Gut eukaryotic communities in pigs: diversity, composition and host genetics contribution

Ramayo-Caldas, Yuliaxis; Prenafeta, F.X; Zingaretti, Laura M.; Gonzales, Olga; Dalmau, Antoni; Quintanilla, Raquel; Ballester, María

doi:10.1101/2020.02.18.941856

Cited by 5 publications

(6 citation statements)

References 54 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…This indicates that the piglet fecal bacteriome likely follows a defined pattern of colonization and succession in healthy developing piglets, whereas in the mycobiome a large portion of the community may be transient and driven by other factors, such as environmental exposure, diet, or host immunity, which may vary by piglet. Other studies have purported similar hypotheses regarding the transient nature of the mycobiome based on compositional variability among sample subjects and association of fungal genera with food or environmental sources [ 36 , 43 , 44 ]. In the pre-wean piglet mycobiome, environmental influence is suggested by the dominance of naturally ubiquitous fungal families Trichosporonaceae , Mucoraceae , and Cladosporiacea , all of which are found in a variety of environments including organic debris, soils, and indoor/outdoor air [ 45 , 46 , 47 ].…”

Section: Discussionmentioning

confidence: 93%

“…One of the most striking differences included a high level of variation in the relative abundances of fungal families Saccharomycetaceae ( K. slooffiae ) and Debaryomcetaceae ( H. burtonii ). K. slooffiae , a persistent fungus in post-weaned piglets [ 30 , 44 ], is hypothesized to be a potential protein source to healthy pigs [ 14 ] and may behave similarly to commensal Candida species in humans [ 13 ]. In a study on human diets, Candida was positively correlated with high carbohydrate consumption [ 50 ] and has been shown to degrade starches [ 51 ].…”

Section: Discussionmentioning

confidence: 99%

“…In piglets, the transition from a milk diet to high carbohydrate nursery feed at weaning may explain the increase in K. slooffiae in post-weaned piglets. In comparison, H. burtonii is a common fungal contaminant of corn [ 52 ] and has not been found to be abundant in other piglet fecal studies regardless of piglet age [ 30 , 44 ]. However, H. burtonii , like Candida , is also able to degrade starch [ 53 ] and may compete with K. slooffiae in the gut environment.…”

Section: Discussionmentioning

confidence: 99%

See 2 more Smart Citations

Temporal Dynamics of the Gut Bacteriome and Mycobiome in the Weanling Pig

2020

View full text Add to dashboard Cite

Weaning is a period of environmental changes and stress that results in significant alterations to the piglet gut microbiome and is associated with a predisposition to disease, making potential interventions of interest to the swine industry. In other animals, interactions between the bacteriome and mycobiome can result in altered nutrient absorption and susceptibility to disease, but these interactions remain poorly understood in pigs. Recently, we assessed the colonization dynamics of fungi and bacteria in the gastrointestinal tract of piglets at a single time point post-weaning (day 35) and inferred interactions were found between fungal and bacterial members of the porcine gut ecosystem. In this study, we performed a longitudinal assessment of the fecal bacteriome and mycobiome of piglets from birth through the weaning transition. Piglet feces in this study showed a dramatic shift over time in the bacterial and fungal communities, as well as an increase in network connectivity between the two kingdoms. The piglet fecal bacteriome showed a relatively stable and predictable pattern of development from Bacteroidaceae to Prevotellaceae, as seen in other studies, while the mycobiome demonstrated a loss in diversity over time with a post-weaning population dominated by Saccharomycetaceae. The mycobiome demonstrated a more transient community that is likely driven by factors such as diet or environmental exposure rather than an organized pattern of colonization and succession evidenced by fecal sample taxonomic clustering with nursey feed samples post-weaning. Due to the potential tractability of the community, the mycobiome may be a viable candidate for potential microbial interventions that will alter piglet health and growth during the weaning transition.

show abstract

Section: Discussionmentioning

confidence: 93%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

See 1 more Smart Citation

Temporal Dynamics of the Gut Bacteriome and Mycobiome in the Weanling Pig

2020

View full text Add to dashboard Cite

show abstract

“…Nevertheless, more additional aspects need to be considered. Firstly, in addition to bacteria, the microbial community of pig fecal samples is characterized by other microorganisms, such as yeasts and fungi (Ramayo-Caldas et al, 2020 ). This may have led to discrepancies between the experimental results of functional metabolism detected by the Ecoplates and the prediction analysis on 16S rRNA performed on the bacterial microbiota.…”

Section: Discussionmentioning

confidence: 99%

Assessment of Biolog EcoplateTM method for functional metabolic diversity of aerotolerant pig fecal microbiota

Checcucci

Luise

Modesto

et al. 2021

Appl Microbiol Biotechnol

View full text Add to dashboard Cite

In the last decades, gut microbiota and its role in mammal host development and health have been increasingly investigated. Metabolites produced by gut microbiota can affect intestinal homeostasis and immune system maturity and activation, and in turn, they can influence the health and growth performance of livestock. Therefore, a better understanding of the functional metabolic capability of the gut microbiota would be appreciated by the scientific community. In this study, the BiologTM Ecoplates technology was applied for studying the metabolic potential of the aerotolerant microbial community of pig fecal samples, evaluating the interference of different storage conditions and cell concentrations. The length of time for which a fecal sample maintained detectable and unchanged microbial metabolic activity was also investigated. Two assays aimed to evaluate differences in the metabolic activities between fresh and snap-frozen fecal samples at different dilutions and at different lengths of times of preservation at −80°C were carried out. The biodiversity and the predicted functionality of the entire bacterial community through a targeted metagenomic approach were also explored. The results highlighted that snap freezing of fecal samples preserved the metabolic activity of the microbial community when compared to fresh feces. Sample storage at −80 °C did not significantly affect the metabolic activity of the microbial community, which was stable for 150 days. Furthermore, the highest metabolic activity was detected with 1:2 to 1:5 dilutions of the stock suspension. BiologTM Ecoplates technology is a rapid and useful method to explore microbial communities’ metabolism in animal fecal samples contributing to investigate host animal physiology. Key points • Freezing of samples can preserve the functional activity of the aerotolerant microbial community for 150 days. • The concentration of microbial cells strongly influences metabolic activity detection. • Sequencing coupled with the BiologTMEcoplates could be a strategy to evaluate the metabolic potential of the microbiota of the fecal sample. Graphical abstract

show abstract

“…Commensal gut populations modulate hosts' immune responses, which in turn can modify the microbiota composition to maintain gut homeostasis [20,21]. Recently, polymorphisms located in immune genes associated with the abundance of microbial communities have been reported [22][23][24][25]. Furthermore, it has been suggested that the pattern recognition receptors, which are proteins capable of recognizing molecules frequently associated with pathogens, may have evolved to mediate the bidirectional crosstalk between microbial symbionts and their hosts [26].…”

Section: Introductionmentioning

confidence: 99%

Leveraging host-genetics and gut microbiota to determine immunocompetence in pigs

Ramayo-Caldas

Zingaretti

Pérez-Pascual

et al. 2021

Preprint

Self Cite

View full text Add to dashboard Cite

The aim of the present work was to identify microbial biomarkers linked to immunity traits and to characterize the contribution of host-genome and gut microbiota to the immunocompetence in healthy pigs. To achieve this goal, we undertook a combination of network, mixed model and microbial-wide association studies (MWAS) for 21 immunity traits and the relative abundance of gut bacterial communities in 389 pigs genotyped for 70K SNPs. The heritability (h2; proportion of phenotypic variance explained by the host genetics) and microbiability (m2; proportion of variance explained by the microbial composition) showed similar values for most of the analyzed immunity traits, except for both IgM and IgG in plasma that were dominated by the host genetics, and the haptoglobin in serum which was the trait with larger m2 (0.275) compared to h2 (0.138). Results from the MWAS suggested a polymicrobial nature of the immunocompetence in pigs and revealed associations between pigs gut microbiota composition and 15 of the analyzed traits. The lymphocytes phagocytic capacity (quantified as mean fluorescence) and the total number of monocytes in blood were the traits associated with the largest number of taxa (6 taxa). Among the associations identified by MWAS, 30% were confirmed by an information theory network approach. The strongest confirmed associations were between Fibrobacter and phagocytic capacity of lymphocytes (r=0.37), followed by correlations between Streptococcus and the percentage of phagocytic lymphocytes (r=-0.34) and between Megasphaera and serum concentration of haptoglobin (r=0.26). In the interaction network, Streptococcus and percentage of phagocytic lymphocytes were the keystone bacterial and immune-trait, respectively. Overall, our findings reveal an important connection between immunity traits and gut microbiota in pigs and highlight the need to consider both sources of information, host genome and microbial levels, to accurately characterize immunocompetence in pigs.

show abstract

Gut eukaryotic communities in pigs: diversity, composition and host genetics contribution

Cited by 5 publications

References 54 publications

Temporal Dynamics of the Gut Bacteriome and Mycobiome in the Weanling Pig

Temporal Dynamics of the Gut Bacteriome and Mycobiome in the Weanling Pig

Assessment of Biolog EcoplateTM method for functional metabolic diversity of aerotolerant pig fecal microbiota

Leveraging host-genetics and gut microbiota to determine immunocompetence in pigs

Contact Info

Product

Resources

About