The piglet mycobiome during the weaning transition: a pilot study1

Abstract

The importance of the microbiota in the gastrointestinal tract of animals is recognized as a critical player in host health. Recently, the significance of the mycobiome has been recognized, but culture-independent studies are limited, especially in swine. Weaning is a time of stress, dietary changes, and a predisposition to infections, making it a time point of interest to industry. In this pilot study, we sought to assess and characterize the mycobiome in the feces of swine from birth through the critical weaning transition to investigate the mycobiome population and its temporal dynamics in piglet feces. Cultured fecal samples demonstrate a significant increase in fungal burden following weaning that does not differ from adult levels, suggesting stable colonization. Culturable fungi were not found in any environmental samples tested, including water, food, sow milk or colostrum. To determine the fungal diversity present and to address the problem of unculturable fungi, we performed a pilot study utilizing ITS and 16S rRNA focused primers for high-throughput sequencing of fungal and bacterial species, respectively. Bacterial populations increase in diversity over the experimental timeline (days 1 to 35 postbirth), but the fungal populations do not demonstrate the same temporal trend. Following weaning, there is a dynamic shift in the feces to a Saccharomycetaceae-dominated population. The shift in fungal population was because of the dominance of Kazachstania slooffiae, a poorly characterized colonizer of animal gastrointestinal tracts. This study provides insights into the early colonization and subsequent establishment of fungi during the weaning transition in piglets. Future studies will investigate the effect of the mycobiome on piglet growth and health during the weaning transition.

The fungal community and its interaction with the concentration of short‐chain fatty acids in the caecum and colon of weaned piglets

“…Results of the current study also revealed a unique fungal composition in the hindgut of piglets. Consistent with previous studies in pigs (Hu et al, 2016;Summers et al, 2019), Ascomycota and Basidiomycota were identified as the two most predominant fungal phyla in the hindgut of piglets, and the two phyla accounted for more than 75% of all fungal populations. As reported in human and mice (Li et al, 2018), Mucoromycota was found as the third abundant fungal phylum in the hindgut of the piglets, suggesting a homogeneous fungal taxonomic composition at phylum level in the gut of pigs, mice and human.…”

“…Furthermore, our results showed that genus Kazachstania (Kazachstania slooffiae) belonging to the phylum Ascomycota was the most common fungal genus in the colon, but not in the caecum, of the piglets. Kazachstania has been shown to be a feature of the gut mycobiota in pigs and considered as a natural inhabitant in the gut of pigs (Summers et al, 2019;Urubschurov, Janczyk, Souffrant, Freyer, & Zeyner, 2011 the results of the current study, we still cannot explain whether fungi from the environment could truly colonized in the GI tract of the piglets or were just excreted as transients. Besides, it still remains unknown that whether those dominant fungal species observed in the hindgut of the piglets play a beneficial role to the host and how they interact with the host still remains unknown.…”

“…So far, most studies on the intestinal fungi focused on human and mice. Only few investigations focused on the fungal community in the faeces or colon of swine (Hu et al, ; Summers et al, ). To the best of our knowledge, this study is the first to report the fungal structure in the different segments of hindgut (caecum and colon) in weaned piglets.…”

“…Furthermore, our results showed that genus Kazachstania ( Kazachstania slooffiae ) belonging to the phylum Ascomycota was the most common fungal genus in the colon, but not in the caecum, of the piglets. Kazachstania has been shown to be a feature of the gut mycobiota in pigs and considered as a natural inhabitant in the gut of pigs (Summers et al, ; Urubschurov, Janczyk, Souffrant, Freyer, & Zeyner, ). While the Candida genus was found to distribute in an extremely low abundance (<0.3%) in both of the two intestinal segments of piglets except for one colonic sample.…”

The fungal community and its interaction with the concentration of short‐chain fatty acids in the faeces of Chenghua, Yorkshire and Tibetan pigs

“…Although several studies have explored the fungal communities in human and mice intestines (Suhr and Hallen-Adams, 2015;Li et al, 2017), studies on the composition and diversity of fungi in the intestines of pigs are still very rare. According to the limited results of deep sequencing, Ascomycota and Basidiomycota have been identified as the two most predominant fungal phyla in the faeces of piglets (Hu et al, 2016;Summers et al, 2019), which is consistent with previous findings in the gut of humans and mice. However, Kazachstania slooffae might be the dominant fungal species in weaning piglets (Summers et al, 2019), while its relative abundance showed extremely low or undetectable in the gut of human and mice (Suhr and Hallen-Adams, 2015;Li et al, 2017).…”