Caecal microbiota compositions from 7-day-old chicks reared in high-performance and low-performance industrial farms and systematic culturomics to select strains with anti-Campylobacter activity

Deep culturing the fecal microbiota of healthy laying hens

BACKGROUND

The microbiota is implicated in several aspects of livestock health and disease. Understanding the structure and function of the poultry microbiota would be a valuable tool for improving their health and productivity since the microbiota can likely be optimized for metrics that are important to the industry such as improved feed conversion ratio, lower greenhouse gas emissions, and higher levels of competitive exclusion against pathogens. Most research into understanding the poultry microbiota has relied on culture-independent methods; however, the pure culture of bacteria is essential to elucidating the roles of individual bacteria in the microbiota and developing novel probiotic products for poultry production.

RESULTS

In this study, we have used a deep culturing approach consisting of 76 culture conditions to generate a culture collection of 1,240 bacterial isolates from healthy chickens. We then compared the taxonomy of cultured isolates to the taxonomic results of metagenomic sequencing to estimate what proportion of the microbiota was cultured. Metagenomic sequencing detected DNA from 545 bacterial species while deep culturing was able to produce isolates for 128 bacterial species. Some bacterial families, such as Comamonadaceae and Neisseriaceae were only detected via culturing - indicating that metagenomic analysis may not provide a complete taxonomic census of the microbiota. To further examine sub-species diversity in the poultry bacteriome, we whole genome sequenced 114 Escherichia coli isolates from 6 fecal samples and observed a great deal of diversity.

CONCLUSIONS

Deep culturing and metagenomic sequencing approaches to examine the diversity of the microbiota within an individual will yield different results. In this project we generated a culture collection of enteric bacteria from healthy laying hens that can be used to further understand the role of specific commensals within the broader microbiota context and have made this collection available to the community. Isolates from this collection can be requested by contacting the corresponding author and will be provided at cost.

Are there consistent effects of gut microbiota composition on performance, productivity and condition in poultry?

Microbiome of the gastrointestinal tract (GIT) has been identified as one of the crucial factors influencing the health and condition of domestic animals. The global poultry industry faces the challenge of understanding the complex relationship between gut microbiota composition and performance-related traits in birds. Considerable variation exists in the results of correlational studies using either 16S rRNA profiling or metagenomics to identify bacterial taxa associated with performance, productivity, or condition in poultry (e.g., body weight, growth rate, feeding efficiency, or egg yield). In this review, we survey the existing reports, discuss variation in research approaches, and identify bacterial taxa consistently linked to improved or deteriorated performance across individual poultry-focused studies. Our survey revealed high methodological heterogeneity, which was in contrast with vastly uniform focus of the research mainly on the domestic chicken (Gallus gallus) as a model. We also show that the bacterial taxa most frequently used in manipulative experiments and commercial probiotics intended for use in poultry (e.g., species of Lactobacillus, Bacillus, Enterococcus, or Bifidobacterium) do not overlap with the bacteria consistently correlated with their improved performance (Candidatus Arthromitus, Methanobrevibacter). Our conclusions urge for increased methodological standardization of the veterinary research in this field. We highlight the need to bridge the gap between correlational results and experimental applications in animal science. To better understand causality in the observed relationships, future research should involve a broader range of host species that includes both agricultural and wild models, as well as a broader range of age groups.

Lactic Acid Bacteria - A Promising Tool for Controlling Chicken Campylobacter Infection

Since 2005, campylobacteriosis has been the most common zoonotic disease in Europe. The main reservoir of pathogenic Campylobacter strains is broilers, which makes raw and undercooked poultry meat two major sources of disease. Infection in chicken flocks is most often asymptomatic, despite a high level of colonization reaching 106-109cfu/g in animal ceca. It is widely believed that controlling the level of colonization of the birds' digestive tract by pathogenic strains is a good way to increase food safety. Many treatments have been proposed to combat or at least reduce the level of colonization in animals reservoirs: probiotics, bacteriophages, vaccines, and anti-Campylobacter bacteriocins. This review focuses on the effects of Campylobacter infection on the chicken microbiome and colonization control strategies using probiotics (mostly lactic acid bacteria, LAB), which are live microorganisms included in the diet of animals as feed additives or supplements. Probiotics are not only an alternative to antibiotics, which were used for years as animal growth promoters, but they also constitute an effective protective barrier against excessive colonization of the digestive system by pathogenic bacteria, including Campylobacter. Moreover, one of the many beneficial functions of probiotics is the ability to manipulate the host's microbiota. Recently, there have also been some promising attempts to use lactic acid bacteria as a delivery system of oral vaccine against Campylobacter. Recombinant LAB strains induce primarily a mucosal immune response against foreign antigens, accompanied by at most a low-level immune response against carrier strains. Since the main barrier against the invasion of pathogens in the gastrointestinal tract is the intestinal mucosal membrane, the development of effective oral vaccines to protect animals against enteric infection is very reasonable.

Microbiota of Chicken Breast and Thigh Fillets Stored under Different Refrigeration Temperatures Assessed by Next-Generation Sequencing

Chicken is one of the most widely consumed meats worldwide. The exploration of the bacterial diversity of chicken meat may provide new insights into the chicken-associated microbiome that will lead to moderation of food spoilage or safety. This study was undertaken to explore the bacterial communities of chicken breast and thigh fillets stored at refrigeration (0 °C and 5 °C) and slightly abuse (10 °C) temperatures for 5 days through conventional cultural methods along with next-generation sequencing (NGS) analysis. Total viable counts (TVC), Brochothrix thermosphacta, Pseudomonas spp., and lactic acid bacteria (LAB) were enumerated, while the bacterial communities were mapped through 16S rRNA gene amplicon sequencing. Chicken breast and thigh fillets possessed a complex bacterial structure that incorporated a total of >200 Operational Taxonomic Units (OTUs) at the genus level. The core microbiota of fresh samples consisted of Acinetobacter, Brochothrix, Flavobacterium, Pseudomonas, Psychrobacter, and Vibrionaceae (family). These genera persisted until the end of storage in >80% of samples, except Psychrobacter and Flavobacterium, while Photobacterium was also identified. Hierarchical clustering showed a distinction of samples based on storage time and chicken part. Conventional plate counting with growth media commonly used in spoilage studies did not always correspond to the microbial community profiles derived from NGS analysis, especially in Pseudomonas, Acinetobacter, Photobacterium, and Vibrionaceae. Results of the present study highlight Photobacterium and Vibrionaceae, in general, as potent chicken meat spoilers and suggest the necessity to combine classical microbiological methods along with NGS technologies to characterize chicken meat spoilage microbiota.

Alternative feed ingredients in the finisher diets for sustainable broiler production

The main objective of this study was to evaluate the utilization of alternative protein feed ingredients including sunflower meal (SFM), corn gluten meal (CGM), and dried distillers' grains with solubles (DDGS) as a mixture in a partial replacement of soybean meal (SBM) in broiler finisher diets with different protein levels and also to evaluate their effect on birds' performance, environmental aspects of litter, cecal microbes, and economic prospects. A total of 576 (19 days old) Cobb 500 broiler chicks were fed eight finisher diets consisting of 4 control (CTL) diets based on SBM with different crude protein (CP) levels (CTL21, CTL20, CTL19, and CTL18, containing 21%, 20%, 19%, and 18% CP, respectively) and 4 test diets with alternative protein sources (APS21, APS20, APS19, and APS18, containing 21%, 20%, 19%, and 18% CP, respectively) using a 15% combination of alternative protein sources (2.5% CGM, 5% SFM, and 7.5% DDGS) until 35 days of age. The results indicated that birds fed test diets APS21 and APS20 recorded the highest (P < 0.05) body weight compared to other treatments, but it was not different than the CTL diets fed at these CP levels. The birds fed CTL18 or APS18 recorded the worst feed conversion ratio (FCR) compared to other treatments. Moreover, birds fed test diet containing APS21 recorded better (P < 0.05) European performance efficiency factor and better economic efficiency when compared to other treatments, but it was not different than CTL21. In addition, birds fed diets APS21 and CTL19 showed significantly increased litter Lactobacillus spp. (P < 0.05) compared to other treatments. Cecal Lactobacillus spp. and Escherichia coli (E. coli) were not affected by CTL or APS diets. The counts of cecal Salmonella spp. increased in the CTL21 group compared to other groups. In conclusion, alternative feed ingredients (protein sources) in broiler finisher diets have positive effects in a sustainable way on the productive performance, litter and cecal microbial counts, and improved economic efficiency when compared to CTL diets.