Can probiotics improve the environmental microbiome and resistome of commercial poultry production?

Interplay of poultry-microbiome interactions - influencing factors and microbes in poultry infections and metabolic disorders

1. The poultry microbiome and its stability at every point in time, either free range or reared under different farming systems, is affected by several environmental and innate factors. The interaction of the poultry birds with their microbiome, as well as several inherent and extraneous factors contribute to the microbiome dynamics. A poor understanding of this could worsen poultry heath and result in disease/metabolic disorders.2. Many diseased states associated with poultry have been linked to dysbiosis state, where the microbiome experiences some perturbation. Dysbiosis itself is too often downplayed; however, it is considered a disease which could lead to more serious conditions in poultry. The management of interconnected factors by conventional and emerging technologies (sequencing, nanotechnology, robotics, 3D mini-guts) could prove to be indispensable in ensuring poultry health and welfare.3. Findings showed that high-throughput technological advancements enhanced scientific insights into emerging trends surrounding the poultry gut microbiome and ecosystem, the dysbiotic condition, and the dynamic roles of intrinsic and exogenous factors in determining poultry health. Yet, a combination of conventional, -omics based and other techniques further enhance characterisation of key poultry microbiome actors, their mechanisms of action, and roles in maintaining gut homoeostasis and health, in a bid to avert metabolic disorders and infections.4. In conclusion, there is an important interplay of innate, environmental, abiotic and biotic factors impacting on poultry gut microbiome homoeostasis, dysbiosis, and overall health. Associated infections and metabolic disorders can result from the interconnected nature of these factors. Emerging concepts (interkingdom or network signalling and neurotransmitter), and future technologies (mini-gut models, cobots) need to include these interactions to ensure accurate control and outcomes.

Probiotics in Poultry Nutrition as a Natural Alternative for Antibiotics

Since the early 1950s, antibiotics have been used in poultry for improving feed efficiency and growth performance. Nevertheless, various side effects have appeared, such as antibiotic resistance, antibiotic residues in eggs and meat, and imbalance of beneficial intestinal bacteria. Consequently, it is essential to find other alternatives that include probiotics that improve poultry production. Probiotics are live microorganisms administered in adequate doses and improve host health. Probiotics are available to be used as feed additives, increasing the availability of the nutrients for enhanced growth by digesting the feed properly. Immunity and meat and egg quality can be improved by supplementation of probiotics in poultry feed. Furthermore, the major reason for using probiotics as feed additives is that they can compete with various infectious diseases causing pathogens in poultry's gastrointestinal tract. Hence, this chapter focuses on the types and mechanisms of action of probiotics and their benefits, by feed supplementation, for poultry health and production.

The possibility of a halal mix probiotic medium for the cultivation of Lactobacillus plantarum N16 and Saccharomyces cerevisiae

This study aimed to determine the effects of interaction between media type (halal mix preparation) and culture mixtures of Lactobacillus plantarum N16 and Saccharomyces cerevisiae (probiotics). A completely randomised factorial design (CRFD) consisting of 2 factors and three replications was used, where factor A was a mixture of Lactobacillus plantarum N16 and Saccharomyces cerevisiae at a ratio of 1:1 (A1); 1:2 (A2) and 2:1 (A3) and factor B was the type of growth media, that is, control (B1), whey tofu, molasses, and fish waste flour (B2), and coconut water, onggok flour and shrimp waste flour (B3). The variables measured were viability, cell biomass, and pH. The results showed interactions between factors A and B, which were significantly different (p <0.05) in terms of viability, cell biomass, and pH. Based on the results of the study, it can be concluded that the mixture of Lactobacillus plantarum N16 and Saccharomyces cerevisiae at a ratio of 2:1 (A3), using coconut water, onggok flour, and shrimp waste flour (B3) as medium and incubated at 36 °C for 24 hours was the best medium. It had a 2.37 viability, 42.33 mg/ml biomass cell, and a pH of 2.37.

Immune Parameters in Chickens Treated with Antibiotics and Probiotics during Early Life

The aim of the study was to compare the effect of the administration of antibiotics or probiotics on chickens in their first week of life, on selected parameters of humoral and cellular immunity, and on the bursa of Fabricius and spleen indices. The experiment was carried out on 90 one-day-old male broilers. The control group received no additive in the drinking water; the group GP received a probiotic providing Enterococcus faecium and Bacillus amyloliquefaciens; and the group GA received 10% enrofloxacin in the drinking water on the first five days of life. Administration of the antibiotic enrofloxacin or a probiotic containing E. faecium and B. amyloliquefaciens strains to chickens in their first week of life exerts pronounced immunomodulatory effects on humoral and cellular defense mechanisms in these birds. The changes in the subpopulations of B and T cells immediately following early administration of enrofloxacin or the probiotic were not observed at the age of 35 days. Early administration of enrofloxacin can pose a risk of suppression of humoral immunity, as indicated by the significant decrease in the total IgY concentration in the plasma of the chickens.

Effects of a direct fed microbial (DFM) on broiler chickens exposed to acute and chronic cyclic heat stress in two consecutive experiments

Two consecutive 35 d experiments were conducted to investigate the effects of a multistrain DFM fed continuously to broiler chickens exposed to HS from 28 to 35 d on broiler performance, body composition, ileal digestibility, and intestinal permeability using serum Fluorescein Isothiocyanate Dextran (FITC-d) concentration. The treatments were arranged as a 2 × 2 factorial with temperature: Elevated (HS: 33 ± 2°C for 6 h and 27.7°C for the remaining 18 h from 28 to 35 days of age) and Thermoneutral (TN: 22 to 24°C over the entire 24-h day from 28 to 35 days of age) and diet: corn-soybean meal based with and without DFM (3-strain Bacillus; Enviva PRO) fed over the entire 35-d period as the two factors. Experimental diets were formulated to meet all nutrient recommendations based on breed standards using a starter (0–10 d), grower (10–21 d), and finisher (21–35 d) period. For each of the 2 experiments, 648 Ross 708 broiler chicks were allotted among the treatments with 9 replicate pens of 18 broilers. Data were analyzed as a 2 × 2 factorial within each experiment in JMP 14. In both experiments, cloacal temperatures were increased (P ≤ 0.05) in the broilers subjected to the HS treatment at both 28 d (acute) and 35 d (chronic). Supplementing birds with DFM reduced cloacal temperatures in the Experiment 1 at 28 d, but not at the other time periods. The HS treatment reduced body weight gain and lean tissue accretion from 0 to 35 d in both experiments (P ≤ 0.05). In Experiment 2, when the litter was reused BWG was increased by 36 g/bird with supplementation of DFM (P ≤ 0.05). Ileal digestibility at 28 d (2 h post HS) was improved with DFM supplementation in both experiments (P ≤ 0.05). Serum FITC-d increased with HS at both 28 and 35 d. Serum FITC-d was generally decreased with DFM at 28 d but the response was inconsistent at 35 d. Overall, the results suggest that HS reduced broiler performance and DFM treatment improved intestinal permeability and nutrient digestibility responses to HS in both experiments but did not improve performance until built up litter was used in Experiment 2.

Prairie strips' effect on transport of antimicrobial resistance indicators in poultry litter

Poultry litter is a valuable nutrient resource for agricultural production but is also a potential source for introducing antibiotic resistance genes (ARGs) and litter-associated bacteria (LAB) to the environment. Prairie strips have been demonstrated as an effective conservation practice to improve environmental quality in agroecosystems. This research aims to assess prairie strips' potential for reducing the transport of LAB and ARGs in runoff after litter application. Plot-scale rainfall simulations were performed using a replicated block design, with soil and surface runoff samples taken during the rainfall event. Microbial taxa and ARGs were characterized in the litter, soil, and water samples. In plots with litter application, LAB and ARGs were mainly detected in runoff, with very low detection in soils. Detection of ARGs in runoff, irrespective of strip installations, is consistent with previous observations of litter as a source of antimicrobial resistance (AMR) risks. The effectiveness of prairie strips to remove LAB and ARGs varied. In two of the three prairie strip plots, fewer AMR indicators were detected relative to control plots, suggesting that the prairie strips can potentially reduce these risks. In one plot, which was also associated with increased flow rate, we observed increased AMR indicators despite the installation of a prairie strip. Our observations highlight the need to prioritize understanding of soil properties even within the same site. Although we show that prairie strips can potentially reduce AMR risks, further research is needed to better understand the influence of rainfall timing, soil, and litter characteristics.

Prevalence and Molecular Characteristics of Avian Pathogenic Escherichia coli in "No Antibiotics Ever" Broiler Farms

Avian pathogenic Escherichia coli (APEC) causes significant economic and welfare concerns to the broiler industry. For several decades, prophylactic supplementation of antimicrobial growth promoters was the primary method to control APEC; however, the recent shift to no antibiotics ever (NAE) production has increased colibacillosis incidence. The objectives of this study were to determine the influence of season, flock age, and sample type on the prevalence and virulence of E. coli and to identify the serogroups and antimicrobial susceptibility of virulent and nonvirulent E. coli in NAE broiler farms. Litter, feces, cloacal swabs, and tracheal swabs were collected from 4 NAE farms during spring and summer seasons, and E. coli was isolated and confirmed by PCR. Confirmed E. coli isolates were tested for 5 APEC-virulence-associated genes (VAGs) using quantitative PCR (qPCR). Further, E. coli isolates with all five VAGs (100 isolates) and E. coli isolates without any VAGs (87 isolates) were screened against 11 antimicrobials through Kirby-Bauer disk diffusion assay, and their serogroups were tested using PCR. Data were analyzed using the GLIMMIX procedure of SAS 9.4, and statistical significance was determined at a P value of ≤0.05. Overall, the prevalence of E. coli was not affected by season, flock age, or sample type. However, the prevalence of all tested VAGs decreased from spring to summer (P ≤ 0.002). The frequency of resistance was highest for tetracycline, and serogroups O8 (31%) and O78 (11%) were most frequent in virulent E. coli. In conclusion, there is a high prevalence of virulent E. coli in NAE farms, especially in the spring season.

IMPORTANCE Avian pathogenic Escherichia coli causes one of the most detrimental bacterial diseases to the United States poultry industry, colibacillosis. Colibacillosis leads to decreased performance, early mortality, and subsequent production loss. Previously, colibacillosis was largely mitigated by the use of antimicrobial growth promoters. Due to concerns about antimicrobial resistance, the use of these promoters has been largely removed from the broiler industry. With recent shifts in the poultry industry to NAE broiler production, there is an increase in bacterial disease and mortality. We do not know how this shift to NAE affects APEC prevalence within broiler farms. Therefore, in the current study, we attempted to assess the prevalence and virulence of E. coli within an antibiotic-free broiler environment, assessed antimicrobial susceptibility, and identified the serogroups of virulent and nonvirulent E. coli.

The Recent Trend in the Use of Multistrain Probiotics in Livestock Production: An Overview

It has been established that introducing feed additives to livestock, either nutritional or non-nutritional, is beneficial in manipulating the microbial ecosystem to maintain a balance in the gut microbes and thereby improving nutrient utilization, productivity, and health status of animals. Probiotic use has gained popularity in the livestock industry, especially since antimicrobial growth promoter's use has been restricted due to the challenge of antibiotic resistance in both animals and consumers of animal products. Their usage has been linked to intestinal microbial balance and improved performance in administered animals. Even though monostrain probiotics could be beneficial, multistrain probiotics containing two or more species or strains have gained considerable attention. Combining different strains has presumably achieved several health benefits over single strains due to individual isolates' addition and positive synergistic adhesion effects on animal health and performance. However, there has been inconsistency in the effects of the probiotic complexes in literature. This review discusses multistrain probiotics, summarizes selected literature on their effects on ruminants, poultry, and swine productivity and the various modes by which they function.

Production of a Potentially Probiotic Product for Animal Feed and Evaluation of Some of Its Probiotic Properties

Nowadays, probiotics have been proposed for substituting antibiotics in animal feed since the European Union banned the latter compounds in 2006 to avoid serious side effects on human health. Therefore, this work aimed to produce a probiotic product for use in animal feed by fed-batch fermentation of whey with a combination of kefir grains, AGK1, and the fermented whole milk used to activate these kefir grains. The probiotic culture obtained was characterized by high levels of biomass (8.03 g/L), total viability (3.6 × 10⁸ CFU/mL) and antibacterial activity (28.26 Activity Units/mL). Some probiotic properties of the probiotic culture were investigated in vitro, including its survival at low pH values, under simulated gastrointestinal conditions, after freezing in skim milk at −20 °C, and in the commercial feed during storage at room temperature. The viable cells of lactic and acetic acid bacteria and yeasts exhibited higher tolerance to acidic pH and simulated gastrointestinal conditions when the cells were protected with skim milk and piglet feed, compared with washed cells. The results indicated the feasibility of producing a probiotic product at a low cost with a potential application in animal feed.

Utilizing the Microbiota and Machine Learning Algorithms To Assess Risk of Salmonella Contamination in Poultry Rinsate

ABSTRACT

Traditional microbiological testing methods are slow, and many molecular-based techniques rely on culture-based enrichment to overcome low limits of detection. Recent advancements in sequencing technologies may make it possible to utilize machine learning to identify patterns in microbiome data to potentially predict the presence or absence of pathogens. In this study, 299 poultry rinsate samples from various points in the processing chain were analyzed to determine if microbiota could inform about a sample's risk for containing Salmonella. Samples were culture confirmed as Salmonella positive or negative following modified U.S. Department of Agriculture Microbiological Laboratory Guidebook protocols. The culture confirmation result was used as a reference to compare with 16S sequencing data. Prechill samples tested positive (71 of 82) at a higher frequency than postchill samples (30 of 217) and contained greater microbial diversity. Due to the larger sample size, postchill samples were analyzed more thoroughly. Analysis of variance identified a significant effect of chilling on the number of genera (P < 0.001), but analysis of similarities failed to provide evidence for microbial dissimilarity between pre- and postchill samples (P = 0.001, R = 0.443). Various machine learning models were trained by using postchill samples to predict if a sample contained Salmonella on the basis of the samples' microbiota preenrichment. The optimal model was a random forest-based model with a performance as follows: accuracy (88%), sensitivity (85%), and specificity (90%). Although the algorithms described in this article are prototypes, these risk-based algorithms demonstrate the potential and need for further studies to provide insight alongside diagnostic tests. Combining risk-based information with diagnostic tools can help poultry processors make informed decisions to help identify and prevent the spread of Salmonella. These data add to the growing body of literature exploring novel ways to utilize microbiome data for predictive food safety.

HIGHLIGHTS

Are There Effective Intervention Measures in Broiler Production against the ESBL/AmpC Producer Escherichia coli?

Extended-spectrum beta-lactamase (ESBL) and AmpC beta-lactamase (AmpC) producing Enterobacteriaceae occur frequently in livestock animals and the subsequent stages of the meat production chain and are therefore considered a risk for human health. Strict biosecurity measures and optimal farm management should reduce or even prevent poultry flock colonization at farm level. This review summarizes and evaluates published information on the effectiveness of specific intervention measures and farm management factors aiming to reduce the occurrence and spread of ESBL/AmpC producing or commensal or pathogenic E. coli in broiler chicken farms. In this systematic literature review, a total of 643 publications were analyzed, and 14 studies with significant outcome about the effectiveness of specific measures against E. coli and ESBL/AmpC producing E. coli in broiler chicken farms were found. Different feed additives seem to have an impact on the occurrence of those microorganisms. The measures ‘cleaning and disinfection’ and ‘competitive exclusion’ showed strong effects in prevention in some studies. In summary, some intervention measures showed potential to protect against or eliminate ESBL/AmpC-producing, commensal or pathogenic E. coli at farm level. Due to the high variability in the outcome of the studies, more specific, detailed investigations are needed to assess the potential of the individual intervention measures.

Ways to minimize bacterial infections, with special reference to Escherichia coli, to cope with the first-week mortality in chicks: an updated overview

On the commercial level, the poultry industry strives to find new techniques to combat bird's infection. During the first week, mortality rate increases in birds because of several bacterial infections of about ten bacterial species, especially colisepticemia. This affects the flock production, uniformity, and suitability for slaughter because of chronic infections. Escherichia coli (E. coli) causes various disease syndromes in poultry, including yolk sac infection (omphalitis), respiratory tract infection, and septicemia. The E. coli infections in the neonatal poultry are being characterized by septicemia. The acute septicemia may cause death, while the subacute form could be characterized through pericarditis, airsacculitis, and perihepatitis. Many E. coli isolates are commonly isolated from commercial broiler chickens as serogroups O₁, O₂, and O₇₈. Although prophylactic antibiotics were used to control mortality associated with bacterial infections of neonatal poultry in the past, the commercial poultry industry is searching for alternatives. This is because of the consumer's demand for reduced antibiotic-resistant bacteria. Despite the vast and rapid development in vaccine technologies against common chicken infectious diseases, no antibiotic alternatives are commercially available to prevent bacterial infections of neonatal chicks. Recent research confirmed the utility of probiotics to improve the health of neonatal poultry. However, probiotics were not efficacious to minimize death and clinical signs associated with neonatal chicks' bacterial infections. This review focuses on the causes of the increased mortality in broiler chicks during the first week of age and the methods used to minimize death.

Novel biotechnological approaches for monitoring and immunization against resistant to antibiotics Escherichia coli and other pathogenic bacteria

The application of next-generation molecular, biochemical and immunological methods for developing new vaccines, antimicrobial compounds, probiotics and prebiotics for zoonotic infection control has been fundamental to the understanding and preservation of the symbiotic relationship between animals and humans. With increasing rates of antibiotic use, resistant bacterial infections have become more difficult to diagnose, treat, and eradicate, thereby elevating the importance of surveillance and prevention programs. Effective surveillance relies on the availability of rapid, cost-effective methods to monitor pathogenic bacterial isolates. In this opinion article, we summarize the results of some research program initiatives for the improvement of live vaccines against avian enterotoxigenic Escherichia coli using virulence factor gene deletion and engineered vaccine vectors based on probiotics. We also describe methods for the detection of pathogenic bacterial strains in eco-environmental headspace and aerosols, as well as samples of animal and human breath, based on the composition of volatile organic compounds and fatty acid methyl esters. We explain how the introduction of these low-cost biotechnologies and protocols will provide the opportunity to enhance co-operation between networks of resistance surveillance programs and integrated routine workflows of veterinary and clinical public health microbiology laboratories.

Prebiotic Driven Increases in IL-17A Do Not Prevent Campylobacter jejuni Colonization of Chickens

Worldwide Campylobacter jejuni is a leading cause of foodborne disease. Contamination of chicken meat with digesta from C. jejuni-positive birds during slaughter and processing is a key route of transmission to humans through the food chain. Colonization of chickens with C. jejuni elicits host innate immune responses that may be modulated by dietary additives to provide a reduction in the number of campylobacters colonizing the gastrointestinal tract and thereby reduce the likelihood of human exposure to an infectious dose. Here we report the effects of prebiotic galacto-oligosaccharide (GOS) on broiler chickens colonized with C. jejuni when challenged at either an early stage in development at 6 days of age or 20 days old when campylobacters are frequently detected in commercial flocks. GOS-fed birds had increased growth performance, but the levels of C. jejuni colonizing the cecal pouches were unchanged irrespective of the age of challenge. Dietary GOS modulated the immune response to C. jejuni by increasing cytokine IL-17A expression at colonization. Correspondingly, reduced diversity of the cecal microbiota was associated with Campylobacter colonization in GOS-fed birds. In birds challenged at 6 days-old the reduction in microbial diversity was accompanied by an increase in the relative abundance of Escherichia spp. Whilst immuno-modulation of the Th17 pro-inflammatory response did not prevent C. jejuni colonization of the intestinal tract of broiler chickens, the study highlights the potential for combinations of prebiotics, and specific competitors (synbiotics) to engage with the host innate immunity to reduce pathogen burdens.

Impacts of environmental complexity on respiratory and gut microbiome community structure and diversity in growing pigs

The limited understanding of the interaction between rearing environment of the growing pig and the pig’s microbial community impedes efforts to identify the optimal housing system to maximize animal health and production. Accordingly, we characterized the impact of housing complexity on shaping the respiratory and gut microbiota of growing pig. A total of 175 weaned pigs from 25 litters were randomly assigned within liter to either simple slatted-floor (S) or complex straw-based rearing ecosystem (C). Beside the floor swabs samples, fecal swabs and mucosal scraping samples from bronchus, ileum, and colon were collected approximately 164 days post-weaning at the time of slaughter. The S ecosystem seems to increase the α-diversity of respiratory and gut microbiota. Moreover, the C-raised pigs showed 35.4, 89.2, and 60.0% reduction in the Firmicutes/Bacteroidetes ratio than the S-raised pigs at bronchus, ileum, and colon, respectively. The unfavorable taxa Psychrobacter, Corynebacterium, Actinobacteria, and Neisseria were the signature taxa of C environment-associated microbial community. Therefore, the microbiota of S-raised pigs seems to show higher density of the most essential and beneficial taxa than the C-raised pigs. We preliminarily conclude that increasing the physical complexity of rearing environment seems to provide suboptimal conditions for establishing a healthy microbial community in the growing pigs.

A Review of Prebiotics Against Salmonella in Poultry: Current and Future Potential for Microbiome Research Applications

Prebiotics are typically fermentable feed additives that can directly or indirectly support a healthy intestinal microbiota. Prebiotics have gained increasing attention in the poultry industry as wariness toward antibiotic use has grown in the face of foodborne pathogen drug resistance. Their potential as feed additives to improve growth, promote beneficial gastrointestinal microbiota, and reduce human-associated pathogens, has been well documented. However, their mechanisms remain relatively unknown. Prebiotics increasing short chain fatty acid (SCFA) production in the cecum have long since been considered a potential source for pathogen reduction. It has been previously concluded that prebiotics can improve the safety of poultry products by promoting the overall health and well-being of the bird as well as provide for an intestinal environment that is unfavorable for foodborne pathogens such as Salmonella. To better understand the precise benefit conferred by several prebiotics, "omic" technologies have been suggested and utilized. The data acquired from emerging technologies of microbiomics and metabolomics may be able to generate a more comprehensive detailed understanding of the microbiota and metabolome in the poultry gastrointestinal tract. This understanding, in turn, may allow for improved administration and optimization of prebiotics to prevent foodborne illness as well as elucidate unknown mechanisms of prebiotic actions. This review explores the use of prebiotics in poultry, their impact on gut Salmonella populations, and how utilization of next-generation technologies can elucidate the underlying mechanisms of prebiotics as feed additives.

Study of the In Vitro Antagonistic Activity of Various Single-Strain and Multi-Strain Probiotics against Escherichia coli

Escherichia coli is an important commensal of our gut, however, many pathogenic strains exist, causing various severe infections in the gut or beyond. Due to several antibiotic resistance patterns of E. coli, research of alternative treatments or adjuvant therapy is important. One of these is the use of probiotics as antagonistic agents against E. coli. Most published studies investigate only one strain of E. coli and single-strain probiotics. The objectives of this study were to evaluate the antagonistic activity of selected single-strain and multi-strain probiotic supplements against selected clinical E. coli pathotypes using the in vitro agar spot test and the co-culturing method. Molecular methods were used to determine the presence of the genus lactobacilli and bifidobacteria as well as certain selected strains in the probiotic supplements. The agar-spot test showed that the multi-strain probiotics were more effective than the single-strain probiotics. On the other hand, the co-culturing method showed the opposite result, indicating that results are importantly influenced by the chosen method. The most effective single-strain probiotics against E. coli strains were Bifidobacterium animalis subsp. lactis BB-12 and Lactobacillus reuteri DSM 17938. The most effective multi-strain probiotics contained lactobacilli, bifidobacteria and enterococci strains, thus proving that most effective probiotics against E. coli strains are the lactic acid bacteria and bifidobacteria. The overall results from both in vitro tests reveal that all selected probiotics exhibited an antagonistic activity against all E. coli strains. From a public health perspective probiotics have thus proved to be successful in inhibiting the growth of E. coli and could therefore be used as adjuvant therapy or alternative therapy in E. coli infections.

Host and Environmental Factors Affecting the Intestinal Microbiota in Chickens

The initial development of intestinal microbiota in poultry plays an important role in production performance, overall health and resistance against microbial infections. Multiplexed sequencing of 16S ribosomal RNA gene amplicons is often used in studies, such as feed intervention or antimicrobial drug trials, to determine corresponding effects on the composition of intestinal microbiota. However, considerable variation of intestinal microbiota composition has been observed both within and across studies. Such variation may in part be attributed to technical factors, such as sampling procedures, sample storage, DNA extraction, the choice of PCR primers and corresponding region to be sequenced, and the sequencing platforms used. Furthermore, part of this variation in microbiota composition may also be explained by different host characteristics and environmental factors. To facilitate the improvement of design, reproducibility and interpretation of poultry microbiota studies, we have reviewed the literature on confounding factors influencing the observed intestinal microbiota in chickens. First, it has been identified that host-related factors, such as age, sex, and breed, have a large effect on intestinal microbiota. The diversity of chicken intestinal microbiota tends to increase most during the first weeks of life, and corresponding colonization patterns seem to differ between layer- and meat-type chickens. Second, it has been found that environmental factors, such as biosecurity level, housing, litter, feed access and climate also have an effect on the composition of the intestinal microbiota. As microbiota studies have to deal with many of these unknown or hidden host and environmental variables, the choice of study designs can have a great impact on study outcomes and interpretation of the data. Providing details on a broad range of host and environmental factors in articles and sequence data repositories is highly recommended. This creates opportunities to combine data from different studies for meta-analysis, which will facilitate scientific breakthroughs toward nutritional and husbandry associated strategies to improve animal health and performance.

An Attenuated Salmonella enterica Serovar Typhimurium Strain and Galacto-Oligosaccharides Accelerate Clearance of Salmonella Infections in Poultry through Modifications to the Gut Microbiome

Salmonella is estimated to cause one million foodborne illnesses in the United States every year. Salmonella-contaminated poultry products are one of the major sources of salmonellosis. Given the critical role of the gut microbiota in Salmonella transmission, a manipulation of the chicken intestinal microenvironment could prevent animal colonization by the pathogen. In Salmonella, the global regulator gene fnr (fumarate nitrate reduction) regulates anaerobic metabolism and is essential for adapting to the gut environment. This study tested the hypothesis that an attenuated Fnr mutant of Salmonella enterica serovar Typhimurium (attST) or prebiotic galacto-oligosaccharides (GOS) could improve resistance to wild-type Salmonella via modifications to the structure of the chicken gut microbiome. Intestinal samples from a total of 273 animals were collected weekly for 9 weeks to evaluate the impact of attST or prebiotic supplementation on microbial species of the cecum, duodenum, jejunum, and ileum. We next analyzed changes to the gut microbiome induced by challenging the animals with a wild-type Salmonella serovar 4,[5],12:r:- (Nal^r) strain and determined the clearance rate of the virulent strain in the treated and control groups. Both GOS and the attenuated Salmonella strain modified the gut microbiome but elicited alterations of different taxonomic groups. The attST produced significant increases of Alistipes and undefined Lactobacillus, while GOS increased Christensenellaceae and Lactobacillus reuteri The microbiome structural changes induced by both treatments resulted in a faster clearance after a Salmonella challenge.IMPORTANCE With an average annual incidence of 13.1 cases/100,000 individuals, salmonellosis has been deemed a nationally notifiable condition in the United States by the Centers for Disease Control and Prevention (CDC). Earlier studies demonstrated that Salmonella is transmitted by a subset of animals (supershedders). The supershedder phenotype can be induced by antibiotics, ascertaining an essential role for the gut microbiota in Salmonella transmission. Consequently, modulation of the gut microbiota and modification of the intestinal microenvironment could assist in preventing animal colonization by the pathogen. Our study demonstrated that a manipulation of the chicken gut microbiota by the administration of an attenuated Salmonella strain or prebiotic galacto-oligosaccharides (GOS) can promote resistance to Salmonella colonization via increases of beneficial microorganisms that translate into a less hospitable gut microenvironment.

Effect of in ovo administration of an adult-derived microbiota on establishment of the intestinal microbiome in chickens

OBJECTIVE To determine effects of in ovo administration of a probiotic on development of the intestinal microbiota of 2 genetic lineages (modern and heritage) of chickens. SAMPLE 10 newly hatched chicks and 40 fertile eggs to determine intestinal microbiota at hatch, 900 fertile eggs to determine effects of probiotic on hatchability, and 1,560 chicks from treated or control eggs. PROCEDURES A probiotic competitive-exclusion product derived from adult microbiota was administered in ovo to fertile eggs of both genetic lineages. Cecal contents and tissues were collected from embryos, newly hatched chicks, and chicks. A PCR assay was used to detect bacteria present within the cecum of newly hatched chicks. Fluorescence in situ hybridization and vitality staining were used to detect viable bacteria within intestines of embryos. The intestinal microbiota was assessed by use of 16S pyrosequencing. RESULTS Microscopic evaluation of embryonic cecal contents and tissues subjected to differential staining techniques revealed viable bacteria in low numbers. Development of the intestinal microbiota of broiler chicks of both genetic lineages was enhanced by in ovo administration of adult microbiota. Although the treatment increased diversity and affected composition of the microbiota of chicks, most bacterial species present in the probiotic were transient colonizers. However, the treatment decreased the abundance of undesirable bacterial species within heritage lineage chicks. CONCLUSIONS AND CLINICAL RELEVANCE In ovo inoculation of a probiotic competitive-exclusion product derived from adult microbiota may be a viable method of managing development of the microbiota and reducing the prevalence of pathogenic bacteria in chickens.

Current Status of the Preharvest Application of Pro- and Prebiotics to Farm Animals to Enhance the Microbial Safety of Animal Products

The selection of microorganisms that act as probiotics and feed additives that act as prebiotics is an ongoing research effort, but a sizable range of commercial pro-, pre- and synbiotic (combining pro- and prebiotics) products are already available and being used on farms. A survey of the composition of commercial products available in the United States revealed that Lactobacillus acidophilus, Enterococcus faecium, and Bacillus subtilis were the three most common species in probiotic products. Of the nearly 130 probiotic products (also called direct-fed microbials) for which information was available, about 50 also contained yeasts or molds. The focus on these particular bacteria and eukaryotes is due to long-standing ideas about the benefits of such strains, research data on effectiveness primarily in laboratory or research farm settings, and regulations that dictate which microorganisms or feed additives can be administered to farm animals. Of the direct-fed microbials, only six made a claim relating to food safety or competitive exclusion of pathogens. None of the approximately 50 prebiotic products mentioned food safety in their descriptions. The remainder emphasized enhancement of animal performance such as weight gain or overall animal health. The reason why so few products carry food safety-related claims is the difficulties in establishing unambiguous cause and effect relationships between the application of such products in varied and constantly changing farm environments and improved food safety of the end product.

Reviewing Classical and Molecular Techniques Regarding Profiling of Probiotic Character of Microorganisms

In recent years the roles of probiotics as functional ingredients in food has been highly adopted by the consumers and are under constant investigation by the scientific community. As a result, several probiotic-containing foods have been introduced in the market with an annual share of several billion dollars. Of particular interest in the probiotics research is the profiling of probiotic character of the microbes involving both in vitro and in vivo approaches. Initially traditional microbiological techniques were used; however they suffer by many limitations and therefore the development of new techniques, which are primarily based on the analysis of nucleic acids have been introduced. The scope of this review is to present current knowledge about the methodological approaches that are used to quantify and characterize the potential probiotic character of microorganisms. Moreover, it will focus on molecular and non-molecular tools and finally will report some new perspectives in the study of probiotics using omics techniques.

Can Bacteriotherapy Using Commercially Available Probiotics, Prebiotics, and Organic Acids Ameliorate the Symptoms Associated With Runting-Stunting Syndrome in Broiler Chickens?

Runting-stunting syndrome (RSS) in poultry has been known for more than 40 years, but the precise etiology remains unknown and a licensed vaccine is consequently not currently available. In order to mitigate the symptoms associated with RSS, a series of experiments was performed to investigate whether a combined bacteriotherapeutic treatment consisting of probiotics, prebiotics, and organic acids could influence the outcome of this disease. Initially two groups of commercial broiler chickens were either left uninoculated or inoculated with filtrate from homogenized intestines of RSS-affected broiler chickens. One group from each of these two challenge groups was treated, with a bacteriotherapeutic regimen. After 12 days chickens were euthanatized, the body weight was measured, and duodenal lesions were enumerated. Five consecutive broiler chicken flocks were then raised either on litter from RSS-affected birds or on fresh wood shavings. Treatment had no beneficial effect on the number and severity of intestinal lesions. There appeared to be a significant build-up of RSS agent(s) in poultry litter, with each consecutive flock placement, independent of bacteriotherapeutic treatment, as more individuals exhibited intestinal lesions on built-up litter in RSS-affected houses (28.9% vs. 44%). While treatment did not appear to consistently reduce intestinal lesions, it did significantly improve the mean body weights (P<0.05) and uniformity of 12-day-old chickens placed on reused litter in houses in which RSS-infected birds were previously raised. A combination of litter management and bacteriotherapy may be needed to ameliorate the adverse effects of RSS on intestinal health and body weight in broiler chickens.

Metagenomic Analysis of Chicken Gut Microbiota for Improving Metabolism and Health of Chickens - A Review

Chicken is a major food source for humans, hence it is important to understand the mechanisms involved in nutrient absorption in chicken. In the gastrointestinal tract (GIT), the microbiota plays a central role in enhancing nutrient absorption and strengthening the immune system, thereby affecting both growth and health of chicken. There is little information on the diversity and functions of chicken GIT microbiota, its impact on the host, and the interactions between the microbiota and host. Here, we review the recent metagenomic strategies to analyze the chicken GIT microbiota composition and its functions related to improving metabolism and health. We summarize methodology of metagenomics in order to obtain bacterial taxonomy and functional inferences of the GIT microbiota and suggest a set of indicator genes for monitoring and manipulating the microbiota to promote host health in future.

Diversity and Persistence of Salmonella enterica Strains in Rural Landscapes in the Southeastern United States

Salmonellosis cases in the in the United States show distinct geographical trends, with the southeast reporting among the highest rates of illness. In the state of Georgia, USA, non-outbreak associated salmonellosis is especially high in the southern low-lying coastal plain. Here we examined the distribution of Salmonella enterica in environmental waters and associated wildlife in two distinct watersheds, one in the Atlantic Coastal Plain (a high case rate rural area) physiographic province and one in the Piedmont (a lower case rate rural area). Salmonella were isolated from the two regions and compared for serovar and strain diversity, as well as distribution, between the two study areas, using both a retrospective and prospective design. Thirty-seven unique serovars and 204 unique strain types were identified by pulsed-field gel electrophoresis (PFGE). Salmonella serovars Braenderup, Give, Hartford, and Muenchen were dominant in both watersheds. Two serovars, specifically S. Muenchen and S. Rubislaw, were consistently isolated from both systems, including water and small mammals. Conversely, 24 serovars tended to be site-specific (64.8%, n = 37). Compared to the other Salmonella serovars isolated from these sites, S. Muenchen and S. Rubislaw exhibited significant genetic diversity. Among a subset of PFGE patterns, approximately half of the environmental strain types matched entries in the USA PulseNet database of human cases. Ninety percent of S. Muenchen strains from the Little River basin (the high case rate area) matched PFGE entries in PulseNet compared to 33.33% of S. Muenchen strains from the North Oconee River region (the lower case rate area). Underlying the diversity and turnover of Salmonella strains observed for these two watersheds is the persistence of specific Salmonella serovars and strain types that may be adapted to these watersheds and landscapes.

Comparative analysis of the intestinal bacterial and RNA viral communities from sentinel birds placed on selected broiler chicken farms

There is a great deal of interest in characterizing the complex microbial communities in the poultry gut, and in understanding the effects of these dynamic communities on poultry performance, disease status, animal welfare, and microbes with human health significance. Investigations characterizing the poultry enteric virome have identified novel poultry viruses, but the roles these viruses play in disease and performance problems have yet to be fully characterized. The complex bacterial community present in the poultry gut influences gut development, immune status, and animal health, each of which can be an indicator of overall performance. The present metagenomic investigation was undertaken to provide insight into the colonization of specific pathogen free chickens by enteric microorganisms under field conditions and to compare the pre-contact intestinal microbiome with the altered microbiome following contact with poultry raised in the field. Analysis of the intestinal virome from contact birds ("sentinels") placed on farms revealed colonization by members of the Picornaviridae, Picobirnaviridae, Reoviridae, and Astroviridae that were not present in pre-contact birds or present in proportionally lower numbers. Analysis of the sentinel gut bacterial community revealed an altered community in the post-contact birds, notably by members of the Lachnospiracea/Clostridium and Lactobacillus families and genera. Members of the avian enteric Reoviridae and Astroviridae have been well-characterized and have historically been implicated in poultry enteric disease; members of the Picobirnaviridae and Picornaviridae have only relatively recently been described in the poultry and avian gut, and their roles in the recognized disease syndromes and in poultry performance in general have not been determined. This metagenomic analysis has provided insight into the colonization of the poultry gut by enteric microbes circulating in commercial broiler flocks, and has identified enteric viruses and virus communities that warrant further study in order to understand their role(s) in avian gut health and disease.

The chicken gastrointestinal microbiome

The domestic chicken is a common model organism for human biological research and of course also forms the basis of a global protein industry. Recent methodological advances have spurred the recognition of microbiomes as complex communities with important influences on the health and disease status of the host. In this minireview, we provide an overview of the current state of knowledge of the chicken gastrointestinal microbiome focusing on spatial and temporal variability, the presence and importance of human pathogens, the influence of the microbiota on the immune system, and the importance of the microbiome for poultry nutrition. Review and meta-analysis of public data showed cecal communities dominated by Firmicutes and Bacteroides at the phylum level, while at finer levels of taxonomic resolution, a phylogenetically diverse assemblage of microorganisms appears to have similar metabolic functions that provide important benefits to the host as inferred from metagenomic data. This observation of functional redundancy may have important implications for management of the microbiome. We foresee advances in strategies to improve gut health in commercial operations through management of the intestinal microbiota as an alternative to in-feed subtherapeutic antibiotics, improvements in pre- and probiotics, improved management of polymicrobial poultry diseases, and better control of human pathogens via colonization reduction or competitive exclusion strategies.

Microorganisms with claimed probiotic properties: an overview of recent literature

Probiotics are defined as live microorganisms, which when administered in adequate amounts, confer a health benefit on the host. Health benefits have mainly been demonstrated for specific probiotic strains of the following genera: Lactobacillus, Bifidobacterium, Saccharomyces, Enterococcus, Streptococcus, Pediococcus, Leuconostoc, Bacillus, Escherichia coli. The human microbiota is getting a lot of attention today and research has already demonstrated that alteration of this microbiota may have far-reaching consequences. One of the possible routes for correcting dysbiosis is by consuming probiotics. The credibility of specific health claims of probiotics and their safety must be established through science-based clinical studies. This overview summarizes the most commonly used probiotic microorganisms and their demonstrated health claims. As probiotic properties have been shown to be strain specific, accurate identification of particular strains is also very important. On the other hand, it is also demonstrated that the use of various probiotics for immunocompromised patients or patients with a leaky gut has also yielded infections, sepsis, fungemia, bacteraemia. Although the vast majority of probiotics that are used today are generally regarded as safe and beneficial for healthy individuals, caution in selecting and monitoring of probiotics for patients is needed and complete consideration of risk-benefit ratio before prescribing is recommended.