The present study aimed at investigating the impact of heat challenges on gut microbiota composition in growing pigs and its relationship with pigs’ performance and thermoregulation responses. From a total of 10 F1 sire families, 558 and 564 backcross Large White × Créole pigs were raised and phenotyped from 11 to 23 wk of age in temperate (TEMP) and in tropical (TROP) climates, respectively. In TEMP, all pigs were subjected to an acute heat challenge (3 wk at 29 °C) from 23 to 26 wk of age. Feces samples were collected at 23 wk of age both in TEMP and TROP climate (TEMP23 and TROP23 samples, respectively) and at 26 wk of age in TEMP climate (TEMP26 samples) for 16S rRNA analyses of fecal microbiota composition. The fecal microbiota composition significantly differed between the 3 environments. Using a generalized linear model on microbiota composition, 182 operational taxonomic units (OTU) and 2 pathways were differentially abundant between TEMP23 and TEMP26, and 1,296 OTU and 20 pathways between TEMP23 and TROP23. Using fecal samples collected at 23 wk of age, pigs raised under the 2 climates were discriminated with 36 OTU using a sparse partial least square discriminant analysis that had a mean classification error-rate of 1.7%. In contrast, pigs in TEMP before the acute heat challenge could be discriminated from the pigs in TEMP after the heat challenge with 32 OTU and 9.3% error rate. The microbiota can be used as biomarker of heat stress exposition. Microbiota composition revealed that pigs were separated into 2 enterotypes. The enterotypes were represented in both climates. Whatever the climate, animals belonging to the Turicibacter–Sarcina–Clostridium sensu stricto dominated enterotype were 3.3 kg heavier (P < 0.05) at 11 wk of age than those belonging to the Lactobacillus-dominated enterotype. This latter enterotype was related to a 0.3 °C lower skin temperature (P < 0.05) at 23 wk of age. Following the acute heat challenge in TEMP, this enterotype had a less-stable rectal temperature (0.34 vs. 0.25 °C variation between weeks 23 and 24, P < 0.05) without affecting growth performance (P > 0.05). Instability of the enterotypes was observed in 34% of the pigs, switching from an enterotype to another between 23 and 26 wk of age after heat stress. Despite a lower microbial diversity, the Turicibacter–Sarcina–Clostridium sensu stricto dominated enterotype was better adapted to heat stress conditions with lower thermoregulation variations.

Microbial population in the gastrointestinal tract plays a central role in health and nutrient digestion. The objective of the present study was to investigate the relationships between microbiota and apparent digestibility coefficients with respect to age and diet. Pigs from Large-White, Duroc or Pietrain breeds were raised under the same housing conditions and fed alternately a low-fiber (LF) and a high-fiber diet (HF) during 4 successive 3-week periods. Data collection for digestibility measurements was achieved during the last week of each period. At the end of each period, fecal microbiota was collected for 16S rRNA gene sequencing. The microbiota remained stable across periods whereas digestibility of energy, crude proteins and cell wall components increased. The microbiota was resilient to diet effect and pigs fed the LF diet were discriminated to those fed the HF diet using 31 predicting OTUs with a mean classification error-rate of 3.9%. Clostridiaceae and Turicibacter were negatively correlated whereas Lactobacillus was positively correlated with protein and energy digestibility coefficients in the LF group. In addition, Lachnospiraceae and Prevotella were negatively correlated with cell wall component digestibility. In contrast, no significant correlation was found between microbiota composition and digestibility coefficients when pigs were fed the HF diet. Interestingly, it was also no longer possible to distinguish animals from different breeds once the animals were fed a HF diet, so that the microbiota could only trace the breed origin in the first period and in the LF group. In our experimental conditions, 3 weeks of adaptation to a new diet seems to be sufficient to observe resilience in growing pigs’ microbiota. We demonstrated that fecal microbiota can be used to classify pigs according to their dietary treatment. Some bacteria are favorable or unfavorable to digestibility. This suggests that manipulations of bacterial populations can improve digestibility and feed efficiency.

The present study aimed at investigating the evolution of pigs’ fecal microbiota composition from post-weaning to finishing in a longitudinal analysis. The experiment was conducted on 160 Pietrain × (Large White × Landrace) castrated male and female pigs in two replicates. Feces were collected at 52, 99, 119, 140, and 154 days of age for further 16S rRNA sequencing to analyze the microbiota composition. Pig microbiota evolved strongly from 52 to 99 days of age with an increased abundance of Streptococcaceae and a decreased abundance of Lactobacillaceae. During the finishing stage, microbiota kept evolving at a slower rate. To link the community structure to the performances, the fecal samples were clustered into enterotypes sharing a similar bacterial composition. At 52 days, two enterotypes dominated either by Lactobacillus or by Prevotella–Sarcina were identified. They differed from the two enterotypes determined from 99 to 154 days which were dominated either by Lactobacillus or by Turicibacter–Clostridium sensu stricto. During this time period, 75% of the pigs switched enterotypes. The enterotypes were not related to differences in the overall growth or feeding performance. The enterotype definition was time-dependent and seemed to be related to the sex type at 99 days of age.

Effects of duration of grain feeding on the concentration of endotoxic lipopolysaccharide (LPS) in digesta throughout the digestive tract and on acute phase proteins and LPS in peripheral blood were determined in Holstein yearling calves. Twenty-five Holstein yearling steer calves received either a forage-based diet containing 92% hay and 8% of a mineral and vitamin pellet on a dry matter basis (CON) or a moderate-grain diet, obtained by replacing 41.5% of the hay in the forage-based diet with barley grain, for 3 (MG3), 7 (MG7), 14 (MG14), or 21 d (MG21) before slaughter. Immediately before slaughter, blood samples were collected from the jugular vein. Immediately after slaughter, digesta samples were collected from the rumen, jejunum, ileum, cecum, colon, and rectum. Rumen liquid digesta, digesta from the intestines, and peripheral blood plasma were analyzed for LPS. Peripheral blood plasma and serum were analyzed for the acute phase proteins amyloid A, haptoglobin, and LPS-binding protein. Feeding the grain diet increased the LPS concentration in rumen fluid linearly from 15,488 endotoxin units (EU)/mL for CON to 70,146 EU/mL for MG7. Concentrations of LPS in rumen fluid in MG14 and MG21 were 61,944 and 56,234 EU/mL, respectively, and did not differ. The LPS concentrations in jejunal digesta were much lower than that in digesta elsewhere in the digestive tract, which suggests that ruminal LPS is broken down in the abomasum or proximal jejunum. The concentration of digesta LPS in the ileum was higher than that of digesta elsewhere in the intestines and similar to that in rumen fluid. The duration of grain feeding increased the LPS concentration in digesta in the ileum and cecum and tended to increase that in the colon cubically. Concentrations of LPS in this part of the digestive tract were highest in the MG3 and MG21 groups. The highest concentrations of LPS in digesta in the cecum, colon, and rectum were 3.7, 3.8, and 5.6 times higher than that in CON, respectively. Grain feeding and the increase in LPS in digesta were not accompanied by an acute phase response or a detectable concentration of LPS in peripheral blood. The absence of LPS in peripheral blood and the lack of increase in acute phase proteins indicated that the grain feeding protocol used in the current study and the accompanying changes in LPS concentrations of the digesta did not result in systemic inflammation.

This study describes the fecal microbiota from piglets reared in different living environments during the weaning transition, and presents the characteristics of microbiota associated with good growth of piglets after weaning. Fecal samples were collected pre- (d26) and post-weaning (d35) from 288 male piglets in 16 conventional indoor commercial farms located in the West of France. The changes one week after weaning on the most abundant microbial families was roughly the same in all farms: alpha diversity increased, the relative abundance of Bacteroidaceae (-61%), Christensenellaceae (-35%), Enterobacteriaceae (-42%), and Clostridiaceae (-32%) decreased, while the relative abundance of Prevotellaceae (+143%) and Lachnospiraceae (+21%) increased. Among all the collected samples, four enterotypes that were ubiquitous in all farms were identified. They could be discriminated by their respective relative abundances of Prevotella, Faecalibacterium, Roseburia, and Lachnospira, and likely corresponded to a gradual maturational shift from pre- to post-weaning microbiota. The rearing environment influenced the frequency of enterotypes, as well as the relative abundance of 6 families at d26 (including Christensenellaceae and Lactobacillaceae), and of 21 families at d35. In all farms, piglets showing the highest relative growth rate during the first three weeks after weaning, which were characterized as more robust, had a higher relative abundance of Bacteroidetes, a lower relative abundance of Proteobacteria, and showed a greater increase in Prevotella, Coprococcus, and Lachnospira in the post-weaning period. This study revealed the presence of ubiquitous enterotypes among the farms of this study, reflecting maturational stages of microbiota from a young suckling to an older cereal-eating profile. Despite significant variation in the microbial profile between farms, piglets whose growth after weaning was less disrupted were, those who had reached the more mature phenotype characterized by Prevotella the fastest.

The present study aimed at describing the impact of a deoxynivalenol (DON) - contaminated diet on microbiota composition. A total of 147 (Large White x Landrace) x Piétrain pigs from two replicates were affected to four different experimental treatments. Pigs in the control group (CC) received a control diet from 99 to 154 days of age. Groups DC, CD, and DD were given the DON-contaminated diet (3.02 mg DON/kg feed) for 7 days at 113, at 134, and at 113 and 134 days of age, respectively. The DON-contaminated diet was formulated with a naturally contaminated corn. The body weight gain and the feed intake were daily recorded from day 99 to 154. Fecal samples were collected at the beginning of the experiment (d99), immediately after the end of the 7-days DON challenges (d119 and 140), and at the end of the experiment (d154) for further 16S rRNA sequencing. During challenge periods, ADFI was decreased by 26% to 32% (P &lt; 0.05) and ADG by 40% to 60% (P &lt; 0.05). Short-term DON challenges induced transient changes in microbiota composition. Two weeks after the end of the DON challenges, this composition went back to control state. Whatever the age, DON challenged pigs could be discriminated from controls in a sparse PLS discriminant analysis based on 88 operational taxonomic units or 27 functional pathways with 16% error-rate. The main predictors raised by this discrimination belonged to Streptococcaceae, Lachnospiraceae and Clostridiaceae families. In our experimental conditions, changes in microbiota composition observed during DON challenges were poorly correlated to changes in ADG and ADFI. This experiment revealed a transient modification of the microbiota composition following the exposition to DON-contaminated diet, with no long-term impact on pigs’ performance. This study is part of the Feed-a-Gene Project funded from the European Union’s H2020 Program (grant 633531).

This study describes the response of piglet microbiota to weaning in various environments, and investigates whether microbiota composition is associated with the robustness of piglets. Faecal samples and growth data were collected just before and 7 days after weaning in 288 piglets from 16 commercial farms characterised by their pathogenic status and antimicrobial use. The effect of weaning on the most abundant microbial families of faecal microbiota was roughly the same in all farms and in agreement with previous findings. Four enterotypes, ubiquitous in all farms, were identified, for which the most discriminating genera were Prevotella, Faecalibacterium, Roseburia, and Lachnospira. They corresponded to a gradual maturational shift from pre to post-weaning microbiota. Besides antimicrobial use, the pathogenic status of the farm had a major influence on the post-weaning microbial evolution of apparently healthy piglets. Regarding individual characteristics, piglets whose growth was less perturbed by weaning had more Bacteroidetes (P < 0.01) and less Proteobacteria (P < 0.001). In response to weaning, they showed a greater increase in Prevotella (P < 0.01), Coprococcus (P< 0.01) and Lachnospira (P < 0.05) than piglets that grew more slowly. Thus, the microbiota of robust piglets shares common characteristics regardless the living environment of animals.

The present study aimed at predicting feed efficiency (FE) based on fecal microbiota, using partial least square regression (PLSR), sparse PLSR, and random forest regression (RF). Fecal samples from 147 Pietrain x (Large White x Landrace) pigs reared in two consecutive batches were collected at 99 days of age. Daily live body weight and feed intake were individually measured in pigs fed ad libitum with a corn soybean diet. The relative abundances of operational taxonomic units (OTU) resulting from fecal 16S rRNA sequencing were used to build the prediction models of FE between 99 and 113 days. From these data, neither PLSR nor RF models have been validated on external datasets. An important over-fitting has been observed in PLSR. With this aim to test the ability of the methods to retrieve information, synthetic OTU were created to fit an artificial Pearson correlation with FE (r² = 0 to 0.9) and were added among the predictors in the dataset. Artificial OTU correlated above 0.37 with FE improved the prediction in sparse PLSR and RF, and reduced the over-fitting. The best predictions were achieved by sparse PLSR. The present study emphasized the ability of sparse PLSR and RF to build valid prediction models of a quantitative phenotype, based on fecal microbiota composition. Since no OTU was correlated above 0.30 with FE in the real dataset, the power of the prediction methods was not enough to extract useful information from the fecal microbiota. The functional redundancy of the microbiota could explain the lack of relevant information in the real dataset to predict pigs’ quantitative phenotype. These results suggest that the best strategy is to run sparse PLSR only if a correlation higher than 0.37 is observed. This study is part of the Feed-a-Gene Project funded from the European Union’s H2020 Program (grant 633531).