second model, the two main conditions were parametrically modulated by the two categories, respectively (SOM, S5.1). The activation of the precuneus was higher for hard dominance-solvable games than for easy ones ( Fig. 4A and table S10). The activation of the insula was higher for the highly focal coordination games than for less focal ones ( Fig. 4B and table S11). Previous studies also found that precuneus activity increased when the number of planned moves increased (40, 41). The higher demand for memory-related imagery and memory retrieval may explain the greater precuneus activation in hard dominance-solvable games. In highly focal coordination games, the participants may have felt quite strongly that the pool students must notice the same salient feature. This may explain why insula activation correlates with NCI.Participants might have disagreed about which games were difficult. We built a third model to investigate whether the frontoparietal activation correlates with how hard a dominance-solvable game is and whether the activation in insula and ACC correlates with how easy a coordination game is. Here, the two main conditions were parametrically modulated by each participant's probability of obtaining a reward in each game (SOM, S2.2 and S5.2). We found a negative correlation between the activation of the precuneus and the participant's probability of obtaining a reward in dominance-solvable games ( Fig. 4C and table S12), which suggests that dominance-solvable games that yielded lower payoffs presented harder mental challenges. In a previous study on working memory, precuneus activity positively correlated with response times, a measure of mental effort (24). Both findings are consistent with the interpretation that subjective measures reflecting harder tasks (higher efforts) correlate with activation in precuneus. A positive correlation between insula activation and the participant's probability of obtaining a reward again suggests that coordination games with a highly salient feature strongly activated the "gut feeling" reported by many participants (Fig. 4D and table S13). A previous study found that the subjective rating of "chills intensity" in music correlates with activation of insula (42). Both findings are consistent with the interpretation that the subjective intensity of how salient a stimulus is correlates with activation in insula.As mentioned, choices were made significantly faster in coordination games than in dominancesolvable games. The results of the second and third models provide additional support for the idea that intuitive and deliberative mental processes have quite different properties. The "slow and effortful" process was more heavily taxed when the dominance-solvable games were harder. The "fast and effortless" process was more strongly activated when coordination was easy.

The rumen is a complex ecosystem composed of anaerobic bacteria, protozoa, fungi, methanogenic archaea and phages. These microbes interact closely to breakdown plant material that cannot be digested by humans, whilst providing metabolic energy to the host and, in the case of archaea, producing methane. Consequently, ruminants produce meat and milk, which are rich in high-quality protein, vitamins and minerals, and therefore contribute to food security. As the world population is predicted to reach approximately 9.7 billion by 2050, an increase in ruminant production to satisfy global protein demand is necessary, despite limited land availability, and whilst ensuring environmental impact is minimized. Although challenging, these goals can be met, but depend on our understanding of the rumen microbiome. Attempts to manipulate the rumen microbiome to benefit global agricultural challenges have been ongoing for decades with limited success, mostly due to the lack of a detailed understanding of this microbiome and our limited ability to culture most of these microbes outside the rumen. The potential to manipulate the rumen microbiome and meet global livestock challenges through animal breeding and introduction of dietary interventions during early life have recently emerged as promising new technologies. Our inability to phenotype ruminants in a high-throughput manner has also hampered progress, although the recent increase in “omic” data may allow further development of mathematical models and rumen microbial gene biomarkers as proxies. Advances in computational tools, high-throughput sequencing technologies and cultivation-independent “omics” approaches continue to revolutionize our understanding of the rumen microbiome. This will ultimately provide the knowledge framework needed to solve current and future ruminant livestock challenges.

The objective of the study was to investigate the fractional rate of volatile fatty acid (VFA) absorption and the expression of genes encoding for transporters and enzymes involved in the absorption and metabolism of VFA in ruminal tissue when cattle were fed high or low concentrate diets. Twelve ruminally cannulated Holstein cows were used in a randomized complete block design. The low concentrate (LC) and high concentrate (HC) diets contained 8 and 64% dietary concentrate (dry matter basis), respectively. Cows were fed their respective diet for at least 28 d, following which data and samples were collected over 6 d. Ruminal pH was measured continuously for 72 h, and the in vivo VFA absorption and passage rates were measured using Co-EDTA and n-valeric acid as markers. Ruminal tissue was collected postslaughter from the ventral sac of the rumen, and gene expression was evaluated using quantitative real-time PCR. Dry matter intake was not affected by treatment, averaging 14.9 kg/d, but cows fed HC had lower mean ruminal pH (6.03 vs. 6.48), and a greater duration (376 vs. 10 min/d) that ruminal pH was <5.8. Ruminal VFA concentration was 24 mM higher for cows fed HC compared with LC; however, the fractional rate of VFA absorption and passage from the rumen was not affected by dietary treatment, averaging 23.4 and 9.6%/h, respectively. The expression of genes encoding for enzymes involved in VFA activation and ketogenesis were not affected by treatment. Cows fed HC tended to have a relative abundance of pyruvate dehydrogenase lipoamide alpha 1 mRNA transcripts that was 1.4 times lower than that of cows fed LC, but other enzymes involved in pyruvate metabolism or regulation of the citric acid cycle were not affected. Collectively, these results suggest that the dietary forage to concentrate ratio does not affect the fractional rate of VFA absorption in vivo, but potentially alters energy metabolism in ruminal tissue.

BackgroundThe emergence and spread of antibiotic resistance in pathogens have led to a restriction on the use of antibiotic growth promoters (AGPs) in animal feed in some countries. The potential negative after-effects of a ban on AGPs could be mitigated by improving animal intestinal health with prebiotic dietary fibers such as xylo-oligosaccharides (XOS). However, the mechanism(s) by which an antibiotic or prebiotic contributes to the health and growth of animals are not well understood. Here, we evaluated XOS and virginiamycin (VIRG)-mediated changes in gut microbiota of broiler chickens using pyrosequencing of the 16S rRNA gene.ResultsThere was a significant change in the relative abundance of certain bacteria, but the overall microbial diversity was not affected by treatment with either XOS or VIRG. Supplementation of HXOS (2 g XOS/kg diet) increased the proportion of Lactobacillus genus in the cecum, whereas Propionibacterium and Corynebacterium genera were enriched in the ileum of VIRG (16 mg/kg) treated birds. Furthermore, an increase in the cecal concentrations of acetate and propionate was observed in HXOS- and VIRG-fed chickens, respectively. These two groups of birds had better feed conversion efficiencies in comparison with the control group from day 7 to 21. In addition, temporal variations in the gut microbiota were evident in the chickens of different ages.ConclusionsTreatments with XOS or VIRG modified the relative abundance but not the presence or absence of specific microbial genus. The increase in both Lactobacillus spp. and acetate production in the cecum of HXOS-treated chickens may promote intestinal health.Electronic supplementary materialThe online version of this article (doi:10.1186/s40168-015-0079-4) contains supplementary material, which is available to authorized users.

Genetic selection for residual feed intake (RFI) is an indirect approach for reducing enteric methane (CH4) emissions in beef and dairy cattle. RFI is moderately heritable (0.26 to 0.43), moderately repeatable across diets (0.33 to 0.67) and independent of body size and production, and when adjusted for off-test ultrasound backfat thickness (RFIfat) is also independent of body fatness in growing animals. It is highly dependent on accurate measurement of individual animal feed intake. Within-animal repeatability of feed intake is moderate (0.29 to 0.49) with distinctive diurnal patterns associated with cattle type, diet and genotype, necessitating the recording of feed intake for at least 35 days. In addition, direct measurement of enteric CH4 production will likely be more variable and expensive than measuring feed intake and if conducted should be expressed as CH4 production (g/animal per day) adjusted for body size, growth, body composition and dry matter intake (DMI) or as residual CH4 production. A further disadvantage of a direct CH4 phenotype is that the relationships of enteric CH4 production on other economically important traits are largely unknown. Selection for low RFIfat (efficient, −RFIfat) will result in cattle that consume less dry matter (DMI) and have an improved feed conversion ratio (FCR) compared with high RFIfat cattle (inefficient; +RFIfat). Few antagonistic effects have been reported for the relationships of RFIfat on carcass and meat quality, fertility, cow lifetime productivity and adaptability to stress or extensive grazing conditions. Low RFIfat cattle also produce 15% to 25% less enteric CH4 than +RFIfat cattle, since DMI is positively related to enteric methane (CH4) production. In addition, lower DMI and feeding duration and frequency, and a different rumen bacterial profile that improves rumen fermentation in −RFIfat cattle may favor a 1% to 2% improvement in dry matter and CP digestibility compared with +RFIfat cattle. Rate of genetic change using this approach is expected to improve feed efficiency and reduce enteric CH4 emissions from cattle by 0.75% to 1.0% per year at equal levels of body size, growth and body fatness compared with cattle not selected for RFIfat.

Our findings suggest that the HPD altered the colonic microbial community, shifted the metabolic profile, and affected the host response in the colons of rats toward an increased risk of colonic disease.

BackgroundPreviously, we identified a major quantitative trait locus (QTL) for host response to Porcine Respiratory and Reproductive Syndrome virus (PRRSV) infection in high linkage disequilibrium (LD) with SNP rs80800372 on Sus scrofa chromosome 4 (SSC4).ResultsWithin this QTL, guanylate binding protein 5 (GBP5) was differentially expressed (DE) (p < 0.05) in blood from AA versus AB rs80800372 genotyped pigs at 7,11, and 14 days post PRRSV infection. All variants within the GBP5 transcript in LD with rs80800372 exhibited allele specific expression (ASE) in AB individuals (p < 0.0001). A transcript re-assembly revealed three alternatively spliced transcripts for GBP5. An intronic SNP in GBP5, rs340943904, introduces a splice acceptor site that inserts five nucleotides into the transcript. Individuals homozygous for the unfavorable AA genotype predominantly produced this transcript, with a shifted reading frame and early stop codon that truncates the 88 C-terminal amino acids of the protein. RNA-seq analysis confirmed this SNP was associated with differential splicing by QTL genotype (p < 0.0001) and this was validated by quantitative capillary electrophoresis (p < 0.0001). The wild-type transcript was expressed at a higher level in AB versus AA individuals, whereas the five-nucleotide insertion transcript was the dominant form in AA individuals. Splicing and ASE results are consistent with the observed dominant nature of the favorable QTL allele. The rs340943904 SNP was also 100 % concordant with rs80800372 in a validation population that possessed an alternate form of the favorable B QTL haplotype.ConclusionsGBP5 is known to play a role in inflammasome assembly during immune response. However, the role of GBP5 host genetic variation in viral immunity is novel. These findings demonstrate that rs340943904 is a strong candidate causal mutation for the SSC4 QTL that controls variation in host response to PRRSV.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1635-9) contains supplementary material, which is available to authorized users.

The objective of this study was to elucidate the effect of feeding a calf starter on the volatile fatty acid (VFA) profile in the rumen and on expression of genes involved in epithelial intracellular pH regulation, butyrate metabolism, and hepatic urea cycle during the weaning transition. Twenty Holstein bull calves were fed either milk replacer and hay (MR) or milk replacer, hay, and a commercial texturized calf starter (MR+S) in a randomized complete block design. All calves were fed 750 g/d of milk replacer as the basal diet. Calves on the MR+S treatment were also fed starter ad libitum, and the energy intake of calves within blocks was maintained by supplementing the MR group with extra milk replacer that was equivalent to the energy intake from calf starter. Calves were killed 3 d after they consumed 680 g/d of calf starter for 3 consecutive days. Calves fed MR+S had higher VFA concentrations in the rumen (99.1±8.1 vs. 64.6±8.6 mM) and a higher molar proportion of butyrate (15.6±1.7 vs. 7.9±1.9%) than calves fed MR. Relative abundance of mRNA for monocarboxylate transporter isoform 1 was higher (1.45 vs. 0.53), and that of Na(+)/H(+) exchanger isoform 3 (0.37 vs. 0.82) and 3-hydroxy-3-methylglutaryl synthase isoform 1 (0.40 vs. 0.94) lower for the MR+S treatment compared with the MR treatment. In the liver, relative mRNA abundances of argininosuccinate synthetase isoform 1 (2.67 vs. 1.56), argininosuccinate lyase (1.44 vs. 0.99), and arginase isoform 1 (3.21 vs. 1.74) were greater for MR+S than for MR calves. Calf starter consumption appeared to increase fermentation in the rumen and affected expression of genes involved in cholesterol synthesis and intracellular pH regulation in ruminal epithelium, and those involved in urea cycle in the liver.