Defining the baseline bacterial microbiome is critical to understanding its relationship with health and disease. In broiler chickens, the core microbiome and its possible relationships with health and disease have been difficult to define, due to high variability between birds and flocks. Presented here are data from a large, comprehensive microbiota-based study in commercial broilers. The primary goals of this study included understanding what constitutes the core bacterial microbiota in the broiler gastrointestinal, respiratory, and barn environments; how these core players change across age, geography, and time; and which bacterial taxa correlate with enhanced bird performance in antibiotic-free flocks. Using 2,309 samples from 37 different commercial flocks within a vertically integrated broiler system and metadata from these and an additional 512 flocks within that system, the baseline bacterial microbiota was defined using 16S rRNA gene sequencing. The effects of age, sample type, flock, and successive flock cycles were compared, and results indicate a consistent, predictable, age-dependent bacterial microbiota, irrespective of flock. The tracheal bacterial microbiota of broilers was comprehensively defined, and was the dominant bacterial taxon in the trachea. Numerous bacterial taxa were identified, which were strongly correlated with broiler chicken performance across multiple tissues. While many positively correlated taxa were identified, negatively associated potential pathogens were also identified in the absence of clinical disease, indicating that subclinical dynamics occur that impact performance. Overall, this work provides necessary baseline data for the development of effective antibiotic alternatives, such as probiotics, for sustainable poultry production. Multidrug-resistant bacterial pathogens are perhaps the greatest medical challenge we will face in the 21st century and beyond. Antibiotics are necessary in animal production to treat disease. As such, animal production is a contributor to the problem of antibiotic resistance. Efforts are underway to reduce antibiotic use in animal production. However, we are also challenged to feed the world's increasing population, and sustainable meat production is paramount to providing a safe and quality protein source for human consumption. In the absence of antibiotics, alternative approaches are needed to maintain health and prevent disease, and probiotics have great promise as one such approach. This work paves the way for the development of alternative approaches to raising poultry by increasing our understandings of what defines the poultry microbiome and of how it can potentially be modulated to improve animal health and performance.

On-farm manure management practices, such as composting, may provide a practical and economical option for reducing antibiotic concentrations in manure before land application, thereby minimizing the potential for environmental contamination. The objective of this study was to quantify degradation of chlortetracycline, monensin, sulfamethazine, and tylosin in spiked turkey (Meleagris gallopavo) litter during composting. Three manure composting treatments were evaluated: a control treatment (manure pile with no disturbance or adjustments after initial mixing), a managed compost pile (weekly mixing and moisture content adjustments), and vessel composting. Despite significant differences in temperature, mass, and nutrient losses between the composting treatments and the control, there was no difference in antibiotic degradation among the treatments. Chlortetracycline concentrations declined rapidly during composting, whereas monensin and tylosin concentrations declined gradually in all three treatments. There was no degradation of sulfamethazine in any of treatments. At the conclusion of the composting period (22-35 d), there was >99% reduction in chlortetracycline, whereas monensin and tylosin reduction ranged from 54 to 76% in all three treatments. Assuming first-order decay, the half-lives for chlortetracycline, monensin, and tylosin were 1, 17, and 19 d, respectively. These data suggest that managed compositing in a manure pile or in a vessel is not better than the control treatment in degrading certain antibiotics in manure. Therefore, low-level manure management, such as stockpiling, after an initial adjustment of water content may be a practical and economical option for livestock producers in reducing antibiotic levels in manure before land application.

Because of concerns related to the use of antibiotics in animal agriculture, antibiotic-free alternatives are greatly needed to prevent disease and promote animal growth. One of the current challenges facing commercial turkey production in Minnesota is difficulty obtaining flock average weights typical of the industry standard, and this condition has been coined “Light Turkey Syndrome” or LTS. This condition has been identified in Minnesota turkey flocks for at least five years, and it has been observed that average flock body weights never approach their genetic potential. However, a single causative agent responsible for these weight reductions has not been identified despite numerous efforts to do so. The purpose of this study was to identify the bacterial community composition within the small intestines of heavy and light turkey flocks using 16S rRNA sequencing, and to identify possible correlations between microbiome and average flock weight. This study also sought to define the temporal succession of bacteria occurring in the turkey ileum. Based upon 2.7 million sequences across nine different turkey flocks, dominant operational taxonomic units (OTUs) were identified and compared between the flocks studied. OTUs that were associated with heavier weight flocks included those with similarity to Candidatus division Arthromitus and Clostridium bartlettii, while these flocks had decreased counts of several Lactobacillus species compared to lighter weight flocks. The core bacterial microbiome succession in commercial turkeys was also defined. Several defining markers of microbiome succession were identified, including the presence or abundance of Candidatus division Arthromitus, Lactobacillus aviarius, Lactobacillus ingluviei, Lactobacillus salivarius, and Clostridium bartlettii. Overall, the succession of the ileum bacterial microbiome in commercial turkeys proceeds in a predictable manner. Efforts to prevent disease and promote growth in the absence of antibiotics could involve target dominant bacteria identified in the turkey ileum that are associated with increased weight gain.

Avian pneumovirus (APV) is the cause of a respiratory disease of turkeys characterized by coughing, ocular and nasal discharge, and swelling of the infraorbital sinuses. Sixty turkey poults were reared in isolation conditions. At 3 weeks of age, serum samples were collected and determined to be free of antibodies against APV, avian influenza, hemorrhagic enteritis, Newcastle disease, Mycoplasma gallisepticum, Mycoplasma synoviae, Mycoplasma meleagridis, Ornithobacterium rhinotracheale, and Bordetella avium. When the poults were 4 weeks old, they were inoculated with cell culture-propagated APV (APV/Minnesota/turkey/2a/97) via the conjunctival spaces and nostrils. After inoculation, four poults were euthanatized every 2 days for 14 days, and blood, swabs, and tissues were collected. Clinical signs consisting of nasal discharge, swelling of the infraorbital sinuses, and frothy ocular discharge were evident by 2 days postinoculation (PI) and persisted until day 12 PI. Mild inflammation of the mucosa of the nasal turbinates and infraorbital sinuses was present between days 2 and 10 PI. Mild inflammatory changes were seen in tracheas of poults euthanatized between days 4 and 10 PI. Antibody to APV was detected by day 7 PI. The virus was detected in tissue preparations and swabs of nasal turbinates and infraorbital sinuses by reverse transcription polymerase chain reaction, virus isolation, and immunohistochemical staining methods between days 2 and 10 PI. Virus was detected in tracheal tissue and swabs between days 2 and 6 PI using the same methods. In this experiment, turkey poults inoculated with tissue culture-propagated APV developed clinical signs similar to those seen in field cases associated with infection with this virus.

Total phosphorus analysis was performed on 20 samples of corn distillers dried grains with solubles (DDGS), and three experiments were conducted to determine the bioavailability of P in different samples of DDGS varying in Lys digestibility and heat processing (autoclaving). Relative bioavailability of P was estimated from tibia ash using the slope ratio method after chicks were fed a P-deficient corn-soybean meal diet supplemented with 0.05 or 0.10% P from KH2PO4 or supplemented with 2 levels of the test DDGS (7 to 25%). The mean total P value for the 20 DDGS samples was 0.73 +/- 0.04% (SD), with an average dry matter value of 88 +/- 0.8% (SD). In experiment 1, the bioavailability coefficient for P in a random sample of DDGS relative to KH2PO4 was 69%. In experiment 2, the relative bioavailabilities of P in low digestible Lys DDGS 1, low digestible Lys DDGS 2, and high digestible Lys DDGS 3 were 102, 82 and 75%, respectively (P < 0.05). For experiment 3, the P bioavailability coefficients for a light-colored nonautoclaved DDGS and the same DDGS autoclaved at 121 degrees C and 124 pKa were 75 and 87%, respectively (P < 0.05). Our results showed that the total P content of DDGS was similar to the 0.72% value reported by the NRC (1994), but the relative P bioavailability is higher than the value estimated from NRC (1994) based on table values for total and nonphytate P content. Our results also indicated that there is substantial variability in P bioavailability among different DDGS samples and suggest that increased heat processing may increase the bioavailability of P in DDGS.