Co-occurring microbial guilds in pig fecal microbiota: key drivers and effects on host performance

Abstract

Background: The pig gut microbiota is a complex ecosystem composed of microbial guilds that remain largely unexplored. Here we decomposed the pig fecal microbiota of two cohorts of 648 healthy Duroc pigs during the transition (n = 400) and growing finish (n = 248) periods in co-occurring bacterial guilds defined as pig enterosignatures (ES).

Results: Our results indicate that fecal microbial ecosystems can accurately be described by combinations of at least six ES, driven by the Prevotella (ES-Prev), Treponema (ES-Trep), Lactobacillus (ES-Lact), Clostridium (ES-Clost), Streptococcus (ES-Strep), and UBA2810 (ES-UBA2) genera. We observed a dynamic shift with age in the composition of ES, where ES-Prev, ES-Strep, and ES-Lact seem to be core components. Our results suggest partial genetic control by the host, with heritabilities of ES composition ranging from 0.24 to 0.36. Furthermore, our findings indicate that stress on the host is associated with assembly of the ES, decreasing ES-Lact abundance, and increasing prevalence of ES-Strep. We noted a positive association of ES-Prev with growth rate at 60-days, which later evolved to become negative, impacting feed efficiency during the growing period. Remarkably, a negative association of the abundance of ES-Lact with levels of hair cortisol was also found during this period.

Conclusions: Our findings provide novel insights into the pig gut microbiota and reveal novels associations with relevant porcine physiological and performance traits. Moreover, while the ES concept has proven valuable in dissecting microbial communities into assemblies of underlying microbial guilds, our results emphasize the relevance of customizing microbial interventions strategies based on the nutritional and health requirements at each stage of the porcine production cycle.

Fig. 1

Relative genera composition of pig enterosignatures (ES) dominated by different microbial genera in 60-day-old pigs: ES_Prev, ES_Trep, ES_Lact, ES_Clos, and ES_Stre. Only genera with a contribution higher than 4% in at least one of the ESs are shown

Fig. 2

Evolution of genus associations with enterosignatures (ES) for the 400 samples from 60-day-old piglets, depending on the rank of the decomposition

Fig. 3

Relative genera composition of enterosignatures (ES) dominated by different microbial genera in 190-day-old pigs: ES_Prev (Prevotella), ES_Lact (Lactobaicllus), ES_UBA2 (UBA2810), and ES_Stre (Streptococcus). Only genera with contribution higher than 4% are shown

Fig. 4

Linear relationship between abundance of enterosignatures (ES) and body weight of 60-day-old pigs. The evolution of ES relative abundances is depicted with the ES faction on the y-axis and BW on the x-axis. P-values are depicted in the legend

Fig. 5

Linear relationship of ESs of 190-day-old pigs with A ADG, B RFI, and C FCR. The relationship of ES relative abundances is depicted with the ES fraction on y-axis and ADG (A), FCR (B) and RFI (C) values in x-axis. P-values are also depicted in the legend at the top-left

Fig. 6

Enterosignatures (ES) composition in stress and control groups of pigs during the growing-finish period

Fig. 7

Relationship between ES-Lact abundance and hair cortisol level of 190-day-old pigs. The black line shows the regression line while the red line shows the local regression fit