Phenotypic characterization and analysis of genetic diversity between commercial crossbred and indigenous chickens from three different agro-ecological zones using DArT-Seq technology.

Indigenous and were used to study genetic diversity and population structure analyses. Polymorphism information content (PIC) values ranged from 0.0 to 0.5, with 21,285 SNP markers (35%) being in the lowest PIC value range (0 to 0.15) while 13,511 (commercial chickens have developed unique adaptations to their environments, which may include nutrition, pathogens, and thermal stress. Besides, environmental pressures and artificial selection have generated significant genome-wide divergence in chickens, as those selection pressures contribute a considerable evolutionary force to phenotypic and genotypic differentiation. Herein, we determined genomic diversity of indigenous chickens from semi-deciduous rainforest (SDR), coastal savannah (CS) and Guinea savannah (GS) agro-ecological zones (AEZs) in Ghana and commercial crossbreds (CC) reared at the Kwame Nkrumah University of Science and Technology (KNUST). We generated SNP markers from 82 chickens (62 indigenous chicken ecotypes and 26 commercial crossbred ecotype) using DArT-Seq technology. A total of 85,396 SNP markers were generated and after filtering the data, 58,353 markers 21%) were in the highest PIC value range (0.45 to 0.50). The CC were more genetically diverse than the indigenous birds, with the highest expected heterozygosity value of 0.220. Between the commercial crossbreds population and the indigenous ecotypes, pairwise FST values were estimated to be 0.105 between CS, 0.096 between SDF, and 0.133 between GS. Furthermore, PCA analysis showed that the CC, SDF and GS chickens clustered together and are genetically distant from the commercial crossbred. We herein show that chickens from the AEZs studied can be considered as one population. However, due the abundance of agro-byproducts in the SDR compared to the CS and GS, chickens from the SDR AEZ had better growth compared to their counterparts. It is suggested that the genetic diversity within the local ecotypes could form the basis for genetic improvement.

Host transcriptome response to heat stress and Eimeria maxima infection in meat-type chickens.

Eimeria (E.) maxima parasite infects chickens' midgut disrupting the jejunal and ileal mucosa causing high morbidity and mortality. Heat stress (HS) is a seasonal stressor that impacts biological functions leading to poor performance. This study elucidates how HS, E. maxima infection, and their combination affect the ileum transcriptome. Two-hundred and forty 2-week-old males Ross708 chickens were randomly allocated into four treatment groups: thermoneutral-control (TNc), thermoneutral-infected (TNi), heat-stress control (HSc), and heat stress-infected (HSi), with 6 replicates each of 10 birds. Infected groups received 200x103 sporulated E. maxima oocysts/bird, and heat-treated groups were raised at 35°C. At 6-day post-treatment, ileums of five randomly selected chickens per group were sampled, RNA was extracted and sequenced. A total of 413, 3377, 1908, and 2304 DEGs were identified when applying the comparisons: TNc vs HSc, TNc vs TNi, HSi vs HSc, and TNi vs HSi, respectively, at cutoff ≥1.2-fold change (FDR: q<0.05). HSc vs TNc showed upregulation of lipid metabolic pathways and degradation/metabolism of multiple amino acids; and downregulation of most immune-related and protein synthesis pathways. TNc vs TNi displayed upregulation of most of immune-associated pathways and eukaryotic mRNA maturation pathways; and downregulation of fatty acid metabolism and multiple amino acid metabolism pathways including tryptophan. Comparing HSi versus HSc and TNi revealed that combining the two stressors restored the expression of some cellular functions, e.g., oxidative phosphorylation and protein synthesis; and downregulate immune response pathways associated with E. maxima infection. During E. maxima infection under HS the calcium signaling pathway was downregulated, including genes responsible for increasing the cytoplasmic calcium concentration; and tryptophan metabolism was upregulated, including genes that contribute to catabolizing tryptophan through serotonin and indole pathways; which might result in reducing the cytoplasmic pool of nutrients and calcium available for the parasite to scavenge and consequently might affect the parasite's reproductive ability.

Methionine sources at different dietary levels alters the growth and expression of genes related to homocysteine remethylation in the jejunum of broilers.

Sulfur amino acids are essential for the proper development of broilers and are required throughout the bird's life to perform important physiological functions. Studies that seek to understand the actions of sulfur amino acids in the body of birds are essential. The present study evaluated the influence of sulfur amino acid supplementation using DL-Methionine (DL-Met) and DL-Methionine hydroxy analogue (DL-HMTBA), on the performance and expression of genes related to methionine metabolism, in the jejunum of broilers. Four hundred and fifty male broilers (Cobb-700 slow feathering) were distributed in a completely randomized design, in a factorial scheme (2x3), with two sources of methionine (DL-Met and DL-HMTBA) and three levels of methionine (deficiency, requirement and excess). The mRNA expression of the MAT1, MTR, BHMT, MTRR, CBG and GSS genes, and performance data such as feed intake, weight gain, and feed conversion were evaluated. DL-HMTBA increased the expression of BHMT (p = 0.0072) and MTRR (p = 0.0003) in the jejunum of the birds. Methionine deficiency increased the expression of BHMT (p = 0.0805) and MTRR (p = 0.0018). Higher expression of GSS was observed in birds that were supplemented with DL-HMTBA (p = 0.0672). Analyzing our results, it is preferable to supplement sulfur amino acids with DL-Met at the requirement level. Birds fed with DL-HMTBA showed worse weight gain (p = 0.0117) and higher feed conversion (p = 0.0170); methionine deficiency resulted in higher feed intake (p = 0.0214), lower weight gain (p<0.0001) and consequently higher feed conversion (p<0.0001). Based on the information found in this work, it is recommended to supplement sulfur amino acids with DL-Met at the level of compliance with the requirement.

Effect of Glucose Supplementation on Apoptosis in the Pectoralis major of Chickens Raised under Thermoneutral or Heat Stress Environment.

Reduced feed intake during heat stress (HS) disrupts glucose homeostasis, thereby resulting in endoplasmic reticulum (ER) stress and triggering apoptosis in chickens. We hypothesize that glucose supplementation could reduce apoptosis in chickens raised under HS. This study comprised 456 28-day-old broiler chickens randomly assigned to four treatment combinations under glucose supplementation and HS. The treatments were TN0, TN6, HS0, and HS6 with two glucose levels (0% and 6%) and two temperature levels (25 °C (thermoneutral-TN) and 35 °C (8.00 AM to 8.00 PM, (HS)). After 7 days post-HS, the blood glucose level for the HS6 group was higher than for TN0, TN6, and HS0. We studied the mRNA expression of genes and caspase-3 activity in the four experimental groups. The expressions of GCN2, ATF4, CHOP, and FOXO3a increased during HS regardless of glucose supplementation, while PERK and MAFbx increased only under HS with glucose supplementation. We show that under TN conditions, glucose supplementation led to a significant increase in cellular apoptosis in the Pectoralis (P.) major. However, under HS with glucose, the level of apoptosis was similar to that of chickens raised under TN conditions with no glucose supplementation. The utility of glucose to curtail apoptosis under HS should be tested under other intense models of HS.

Glucose Supplementation Improves Performance and Alters Glucose Transporters' Expression in Pectoralis major of Heat-Stressed Chickens.

Glucose level in birds' tissue decreases due to heat stress (HS)-induced reduction in feed intake (FI); impairing metabolism and growth. The effect of glucose supplementation on the performance of broiler chickens was evaluated under thermoneutral (TN) and HS conditions. Glucose was supplemented at 0 and 6% under TN-(25 °C) and HS-(25 °C-35 °C-25 °C) conditions. The treatments were TN + 0%-glucose (TN0); TN + 6%-glucose (TN6), HS + 0%-glucose (HS0) and HS + 6%-glucose (HS6). There were 6 replicates (19 birds each)/treatment. Heat and glucose supplementation were applied from d28-35. At d35, Pectoralis (P.) major was sampled from one bird/replicate to determine glucose transporters' mRNA expression. Heat application lowered (p < 0.05) FI, body weight gain, and increased feed and water conversion ratios. Glucose supplementation increased total energy intake by 4.9 and 3.2% in TN and HS groups, respectively but reduced FI under TN and HS conditions. The P. major- and drumstick-yield reduced (p < 0.05) in HS0 compared to TN0, TN6 and HS6. Under HS, glucose supplementation improved eviscerated carcass weight by 9% and P. major yield by 14%. Glucose supplementation increased SGLT1 expression with/without heat treatment while HS independently increased the expression of GLUT 1, 5 and 10. Glucose supplementation under HS could improve performance of broilers.

Growth Rate Distribution and Potential Non-Linear Relationship between Body Weight and Walking Ability in Turkeys.

The aim of this study was to investigate the potential non-linear relationship between growth and walking ability (WA). The phenotypic data included body weights at 12 and 20 weeks and WA at 20 weeks of age measured on 276,059 male turkeys. The growth rate at three age periods (0 to 12, 12 to 20 and 0 to 20 weeks) was calculated. Each bird was assigned to one of the quartiles of the growth rate distribution for each age period. Between the first and fourth quartiles, the incidence of score 1 (bad WA) increased by 31, 18, and 33% for the first, second, and third age periods, respectively. For good WA (scores 4, 5, and 6), the incidence decreased by 55, 66, and 72% between the first and fourth quartiles for the first, second, and third age periods, respectively. Estimates of heritability of WA ranged between 0.18 and 0.26. The genetic correlations between adjacent growth rate quartiles were high and decayed as the interval between quartiles increased. The magnitude of the variation in the incidence of walking scores and genetic correlations across the growth rate quartiles point towards a non-linear relationship between growth and mobility suggesting other factors may affect walking ability.

Quantitative and molecular aspects of water intake in meat-type chickens.

Even though water is the most essential nutrient for poultry production, adequate data on individual water intake in broiler chickens and its relationship with other traits of economic importance is scant. Water is provided to chickens in an unrestricted manner in spite of being a finite resource. Climate change continues to affect water sources and efficient bird use of water is long overdue. Understanding the biological basis of water intake is essential for sustainability of the poultry industry. Individual water and feed intake, and growth data was collected on 520 commercial broilers aged 14 to 42 days. We introduced the concepts of water conversion ratio (WCR) and residual water intake (RWI) as parameters that can be used to assess water intake efficiency. Water conversion ratio was defined as the amount of water consumed per unit of body weight gain, and RWI was defined as the difference between the actual water intake (WI) of a given bird and the expected WI by an average bird from the population with the same metabolic body weight, feed intake (FI) and body weight gain (BWG). The correlation between WI and FI was positive (r=0.77; P<0.0001), and the correlation between WI and BWG was positive (r=0.80; P<0.0001). Based on the distribution of RWI, the bottom 5 birds (LRWI) and the top 5 birds (HRWI) for RWI were selected for mRNA expression differences. The average broiler consumed about 7.8 L (± 1L) of water from 14 to 42 days of age. The mRNA expression of arginine vasopressin (AVP) antidiuretic hormone, calcium sensing receptor (CasR), sodium channel epithelial 1 subunit alpha (SCNN1A) and SCNN1D in the hypothalamus was upregulated in the LRWI group compared to the HRWI group. Similarly, kidney aquaporins (AQP) 2, 3, and 4 were upregulated in the LRWI group compared with the HRWI group. Given that water was provided ad libitum, the up-regulation of AVP and AQP gene mRNA expressions seem to indicate that the LRWI birds were more efficient in water reabsorption in the kidney compared to their HRWI counterparts. Increased water reabsorption will reduce the amount of water consumed to attain hydration. The water reabsorption potential was reflected in the excreta moisture levels as the LRWI birds had significantly lower excreta moisture than the HRWI birds. Excreta moisture level require further studies and could be considered as a potential proxy trait for water intake.

Research Note: Analysis of body weight and walking ability in turkeys and the prediction of categorical responses across systematic effect classes using a linear threshold model.

Heavy selection for growth in turkeys has led to a decay in leg soundness and walking ability. In this study, different models and traits were used to investigate the genetic relationships between body weight (BW) and walking ability (WA) in a turkey population. The data consisted of BW and WA traits collected on 276,059 male birds. Body weight was measured at 12 and 20 wk and WA at 20 wk of age. For WA, birds were scored based on a 1 (bad) to 6 (good) grading system. Due to the small number of records with scores 5 and 6, birds with WA scores of 4, 5, and 6 were grouped together resulting in only 4 classes. Additionally, a binary classification of WA (scores 1 and 2 = Similarly, an estimate of the genetic correlation between WA and BW at 20 wk was -0.45, indicating a more pronounced class 1; scores 3, 4, 5, and 6 = class 2) was evaluated. The inheritability estimates of WA ranged between 0.25 and 0.27 depending on the number of classes. The Heritability of BW at 12 and 20 wk was 0.44 and 0.51, respectively. The genetic correlation between WA and BW at 12 wk was around -0.35, indicating that heavy birds tend to have poor WA. antagonistic relationship between BW and WA. The genetic correlation between BW at 12 and 20 wk was positive and high (0.80). The residual correlation between WA and BW at 12 and 20 wk of age was -0.07 and -0.02, respectively. The residual correlation between body weight traits was 0.57. Similar results were observed when a binary classification was adopted for WA. The probability of an individual with a given genetic merit expressing a certain class of WA was determined for different fixed effect designations. Predictive probabilities clearly showed that birds when hatched in the winter would have a small chance to exhibit good WA phenotypes.

Temporal dynamics of the cecal and litter microbiome of chickens raised in two separate broiler houses.

In this study, we investigated the dynamics of the ceca and litter microbiome of chickens from post-hatch through pre-harvest. To achieve this, six hundred one-day old Cobb 500 broiler chicks were raised on floor pens for 49 days in two separate houses. We performed short-read and full-length sequencing of the bacterial 16S rRNA gene present in the meconium and in cecal and litter samples collected over the duration of the study. In addition, we determined the antimicrobial resistance (AMR) phenotype of Escherichia coli and Enterococcus spp. isolated from the meconium and the ceca of 49-day old chickens. We monitored the relative humidity, temperature, and ammonia in each house daily and the pH and moisture of litter samples weekly. The overall microbial community structure of the ceca and litter consistently changed throughout the course of the grow-out and correlated with some of the environmental parameters measured (p < 0.05). We found that the ceca and litter microbiome were similar in the two houses at the beginning of the experiment, but over time, the microbial community separated and differed between the houses. When we compared the environmental parameters in the two houses, we found no significant differences in the first half of the growth cycle (day 0-21), but morning temperature, morning humidity, and ammonia significantly differed (p < 0.05) between the two houses from day 22-49. Lastly, the prevalence of AMR in cecal E. coli isolates differed from meconium isolates (p < 0.001), while the AMR phenotype of cecal Enterococcus isolates differed between houses (p < 0.05).

Monitoring Behaviors of Broiler Chickens at Different Ages with Deep Learning.

Animal behavior monitoring allows the gathering of animal health information and living habits and is an important technical means in precision animal farming. To quickly and accurately identify the behavior of broilers at different days, we adopted different deep learning behavior recognition models. Firstly, the top-view images of broilers at 2, 9, 16 and 23 days were obtained. In each stage, 300 images of each of the four broilers behaviors (i.e., feeding, drinking, standing, and resting) were segmented, totaling 4800 images. After image augmentation processing, 10,200 images were generated for each day including 8000 training sets, 2000 validation sets, and 200 testing sets. Finally, the performance of different convolutional neural network models (CNN) in broiler behavior recognition at different days was analyzed. The results show that the overall performance of the DenseNet-264 network was the best, with the accuracy rates of 88.5%, 97%, 94.5%, and 90% when birds were 2, 9, 16 and 23 days old, respectively. In addition, the efficient channel attention was introduced into the DenseNet-264 network (ECA-DenseNet-264), and the results (accuracy rates: 85%, 95%, 92%, 89.5%) confirmed that the DenseNet-264 network was still the best overall. The research results demonstrate that it is feasible to apply deep learning technology to monitor the behavior of broilers at different days.

Fuzzy Logic as a Strategy for Combining Marker Statistics to Optimize Preselection of High-Density and Sequence Genotype Data.

The high dimensionality of genotype data available for genomic evaluations has presented a motivation for developing strategies to identify subsets of markers capable of increasing the accuracy of predictions compared to the current commercial single nucleotide polymorphism (SNP) chips. In this simulation study, an algorithm for combining statistics used in the preselection and prioritization of SNP markers from a high-density panel (1.3 million SNPs) into a composite "fuzzy" ranking score based on a Sugeno-type fuzzy inference system (FIS) was developed and evaluated for performance in preselection for genomic predictions. FST scores, and p-values were evaluated as inputs for the FIS. The accuracy of genomic predictions for fuzzy-score-preselected panel sizes of 1-50 k SNPs ranged from -0.4-11.7 and -0.3-3.8% higher than FST and p-value preselection, respectively. Though gains in prediction accuracies using only two inputs to the FIS were modest, preselection based on fuzzy scores yielded more accurate predictions than both FST scores and p-values for the majority of evaluated panel sizes under all genetic architectures. FIS have the potential to aggregate information from multiple criteria that reflect SNP-trait associations and biological relevance in a flexible and efficient way to yield higher quality genomic predictions.

Thrombin as a Potential Proxy to Select for Horn Fly Abundance in Beef Cattle.

Horn flies are a major nuisance to cattle and induce significant economic losses. Fly abundance varies within and across breeds and genetic analyses have shown sufficient genetic variation to permit selection. A major bottleneck for selecting against horn fly abundance is the complexity of measuring fly attraction phenotypes. Easy-to-measure proxy phenotypes could be an attractive option to indirectly estimate fly abundance. In the current study, thrombin was investigated as a potential proxy to assess fly abundance. Fly counts and blood samples were collected on 355 cows. Pearson correlation between subjective fly count and thrombin was -0.13, indicating a decrease in fly abundance with the increase in thrombin concentration. When thrombin was discretized into three classes, there was a 22% difference in fly count between the top and bottom classes. Heritability estimates of thrombin were 0.38 and 0.39 using linear and threshold models, respectively. The correlation between estimated thrombin breeding values and fly count was around -0.18. There was a noticeably lower density of high fly counts among animals with high breeding values for thrombin. These results indicate that thrombin could be used in combination with other biological factors to estimate fly abundance and as a proxy for selection against fly abundance.

Cecal Microbial Hydrogen Cycling Potential Is Linked to Feed Efficiency Phenotypes in Chickens.

In chickens, early life exposure to environmental microbes has long-lasting impacts on gastrointestinal (GI) microbiome development and host health and growth, via mechanisms that remain uncharacterized. In this study, we demonstrated that administrating a fecal microbiome transplant (FMT) from adults to day-of-hatch chicks results in significantly higher body mass of birds and decreased residual feed intake (RFI), implying enhanced feed efficiency, at 6 weeks of age. To assess the potential mechanisms through which FMT affects adult bird phenotype, we combined 16 S rRNA gene amplification, metagenomic, and comparative genomic approaches to survey the composition and predicted activities of the resident microbiome of various GI tract segments. Early life FMT exposure had a long-lasting significant effect on the microbial community composition and function of the ceca but not on other GI segments. Within the ceca of 6-week-old FMT birds, hydrogenotrophic microbial lineages and genes were most differentially enriched. The results suggest that thermodynamic regulation in the cecum, in this case via hydrogenotrophic methanogenic and sulfur-cycling lineages, potentially serving as hydrogen sinks, may enhance fermentative efficiency and dietary energy harvest capacity. Our study provides a specific mechanism of action through which early-life microbiome transplants modulate market-relevant phenotypes in poultry and, thereby, may represent a significant advance toward microbiome-focused sustainable agriculture.

Heat Stress Alters the Effect of Eimeria maxima Infection on Ileal Amino Acids Digestibility and Transporters Expression in Meat-Type Chickens.

Eimeria (E.) maxima invades the midgut of chickens and destroys the intestinal mucosa, impacting nutrient digestibility and absorption. Heat stress (HS) commonly affects the broiler chicken and contributes to inflammation and oxidative stress. We examined the independent and combined effects of HS and E. maxima infection on apparent amino acid ileal digestibility (AID) and mRNA expression of amino acid transporters in broiler chickens (Ross 708). There were four treatment groups: thermoneutral-control (TNc) and infected (TNi), heat-stress control (HSc) and infected (HSi), six replicates of 10 birds/treatment. Ileal content and tissue were sampled at 6 d post infection to determine AID and transporters expression. Surprisingly, the HSi chickens exposed to two critical stressors exhibited normal AID. Only the TNi group displayed reduction in AID. Using TNc as control, the HSc group showed upregulated CAT1, LAT4, TAT1, SNAT1, and SNAT7. The HSi group showed upregulated CAT1 and LAT1, and downregulated b0,+AT, rBAT, SNAT1, and SNAT2. The TNi group showed upregulated CAT1, LAT1, and SNAT1 and downregulated B0AT1, b0,+AT, rBAT, LAT4, and TAT1. The expression of all enterocytic-apical and about half of the basolateral transporters was higher in the HSi group than in the TNi group, indicating that HS can putatively alleviate the E. maxima adverse effect on ileal digestion and absorption.

Heat stress modulates the disruptive effects of Eimeria maxima infection on the ileum nutrient digestibility, molecular transporters, and tissue morphology in meat-type chickens.

Eimeria (E.) maxima is one of the most pathogenic Eimeria spp persistently invading the middle jejunum and ileum, damaging the intestinal mucosa of chickens. Heat stress (HS) is a common stressor and equally contributes to inflammation and oxidative stress. We investigated the effect of E. maxima infection and HS on ileal digestibility, mRNA expression of nutrient transporters, and ileal tissue morphology in broiler chickens. There were four treatment groups: thermoneutral control (TNc), thermoneutral infected (TNi), heat stress control (HSc), and heat stress infected (HSi), 6 replicates each of 10 birds per treatment. Chickens were fed a diet containing 0.2% TiO2. At 6-day-post infection, ileal content and tissue were collected to quantify ileal digestibility of crude protein and fat, mRNA levels of nutrient transporters and histopathology. Growth and feed intake were reduced in all treatment groups, compared with the TNc. Contrary to expectation, the combination of two major stressors (E. maxima and HS) in the TNi group exhibited almost normal digestibility while only the TNi birds expressed severe digestibility depression, compared with the TNc group. The TNi group showed the lowest mRNA expression of the transporters: SGLT1, GLUT2-5-8-10-12, FABP1-2-6, and PEPT1 compared with the other treatment groups. The expression of the absorptive enterocytes' gene markers (ACSL5, IAP, and SGLT1) supported by the ileal tissue morphology indicated that the TNi group had the highest enterocytic destruction. The expression of oxidative genes (iNOS and CYBB) dramatically increased only in the TNi group compared with the other treatment groups. Our results showed that exposing broiler chickens to HS can mitigate the disruptive effect of E. maxima on the ileal digestibility and absorption by limiting the parasite-induced tissue injury and suppressing the enterocytic inducible oxidative damage.

Mexican Creole chickens: effect of data collection periods on goodness-of-fit and parameter precision of growth models.

The objective of this study was to estimate the good-of-fitness and precision of parameters of the Gompertz-Laird, Logistic, Richards, and Von Bertalanffy growth models, using different data collection periods (DCP). Two hundred and sixty-two Mexican Creole chicks (116 females and 146 males), were individually weighed to form the following sets of data for each sex: DCP1 (weights recorded weekly from hatching to 63 d, and every 2 wk, from 63 to 133 d of age), DCP2 (weights recorded weekly from hatching to 133 d of age), DCP3 (weights recorded every third day, from hatching to 63 d, and every 14 d, from 63 to 133 d of age), and DCP4 (weights recorded every third day, from hatching to 63 d, and weekly, from 63 to 133 d of age). Data were analyzed using the NLIN procedure of SAS (Marquardt algorithm). For all growth models, the width of confidence interval (CI) of each parameter, was estimated (α = 0.05). The adjusted coefficient of determination (AR2), as well as the Akaike (AIC) and Bayesian information criteria (BIC) were used to select the best model. The higher the AR2, and the lower the width of CI, as well as the AIC and BIC values, the better the model. The Gompertz-Laird model, more frequently showed the highest AR2, and the lowest AIC and BIC values compared to the other models. Moreover, for all models, both sexes and all parameters, most confidence interval widths (all with the Gompertz-Laird model) were the lowest with DCP3 when compared to the other sets of data. In conclusion, the Gompertz-Laird model was the best provided that the chickens are weighed every third day from hatching until 63 d of age, and every 2 wk thereafter.

Litter Commensal Bacteria Can Limit the Horizontal Gene Transfer of Antimicrobial Resistance to Salmonella in Chickens.

Fostering a "balanced" gut microbiome through the administration of beneficial microbes that can competitively exclude pathogens has gained a lot of attention and use in human and animal medicine. However, little is known about how microbes affect the horizontal gene transfer of antimicrobial resistance (AMR). To shed more light on this question, we challenged neonatal broiler chicks raised on reused broiler chicken litter-a complex environment made up of decomposing pine shavings, feces, uric acid, feathers, and feed-with Salmonella enterica serovar Heidelberg (S. Heidelberg), a model pathogen. Neonatal chicks challenged with S. Heidelberg and raised on reused litter were more resistant to S. Heidelberg cecal colonization than chicks grown on fresh litter. Furthermore, chicks grown on reused litter were at a lower risk of colonization with S. Heidelberg strains that encoded AMR on IncI1 plasmids. We used 16S rRNA gene sequencing and shotgun metagenomics to show that the major difference between chicks grown on fresh litter and those grown on reused litter was the microbiome harbored in the litter and ceca. The microbiome of reused litter samples was more uniform and enriched in functional pathways related to the biosynthesis of organic and antimicrobial molecules than that in fresh litter samples. We found that Escherichia coli was the main reservoir of plasmids encoding AMR and that the IncI1 plasmid was maintained at a significantly lower copy per cell in reused litter compared to fresh litter. These findings support the notion that commensal bacteria play an integral role in the horizontal transfer of plasmids encoding AMR to pathogens like Salmonella. IMPORTANCE Antimicrobial resistance spread is a worldwide health challenge, stemming in large part from the ability of microorganisms to share their genetic material through horizontal gene transfer. To address this issue, many countries and international organizations have adopted a One Health approach to curtail the proliferation of antimicrobial-resistant bacteria. This includes the removal and reduction of antibiotics used in food animal production and the development of alternatives to antibiotics. However, there is still a significant knowledge gap in our understanding of how resistance spreads in the absence of antibiotic selection and the role commensal bacteria play in reducing antibiotic resistance transfer. In this study, we show that commensal bacteria play a key role in reducing the horizontal gene transfer of antibiotic resistance to Salmonella, provide the identity of the bacterial species that potentially perform this function in broiler chickens, and also postulate the mechanism involved.

Insights into the proteomic profile of newly harvested corn and metagenomic analysis of the broiler intestinal microbiota.

BACKGROUND: The use of newly harvested corn in feed causes wet droppings in broilers and increased feed cost which was termed as "new season grain problem". The present study was conducted to evaluate the proteomic profile of newly harvested corn and the subsequent influence on intestinal microbiol community for broiler chickens. METHODS: Newly harvested corn stored for either half a month (HM) or two months (TM) was used, and the pasting properties, total soluble sugars, and proteomic analysis technology was used to explore the influence of storage on natural aging corn properties. Additionally, seventy-two 7-day-old Ross 308 male broiler chicken were fed with different stored corn. Apparent metabolizable energy (AME), digesta viscosity, intestinal morphology and microbiota were examined to explore the influence of feed corn storage on broiler chickens. RESULTS: Pasting properties in the TM corn exhibited decreased viscoelastic properties. Proteomic studies found a total of 26 proteins that were differentially expressed between the two treatment groups. Proteins involved in starch and polysaccharides biosynthesis were upregulated in TM compared with HM. Chickens fed on TM diet had higher relative energy utilization compared to the HM birds. With increased corn storage, the relative digesta viscosity decreased significantly (P ≤ 0.05). The total number of goblet cells and lymphocytes was lower in chickens fed the TM diet. The microbiota data showed that the TM chickens had decreased abundance of diarrheal bacteria such as Hungatella hathewayi and Bacteroides fragilis, and increased butyrate-producing bacteria such as Alistipes compared to the HM chickens. CONCLUSIONS: Storage of newly harvested corn induced the synthetic reaction of large molecules and changed the solubility of starch and protein with increasing soluble sugars and decreasing pasting properties that may improve the fermentation of intestinal microbiota, improve the energy utilization and protect gut health without the risk of diarrhea.

Dissection of the impact of prioritized QTL-linked and -unlinked SNP markers on the accuracy of genomic selection1.

BACKGROUND: Use of genomic information has resulted in an undeniable improvement in prediction accuracies and an increase in genetic gain in animal and plant genetic selection programs in spite of oversimplified assumptions about the true biological processes. Even for complex traits, a large portion of markers do not segregate with or effectively track genomic regions contributing to trait variation; yet it is not clear how genomic prediction accuracies are impacted by such potentially nonrelevant markers. In this study, a simulation was carried out to evaluate genomic predictions in the presence of markers unlinked with trait-relevant QTL. Further, we compared the ability of the population statistic FST and absolute estimated marker effect as preselection statistics to discriminate between linked and unlinked markers and the corresponding impact on accuracy. RESULTS: We found that the accuracy of genomic predictions decreased as the proportion of unlinked markers used to calculate the genomic relationships increased. Using all, only linked, and only unlinked marker sets yielded prediction accuracies of 0.62, 0.89, and 0.22, respectively. Furthermore, it was found that prediction accuracies are severely impacted by unlinked markers with large spurious associations. FST-preselected marker sets of 10 k and larger yielded accuracies 8.97 to 17.91% higher than those achieved using preselection by absolute estimated marker effects, despite selecting 5.1 to 37.7% more unlinked markers and explaining 2.4 to 5.0% less of the genetic variance. This was attributed to false positives selected by absolute estimated marker effects having a larger spurious association with the trait of interest and more negative impact on predictions. The Pearson correlation between FST scores and absolute estimated marker effects was 0.77 and 0.27 among only linked and only unlinked markers, respectively. The sensitivity of FST scores to detect truly linked markers is comparable to absolute estimated marker effects but the consistency between the two statistics regarding false positives is weak. CONCLUSION: Identification and exclusion of markers that have little to no relevance to the trait of interest may significantly increase genomic prediction accuracies. The population statistic FST presents an efficient and effective tool for preselection of trait-relevant markers.