BackgroundThe complex microbiome of the ceca of chickens plays an important role in nutrient utilization, growth and well-being of these animals. Since we have a very limited understanding of the capabilities of most species present in the cecum, we investigated the role of the microbiome by comparative analyses of both the microbial community structure and functional gene content using random sample pyrosequencing. The overall goal of this study was to characterize the chicken cecal microbiome using a pathogen-free chicken and one that had been challenged with Campylobacter jejuni.Methodology/Principal FindingsComparative metagenomic pyrosequencing was used to generate 55,364,266 bases of random sampled pyrosequence data from two chicken cecal samples. SSU rDNA gene tags and environmental gene tags (EGTs) were identified using SEED subsystems-based annotations. The distribution of phylotypes and EGTs detected within each cecal sample were primarily from the Firmicutes, Bacteroidetes and Proteobacteria, consistent with previous SSU rDNA libraries of the chicken cecum. Carbohydrate metabolism and virulence genes are major components of the EGT content of both of these microbiomes. A comparison of the twelve major pathways in the SEED Virulence Subsystem (metavirulome) represented in the chicken cecum, mouse cecum and human fecal microbiomes showed that the metavirulomes differed between these microbiomes and the metavirulomes clustered by host environment. The chicken cecum microbiomes had the broadest range of EGTs within the SEED Conjugative Transposon Subsystem, however the mouse cecum microbiomes showed a greater abundance of EGTs in this subsystem. Gene assemblies (32 contigs) from one microbiome sample were predominately from the Bacteroidetes, and seven of these showed sequence similarity to transposases, whereas the remaining sequences were most similar to those from catabolic gene families.Conclusion/SignificanceThis analysis has demonstrated that mobile DNA elements are a major functional component of cecal microbiomes, thus contributing to horizontal gene transfer and functional microbiome evolution. Moreover, the metavirulomes of these microbiomes appear to associate by host environment. These data have implications for defining core and variable microbiome content in a host species. Furthermore, this suggests that the evolution of host specific metavirulomes is a contributing factor in disease resistance to zoonotic pathogens.

A prospective cohort study was performed to evaluate the prevalences and loads of Salmonella and Campylobacter spp. in farm and processing plant samples collected from 55 commercial broiler chicken flocks. Environmental samples were collected from broiler houses within 48 h before slaughter, and carcass rinses were performed on birds from the same flocks at 4 different stages of processing. Salmonella was detected in farm samples of 50 (90.9%) flocks and in processing samples of 52 (94.5%) flocks. Campylobacter was detected in farm samples of 35 (63.6%) flocks and in processing samples of 48 (87.3%) flocks. There was a significant positive relationship between environmental farm samples and processing plant carcass rinses with respect to both Salmonella and Campylobacter prevalences and loads. Campylobacter loads were significantly higher than Salmonella loads, and the correlations between samples collected from the same flocks were higher for Campylobacter than they were for Salmonella. Boot socks were the most sensitive sample type for detection of Salmonella on the farm, whereas litter samples had the strongest association with Salmonella loads in pre-and postchill carcass rinses. Boot socks, drag swabs, and fecal samples all had similar sensitivities for detecting Campylobacter on the farm, and all were more strongly associated with Campylobacter loads in carcass rinses than were litter samples. Farm samples explained a greater proportion of the variability in carcass rinse prevalences and loads for Campylobacter than they did for Salmonella. Salmonella and Campylobacter prevalences and loads both decreased significantly as birds progressed through the processing plant.

The emergence of antibiotic-resistant Salmonella is of concern to food processors. The objective of this research was to identify antimicrobial activities of cinnamaldehyde and carvacrol against antibiotic-resistant Salmonella enterica in phosphate-buffered saline (PBS) and on celery and oysters. Twenty-three isolates were screened for resistance to seven antibiotics. Two resistant and two susceptible strains were chosen for the study. S. enterica cultures (10(5) CFU/ml) were added to different concentrations of cinnamaldehyde and carvacrol (0.1, 0.2, 0.3, and 0.4% [vol/vol]) in PBS, mixed, and incubated at 37 degrees C. Samples were taken at 0, 1, 5, and 24 h for enumeration. Celery and oysters were inoculated with S. enterica (10(6-7) CFU/ml), treated with 1% cinnamaldehyde or 1% carvacrol, incubated at 4 degrees C, and then sampled for enumeration on days 0 and 3. Both antimicrobials induced complete inactivation of S. enterica in PBS at 0.3 and 0.4% on exposure, and on 0.2% in 1 h. Exposure to cinnamaldehyde at 0.1% inactivated all pathogens at 1 h, and survivors were observed only for Salmonella Newport with 0.1% carvacrol at 1 h. In celery, 1% carvacrol reduced S. enterica populations to below detection on day 0, while 1% cinnamaldehyde reduced populations by 1 and 2.3 log on day 0 and day 3, respectively. In oysters, both antimicrobials caused about 5-log reductions on day 3. These results show the potential antimicrobial effects of carvacrol and cinnamaldehyde against antibiotic-resistant S. enterica in vitro and in foods.

ABSTRACTIn this work, we investigated theCampylobacter jejuni dps(DNA binding protein from starved cells) gene for a role in biofilm formation and cecal colonization in poultry.In vitrobiofilm formation assays were conducted with stationary-phase cells in cell culture plates under microaerophilic conditions. These studies demonstrated a significant (>50%) reduction in biofilm formation by theC. jejuni dpsmutant compared to that by the wild-type strain. Studies in poultry also demonstrated the importance of thedpsgene in host colonization byC. jejuni. Real-time PCR analysis of mRNA extracted from the cecal contents of poultry infected with wild-typeC. jejuniindicated that thedpsgene is upregulated 20-fold during poultry colonization. Cecal colonization was greater than 5 log CFU lower in chicks infected with thedpsmutant than chicks infected with the wild-typeC. jejunistrain. Moreover, thedpsmutant failed to colonize 75% of the chicks following challenge with 105CFU. Preliminary studies were conducted in chicks by parenteral vaccination with a recombinant Dps protein or through oral vaccination with a recombinant attenuatedSalmonella entericastrain synthesizing theC. jejuniDps protein. No reduction inC. jejuniwas noted in chicks vaccinated with the parenteral recombinant protein, whereas, a 2.5-log-unit reduction ofC. jejuniwas achieved in chicks vaccinated with the attenuatedSalmonellavector after homologous challenge. Taken together, this work demonstrated the importance of Dps for biofilm formation and poultry colonization, and the study also provides a basis for continued work using the Dps protein as a vaccine antigen when delivered through aSalmonellavaccine vector.

Sixty-three Campylobacter jejuni isolates were screened for their resistance to the antibiotics ampicillin, cefaclor, ciprofloxacin, erythromycin, gentamycin, tetracycline, and trimethoprim-sulfamethoxazole. Based on this screen, the resistant strains D28a and H2a and the nonresistant strain A24a were selected for evaluation of their resistance and susceptibility to inactivation by cinnamaldehyde and carvacrol, the main constituents of plant-derived cinnamon and oregano oils, respectively. Different concentrations (0.05, 0.1, and 0.2% [vol/vol] in sterile phosphate-buffered saline) of cinnamaldehyde and carvacrol were added to C. jejuni cultures with initial populations of 10(4) CFU/ml. The samples were then mixed thoroughly and incubated at 37 degrees C. Viable bacterial populations were enumerated at incubation periods of 0, 30, 60, and 120 min. The results indicate that the extent of inhibition of microbial survival was related to both the nature and concentration of antimicrobials and the incubation time. Both cinnamaldehyde and carvacrol exhibited rapid antimicrobial activity against both antibiotic-resistant and non-resistant C. jejuni strains, at concentrations of approximately 0.1% and higher. The antimicrobial efficacy of cinnamaldehyde was greater than that of carvacrol. The possible significance of the results for microbiological food safety is discussed.