Raquel Rio-Lopez

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.

Stress significantly affects the health, welfare, and productivity of farm animals. We performed a longitudinal study to evaluate stress’s effects on pig performance, feeding behavior, and fecal microbiota composition. This study involved 64 Duroc pigs during the fattening period, divided into two experimental groups: a stress group (n = 32) and a control group (n = 32). Stressed groups had less space and were mixed twice during the experiment. We monitored body weight, feed efficiency, feeding behavior, and fecal microbiota composition. Compared to the control group, the stressed pigs exhibited reduced body weight, feed efficiency, fewer feeder visits, and longer meal durations. In the fecal microbiota, resilience was observed, with greater differences between groups when sampling was closer to the stressful stimulus. Stressed pigs showed an increase in opportunistic bacteria, such as Streptococcus, Treponema and members of the Erysipelotrichaceae family, while control pigs had more butyrate- and propionate-producing genera like Anaerobutyricum, Coprococcus and HUN007. Our findings confirm that prolonged stress negatively impacts porcine welfare, behavior, and performance, and alters their gut microbiota. Specific microorganisms identified could serve as non-invasive biomarkers for stress, potentially informing both animal welfare and similar gut-brain axis mechanisms relevant to human research.

Pigs are a social species, and they establish hierarchies for better use of resources and to reduce conflicts. However, in pig production, the opportunities for growth can differ between dominant and subordinate animals. In the present study, a system was tested to perform a dominant versus subordinate test in growing pigs to investigate how the hierarchy affects feeding behaviour, growth, and gut microbiota assessed in faeces. Sixty-four animals housed in eight different pens were used, with four castrated males and four females in each one, weighing 18 kg at arrival and maintained during the whole growing period, until 140 kg. Three stool samples were obtained from the animals directly from the anus to avoid contamination of the faeces 58, 100, and 133 days after the start of the study to investigate the microbiota composition. The dominant animals had higher gains during the growing period than the subordinates. In addition, they were performing more visits to the feeder throughout the day. Differential abundance patterns were observed in five bacterial genera, with Oliverpabstia, Peptococcus, and Faecalbacterium being more abundant in dominant animals and Holdemanella and Acetitomaculum being overrepresented in subordinate ones. This microbial biomarker accurately classified dominant versus subordinate groups of samples with an AUC of 0.92.

Pigs are a social species and they stablish hierarchies for a better use of resources and to reduce conflicts. However, in pig production, the opportunities for growing can differ in dominant and subordinate animals. In the present study a system was tested to perform a Dominance versus Subordinate test in growing pigs to investigate how the hierarchy affects feeding behaviour, growth and gut microbiota assessed in faeces. 64 animals housed in eight different pens were used, with four castrated males and four females in each one, weighing 18kg at arrival and maintained during the whole growing period, until 140 kg. Three stool samplings were obtained from the animals directly from the anus to avoid contamination of the faeces on 58, 100 and 133 days after the start of the study to investigate the microbiota composition. The dominant animals had higher gains during the growing period that the subordinate. In addition, they were performing more visits to the feeder throughout the day. Differential abundance patterns were observed in five bacterial genera, Oliverpabstia, Peptococcus, and Faecalbacterium being more abundant in dominant animals and Holdemanella and Acetitomaculum being overrepresented in subordinate ones. This microbial biomarker accurately classified dominant versus subordinate groups of samples with an AUC of 0.92.

The pig gut microbiota is a complex ecosystem composed of microbial guilds, which until recently were unknown. Here, we decomposed the pig fecal microbiota of 648 healthy pigs during the transition (n=400) and growing-finishing (n=248) periods in co-occurring bacterial communities defined as pig enterosignatures (pig ES). Our results indicate that fecal microbial ecosystems can accurately be described by combinations of at least six pig ES, driven by 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 in the composition of pig ES, where ES-Prev, ES-Strep, and ES-Lact seem to be core components, while ES-Trep, ES-Clost, and ES-UBA play age-specific roles. Our results suggest partial genetic control by the host, with heritabilities of pig ES composition ranging from 0.30 to 0.42. Furthermore, our findings indicate that stress can impact pig ES assembly, decreasing ES-Lact abundance while increasing the prevalence of ES-Strep. We noted a positive link between ES-Prev and growth at 60 days, which later evolved negatively, impacting feed efficiency during the finish-growing period. Additionally, we observed a negative association of ES-Strep and a positive impact of ES-Lact on growth and feed efficiency during the growing period. Remarkably, a negative association between the abundance of ES-Lact and levels of hair cortisol was also observed during this period. Overall, our findings confirm the key ecological roles of Prevotella, Treponema, Lactobacillus, and Streptococcus from previous studies in pigs and reveal novels links with relevant porcine physiological and performance traits. Finally, despite pig ES proving valuable in dissecting microbial communities into assemblies of underlying microbial guilds, showcasing its potential as a novel tool in breeding and precision farming. Our findings emphasize the importance of customizing microbial consortia to meet the nutritional and health requirements at each stage or category of the porcine production chain.