Relationship of the Poultry Microbiome to Pathogen Colonization, Farm Management, Poultry Production, and Foodborne Illness Risk Assessment

Despite the continuous progress in food science and technology, the global burden of foodborne illnesses remains substantial, with pathogens in food causing millions of infections each year. Traditional microbiological culture methods are inadequate in detecting the full spectrum of these microorganisms, highlighting the need for more comprehensive detection strategies. This review paper aims to elucidate the relationship between foodborne pathogen colonization and the composition of the poultry microbiome, and how this knowledge can be used for improved food safety. Our review highlights that the relationship between pathogen colonization varies across different sections of the poultry microbiome. Further, our review suggests that the microbiome profile of poultry litter, farm soil, and farm dust may serve as potential indicators of the farm environment's food safety issues. We also agree that the microbiome of processed chicken samples may reveal potential pathogen contamination and food quality issues. In addition, utilizing predictive modeling techniques on the collected microbiome data, we suggest establishing correlations between particular taxonomic groups and the colonization of pathogens, thus providing insights into food safety, and offering a comprehensive overview of the microbial community. In conclusion, this review underscores the potential of microbiome analysis as a powerful tool in food safety, pathogen detection, and risk assessment.

Uncovering changes in microbiome profiles across commercial and backyard poultry farming systems

The microbiome profiles of poultry production systems significantly impact bird health, welfare, and the environment. This study investigated the influence of broiler-rearing systems on the microbiome composition of commercial and backyard chicken farms and their environment over time. Understanding these effects is vital for optimizing animal growth, enhancing welfare, and addressing human and environmental health implications. We collected and analyzed various samples from commercial and backyard farms, revealing significant differences in microbial diversity measurements between the two systems. Backyard farms exhibited higher alpha diversity measurements in soil and water samples, while commercial farms showed higher values for litter and feeder samples. The differences in microbial diversity were also reflected in the relative abundance of various microbial taxa. In backyard farms, Proteobacteria levels increased over time, while Firmicutes levels decreased. Campilobacterota, including the major poultry foodborne pathogen Campylobacter, increased over time in commercial farm environments. Furthermore, Bacteroides, associated with improved growth performance in chickens, were more abundant in backyard farms. Conversely, pathogenic Acinetobacter was significantly higher in backyard chicken fecal and feeder swab samples. The presence of Brevibacterium and Brachybacterium, associated with low-performing broiler flocks, was significantly higher in commercial farm samples. The observed differences in microbial composition and diversity suggest that farm management practices and environmental conditions significantly affect poultry health and welfare and have potential implications for human and environmental health. Understanding these relationships can inform targeted interventions to optimize poultry production, improve animal welfare, and mitigate foodborne pathogens and antimicrobial resistance risks. IMPORTANCE The microbiome of poultry production systems has garnered significant attention due to its implications on bird health, welfare, and overall performance. The present study investigates the impact of different broiler-rearing systems, namely, commercial (conventional) and backyard (non-conventional), on the microbiome profiles of chickens and their environment over time. Understanding the influence of these systems on microbiome composition is a critical aspect of the One-Health concept, which emphasizes the interconnectedness of animal, human, and environmental health. Our findings demonstrate that the type of broiler production system significantly affects both the birds and their environment, with distinct microbial communities associated with each system. This study reveals the presence of specific microbial taxa that differ in abundance between commercial and backyard poultry farms, providing valuable insights into the management practices that may alter the microbiome in these settings. Furthermore, the dynamic changes in microbial composition over time observed in our study highlight the complex interplay between the poultry gut microbiome, environmental factors, and production systems. By identifying the key microbial players and their fluctuations in commercial and backyard broiler production systems, this research offers a foundation for developing targeted strategies to optimize bird health and welfare while minimizing the potential risks to human and environmental health. The results contribute to a growing body of knowledge in the field of poultry microbiome research and have the potential to guide future improvements in poultry production practices that promote a sustainable and healthy balance between the birds, their environment, and the microbial communities they host.

Effects of different duck rearing systems on egg flavor and quality and microbial diversity

The fishy odor of duck eggs has restricted their consumption and industrial development, a problem that producers need to address. We estimated the effects of cage, floor, and pond rearing systems on duck egg flavor, egg quality, and microbial diversity by evaluating yolk trimethylamine (TMA) content, egg quality, and the differences between duck cecum (cage cecum, CC; floor cecum, FC; pond cecum, PC) and the environment (cage environment, CE; floor environment, FE; pond environment, PE). The results show that the yolk TMA content of the floor-rearing and pond-rearing systems was significantly higher than that of the cage-rearing system (P < 0.001), with no difference between the floor and pond-rearing systems. No significant differences were detected in egg quality among the rearing systems. Firmicutes, Actinobacteria, and Bacteroidetes were the dominant phyla in the cecum, and in the rearing environment, Firmicutes, Actinobacteria, Bacteroidetes, and Proteobacteria were the dominant phyla. The results of α and β diversity analyses show that changes in the rearing system affected the composition and diversity of duck cecal microbes. In addition, we screened several genera that may be related to the production of TMA in duck cecum under different rearing systems using LEfSe analysis; for example, Subdoligranulum in the CC group; Romboutsia in the FC group; and Lactobacillus, Clostridium, and Streptococcus in the PC group. In conclusion, the rearing system affects the cecal microbes of ducks, which in turn affect the deposition of TMA in duck eggs but have no adverse effect on egg quality. This study provides a basis for the development of rearing strategies to reduce the fishy odor of egg yolk in the duck industry.

Survival and inactivation kinetics of Salmonella enterica serovar Typhimurium in irradiated and natural poultry litter microcosms

The use of poultry litter as a biological soil amendment presents a risk for the preharvest contamination of fresh produce by Salmonella. In order to properly assess this risk, it is important to understand the factors influencing the persistence of Salmonella in poultry litter. This research was performed to investigate the influence of indigenous microflora on the survival of Salmonella Typhimurium in poultry litter. Microcosms of irradiated (sterilized) and natural poultry litter were inoculated with S. Typhimurium, adjusted to pH 8.0, 0.92 water activity (a_w), and stored at 30°C for 6 days. S. Typhimurium populations (log CFU g^-1) declined in both litter treatments and there were no significant differences (P > 0.05) in recovery between litter treatments on any sampling days (0 to 6). The pH of the natural litter significantly increased (P < 0.05) from 8.42 on day 0 to 9.00 on day 6. By day 6, S. Typhimurium populations in both litter treatments fell below the limit of detection (1 log CFU g^-1). The inactivation kinetics of S. Typhimurium in both litter treatments were described by the Weibull model. Under the experimental conditions (pH 8.0, 0.92 a_w, 30°C), the presence or absence of poultry litter microflora did not significantly influence the survival of S. Typhimurium. This study demonstrates that the mere presence of poultry litter microflora will not inhibit Salmonella survival. Instead, inhibitory interactions between various microorganisms in litter and Salmonella are likely dependent on more favorable environmental conditions (e.g., a_w, pH) for growth and competition.

Considerations and best practices in animal science 16S ribosomal RNA gene sequencing microbiome studies

Microbiome studies in animal science using 16S rRNA gene sequencing have become increasingly common in recent years as sequencing costs continue to fall and bioinformatic tools become more powerful and user-friendly. The combination of molecular biology, microbiology, microbial ecology, computer science, and bioinformatics-in addition to the traditional considerations when conducting an animal science study-makes microbiome studies sometimes intimidating due to the intersection of different fields. The objective of this review is to serve as a jumping-off point for those animal scientists less familiar with 16S rRNA gene sequencing and analyses and to bring up common issues and concerns that arise when planning an animal microbiome study from design through analysis. This review includes an overview of 16S rRNA gene sequencing, its advantages, and its limitations; experimental design considerations such as study design, sample size, sample pooling, and sample locations; wet lab considerations such as field handing, microbial cell lysis, low biomass samples, library preparation, and sequencing controls; and computational considerations such as identification of contamination, accounting for uneven sequencing depth, constructing diversity metrics, assigning taxonomy, differential abundance testing, and, finally, data availability. In addition to general considerations, we highlight some special considerations by species and sample type.

Probiotics and potential applications for alternative poultry production systems

Concerns over animal welfare continue to be a critical component of law and policies associated with commercial food animal production. Social and market pressures are the driving forces behind the legislation and result in the change of poultry production management systems. As a result, the movement toward cage-free and aviary-based egg production systems has become standard practices. Cage-based systems being replaced by alternative methods that offer a suitable housing environment to meet or exceed poultry welfare needs and require different management, including the ban of antibiotics in poultry diets. For broiler production, pasture- raised and free-range management systems have become more popular. However, challenges remain from exposure to disease-causing organisms and foodborne pathogens in these environments. Consequently, probiotics can be supplemented in poultry diets as commercial feed additives. The present review discusses the impacts of these probiotics on the performance of alternative poultry production systems for improving food safety and poultry health by mitigating pathogenic organisms and improving egg and meat quality and production.

Comparison between cage and free-range egg production on microbial composition, diversity and the presence of Salmonella enterica

The microbial composition of the food production environment plays an important role in food safety and quality. This study employed both 16 S rRNA gene sequencing technology and culture-based techniques to investigate the bacterial microbiota of an egg production facility comprising of both free-range and conventional cage housing systems. The study also aimed to detect the presence of Salmonella enterica and determine whether its presence was positively or negatively associated with other taxa. Our findings revealed that microbiota profiles of free-range and cage houses differ considerably in relation to the relative abundance and diversity with a number of taxa unique to each system and to individual sampling sites within sheds. Core to each housing system were known inhabitants of the poultry gastrointestinal tracts, Romboutsia and Turicibacter, as well as common spoilage bacteria. Generally, free-range samples contained fewer taxa and were dominated by Staphylococcus equorum, differentiating them from the cage samples. Salmonella enterica was significantly associated with the presence of a taxa belonging to the Carnobacteriaceae family. The results of this study demonstrate that the diversity and composition of the microbiota is highly variable across egg layer housing systems, which could have implications for productivity, food safety and spoilage.

Effect of sodium bisulfate amendments on bacterial populations in broiler litter

The accumulation of ammonia in poultry houses is of concern to bird and human health. Acidification of the litter by application of acidifying amendments such as sodium bisulfate (SBS) retains ammonia generated by microbial degradation of uric acid as harmless ammonium in the litter. Although some studies on the effects of litter amendments on specific bacteria and groups of bacteria have been carried out previously, wide gaps in knowledge remain. In the present study, 2 types of samples were prepared and either left unamended or amended with 2.5 or 10% SBS. One set of samples consisted of a 1:1 mixture of built-up litter and fresh poultry manure (L/M); the other of fresh wood shavings and fresh poultry manure (S/M). The samples were kept in the laboratory at room temperature for 35 d. The pH of unamended mixtures increased to 7.3 and 6.9 for L/M and S/M, respectively. A pH of 6.7 and 3.9 on day 35 was observed for L/M and SM with 2.5% SBS, respectively. The corresponding values for LM and SM amended with 10% SBS were 3.5 and 2.5, respectively. Plating data indicated that coliforms became less numerous in the unamended samples than the SBS-amended samples. This difference was also seen in data obtained by high-throughput sequencing of 16S rDNA. The sequencing data also indicated that sequences from the genus Oceanisphaera accounted for as much as 80% of the sequences from L/M and about 40% of those from S/M samples early on. Sequences from members of the order Clostridiales were enriched in L/M and S/M amended with 10% SBS as were sequences from the genus Turicibacter. Weisella species sequences were more prevalent in SBS-amended samples than in unamended ones. Sequences from the genus Corynebacterium, Brachybacterium, and Arthrobacter were more common in L/M samples than in S/M samples regardless of the SBS content. The data indicate that litter amendments affect some bacteria populations and not others. Further studies are required to determine if the observed population changes such as increased survival of coliforms warrant actions to improve the microbial quality of litter to be reused.

Soil bacterial biodiversity is driven by long-term pasture management, poultry litter, and cattle manure inputs

Soil microorganisms are important for maintaining soil health, decomposing organic matter, and recycling nutrients in pasture systems. However, the impact of long-term conservation pasture management on soil microbial communities remains unclear. Therefore, soil microbiome responses to conservation pasture management is an important component of soil health, especially in the largest agricultural land-use in the US. The aim of this study was to identify soil microbiome community differences following 13-years of pasture management (hayed (no cattle), continuously grazed, rotationally grazed with a fenced, un-grazed and unfertilized buffer strip, and a control (no poultry litter or cattle manure inputs)). Since 2004, all pastures (excluding the control) received annual poultry litter at a rate of 5.6 Mg ha^-1. Soil samples were collected at a 0-15 cm depth from 2016-2017 either pre or post poultry litter applications, and bacterial communities were characterized using Illumina 16S rRNA gene amplicon sequencing. Overall, pasture management influenced soil microbial community structure, and effects were different by year (P < 0.05). Soils receiving no poultry litter or cattle manure had the lowest richness (Chao). Continuously grazed systems had greater (P < 0.05) soil community richness, which corresponded with greater soil pH and nutrients. Consequently, continuously grazed systems may increase soil diversity, owing to continuous nutrient-rich manure deposition; however, this management strategy may adversely affect aboveground plant communities and water quality. These results suggest conservation pasture management (e.g., rotationally grazed systems) may not improve microbial diversity, albeit, buffer strips were reduced nutrients and bacterial movement as evident by low diversity and fertility in these areas compared to areas with manure or poultry litter inputs. Overall, animal inputs (litter or manure) increased soil microbiome diversity and may be a mechanism for improved soil health.