Impact of a probiotic-based cleaning product on the microbiological profile of broiler litters and chicken caeca microbiota

Ontogeny and function of the intestinal epithelial and innate immune cells during early development of chicks: to explore in ovo immunomodulatory nutrition

Intestinal epithelial cells (IECs) and innate immune cells in the gastrointestinal tract (GIT) of chickens play crucial roles in pathogens defense and maintaining gut health. However, their effectiveness influenced with their developmental and functional stages during pre and post hatch periods of chick. During embryonic development, differentiation and migration of these innate immune systems are tightly regulated by diverse cellular and molecular factors. The maturation and functionality of IECs are histologically evident starting embryonic day (ED) 14. Moreover, the innate immun cells, such as dendritic cells (DCs), macrophages, natural killer (NK) cells, and gamma-delta (γδ) T cells have showed developmental expression varation, while most identified by the 3rd days of incubation and capable of responsing to their cognate ligands of pathogens by ED 17, it may not efficient during posthatch period. In modern poultry production, in ovo feeding of bioactive substances is a topic of interest to maximize the protection capability of hatched chicks by enhancing improvement on the development of innate immune systems. However, their actions and effects on each distinct innate immune involved response are inconsistent and not clearly understood. Thus, summarizing the ontogeny and function of IECs, innate immunity systems, and interaction mechanisms of in ovo feeding of bioactive substances could provide baseline information for designing targeted in ovo feeding interventions to modulate cell waise specific innate immune systems.

The growth-promoting effect of water extract of Chuanminshen violaceum stem and leaf on broilers

Currently, developing nonantibiotic growth promoters is a broad consensus in broiler industry, which is one of the effective ways to reduce drug-resistant strains. Chuanminshen violaceum is a traditional Chinese medicinal herb that is commonly used for its roots, while the stems and leaves are often discarded, resulting in a huge amount of waste. This study optimized the preparation process of water extract of Chuanminshen violaceum stems and leaves (CVSLE) by response surface analysis based on the yields of polysaccharide and protein. The CVSLE and herbal powder (CVSL) were then processed into granules before being used as feed additives. The Macleaya cordata powder was used as positive control. The results showed that the addition of CVSLE (0.5% of the feed) showed the highest growth-promoting activity than other CVSLE groups (0.2% and 1%), 1% CVSL group and positive control (0.05%). CVSLE at the dosage of 0.5% could significantly increase the ADG and reduce the FCR from d 21 to 42, d 0 to 42. The HI antibody titers against Newcastle disease virus and avian influenza virus were significantly enhanced at 21, 28 and 42 d. CVSLE did not affect the slaughtering performances, but could significantly elevate the spleen, thymus and bursa of Fabricius indices and the transcriptional levels of IL-2, IL-4, IL-10 and IFN-γ in spleen. The intestinal barrier function of broilers was significantly enhanced by increased levels of immune barrier (sIgA), physical barrier (ZO-1, OCL and Muc-2) and flora barrier (Lactobacillus and Bifidobacterium). These results suggest that CVSLE was a promising herbal additive candidate for broilers.

A conventional hatchery vs "on-farm" hatching of broiler chickens in terms of microbiological and microclimatic conditions

"On-farm hatching" is one of the proposed alternatives to conventional hatchery-hatching. This solution reduces distress and improves the welfare of the chicks around the hatching period. Therefore, it seemed interesting to compare conventional hatchery and "on-farm" hatching in terms of microbiological and microclimatic conditions. Hatching eggs (Ross 308) were incubated in a commercial hatchery. The control group (HH, 683 eggs) hatched in a conventional hatcher, while the other eggs were transported into the experimental chicken-hall for on-farm hatching, and set in pens directly on litter (OL, 667 eggs) or plastic trays (OT, 678 eggs). One-day-old chicks were also placed in the experimental hall. Microclimatic parameters were controlled every 12 h. The microbiological status of the surface of the eggshells and the litter was assessed based on the total number of aerobic mesophilic microorganisms and also the selected individual genus/species of bacteria. The hatchability of HH was 96.4% in comparison to 93.9% and 95.8% for OL and OT, respectively (P > 0.05). On the other hand, 2.1% of the HH chicks were found injured/dead, while only 0.2-0.3% of the on-farm groups were. The total number of aerobic mesophilic microflora on the surface of as-hatched shells was 4.93 ± 0.629 log CFU/g in HH, while only 1.14 ± 0.995 and 1.93 ± 1.709 log CFU/g in OL and OT, respectively (P < 0.001). Similarly, the total count of bacteria in the litter in the on-farm hatched pens was 1.9-fold lower than in pens set with HH chicks (P < 0.001). In summary, on-farm hatching results in hatchability that is no worse than in a conventional hatcher, while the microbiological status of as-hatched eggshells and litter is significantly better. Therefore, on-farm hatching seems to provide appropriate environmental conditions for newly hatched chicks and poses no epizootic risk.

Tackling transmission of infectious diseases: A probiotic-based system as a remedy for the spread of pathogenic and resistant microbes

Built environments (BEs) currently represent the areas in which human beings spend most of their life. Consistently, microbes populating BEs mostly derive from human occupants and can be easily transferred from BE to occupants. The hospital microbiome is a paradigmatic example, representing a reservoir for harmful pathogens that can be transmitted to susceptible patients, causing the healthcare-associated infections (HAIs). Environmental cleaning is a crucial pillar in controlling BE pathogens and preventing related infections, and chemical disinfectants have been largely used so far towards this aim. However, despite their immediate effect, chemical-based disinfection is unable to prevent recontamination, has a high environmental impact, and can select/increase antimicrobial resistance (AMR) in treated microbes. To overcome these limitations, probiotic-based sanitation (PBS) strategies were recently proposed, built on the use of detergents added with selected probiotics able to displace surrounding pathogens by competitive exclusion. PBS was reported as an effective and low-impact alternative to chemical disinfection, providing stable rebalance of the BE microbiome and significantly reducing pathogens and HAIs compared to disinfectants, without exacerbating AMR and pollution concerns. This minireview summarizes the most significant results obtained by applying PBS in sanitary and non-sanitary settings, which overall suggest that PBS may effectively tackle the infectious risk meanwhile preventing the further spread of pathogenic and resistant microbes.

Metagenomic insights into the impact of litter from poultry Concentrated Animal Feeding Operations (CAFOs) to adjacent soil and water microbial communities

In recent decades, human food consumption has led to an increased demand for animal-based foods, particularly chicken meat production. The state of Georgia, USA is one of the top broiler chicken producers in the United States, where animals are raised in Concentrated Animal Feeding Operations (CAFOs). Without proper management, CAFOs could negatively impact the environment and become a public health risk as a source of water and air pollution and/or by spreading antimicrobial resistance genes. In this study, we used metagenome sequencing to investigate the impact of the application of the CAFO's litter on adjacent soils and downstream creek waters in terms of microbial diversity and antimicrobial resistance profile changes. Our data indicate that while a few microbial groups increased in abundance within a short period of time after litter application, these populations subsequently decreased to levels similar to those found prior to the litter application or to below the detection limit of our metagenome sequencing effort. Microbial taxonomic composition analyses, relative abundance of Metagenome-Assembled Genomes (MAGs) and detection of Antimicrobial Resistance Genes (ARGs) allow us to conclude that this practice of litter application had a negligible effect on the microbiome or resistome profile of these soils and nearby waterways, likely due to its dilution in the field and/or outcompetition by indigenous microbes, revealing a minimal impact of these poultry facilities on the natural microbial communities.

Biophysiology of in ovo administered bioactive substances to improve gastrointestinal tract development, mucosal immunity, and microbiota in broiler chicks

Early embryonic exogenous feeding of bioactive substances is a topic of interest in poultry production, potentially improving gastrointestinal tract (GIT) development, stimulating immunization, and maximizing the protection capability of newly hatched chicks. However, the biophysiological actions and effects of in ovo administered bioactive substances are inconsistent or not fully understood. Thus, this paper summarizes the functional effects of bioactive substances and their interaction merits to augment GIT development, the immune system, and microbial homeostasis in newly hatched chicks. Prebiotics, probiotics, and synbiotics are potential bioactive substances that have been administered in embryonic eggs. Their biological effects are enhanced by a variety of mechanisms, including the production of antimicrobial peptides and antibiotic responses, regulation of T lymphocyte numbers and immune-related genes in either up- or downregulation fashion, and enhancement of macrophage phagocytic capacity. These actions occur directly through the interaction with immune cell receptors, stimulation of endocytosis, and phagocytosis. The underlying mechanisms of bioactive substance activity are multifaceted, enhancing GIT development, and improving both the innate and adaptive immune systems. Thus summarizing these modes of action of prebiotics, probiotics and synbiotics can result in more informed decisions and also provides baseline for further research.

Bacillus-based probiotic cleansers reduce the formation of dry biofilms on common hospital surfaces

In the absence of liquid suspension, dry biofilms can form upon hard surfaces within a hospital environment, representing a healthcare-associated infection risk. Probiotic cleansers using generally recognized as safe organisms, such as those of the Bacillus genus, represent a potential strategy for the reduction of dry biofilm bioburden. The mechanisms of action and efficacy of these cleaners are, however, poorly understood. To address this, a preventative dry biofilm assay was developed using steel, melamine, and ceramic surfaces to assess the ability of a commercially available Bacillus spp. based probiotic cleanser to reduce the surface bioburden of Escherichia coli and Staphylococcus aureus. Via this assay, phosphate-buffered saline controls were able to generate dry biofilms within 7 days of incubation, with the application of the probiotic cleanser able to prevent >97.7% of dry biofilm formation across both pathogen analogs and surface types. Further to this, surfaces treated with the probiotic mixture alone also showed a reduction in dry biofilm across both pathogen and surface types. Confocal laser scanning microscopy imaging indicated that the probiotic bacteria were able to germinate and colonize surfaces, likely forming a protective layer upon these hard surfaces.

Salmonella spp. in poultry production-A review of the role of interventions along the production continuum

Salmonella is a significant pathogen of human and animal health and poultry are one of the most common sources linked with foodborne illness worldwide. Global production of poultry meat and products has increased significantly over the last decade or more as a result of consumer demand and the changing demographics of the world's population, where poultry meat forms a greater part of the diet. In addition, the relatively fast growth rate of birds which is significantly higher than other meat species also plays a role in how poultry production has intensified. In an effort to meet the greater demand for poultry meat and products, modern poultry production and processing practices have changed and practices to target control and reduction of foodborne pathogens such as Salmonella have been implemented. These strategies are implemented along the continuum from parent and grandparent flocks to breeders, the farm and finished broilers to transport and processing and finally from retail to the consumer. This review focuses on common practices, interventions and strategies that have potential impact for the control of Salmonella along the poultry production continuum from farm to plate.

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.

Microbiota of Chickens and Their Environment in Commercial Production

Chickens in commercial production are subjected to constant interaction with their environment, including the exchange of microbiota. In this review, we therefore focused on microbiota composition in different niches along the whole line of chicken production. We included a comparison of microbiota of intact eggshells, eggshell waste from hatcheries, bedding, drinking water, feed, litter, poultry house air and chicken skin, trachea, crop, small intestine, and cecum. Such a comparison showed the most frequent interactions and allowed for the identification of microbiota members that are the most characteristic for each type of sample as well as those that are the most widespread in chicken production. Not surprisingly, Escherichia coli was the most widely distributed species in chicken production, although its dominance was in the external aerobic environment and not in the intestinal tract. Other broadly distributed species included Ruminococcus torque, Clostridium disporicum, and different Lactobacillus species. The consequence and meaning of these and other observations are evaluated and discussed.

Influence of dietary Bacillus coagulans and/or Bacillus licheniformis-based probiotics on performance, gut health, gene expression, and litter quality of broiler chickens

Probiotics are non-pathogenic microorganisms that are potentially important non-antibiotic alternatives. This study aimed to compare novel multi-strain and single-strain Bacillus probiotics and their respective influences on broiler chickens' performance, gut health, litter quality, immune response, and NBN and TLR gene expression. A total of 1200 Arbor-Acres 1-day-old broiler chicks were randomly allocated into three treatments (T1 was a control, T2 was supplemented with a combined Bacillus coagulans (2 × 10⁹ cfu/g) and Bacillus licheniformis (8 × 10⁹ cfu/g) probiotic strains (0.2 kg/ton of feed), and T3 was supplemented with Bacillus licheniformis (3.2 × 10⁹ cfu/g) probiotic (0.5 kg/ton of feed) with eight replicas of each. Supplementing the broiler diet with either the single-strain (T3) or the multi-strain (T2) Bacillus-based probiotic raised the overall birds' body weight, body weight gain, feed conversion ratio, and European production efficiency factor compared to the control (T1), with a significant enhancement achieved by the multi-strain Bacillus product (P = 0.005). T2 and T3 exhibited significantly improved cholesterol, Alanine aminotransferase, aspartate aminotransferase, lactate dehydrogenase, and alkaline phosphatase levels than the control (P ≤ 0.05). The transcript levels of both NBN and TLR genes were upregulated in the liver in the T2 and T3 groups. The T2 group experienced significant reductions in gut bacterial counts, especially for Clostridia, and recorded the lowest litter moisture and nitrogen. In conclusion, supplementing broiler diets with probiotics of multiple Bacillus strains increased production profitability by promoting bird growth, improving feed intake, enhancing gut mucosa and immune organs, and upregulating genes responsible for immunity. All these inhibit the overgrowth of enteric pathogens and sustain litter quality.

Succession, Replacement, and Modification of Chicken Litter Microbiota

Chickens are in constant interaction with their environment, e.g., bedding and litter, and their microbiota. However, how litter microbiota develops over time and whether bedding and litter microbiota may affect the cecal microbiota is not clear. We addressed these questions using sequencing of V3/V4 variable region of 16S rRNA genes of cecal, bedding, and litter samples from broiler breeder chicken flocks for 4 months of production. Cecal, bedding, and litter samples were populated by microbiota of distinct composition. The microbiota in the bedding material did not expand in the litter. Similarly, major species from litter microbiota did not expand in the cecum. Only cecal microbiota was found in the litter forming approximately 20% of total litter microbiota. A time-dependent development of litter microbiota was observed. Escherichia coli, Staphylococcus saprophyticus, and Weissella jogaejeotgali were characteristic of fresh litter during the first month of production. Corynebacterium casei, Lactobacillus gasseri, and Lactobacillus salivarius dominated in a 2-month-old litter, Brevibacterium, Brachybacterium, and Sphingobacterium were characteristic for 3-month-old litter, and Salinococcus, Dietzia, Yaniella, and Staphylococcus lentus were common in a 4-month-old litter. Although the development was likely determined by physicochemical conditions in the litter, it might be interesting to test some of these species for active modification of litter to improve the chicken environment and welfare. IMPORTANCE Despite intimate contact, the composition of bedding, litter, and cecal microbiota differs considerably. Species characteristic for litter microbiota at different time points of chicken production were identified thus opening the possibility for active manipulation of litter microbiota.

In critique of anthropocentrism: a more-than-human ethical framework for antimicrobial resistance

Antimicrobial resistance (AMR) is often framed as a One Health issue, premised on the interdependence between human, animal and environmental health. Despite this framing, the focus across policymaking, implementation and the ethics of AMR remains anthropocentric in practice, with human health taking priority over the health of non-human animals and the environment, both of which mostly appear as secondary elements to be adjusted to minimise impact on human populations. This perpetuates cross-sectoral asymmetries whereby human health institutions have access to bigger budgets and technical support, limiting the ability of agricultural, animal health or environmental institutions to effectively implement policy initiatives. In this article, we review these asymmetries from an ethical perspective. Through a review and analysis of contemporary literature on the ethics of AMR, we demonstrate how the ethical challenges and tensions raised still emerge from an anthropocentric framing, and argue that such literature fails to address the problematic health hierarchies that underlie policies and ethics of AMR. As a consequence, they fail to provide the necessary tools to ethically evaluate the more-than-human challenges that the long list of actors involved in managing AMR face in their everyday practices. In response to such shortcomings, and to make sense of these challenges and tensions, this article develops an ethical framework based on relationality, care ethics and ambivalence that attends to the more-than-human character of AMR. We formulate this approach without overlooking everyday challenges of implementation by putting the framework in conversation with concrete situations from precarious settings in West Africa. This article concludes by arguing that a useful AMR ethics framework needs to consider and take seriously non-human others as an integral part of both health and disease in any given ecology.

Positive biofilms to guide surface microbial ecology in livestock buildings

The increase in human consumption of animal proteins implies changes in the management of meat production. This is followed by increasingly restrictive regulations on antimicrobial products such as chemical biocides and antibiotics, used in particular to control pathogens that can spread zoonotic diseases. Aligned with the One Health concept, alternative biological solutions are under development and are starting to be used in animal production. Beneficial bacteria able to form positive biofilms and guide surface microbial ecology to limit microbial pathogen settlement are promising tools that could complement existing biosecurity practices to maintain the hygiene of livestock buildings. Although the benefits of positive biofilms have already been documented, the associated fundamental mechanisms and the rationale of the microbial composition of these new products are still sparce. This review provides an overview of the envisioned modes of action of positive biofilms used on livestock building surfaces and the resulting criteria for the selection of the appropriate microorganisms for this specific application. Limits and advantages of this biosecurity approach are discussed as well as the impact of such practices along the food chain, from farm to fork.

Potential Feed Additives as Antibiotic Alternatives in Broiler Production

This article aimed to describe the current use scenario, alternative feed additives, modes of action and ameliorative effects in broiler production. Alternative feed additives have promising importance in broiler production due to the ban on the use of certain antibiotics. The most used antibiotic alternatives in broiler production are phytogenics, organic acids, prebiotics, probiotics, enzymes, and their derivatives. Antibiotic alternatives have been reported to increase feed intake, stimulate digestion, improve feed efficiency, increase growth performance, and reduce the incidence of diseases by modulating the intestinal microbiota and immune system, inhibiting pathogens, and improving intestinal integrity. Simply, the gut microbiota is the target to raise the health benefits and growth-promoting effects of feed additives on broilers. Therefore, naturally available feed additives are promising antibiotic alternatives for broilers. Then, summarizing the category, mode of action, and ameliorative effects of potential antibiotic alternatives on broiler production may provide more informed decisions for broiler nutritionists, researchers, feed manufacturers, and producers.

Probiotic Lactobacilli Do Not Protect Chickens against Salmonella Enteritidis Infection by Competitive Exclusion in the Intestinal Tract but in Feed, Outside the Chicken Host

Lactobacilli are commonly used as probiotics in poultry to improve production parameters and to increase chicken resistance to enteric infections. However, lactobacilli do not efficiently colonise the chicken intestinal tract, and also, their anti-infection effect in vivo is sometimes questionable. In this study, we therefore evaluated the potential of a mixture of four Lactobacillus species (L. salivarius, L. reuteri, L. ingluviei and L. alvi) for the protection of chickens against Salmonella Enteritidis infection. Whenever the chickens were inoculated by lactobacilli and S. Enteritidis separately, there was no protective effect of lactobacilli. This means that when lactobacilli and S. Enteritidis are exposed to each other as late as in the crop of chickens, lactobacilli did not influence chicken resistance to S. Enteritidis at all. The only positive effect was recorded when the mixture of lactobacilli and S. Enteritidis was used for the inoculation of feed and the feed was anaerobically fermented for 1 to 5 days. In this case, chickens fed such a diet remained S. Enteritidis negative. In vitro experiments showed that the protective effect was caused by acidification of feed down to pH 4.6 due to lactobacilli fermentation and was associated with S. Enteritidis inactivation. The probiotic effect of lactobacilli was thus expressed in the feed, outside the chicken host.

Pilot Study on Poultry Meat from Antibiotic Free and Conventional Farms: Can Metagenomics Detect Any Difference?

Antibiotic free farms are increasing in the poultry sector in order to address new EU regulations and consumer concerns. In this pilot study, we investigated whether the efforts of raising chickens without the use antibiotics make any difference in the microbiome of poultry meat eaten by consumers. To this aim we compared the microbiomes characterizing caeca and the corresponding carcasses of two groups of chickens reared, one reared on a conventional farm and one on an antibiotic-free intensive farm. The results showed a clear separation between the taxonomic, functional and antibiotic resistant genes in the caeca of the birds reared on the conventional and antibiotic free farm. However, that separation was completely lost on carcasses belonging to the two groups. The antibiotic-free production resulted in statistically significant lower antimicrobial resistance load in the caeca in comparison to the conventional production. Moreover, the antimicrobial resistance load on carcasses was much higher than in the caeca, without any significant difference between carcasses coming from the two types of farms. All in all, the results of this research highlighted the need to reduce sources of microbial contamination and antimicrobial resistance not only at the farm level but also at the post-harvest one.

The Potential of Probiotics to Eradicate Gut Carriage of Pathogenic or Antimicrobial-Resistant Enterobacterales

Probiotic supplements have been used to decrease the gut carriage of antimicrobial-resistant Enterobacterales through changes in the microbiota and metabolomes, nutrition competition, and the secretion of antimicrobial proteins. Many probiotics have shown Enterobacterales-inhibiting effects ex vivo and in vivo. In livestock, probiotics have been widely used to eradicate colon or environmental antimicrobial-resistant Enterobacterales colonization with promising efficacy for many years by oral supplementation, in ovo use, or as environmental disinfectants. In humans, probiotics have been used as oral supplements for infants to decease potential gut pathogenic Enterobacterales, and probiotic mixtures, especially, have exhibited positive results. In contrast to the beneficial effects in infants, for adults, probiotic supplements might decrease potentially pathogenic Enterobacterales, but they fail to completely eradicate them in the gut. However, there are several ways to improve the effects of probiotics, including the discovery of probiotics with gut-protection ability and antimicrobial effects, the modification of delivery methods, and the discovery of engineered probiotics. The search for multifunctional probiotics and synbiotics could render the eradication of “bad” Enterobacterales in the human gut via probiotic administration achievable in the future.

Eggshell and Feed Microbiota Do Not Represent Major Sources of Gut Anaerobes for Chickens in Commercial Production

In this study, we addressed the origin of chicken gut microbiota in commercial production by a comparison of eggshell and feed microbiota with caecal microbiota of 7-day-old chickens, using microbiota analysis by 16S rRNA sequencing. In addition, we tested at which timepoint during prenatal or neonatal development it is possible to successfully administer probiotics. We found that eggshell microbiota was a combination of environmental and adult hen gut microbiota but was completely different from caecal microbiota of 7-day-old chicks. Similarly, we observed that the composition of feed microbiota was different from caecal microbiota. Neither eggshell nor feed acted as an important source of gut microbiota for the chickens in commercial production. Following the experimental administration of potential probiotics, we found that chickens can be colonised only when already hatched and active. Spraying of eggs with gut anaerobes during egg incubation or hatching itself did not result in effective chicken colonisation. Such conclusions should be considered when selecting and administering probiotics to chickens in hatcheries. Eggshells, feed or drinking water do not act as major sources of gut microbiota. Newly hatched chickens must be colonised from additional sources, such as air dust with spores of Clostridiales. The natural colonisation starts only when chickens are already hatched, as spraying of eggs or even chickens at the very beginning of the hatching process did not result in efficient colonisation.

A Review of the Effects and Production of Spore-Forming Probiotics for Poultry

Simple Summary

Spore-forming probiotics are widely used in the poultry industry for their beneficial impact on host health. The main feature that separates spore-forming probiotics from the more common lactic acid probiotics is their high resistance to external and internal factors, resulting in higher viability in the host and correspondingly, greater efficiency. Their most important effect is the ability to confront pathogens, which makes them a perfect substitute for antibiotics. In this review, we cover and discuss the interactions of spore-forming probiotic bacteria with poultry as the host, their health promotion effects and mechanisms of action, impact on poultry productivity parameters, and ways to manufacture the probiotic formulation. The key focus of this review is the lack of reproducibility in poultry research studies on the evaluation of probiotics’ effects, which should be solved by developing and publishing a set of standard protocols in the professional community for conducting probiotic trials in poultry.

Abstract

One of the main problems in the poultry industry is the search for a viable replacement for antibiotic growth promoters. This issue requires a “one health” approach because the uncontrolled use of antibiotics in poultry can lead to the development of antimicrobial resistance, which is a concern not only in animals, but for humans as well. One of the promising ways to overcome this challenge is found in probiotics due to their wide range of features and mechanisms of action for health promotion. Moreover, spore-forming probiotics are suitable for use in the poultry industry because of their unique ability, encapsulation, granting them protection from the harshest conditions and resulting in improved availability for hosts’ organisms. This review summarizes the information on gastrointestinal tract microbiota of poultry and their interaction with commensal and probiotic spore-forming bacteria. One of the most important topics of this review is the absence of uniformity in spore-forming probiotic trials in poultry. In our opinion, this problem can be solved by the creation of standards and checklists for these kinds of trials such as those used for pre-clinical and clinical trials in human medicine. Last but not least, this review covers problems and challenges related to spore-forming probiotic manufacturing.

Modulatory Effects of Bacillus subtilis on the Performance, Morphology, Cecal Microbiota and Gut Barrier Function of Laying Hens

We investigated the efficacy of a single bacterium strain, Bacillus subtilis (B. subtilis) YW1, on the performance, morphology, cecal microbiota, and intestinal barrier function of laying hens. A total of 216 28-week-old Hy-line Brown laying hens were divided into three dietary treatment groups, with six replicates of 12 birds each for 4 weeks. The control group (Ctr) was fed a basal diet and the treatment groups, T1 and T2, were fed a basal diet supplemented with B. subtilis at a dose rate of 5 × 108 CFU/kg and 2.5 × 109 CFU/kg, respectively. Dietary supplementation with B. subtilis did not significantly affect overall egg production in both groups, with no obvious changes in average egg weight and intestine morphology. B. subtilis administration also improved the physical barrier function of the intestine by inducing significantly greater expression levels of the tight junction protein occludin in T1 (p = 0.07) and T2 (p < 0.05). Further, supplementation with B. subtilis effectively modulated the cecal microbiota, increasing the relative level of beneficial bacteria at the genus level (e.g., Bifidobacterium p < 0.05, Lactobacillus p = 0.298, Bacillus p = 0.550) and decreasing the level of potential pathogens (e.g., Fusobacterium p < 0.05, Staphylococcus p < 0.05, Campylobacter p = 0.298). Overall, B. subtilis YW1 supplementation cannot significantly improve the egg production; however, it modulated the cecal microbiota towards a healthier pattern and promoted the mRNA expression of the tight junction protein occludin in laying hens, making B. subtilis YW1 a good probiotic candidate for application in the poultry industry, and further expanding the resources of strains of animal probiotics.

Antimicrobial and bacteriostatic activity of surfactants against B. subtilis for microbial cleaner formulation

Cleaning products containing live bacteria that form spores of Bacillus spp. as active substances are becoming increasingly common in probiotic cleaner formulation. The quality of cleaning performance for the production of probiotic cleaners does not only depend on the potential of the bacterial strains used, but also on the chemical components of the formulations. In this study, the surfactants and other additives were investigated as biocidal or bacteriostatic against B. subtilis, and the viability of B. subtilis was examined at different pH ranges for microbial cleaner formulation. As a result, it was discovered that the B. subtilis, which can be used in the microbial cleaner formulation, shows higher growth and viability at the neutral pH, and it passes into the death phase at pH 3. According to antagonistic activity results, the Gram-positive S. aureus and K. pneumoniae were the most sensitive bacteria while B. cereus was the most resistant bacteria. The anionic surfactants such as linear alkylbenzene sulfonic acid and sodium lauryl ether sulfate act as bacteriostatic on Bacillus spp. and do not cause cell death. In the view of these results, the usage of appropriate bacterial cultures and the correct stabilization of the formulations are also critical elements in the development of microbial cleaner formulations.

Comparison between 16S rRNA and shotgun sequencing data for the taxonomic characterization of the gut microbiota

In this paper we compared taxonomic results obtained by metataxonomics (16S rRNA gene sequencing) and metagenomics (whole shotgun metagenomic sequencing) to investigate their reliability for bacteria profiling, studying the chicken gut as a model system. The experimental conditions included two compartments of gastrointestinal tracts and two sampling times. We compared the relative abundance distributions obtained with the two sequencing strategies and then tested their capability to distinguish the experimental conditions. The results showed that 16S rRNA gene sequencing detects only part of the gut microbiota community revealed by shotgun sequencing. Specifically, when a sufficient number of reads is available, Shotgun sequencing has more power to identify less abundant taxa than 16S sequencing. Finally, we showed that the less abundant genera detected only by shotgun sequencing are biologically meaningful, being able to discriminate between the experimental conditions as much as the more abundant genera detected by both sequencing strategies.

Comparison of Different Invasive and Non-Invasive Methods to Characterize Intestinal Microbiota throughout a Production Cycle of Broiler Chickens

In the short life of broiler chickens, their intestinal microbiota undergoes many changes. To study underlying biological mechanisms and factors that influence the intestinal microbiota development, longitudinal data from flocks and individual birds is needed. However, post-mortem collection of samples hampers longitudinal data collection. In this study, invasively collected cecal and ileal content, cloacal swabs collected from the same bird, and boot sock samples and cecal droppings from the litter of the broilers' poultry house, were collected on days 0, 2, 7, 14 and 35 post-hatch. The different sample types were evaluated on their applicability and reliability to characterize the broiler intestinal microbiota. The microbiota of 247 samples was assessed by 16S ribosomal RNA gene amplicon sequencing. Analyses of α and β measures showed a similar development of microbiota composition of cecal droppings compared to cecal content. Furthermore, the composition of cecal content samples was comparable to that of the boot socks until day 14 post-hatch. This study shows that the value of non-invasive sample types varies at different ages and depends on the goal of the microbiota characterization. Specifically, cecal droppings and boot socks may be useful alternatives for cecal samples to determine intestinal microbiota composition longitudinally.