, COURTNEY - Kansas State University; POGRANICHNIY, SOPHIA - Kansas State University; WARD, KAITLYN - Kansas State University; GOODBAND, ROBERT - Kansas State University; NIEDERWERDER, MEGAN - Kansas State University; Summers, Katie; LEE, SONNY - Kansas State University

Submitted to: Nature Scientific Reports
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/24/2022
Publication Date: 9/5/2022
Citation: Freehan, B., Ran, Q., Dorman, V., Rumback, C., Pogranichniy, S., Ward, K., Goodband, R., Niederwerder, M., Summers, K.L., Lee, S.T. 2022. Stability and volatility shape the gut bacteriome and mycobiome dynamics in a pig model. Nature Scientific Reports. 12:15080. https://doi.org/10.1038/s41598-022-19093-9.
DOI: https://doi.org/10.1038/s41598-022-19093-9

Interpretive Summary: The interactions between the bacteria (bacteriome) and fungi (mycobiome) in the gastrointestinal tract of piglets have complex interactions that result in altered host development, growth, and disease pathogenesis. Due to the large number of microbes in the gut and the inability to culture many of these microbial members, these interactions remain poorly understood. Scientists at Kansas State University and at the Agricultural Research Service, Beltsville, Maryland analyzed the bacteriome and the levels of a specific fungus, Kazachstania slooffiae, in pigs from 2 days to 157 days of age. The scientists demonstrated the dynamic changes in the bacteriome at the preweaning stage with the progression to a more stable bacteriome in the nursery and finisher stages that corresponded with the elevation of K. slooffiae levels. K. slooffiae demonstrated negative inferred interactions with the bacteriome during the nursery stage with a shift to positive and negative interactions in adult pigs. These longitudinal interactions provide insight into the piglet gut ecosystem during development and further studies will investigate their role in piglet growth performance and disease pathogenesis.

Technical Abstract: The gut microbiome plays important roles in the maintenance of health and pathogenesis of diseases in the growing host. In order to fully comprehend the interplay of the gut microbiome and host, a foundational understanding of longitudinal bacteriome and mycobiome development is necessary. In this study, we evaluated enteric bacterial, fungal and host dynamics throughout the host lifetime. We collected a total of 234 fecal samples from 9 swine hosts across 31 time points in 3 developmental stages (5 preweaning, 15 nursery, and 11 growth adult). We then performed 16S rRNA amplicon sequencing for bacterial profiles and qPCR for the fungus Kazachstania slooffiae. We identified distinct bacteriome clustering according to the host developmental stage, with the preweaning stage exhibiting low bacterial diversity and high volatility amongst samples. We further recovered clusters of bacterial populations that were considered core, transient and increasing throughout the host lifetime, suggesting distinct yet important roles which these differing bacterial population clusters played in the different host stages. Kazachstania slooffiae was absent in the preweaning host but peaked during the nursery stage of the host. We determined that all host growth stages contained negative correlations between K. slooffiae and bacterial genera, with only the growth adult stage containing positive correlates. The lack of positive correlates and shared K. slooffiae-bacteria interactions between stages warrants future research into the interactions amongst these kingdoms for host health. This research is foundational for understanding how the bacteriome and mycobiome develop singularly, as well as a system in the host’s gut environment.