Investigating the cecal microbiota of broilers raised in extensive and intensive production systems

Intensive broiler production practices are structured to prevent the introduction and spread of pathogens; however, they can potentially minimize the exposure of broilers to beneficial commensal bacteria. In this study, we used 16S rRNA amplicon sequencing to characterize the cecal microbiota of 35-day-old broilers from 22 independent commercial farms rearing broilers under intensive (IPS) or extensive production systems (EPS). We aimed to determine which bacteria are normal inhabitants of the broiler ceca and which bacteria might be missing from broilers in IPS. In addition, we generated a collection of 410 bacterial isolates, including 87 different species, to be used as a resource to further explore the effects of selected isolates on bird physiology and to elucidate the role of individual species within the cecal microbial community. Our results indicated significant differences in the microbiota of broilers between systems: the microbiota of broilers from EPS was dominated by Bacteroidetes {55.2% ± 8.9 [mean ± standard deviation (SD)]}, whereas Firmicutes dominated the microbiota of broilers from IPS (61.7% ± 14.4, mean ± SD). Bacterial taxa found to be core in the EPS microbiota, including Olsenella, Alistipes, Bacteroides, Barnesiella, Parabacteroides, Megamonas, and Parasutterella, were shown to be infrequent or absent from the IPS microbiota, and the EPS microbiota presented higher phylogenetic diversity and greater predicted functional potential than that of broilers in IPS. The bacteria shown to be depleted in broilers from IPS should be further investigated for their effects on bird physiology and potential application as next-generation probiotics. IMPORTANCE Production practices in intensive farming systems significantly reduce the introduction and spread of pathogens; however, they may potentially minimize the exposure of animals to beneficial commensal microorganisms. In this study, we identified core bacteria from the cecal microbiota of broilers raised in extensive production systems that are missing or reduced in birds from intensive systems, including Olsenella, Alistipes, Bacteroides, Barnesiella, Parabacteroides, Megamonas, and Parasutterella. Furthermore, the cecal microbiota of broilers from extensive systems showed higher diversity and greater functional potential than that of broilers from intensive systems. In addition, a collection of bacterial isolates containing 87 different species was generated from the current study, and this important resource can be used to further explore the role of selected commensal bacteria on the microbial community and bird physiology.

Assessment of Rumen Mucosa, Lung, and Liver Lesions at Slaughter as Benchmarking Tool for the Improvement of Finishing Beef Cattle Health and Welfare

Abattoir post-mortem inspections offer a useful tool for animal disease surveillance. The present cross-sectional study aimed at assessing the prevalence of rumen mucosa, lung, and liver lesions in 153 randomly selected batches of finishing beef cattle through a post-mortem inspection at the abattoir. At least 15 animals per batch were inspected at slaughter by two veterinarians for a total of 2,161 animals (1,376 bulls; 785 heifers) coming from 80 Italian commercial farms. Rumens were inspected by recording as binary variables (presence/absence) signs of hyperkeratosis, ruminitis, ulcer, and star scars. Similarly, lungs were inspected for signs of pneumonia and livers for signs of lipidosis, abscesses, and/or adherence. Hyperkeratosis of the mucosa and signs of ruminitis were detected in 58 and 30% of the inspected rumens, respectively. Ruminal star scars were more prevalent in bulls than in heifers (18 vs. 11%; P < 0.05). Signs of severe pneumonia were observed in 10% of the lungs; abscess and/or adherence in 4% of the livers. Hyperkeratosis of rumen mucosa was correlated to signs of ruminitis, and signs of ruminitis were correlated to star scars. No correlations were found between hepatic lesions and any other rumen or lung disorders. The wide variability observed among batches for the prevalence of specific lesions suggested the development of a benchmarking system to provide feedback to the farm veterinarians, as these lesions can be reflective of a subclinical disease status not easy to be detected in the live animal. Quartiles of the batch prevalence of rumen, lung, and liver alterations (if ≥1%) were calculated as a benchmarking tool, and third quartile value was proposed as an alarm threshold for each lesion. The use of the benchmarking system could allow to allocate each inspected batch to a specific "health class." Critical batches with a prevalence above the alarm threshold for a given lesion should be reported to veterinarians of the origin farms where actions should be taken in order to identify and lower the risk factors for that specific health issue. Knowledge of post-mortem inspection data along with the implementation of the proposed benchmarking system should help farm veterinarians to improve herd management from a health and welfare perspective.