Feed efficiency (FE) is critical in pig production for both economic and environmental reasons. As the intestinal microbiota plays an important role in energy harvest, it is likely to influence FE. Therefore, our aim was to characterize the intestinal microbiota of pigs ranked as low, medium, and high residual feed intake ([RFI] a metric for FE), where genetic, nutritional, and management effects were minimized, to explore a possible link between the intestinal microbiota and FE. Eightyone pigs were ranked according to RFI between weaning and day 126 postweaning, and 32 were selected as the extremes in RFI (12 low, 10 medium, and 10 high). Intestinal microbiota diversity, composition, and predicted functionality were assessed by 16S rRNA gene sequencing. Although no differences in microbial diversity were found, some RFI-associated compositional differences were revealed, principally among members of Firmicutes, predominantly in feces at slaughter (albeit mainly for low-abundance taxa). In particular, microbes associated with a leaner and healthier host (e.g., Christensenellaceae, Oscillibacter, and Cellulosilyticum) were enriched in low RFI (more feed-efficient) pigs. Differences were also observed in the ileum of low RFI pigs; most notably, Nocardiaceae (Rhodococcus) were less abundant. Predictive functional analysis suggested improved metabolic capabilities in these animals, especially within the ileal microbiota. Higher ileal isobutyric acid concentrations were also found in low RFI pigs. Overall, the differences observed within the intestinal microbiota of low RFI pigs compared with that of their high RFI counterparts, albeit relatively subtle, suggest a possible link between the intestinal microbiota and FE in pigs.IMPORTANCE This study is one of the first to show that differences in intestinal microbiota composition, albeit subtle, may partly explain improved feed efficiency (FE) in low residual feed intake (RFI) pigs. One of the main findings is that, although microbial diversity did not differ among animals of varying FE, specific intestinal microbes could potentially be linked with porcine FE. However, as the factors impacting FE are still not fully understood, intestinal microbiota composition may not be a major factor determining differences in FE. Nonetheless, this work has provided a potential set of microbial biomarkers for FE in pigs. Although culturability could be a limiting factor and intervention studies are required, these taxa could potentially be targeted in the future to manipulate the intestinal microbiome so as to improve

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BackgroundThis study aimed at (1) deriving Bayesian methods to predict breeding values for ratio (i.e. feed conversion ratio; FCR) or linear (i.e. residual feed intake; RFI) traits; (2) estimating genetic parameters for average daily feed consumption (ADFI), average daily weight gain (ADG), lean meat percentage (LMP) along with the derived traits of RFI and FCR; and (3) deriving Bayesian estimates of direct and correlated responses to selection on RFI, FCR, ADG, ADFI, and LMP. Response to selection was defined as the difference in additive genetic mean of the selected top individuals, expected to be parents of the next generation, and the total population after integrating genetic trends out of the posterior distribution of selection responses. Inferences were based on marginal posterior distributions obtained from the Bayesian method for integration over unknown population parameters and “fixed” environmental effects and for appropriate handling of ratio traits. Terminal line pigs (n = 3724) were used for a multi-variate model for ADFI, ADG, and LMP. RFI was estimated from the conditional distribution of ADFI given ADG and LMP, using either genetic (RFIG) or phenotypic (RFIP) partial regression coefficients. The posterior distribution of the FCR’s breeding values was derived from the posterior distribution of “fixed” environmental effects and additive genetic effects on ADFI and ADG.ResultsPosterior means of heritability were 0.32, 0.26, 0.56, 0.20, and 0.15 for ADFI, ADG, LMP, RFIP, and RFIG, respectively. Selection against RFIG showed a direct response of − 0.16 kg/d and correlated responses of − 0.16 kg/kg for FCR and − 0.15 kg/d for ADFI, with no effect on other production traits. Selection against FCR resulted in a direct response of − 0.17 kg/kg and correlated responses of − 0.14 kg/d for RFIG, − 0.18 kg/d for ADFI, and 0.98% for LMP.ConclusionsThe Bayesian methodology developed here enables prediction of breeding values for FCR and RFI from a single multi-variate model. In addition, we derived posterior distributions of direct and correlated responses to selection. Genetic parameter estimates indicated a genetic basis for the studied traits and that genetic improvement through selection was possible. Direct selection against FCR or RFIP resulted in unexpected responses in production traits.

Seaweed extracts (SWE) rich in laminarin and fucoidan have shown promise as a supplement for weaned piglets. However, successful application in pig nutrition depends on their bioactivity in the presence of additives such as ZnO. In the present study, a 2 £ 2 factorial experiment was carried out to investigate the effect of the interaction between SWE and ZnO on the growth performance, digestibility and faecal characteristics of 192 weaned piglets (6·5 kg). The piglets were penned in groups of 4 (n 12 pens). The study consisted of two phases after weaning: a starter diet period from the day of weaning (0 d) to 21 d and a transition diet period from 21 to 40 d. The dietary treatments were as follows: (1) control diet; (2) control diet þ ZnO; (3) control diet þ SWE; (4) control diet þ ZnO þ SWE. Diets containing ZnO improved the faecal consistency of the piglets throughout the experimental period (0-40 d). An effect of the interaction between ZnO and SWE on several variable was observed. The diet containing only SWE or ZnO improved the feed conversion efficiency of the piglets during the transition diet period; however, this effect was not observed when the diet containing both ZnO and SWE was fed. The diet containing only SWE increased the N and organic matter digestibility of the piglets; however, this effect was not observed in the presence of ZnO. An interaction between ZnO and SWE was observed, whereby the faecal counts of Escherichia coli were decreased when piglets were fed the diet containing only SWE, but not when fed the diet containing both SWE and ZnO. In summary, SWE and ZnO improve growth performance when given alone, but not when given in combination. The biological effect of SWE on selected digestibility and faecal characteristics was markedly different when compared with that of ZnO.Key words: Laminarin: Fucoidan: Zinc oxide: Weaned pigletsThe commercial practice of abrupt weaning exposes piglets to several environmental and nutritional challenges, including the absence of sows, new littermates, and changes in the source and delivery of nutrition (1) . Among these, the rapid dietary transition from liquid milk to solid feed principally disrupts digestive processes, temporarily impeding growth performance. However, frequently the weaning process results in a physiological damage to the gastrointestinal tract as microbial pathogens take advantage of a turbulent immune status. The consequences of this microbial dysbiosis are poor nutrient utilisation, faecal scouring, increased number of faecal coliforms such as Escherichia coli, and impaired feed conversion efficiency (FCE). The practice of in-feed antibiotic inclusion was popular as a means of buffering the weaning transition in piglets to overcome the disruption of growth performance after weaning. However, concerns of increased microbial tolerance to antibiotics eventually resulted in a ban on prophylactic antibiotic use, upheld in the European Union since 2006. Consequently, the prescribed inclusion of ZnO at rates above nutritional requi...

The consideration of feed efficiency traits is highly relevant in animal breeding due to economic and ecologic impacts of the efficient usage and utilization of feed resources. In pigs, corresponding observations are recorded using automatic feeding stations and serve as one of the main criteria in most pig selection programmes. Simultaneously, feeding stations also generate feeding behaviour data which represent a nearly unused resource and provide a valuable proxy measure of health status, animal welfare, and management practices. In the current study, an integrated approach was applied to a feed efficiency tested and genome-wide genotyped terminal sire line population. Therefore, genetic analyses were performed combining a single-marker based approach and a Bayesian multi-marker algorithm. Major quantitative trait loci (QTL) for feeding behaviour traits comprising daily occupation time, daily feeder visit, and daily feeding rate were identified on chromosomes 1, 4, 6, 7, 8, and 14. Feed efficiency was represented by feed conversion ratio and daily feed intake revealing prominent genomic regions on chromosomes 1, 6, 9, and 11. The positional and functional candidate genes identified are involved in transport processes like AQP4, SLC22A23, and SLC6A14 as well as energy sensing, generation, and utilization as exemplified by PPP3CA, IQGAP3, ECI2, and DnaJC15. These molecular features provide the first step towards the dissection of the genetic connection between distinct feeding behaviour patterns, feed efficiency and performance, health, and welfare traits driving the implementation of these traits in breeding programmes and pig husbandry.Electronic supplementary materialThe online version of this article (doi:10.1007/s00438-017-1325-1) contains supplementary material, which is available to authorized users.