Antibiotic growth promoters virginiamycin and bacitracin methylene disalicylate alter the chicken intestinal metabolome

Bacitracin Methylene Disalicylate (BMD) Treatment Affects Spleen Proteome in Broiler Chicks Infected with Salmonella enteritidis

Bacitracin Methylene Disalicylate (BMD), as a feed additive to poultry diets, enhances digestion, prevents Salmonella enteritidis (SE) colonization, and treats current infections. The objective of this study was to utilize a quantitative proteomic approach to determine the effect of BMD feed additive on broiler chickens challenged with SE in the spleen proteome. At 1 d of age, chicks were randomly allocated into four groups: control with and without SE challenge (CON, n = 60; CON-SE, n = 60), BMD with and without SE challenge (BMD, n = 60; BMD-SE, n = 60). Birds in the CON-SE and BMD-SE treatment were administered SE inoculum by oral gavage. On day three and day seven post-gavage, the spleen was collected aseptically from birds in each treatment group (CON, n = 4/day; CON-SE, n = 4/day; BMD, n = 4/day; BMD-SE, n = 4/day). Proteomic analysis by liquid chromatography-tandem mass spectrometry (LC-MS/MS) showed an increased abundance of 115 proteins and decreased of 77 due to the BMD. Proteins that decreased in abundance were enriched for fibrinogen complex and extracellular space, whereas proteins that increased in abundance were enriched for proteasome-mediated ubiquitin-dependent protein catabolic process and mitochondrion. Analysis of the interaction between BMD and the Salmonella challenge found 230 differentially abundant proteins including proteins associated with RNA binding, spliceosome, protein transport, and cell adhesion among the upregulated proteins, and those associated with protein folding, carbon metabolism, biosynthesis of nucleotide sugars, response to oxidative stress, positive regulation of NIK/NF-kappaB signaling, and inflammatory response among the downregulated proteins. The impact of BMD treatment on spleen proteome indicates an anti-apoptotic effect. BMD also modified the response of the spleen to the SE challenge with a marked decrease in proteins that prompt cytokine synthesis and an increase in proteins involved in the selective removal of unfolded proteins.

Bacillus subtilis RBT-7/32 and Bacillus licheniformis RBT-11/17 as New Promising Strains for Use in Probiotic Feed Additives

The normal functioning of a gastrointestinal microflora in poultry and livestock is of significant importance, since its imbalance negatively influences an organism's functions. In this study, the UV mutagenesis and selection were used to obtain two Bacillus strains possessing antagonistic activity towards Escherichia coli and Staphylococcus aureus, and their potential as a probiotic feed additive was evaluated. Compared to the parental strains, the ability of B. subtilis RBT-7/32 and B. licheniformis RBT-11/17 strains to suppress E. coli increased by 77 and 63%, respectively; the corresponding ability of these strains to suppress S. aureus increased by 80 and 79%, respectively. RBT-11/17 could not utilize microcrystalline cellulose and carboxymethyl cellulose, whereas cellulolytic activity of RBT-7/32 was doubled compared to the initial strain. The amylolytic activity of new strains was increased by 40%. Cultivation of strains on media containing soybean, pea, and corn meal did not provide any difference in the biomass production compared to the control. The heating of a water suspension of a dried biomass of the strains for 10-20 min at 80 and 100 °C or incubation in water solutions of citric, ascorbic, acetic, and formic acids (pH 3.0) for 3 and 24 h at 40 °C did not provide any negative influence on the spore survivability. Both strains were evaluated for their resistance to a number of veterinary antibiotics. Thus, RBT-7/32 and RBT-11/17 strains have good prospects for use in feed additives.

Potency of Origanum vulgare and Andrographis paniculata extracts on growth performance in poultry

The objective of this study was to investigate the effect of phytobiotics combination of Origanum vulgare and Andrographis paniculata water extracts (FOA) mixed into the feed of broiler and specific-pathogen-free chickens as an alternative to Antibiotics Growth Promoter (AGP). Performance, intestinal bacteria characteristic, and oocysts of Eimeria spp. in feces were measured and compared with the AGP-added group. The first experiment in broiler chickens compared FOA, Zinc Bacitracin (ZB, as an AGP group), and negative control. On day 28, FOA group and ZB group showed significantly higher body weight than the control group (P < 0.05). The FCR of ZB group was better than FOA group. However, FOA group displayed better microbiota profile than ZB group and negative control, with more Lactobacillus spp. and Bacillus spp., and less Escherichia coli and Salmonella spp. isolated from intestines. The second experiment in specific-pathogen-free chickens showed the anticoccidial effect of FOA addition to reduce the number of oocysts per gram (OPG) from live coccidia vaccine. FOA group and Amprolium group showed OPG reduction (82.53% and 92.02%, respectively) after 7 days of treatment. In conclusion, the combination of Origanum vulgare and Andrographis paniculata extract can function as an AGP replacement in feed.

Effects of a synbiotic as an antibiotic alternative on behavior, production performance, cecal microbial ecology, and jejunal histomorphology of broiler chickens under heat stress

The aim of this study was to examine if synbiotics present similar efficiency to a common antibiotic used in poultry production under heat stress (HS) conditions. Two hundred and forty-one-day-old male Ross 708 broiler chicks were distributed among 3 treatments with 8 pens per treatment of 80 birds each for a 42-day trial. From day 15, birds were heat stressed (32°C for 9 h daily, HS) and fed the basal diet (CONT), the basal diet mixed with an antibiotic (Bactiracin Methylene Disalicylate) (0.05 g/kg of feed, BMD) or a synbiotic (0.5 g/kg of feed, SYN). The treatment effects on bird behavior, production performance, jejunal histomorphology, and cecal microbial ecology were examined. Behavioral observation was recorded by using instantaneous scan sampling technique. Production parameters were measured on day 14, 28, and 42. Cecal microbial populations of Escherichia coli and Lactobacilli and jejunal histomorphological parameters were measured at day 42. The results showed that, SYN birds exhibited more feeding and preening but less drinking and panting behaviors compared with both BMD and CONT birds (P < 0.05). The SYN birds also had higher body weight (BW) at both day 28 and 42 compared to CONT birds (P < 0.05). At the end of the experiment, the counts of Escherichia coli of SYN birds were at the similar levels of BMD but were lower than that of CONT birds (P < 0.05); while there were no treatment effects on the populations of Lactobacilli (P > 0.05). In addition, SYN birds had greater villus height compared with both CONT and BMD birds (P < 0.05). These findings suggest that the dietary synbiotic supplement has significant performance and welfare benefits, with the potential to be used as an alternative to antibiotics for poultry meat production, especially during hot seasons.

The immune-neuroendocrine system, a key aspect of poultry welfare and resilience

There is increasing societal concern regarding the negative impact of intensive poultry production on animal welfare, human health, and on the environment. This is leading to the inclusion of animal welfare as an imperative aspect for sustainable production. Certain environmental factors may challenge domesticated birds, resulting in poor health and welfare status. Resilience is the capacity to rapidly return to prechallenge status after coping with environmental stressors, thus resilient individuals have better chances to maintain good health and welfare. Immune-neuroendocrine system, thoroughly characterized in the domestic bird species, is the physiological scaffold for stress coping and health maintenance, influencing resilience and linking animal welfare status to these vital responses. Modern domestic bird lines have undergone specific genetic selective pressures for fast-growing, or high egg-production, leading to a diversity of birds that differ in their coping capacities and resilience. Deepening the knowledge on pro/anti-inflammatory milieus, humoral/cell-mediated immune responses, hormonal regulations, intestinal microbial communities and mediators that define particular immune and neuroendocrine configurations will shed light on coping strategies at the individual and population level. The understanding of the profiles leading to differential coping and resilience potential will be highly relevant for improving bird health and welfare in a wider range of challenging scenarios and, therefore, crucial to scientifically tackle long term sustainability.

Dietary Bacitracin Methylene Disalicylate Improves Growth Performance by Mediating the Gut Microbiota in Broilers

The growth performance of livestock and poultry has always been a concern. However, much work is currently focused on the selection of breeds and diets to improve the growth performance of livestock and poultry. Furthermore, numerous studies have shown that the gut microbiota is closely related to the growth performance of livestock and poultry. At present, there are many reports on the impact of antibiotic intervention on the structure of gut microbiota. However, there are few reports on the influence of antibiotic intervention on the structure of intestinal microbes and the effect of this change on growth performance. Bacitracin methylene disalicylate (BMD) intervention changes the microbial structure in the caecum of broilers at different growth stages, as shown in this study. To further reveal the potential relationship between gut microbiota changes and growth performance caused by BMD intervention, correlation analysis was used for analysis. A total of 144 1-day-old male Cobb-Vantress were randomly divided into two groups. In addition to antibiotic-free starter mash diets, starter mash diets supplemented with 55 mg/kg BMD were also used, called the CON group and the BMD group, and lasted 28 days. (1) These study results showed that adding BMD to the diet had a significant effect on the growth performance of broilers. Compared with the CON group, the body weight of the BMD group increased significantly by 11.08% and 20.13% on Days 14 and 28, respectively (p < 0.05). Similarly, at 0−14, 14−28 and 0−28 days of age, the average daily gain of the BMD group increased significantly by 12.28%, 24.49% and 20.80%, respectively. The average daily feed intake of the BMD group increased significantly by 18.28%, 27.39% and 24.97% (p < 0.05). In addition, at 0−28 days of age, the feed conversion ratio increased significantly by 5.5% (p < 0.05). (2) Alpha diversity results show that BMD intervention has an impact on gut microbiota at different growth stages. (3) The early intervention significantly affected 7 taxa by Day 14, followed by 22 taxa by Day 28, which is similar to the results in the caecal flora. Compared with the CON group, the Christensenellaceae R-7 group had the highest linear discriminant analysis (LDA) score on Day 28. In addition, Pearson’s correlation analysis showed that the Lachnospiraceae FCS020 group was significantly negatively correlated with growth performance. In general, these results indicate that dietary supplementation of BMD has an effect on broiler gut microbiota structure and growth performance. However, changes in growth performance may be caused by the gut microbiota structure.

Identification of Metabolomic Biomarkers of Long-Term Stress Using NMR Spectroscopy in a Diving Duck

Human-induced environmental changes that act as long-term stressors pose significant impacts on wildlife health. Energy required for maintenance or other functions may be re-routed towards coping with stressors, ultimately resulting in fluctuations in metabolite levels associated with energy metabolism. While metabolomics approaches are used increasingly to study environmental stressors, its use in studying stress in birds is in its infancy. We implanted captive lesser scaup (Aythya affinis) with either a biodegradable corticosterone (CORT) pellet to mimic the effects of a prolonged stressor or a placebo pellet. 1D ¹H nuclear magnetic resonance (NMR) spectroscopy was performed on serum samples collected over 20 days after implant surgery. We hypothesized that CORT pellet-induced physiological stress would alter energy metabolism and result in distinct metabolite profiles in ducks compared with placebo (control). Quantitative targeted metabolite analysis revealed that metabolites related to energy metabolism: glucose, formate, lactate, glutamine, 3-hydroxybutyrate, ethanolamine, indole-3- acetate, and threonine differentiated ducks with higher circulatory CORT from controls on day 2. These metabolites function as substrates or intermediates in metabolic pathways related to energy production affected by elevated serum CORT. The use of metabolomics shows promise as a novel tool to identify and characterize physiological responses to stressors in wild birds.

Current perspective on veterinary drug and chemical residues in food of animal origin

The marked increase in the demand for animal protein of high quality necessitates protecting animals from infectious diseases. This requires increasing the use of veterinary therapeutics. The overuse and misuse of veterinary products can cause a risk to human health either as short-term or long-term health problems. However, the biggest problem is the emergence of resistant strains of bacteria or parasites. This is in addition to economic losses due to the discarding of polluted milk or condemnation of affected carcasses. This paper discusses three key points: possible sources of drug and chemical residues, human health problems, and the possible method of control and prevention of veterinary drug residues in animal products.

Assessing the Impact of Flavophospholipol and Virginiamycin Supplementation on the Broiler Microbiota: a Prospective Controlled Intervention Study

The antibiotic growth promoters (AGPs) flavophospholipol and virginiamycin have been widely used for decades in food animal production. AGP activity is believed to be partly modulated by gut microbial composition although exact AGP-induced changes remain unclear. In a controlled intervention study, we studied the effect of flavophospholipol and virginiamycin on the broiler chicken ileal microbiota spanning from birth to 39 days. Using 16S rRNA gene profiling and prediction of metabolic activity, we show that both AGPs result in dynamic microbial shifts that potentially increase anti-inflammatory mechanisms and bioavailability of several essential nutrients by decreasing degradation (flavophospholipol) or increasing biosynthesis (virginiamycin). Further, virginiamycin-supplemented broilers showed increased colonization with potentially pathogenic bacteria, Clostridium perfringens, Campylobacter, and Escherichia/Shigella spp. Overall, we show that both AGPs induce microbial changes potentially beneficial for growth. However, the increase in (foodborne) pathogens shown here with virginiamycin use could impact not only broiler mortality but also human health. IMPORTANCE Antibiotic growth promoters (AGPs) are commonly used within poultry farming to increase muscle growth. Microbial composition in the gut is known to be influenced by AGP use although exact AGP-induced changes remain unclear. Utilizing 16S rRNA gene profiling, this study provides a first head-to-head comparison of the effect of the two most commonly used AGPs, flavophospholipol and virginiamycin, on the broiler chicken ileum microbiota over time. We found that supplementation with both AGPs altered ileal microbial composition, thereby increasing potential bioavailability of essential nutrients and weight gain. Flavophospholipol showed a slight benefit over virginiamycin as the latter resulted in more extensive microbial perturbations including increased colonization by enteropathogens, which could impact broiler mortality.

Biodiversity of Secondary Metabolites Compounds Isolated from Phylum Actinobacteria and Its Therapeutic Applications

The current review aims to summarise the biodiversity and biosynthesis of novel secondary metabolites compounds, of the phylum Actinobacteria and the diverse range of secondary metabolites produced that vary depending on its ecological environments they inhabit. Actinobacteria creates a wide range of bioactive substances that can be of great value to public health and the pharmaceutical industry. The literature analysis process for this review was conducted using the VOSviewer software tool to visualise the bibliometric networks of the most relevant databases from the Scopus database in the period between 2010 and 22 March 2021. Screening and exploring the available literature relating to the extreme environments and ecosystems that Actinobacteria inhabit aims to identify new strains of this major microorganism class, producing unique novel bioactive compounds. The knowledge gained from these studies is intended to encourage scientists in the natural product discovery field to identify and characterise novel strains containing various bioactive gene clusters with potential clinical applications. It is evident that Actinobacteria adapted to survive in extreme environments represent an important source of a wide range of bioactive compounds. Actinobacteria have a large number of secondary metabolite biosynthetic gene clusters. They can synthesise thousands of subordinate metabolites with different biological actions such as anti-bacterial, anti-parasitic, anti-fungal, anti-virus, anti-cancer and growth-promoting compounds. These are highly significant economically due to their potential applications in the food, nutrition and health industries and thus support our communities' well-being.

Overview of the Use of Probiotics in Poultry Production

Simple Summary

Probiotics are feed additives that have gained popularity in poultry production following the ban of antibiotic growth promoters (AGP). They are one of the more universal feed additives and can be easily combine with other additives. Probiotics, above all, have many advantages, including stimulation of the host microflora or immunomodulation. The statement “immunity comes from the intestines” has become more important in the poultry industry because probiotics have proven helpful in the fight against diseases of bacterial origin and against zoonoses. Positive effects on the organism have already been studied at the cellular level, where probiotics were responsible for changes in gene expression, leading to alleviation of heat stress. In addition to the health benefits, the utility value of the animals increases. The numerous advantages are overshadowed by a few drawbacks, which include the possibility of lowering semen quality in roosters and the diversity of production processes affecting the persistence of the probiotic. In addition to bird health, probiotics have improved the taste and quality of poultry products. Future prospects are promising as scientists are working to maximize the positive effects of probiotics by increasing the integrity of probiotics within the bird organism, taking into account, among others, bacterial metabolites.

Abstract

In recent years, probiotics have become more popular in the world of dietary supplements and feed additives within the poultry industry, acting as antibiotic substitutes. Above all, probiotics are universal feed additives that can be used in conjunction with other additives to promote improved performance and health. Their positive effects can be observed directly in the gastrointestinal tract and indirectly in immunomodulation of the poultry immune system. Nutritional effects seen in flocks given probiotics include increased laying and egg quality, increased daily increments, and improved feed conversion ratio (FCR). There has also been an improvement in the quality of meat. This suggests producers can improve production results through the use of probiotics. In addition to these production effects, bird immunity is improved by allowing the organism to better protect itself against pathogens and stress. The lack of accuracy in the formulation of non-European preparations needs to be further developed due to unknown interactions between probiotic bacteria strains as well as their metabolites. The versatility of probiotics and the fact that the bacteria used in their production are an integral part of animal digestive tracts make them a safe feed additives. Despite restrictions from the European Union, probiotics have potential to improve production and health within the poultry industry and beyond. The following article will review the use of probiotics in poultry production.

Molecular Characterization of Enterococcus Isolates From Different Sources in Estonia Reveals Potential Transmission of Resistance Genes Among Different Reservoirs

In this study, we aimed to characterize the population structure, drug resistance mechanisms, and virulence genes of Enterococcus isolates in Estonia. Sixty-one Enterococcus faecalis and 34 Enterococcus faecium isolates were collected between 2012 and 2014 across the country from various sites and sources, including farm animals and poultry (n = 53), humans (n = 12), environment (n = 24), and wild birds (n = 44). Clonal relationships of the strains were determined by whole-genome sequencing and analyzed by multi-locus sequence typing. We determined the presence of acquired antimicrobial resistance genes and 23S rRNA mutations, virulence genes, and also the plasmid or chromosomal origin of the genes using dedicated DNA sequence analysis tools available and/or homology search against an ad hoc compiled database of relevant sequences. Two E. faecalis isolates from human with vanB genes were highly resistant to vancomycin. Closely related E. faecalis strains were isolated from different host species. This indicates interspecies spread of strains and potential transfer of antibiotic resistance. Genomic context analysis of the resistance genes indicated frequent association with plasmids and mobile genetic elements. Resistance genes are often present in the identical genetic context in strains with diverse origins, suggesting the occurrence of transfer events.

Immunosecurity: immunomodulants enhance immune responses in chickens

The global population has increased with swift urbanization in developing countries, and it is likely to result in a high demand for animal-derived protein-rich foods. Animal farming has been constantly affected by various stressful conditions, which can be categorized into physical, environmental, nutritional, and biological factors. Such conditions could be exacerbated by banning on the use of antibiotics as a growth promoter together with a pandemic situation including, but not limited to, African swine fever, avian influenza, and foot-and-mouth disease. To alleviate these pervasive tension, various immunomodulants have been suggested as alternatives for antibiotics. Various studies have investigated how stressors (i.e., imbalanced nutrition, dysbiosis, and disease) could negatively affect nutritional physiology in chickens. Importantly, the immune system is critical for host protective activity against pathogens, but at the same time excessive immune responses negatively affect its productivity. Yet, comprehensive review articles addressing the impact of such stress factors on the immune system of chickens are scarce. In this review, we categorize these stressors and their effects on the immune system of chickens and attempt to provide immunomodulants which can be a solution to the aforementioned problems facing the chicken industry.

16S rRNA Sequencing Analysis of the Gut Microbiota in Broiler Chickens Prophylactically Administered with Antimicrobial Agents

In poultry production, gut microbiota (GM) plays a pivotal role and influences different host functions related to the efficiency of production performances. Antimicrobial (AM) use is one of the main factors affecting GM composition and functions. Although several studies have focused their attention on the role of AMs as growth promoters in the modulation of GM in broilers, the consequences of higher AM concentrations administered during prophylactic treatments need to be better elucidated. For this purpose, 16S rRNA gene sequencing was performed to evaluate the impact of different prophylactic AM protocols on the composition and diversity of the broiler GM. Diversity analysis has shown that AM treatment significantly affects alpha diversity in ileum and beta diversity in both ileum and caecum. In ileal samples, the Enterobacteriaceae family has been shown to be particularly affected by AM treatments. AMs have been demonstrated to affect GM composition in broiler. These findings indicate that withdrawal periods were not enough for the restoral of the original GM. Further studies are needed for a better elucidation of the negative effects caused by an altered GM in broilers.

Composting of chicken litter from commercial broiler farms reduces the abundance of viable enteric bacteria, Firmicutes, and selected antibiotic resistance genes

We examined the ability of composting to remove ARGs and enteric bacteria in litter obtained from broiler chickens fed with a diet supplemented with Bacitracin methylene disalicylate (BDM) (conventional chicken litter), or an antibiotic-free diet (raised without antibiotic (RWA) chicken litter). This was done by evaluating the litter before and after composting for the abundance of ten gene targets associated with antibiotic resistance or horizontal gene transfer, the composition of the bacterial communities, and the abundance of viable enteric bacteria. The abundance of gene targets was determined by qPCR and the microbial community composition of chicken litter determined by 16S rRNA gene amplicon sequencing. Enteric bacteria were enumerated by viable plate count. A majority of the gene targets were more abundant in conventional than in RWA litter. In both litter types, the absolute abundance of all of the target genes decreased after composting except sul1, intI1, incW and erm(F) that remained stable. Composting significantly reduced the abundance of enteric bacteria, including those carrying antibiotic resistance. The major difference in bacterial community composition between conventional and RWA litter was due to members affiliated to the genus Pseudomonas, which were 28% more abundant in conventional than in RWA litter. Composting favoured the presence of thermophilic bacteria, such as those affiliated with the genus Truepera, but decreased the abundance of those bacterial genera associated with cold-adapted species, such as Carnobacterium, Psychrobacter and Oceanisphaera. The present study shows that chicken litter from broilers fed with a diet supplemented with antibiotic has an increased abundance of some ARGs, even after composting. However, we can conclude that fertilization with composted litter represents a reduced risk of transmission of antibiotic resistance genes and enteric bacteria of poultry origin to soil and crops than will fertilization with raw litter.

A Role for the Microbiota in the Immune Phenotype Alteration Associated with the Induction of Disease Tolerance and Persistent Asymptomatic Infection of Salmonella in the Chicken

Previous studies have shown a tissue immune phenotype-altering event occurring on days 2 and 4 in the ceca post-Salmonella challenge. To evaluate the involvement of the cecal microbiota in the phenotype reprogramming, we hypothesized that the addition of subtherapeutic bacitracin (BMD) will affect the cecal microbiota. Therefore, the objective of this study was to determine if the antibiotic-mediated changes in the microbiota composition influenced the immune phenotype induced by Salmonella enteritidis infection of the chicken cecum. A total of 112 fertile eggs were obtained for each experiment, repeated for a total of three separate times. The ceca and cecal contents were collected on days 2 and 4 post-infection for mRNA expression TaqMan assay and 16S rRNA gene microbiota sequencing. The results demonstrate the effects of bacitracin on cecal composition and its interaction with Salmonella enteritidis in young chicks. There is a preliminary indication of phenotype change in the Salmonella-challenged group provided subtherapeutic BMD due to the shifting cecal microbiota and cecal immune response, indicating the addition of bacitracin during infection altered the cecal phenotype. These data demonstrate the potential involvement of the microbiota in reprogramming immune phenotype (disease resistance to disease tolerance) induced by Salmonella in the chicken cecum.

Broiler chickens and early life programming: Microbiome transplant-induced cecal community dynamics and phenotypic effects

The concept of successional trajectories describes how small differences in initial community composition can magnify through time and lead to significant differences in mature communities. For many animals, the types and sources of early-life exposures to microbes have been shown to have significant and long-lasting effects on the community structure and/or function of the microbiome. In modern commercial poultry production, chicks are reared as a single age cohort and do not directly encounter adult birds. This scenario is likely to initiate a trajectory of microbial community development that is significantly different than non-industrial settings where chicks are exposed to a much broader range of environmental and fecal inocula; however, the comparative effects of these two scenarios on microbiome development and function remain largely unknown. In this work, we performed serial transfers of cecal material through multiple generations of birds to first determine if serial transfers exploiting the ceca in vivo, rather than the external environment or artificial incubations, can produce a stable microbial community. Subsequently, we compared microbiome development between chicks receiving this passaged, i.e. host-selected, cecal material orally, versus an environmental inoculum, to test the hypothesis that the first exposure of newly hatched chicks to microbes determines early GI microbiome structure and may have longer-lasting effects on bird health and development. Cecal microbiome dynamics and bird weights were tracked for a two-week period, with half of the birds in each treatment group exposed to a pathogen challenge at 7 days of age. We report that: i) a relatively stable community was derived after a single passage of transplanted cecal material, ii) this cecal inoculum significantly but ephemerally altered community structure relative to the environmental inoculum and PBS controls, and iii) either microbiome transplant administered at day-of-hatch appeared to have some protective effects against pathogen challenge relative to uninoculated controls. Differentially abundant taxa identified across treatment types may inform future studies aimed at identifying strains associated with beneficial phenotypes.

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.

Impact of industrial production system parameters on chicken microbiomes: mechanisms to improve performance and reduce Campylobacter

BACKGROUND

The factors affecting host-pathogen ecology in terms of the microbiome remain poorly studied. Chickens are a key source of protein with gut health heavily dependent on the complex microbiome which has key roles in nutrient assimilation and vitamin and amino acid biosynthesis. The chicken gut microbiome may be influenced by extrinsic production system parameters such as Placement Birds/m2 (stocking density), feed type and additives. Such parameters, in addition to on-farm biosecurity may influence performance and also pathogenic bacterial numbers such as Campylobacter. In this study, three different production systems 'Normal' (N), 'Higher Welfare' (HW) and 'Omega-3 Higher Welfare' (O) were investigated in an industrial farm environment at day 7 and day 30 with a range of extrinsic parameters correlating performance with microbial dynamics and Campylobacter presence.

RESULTS

Our data identified production system N as significantly dissimilar from production systems HW and O when comparing the prevalence of genera. An increase in Placement Birds/m2 density led to a decrease in environmental pressure influencing the microbial community structure. Prevalence of genera, such as Eisenbergiella within HW and O, and likewise Alistipes within N were representative. These genera have roles directly relating to energy metabolism, amino acid, nucleotide and short chain fatty acid (SCFA) utilisation. Thus, an association exists between consistent and differentiating parameters of the production systems that affect feed utilisation, leading to competitive exclusion of genera based on competition for nutrients and other factors. Campylobacter was identified within specific production system and presence was linked with the increased diversity and increased environmental pressure on microbial community structure. Addition of Omega-3 though did alter prevalence of specific genera, in our analysis did not differentiate itself from HW production system. However, Omega-3 was linked with a positive impact on weight gain.

CONCLUSIONS

Overall, our results show that microbial communities in different industrial production systems are deterministic in elucidating the underlying biological confounders, and these recommendations are transferable to farm practices and diet manipulation leading to improved performance and better intervention strategies against Campylobacter within the food chain. Video Abstract.

Characterization and assessment of naturally mutant non-pathogenic O27 strain Escherichia coli and their potential use as poultry probiotics

Objective

The purpose of the current study was to evaluate the molecular characteristics of naturally mutant non-pathogenic O27 strain of Escherichia coli and its efficacy as probiotic in broilers and determine the best age at which it can be administered.

Materials and methods

A total of 24 virulence genes using 24 sets of primers were detected using the polymerase chain reaction technique. For probiotics experiments, 60 chicks (day 1 old) were divided into three groups, 20 per group, and reared for 4 weeks. The first group was considered as a negative control. The second group was treated orally with O27 strain at first day of life for three successive days and repeated at day 21. The third group was administered orally with O27 strain at day 10 old, and repeated at day 21 old.

Results

The data revealed that type 1 fimbrial adhesion, salmochelin siderophore receptor, and sigma factor-binding protein were detected in O27 strain, but temperature-sensitive hemagglutinin, hemolysin secretion gene, pyelonephritis-associated Pili gene, polysaccharide capsule synthesis gene, Shiga-toxin1 gene, Shiga-toxin2 gene, Brain microvascular endothelial cell invasion, E. coli attaching and effacing gene, heat-stable enterotoxin, heat-labile enterotoxin, east 1 toxin, colicin V, verotoxin type 2, necrotizing cytotoxic factor type 1, colonization factor antigen I, colonization factor antigen III, coli surface 2, coli surface 4, serine protease pic autransporter, vacuolating autotransporter toxin, and serine protease EspP precursor were not detected in O27 strain. Group 2 performance parameters were significantly better (p < 0.01) than groups 3 and 1. Hematological and biochemical parameters did not be influenced (p > 0.05) by the administration of O27 strain. Antibody titers of infectious bursal disease virus and Newcastle disease virus in groups 2 and 3 were improved as compared to group 1. Group 2 had significantly higher titers than group 3. Histopathologically, all groups showed normal histopathological pictures. However, jejunum in groups 2 and 3 showed more tall, intact, and densely packed microvilli and more crypt depth than the control group.

Conclusion

The O27 strain of E. coli is non-pathogenic bacteria. Its effects on growth performances and enhancement of immunity in broilers match with the same impact of probiotics, and these candidates will fit to be a good probiotic in the future. The results revealed that the effects of O27 strain at the day 1 old of life for three successive days and repeated at day 21 old are better for improving the performance and immunity of the birds. More research works about the characterized non-pathogenic E. coli strain O27 are required for field and commercial use.

Enhanced modulation of gut microbial dynamics affecting body weight in birds triggered by natural growth promoters administered in conventional feed

This study explored the effects of natural growth promoters (phytogenic feed additives and organic acids) on animal performance, carcass characteristics, blood parameters, gut microflora composition, and microbe–host interactions in broiler chickens over a 42-day feeding period. Two-hundred-fifty-day-old chicks were randomly assigned to one of five treatments: (i) control diets (CON); (ii) control diets + 40 g/tons antibiotic growth promoter (AB); (iii) control diets + 3 kg/tons organic acids (ORG); (iv) control diets + 3 kg/tons phytogenic feed additives (PHY); (v) control diets + 3 kg/tons organic acids + phytogenic feed additive combination (COM). A non-significant differences (p > 0.05) were observed in broiler performance among treatments at 21 days of age; however, a gradually increasing body weight gain and reduced feed conversion ratio were observed at 42 days in treatments versus control group. Biochemical indices were non-significant (p > 0.05) except for decreased cholesterol (p < 0.05) and increased A/G ratio (p < 0.05) recorded in the treatment groups. The addition of PHY and ORG improved total counts of Enterococcus spp. and Lactobacillus spp. (p < 0.05) as well as reduced caecal and ileal Campylobacter spp. and Escherichia coli (p < 0.05). Correlation analysis elucidated beneficial bacteria (Enterococcus spp. and Lactobacillus spp.) were positively and pathogenic bacteria (Campylobacter spp. and E. coli) were negatively correlated (p < 0.05) with host weight gain. The findings indicated that dietary supplementation of PHY and ORG sustained balanced gut microflora, which in turn improved body weight. This study broadens the significance of using PHY and ORG as safe alternatives to antibiotic growth promoters for achieving healthier and economical broiler production.

Study of the antibiotic residues in poultry meat in some of the EU countries and selection of the best compositions of lactic acid bacteria and essential oils against Salmonella enterica

In this study, the presence of antibiotics (ANB) residues was evaluated in poultry meat purchased from German and Lithuanian markets. In addition, the antimicrobial activity of 13 lactic acid bacteria (LAB) strains, 2 essential oils (EO) (Thymus vulgaris and Origanum vulgare L.), and their compositions were tested for the purpose of inhibiting antibiotic-resistant Salmonella spp. ANB residues were found in 3 out of the 20 analyzed poultry meat samples: sample no. 8 contained enrofloxacin (0.46 μg/kg), sample no. 14 contained both enrofloxacin and doxycycline (0.05 and 16.8 μg/kg, respectively), and sample no. 18 contained enrofloxacin (2.06 μg/kg). The maximum residue limits (MRLs) for the sum of enrofloxacin and ciprofloxacin and for doxycycline in the poultry muscle are 100 μg/kg. Finally, none of the tested poultry meat samples exceeded the suggested MRLs; however, the issue of ANB residues still requires monitoring of the poultry industry in Germany, Poland, and Lithuania, despite the currently established low ANB concentrations. These findings can be explained by the increased use of alternatives to ANB in the poultry industry. Our results showed that an effective alternative to ANB, which can help to reduce the occurrence of antibiotic-resistant salmonella, is a composition containing 1.0% of thyme EO and the following LAB strains: Lactobacillus plantrum LUHS122, Enteroccocus pseudoavium LUHS242, Lactobacillus casei LUHS210, Lactobacillus paracasei LUHS244, Lactobacillus plantarum LUHS135, Lactobacillus coryniformins LUHS71, and Lactobacillus uvarum LUHS245, which can be recommended for poultry industry as components of feed or for the treatment of surfaces, to control the contamination with Salmonella strains. However, it should be mentioned that most of the tested LAB strains were inhibited by thyme EO at the concentrations of 0.5 and 1.0%, except for LUHS122, LUHS210, and LUHS245. Finally, it can be noted that the agents responsible for the inhibitory effect on Salmonella are not the viable LAB strains but rather their metabolites, and further studies are needed to identify which metabolites are the most important.

Withdrawal of antibiotic growth promoters from broiler diets: performance indexes and economic impact

This study aimed to estimate the productive and economic impacts caused by the withdrawal of antibiotic growth promoters (AGP) from broilers diet. Indexed publications that compared diets with or without AGP (AGP+/AGP-) for broilers (from initial to final phase) were collected and the results of feed intake, weight gain, and feed conversion were compiled in a database. A meta-analysis was performed following sequential analyses: graphical approach (to observe biological data coherence), correlation (to identify related factors), and variance-covariance (to compare groups). The annual number of broiler slaughtered in Brazil, target weight gain and feed conversion for each phase, the variation in feed conversion, feed cost, and AGP costs were used to build a model to estimate the effects of the AGP withdrawal on feeding costs. The database comprised 174 scientific articles containing 183 experiments, totaling 121,643 broilers, most of which were Ross (52% of the studies). The most frequent AGP sources/forms in the database were Avilamycin (41% of the AGP+ treatments), Flavomycin (19%), Virginiamycin (16%), and Bacitracin (14%). Higher feed intake, weight gain, and lower feed conversion were attributed (P < 0.05) to AGP+ diets during Initial phase (1 to 21 D). In Final phase (22 to 42 D) no differences were observed in performance variables. Treatments AGP+ presented higher weight gain and better feed conversion in the Total period (1 to 42 D). The results of feed conversion were improved (P < 0.05) with Avilamycin and Flavomycin; Virginiamycin improved weight gain and feed conversion. In the Total period, the economic impact was $0.03 per animal and a total of $183,560,232 per year. It was concluded that broilers fed AGP+ diets have higher weight gain and better feed conversion than those fed AGP- diets, and withdrawing AGP increases production costs.

Microbiota and metabolome responses in the cecum and serum of broiler chickens fed with plant essential oils or virginiamycin

This study investigated the cecal microbiota and serum metabolite profile of chickens fed with plant essential oils (PEO) or virginiamycin (VIRG) using high-throughput 16S rRNA gene sequencing and untargeted metabolomics approach. The main aim of this work was to explore the biochemical mechanisms involved in the improved growth performance of antibiotics and their alternatives in animal production. The results showed that both PEO and VIRG treatment significantly increased the relative abundance of phyla Bacteroidetes and decreased the abundance of phyla Firmicutes and genus of Lactobacillus in cecal microbiota of chickens. Compared to the control group (CT group), the relative abundance of genus of Alistipes, unclassified Rikenellaceae, Roseburia, and Anaeroplasma was enriched in the PEO group; that of genus Bacteroides, Lachnospiraceae, and unclassified Enterobacteriaceae was enriched in the cecal microbiota of the VIRG group. Untargeted metabolomics analyses revealed that the PEO treatment modified 102 metabolites and 3 KEGG pathways (primary bile acid biosynthesis and phenylalanine metabolism) in the cecal microbiota, and 81 metabolites and relevant KEGG pathways (fructose and mannose metabolism, biosynthesis of unsaturated fatty acids, and linoleic acid.) in the serum of the chicken. Compared to the CT group, VIRG treatment group differed 217 metabolites and 10 KEGG pathways in cecal contents and 142 metabolites and 7 KEGG pathways in serum of chickens. Pearson’s correlation analysis showed that phyla Bacteroidetes and genus of Bacteroides, Alistipes, and unclassified Rikenellaceae (in the VIRG and PE group) were positively correlated with many lipid metabolites. However, phyla Firmicutes and genera Lactobacillus (higher in the CT group) were negatively correlated with the lipid and thymine metabolism, and positively correlated with hydroxyisocaproic acid, cytosine, and taurine. This study shows that dietary supplementation with PEO and VIRG altered the composition and metabolism profile of the cecal microbiota, modified the serum metabolism profile.

Dietary Supplementation With Magnolia Bark Extract Alters Chicken Intestinal Metabolite Levels

Magnolia bark extract administered as a dietary supplement to poultry confers a performance and health benefit, but the mechanisms are unknown. Here, a metabolomics approach was used to identify changes in intestinal metabolite levels in chickens fed an unsupplemented diet or a diet supplemented with magnolia bark extract. Total body weight gains of chickens fed magnolia bark-supplemented diets were increased 2% (from 861 to 878 g/chicken), compared with chickens fed an unsupplemented diet. Compared with unsupplemented controls, the levels of 278 intestinal biochemicals (metabolites) were altered (165 increased, 113 decreased) in chickens given the magnolia-supplemented diet. Data for biochemicals of intestinal contents of chickens fed the unsupplemented diet clustered on the left side of the PCA score plot, while those of the magnolia-supplemented diet were separated and clustered on the right side. The biochemicals included changes in the levels of amino acids, fatty acids, peptides, and nucleosides, which provided a distinctive biochemical signature unique to the magnolia-supplemented group, compared with the unsupplemented group. These results provide the foundation for future studies to identify naturally-produced biochemicals that might be used to improve poultry growth performance.

Molecular Detection of Multidrug Resistant Salmonella Species Isolated from Broiler Farm in Bangladesh

Multidrug resistant (MDR) Salmonella are a leading cause of foodborne diseases and serious human health concerns worldwide. In this study we detected MDR Salmonella in broiler chicken along with the resistance genes and class 1 integron gene intl1. A total of 100 samples were collected from broiler farms comprising 50 cloacal swabs, 35 litter and 15 feed samples. Overall prevalence of Salmonella was 35% with the highest detected in cloacal swabs. Among the Salmonella, 30 isolates were confirmed as S. enterica serovar Typhimurium using molecular methods of PCR. Disk diffusion susceptibility test revealed that all the Salmonella were classified as MDR with the highest resistance to tetracycline (97.14%), chloramphenicol (94.28%), ampicillin (82.85%) and streptomycin (77.14%). The most prevalent resistance genotypes were tetA (97.14%), floR (94.28%), bla_TEM-1 (82.85%) and aadA1 (77.14%). In addition, among the MDR Salmonella, 20% were positive for class 1 integron gene (intl1). As far as we know, this is the first study describing the molecular basis of antibiotic resistance in MDR Salmonella from broiler farms in Bangladesh. In addition to tetA, floR, bla_TEM-1, aadA1 and intl1 were also detected in the isolated MDR Salmonella. The detection of MDR Salmonella in broiler chicken carrying intl1 is of serious public health concern because of their zoonotic nature and possibilities to enter into the food chain.

Dietary Supplementation With Bacillus subtilis Direct-Fed Microbials Alters Chicken Intestinal Metabolite Levels

Direct-fed microbials (DFMs) are dietary supplements containing live microorganisms which confer a performance and health benefit to the host, but the mechanisms are unclear. Here, a metabolomics approach was used to identify changes in intestinal metabolite levels in chickens fed an unsupplemented diet or a diet supplemented with B. subtilis strain 1781 or strain 747. Body weight gains of chickens fed the B. subtilis-supplemented diets were increased up to 5.6% in the B. subtilis 1781 group and 7.6% in the B. subtilis 747 group compared with chickens fed the unsupplemented diet. Compared with unsupplemented controls, the levels of 83 metabolites were altered (p < 0.05) (25 increased, 58 decreased) in chickens given the B. subtilis 1781-supplemented diet, while 50 were altered (p < 0.05) (12 increased, 38 decreased) with the B. subtilis 747-supplemented diet. Twenty-two metabolites were altered (p < 0.05) (18 increased, 4 decreased) in the B. subtilis 1781 vs. B. subtilis 747 groups. A random forest analysis of the B. subtilis 1781 vs. control groups gave a predictive accuracy of 87.5%, while that of the B. subtilis 747 vs. control groups was 62.5%. A random forest analysis of the B. subtilis 1781 vs. B. subtilis 747 groups gave a predictive accuracy of 75.0%. Changes in the levels of these intestinal biochemicals provided a distinctive biochemical signature unique to each B. subtilis-supplemented group, and were characterized by alterations in the levels of dipeptides (alanylleucine, glutaminylleucine, phenylalanylalanine, valylglutamine), nucleosides (N1-methyladenosine, N6-methyladenosine, guanine, 2-deoxyguanosine), fatty acids (sebacate, valerylglycine, linoleoylcholine), and carbohydrates (fructose). These results provide the foundation for future studies to identify biochemicals that might be used to improve poultry growth performance in the absence of antibiotic growth promoters.

The Effect of Addition of Probiotic Bacteria (Bacillus Subtilis or Enterococcus faecium) or Phytobiotic Containing Cinnamon Oil to Drinking Water on the Health and Performance of Broiler Chickens

The aim of the study was to test whether the use of probiotic bacteria Bacillus subtilis or Enterococcus faecium or a phytobiotic containing cinnamon oil can improve the metabolic parameters, immune status, gut microbiota and histology, and growth performance of broiler chickens. The experiment was carried out on 560 one-day-old male Ross 308 broiler chickens raised until the age of 42 days. The broiler chickens were assigned to 4 experimental groups of 140 birds each (7 replications of 20 individuals each). The control group (Control) did not receive additives. A probiotic preparation containing live bacterial cultures of Enterococcus faecium (EF, in the amount of 0.25 g/l) or Bacillus subtilis (BS, 0.25 g/l) or a phytobiotic preparation containing cinnamon oil (OC, 0.25 ml/l) was administered to the broiler chickens with their drinking water throughout the rearing period. The most important results indicate that the use of BS and OC resulted in: a significant (P≤0.05) increase in the level of ferric reducing ability of plasma (FRAP), high-density cholesterol (HDL) and glutathione (GSH + GSSH) and a significant (P≤0.05) decrease in the level of malondialdehyde (MDA), lipid hydroperoxides (LOOH), total cholesterol (TC), triacylglycerols (TAG), nonesterified fatty acids (NEFA) and interleukin 6 (IL-6), a ratio of heterophils : leukocytes (H:L) and alkaline phosphatase (ALP) activity, alanine aminotransferase (ALT), acidic phosphatase (AC) and creatinine kinase (CK), relative to the C group. In the blood of broiler chickens from the OC treatment, aspartate aminotransferase (AST), lactate dehydrogenase activity and 3-hydroxy-butyrate dehydrogenase (HBDH) significantly (P≤0.05) decreased in relation to the C group, and in broiler chickens from EF and BS treatments there was an increase (P≤0.05) in haemoglobin (Hb) content. Compared with group C, in the broiler chickens’ nutritional content from EF, BS and OC treatments, the total number of coliforms and number of fungi significantly (P≤0.05) dropped and the number of aerobic bacteria increased (P≤0.05) in the length of the villus and the depth of the crypt. It has been found that Bacillus subtilis, Enterococcus faecium and phytobiotic containing cinnamon oil can improve the microbiological and histological appearance of broiler chicken intestine. The addition of probiotic bacteria Bacillus subtilis or phytobiotic containing cinnamon oil to drinking water is more preferable than Enterococcus faecium regarding stimulation of the immune system, blood redox status parameters, parameters of metabolic changes and the gut microbiome and morphometry.

The effects of dietary Bacillus subtilis supplementation, as an alternative to antibiotics, on growth performance, intestinal immunity, and epithelial barrier integrity in broiler chickens infected with Eimeria maxima

The objective of this study was to investigate the effects of dietary Bacillus subtilis supplementation on growth performance, jejunal lesion scores, oocyst shedding, and cytokine and tight junction protein expression in broiler chickens infected with Eimeria maxima. A total of 196 male day-old Ross 708 broilers were given a nonexperimental diet until 14 D of age. Then, all chickens were randomly assigned to one of seven dietary treatments: 2 basal diets (CON and NC); CON + virginiamycin (AB1); CON + bacitracin methylene disalicylate (BMD; AB2); CON + B. subtilis 1781 (PB1); CON + B. subtilis 747 (PB2); or CON + B. subtilis 1781 + 747 (PB3). At day 21, all chickens except those in the CON group were orally inoculated with E. maxima oocysts. At 7 D after E. maxima infection, the body weight gains of chickens fed PB2 and PB3 increased (P = 0.032) as much as those in chickens fed AB2. The body weight gain and feed efficiency of chickens fed PB2 were significantly increased (P < 0.001), and PB2 chickens showed (P = 0.005) the lowest lesion scores after E. maxima infection. Chickens fed PB2 showed (P < 0.05) lower mRNA expression of IL-1β in infected chicken groups. Chickens in the AB1, AB2, PB1, PB2, and PB3 groups showed (P < 0.05) greater mRNA expression of junctional adhesion molecule 2 in jejunal tissue, whereas occludin expression increased (P < 0.05) in the jejunal tissue of chickens fed AB2 or PB2. Dietary B. subtilis supplementation significantly improved the growth performance of young chickens to a level comparable with that induced by virginiamycin or BMD without E. maxima infection. After infection with E. maxima, dietary virginiamycin and BMD significantly enhanced the epithelial barrier integrity, and the dietary B. subtilis 747 showed significantly enhanced growth performance, intestinal immunity, and epithelial barrier integrity. Together our results indicated that certain strains of B. subtilis provide beneficial effects on the growth of young broiler chickens and have the potential to replace antibiotic growth promoters.

Dietary Antibiotic Growth Promoters Down-Regulate Intestinal Inflammatory Cytokine Expression in Chickens Challenged With LPS or Co-infected With Eimeria maxima and Clostridium perfringens

Subtherapeutic levels of dietary antibiotics increase growth performance in domestic animals, but the mechanisms are poorly understood. Here, 1-week-old broiler chickens were challenged with LPS (experiment 1), or co-infected with Eimeria maxima and Clostridium perfringens as an experimental model of necrotic enteritis (experiment 2), and fed a standard basal diet or a basal diet supplemented with virginiamycin or bacitracin methylene disalicylate. In experiment 1, LPS-challenged chickens fed the unsupplemented diet had decreased body weight gains, compared with unsupplemented controls given the PBS control. In contrast, antibiotic supplementation increased body weight gains in both the LPS-challenged and PBS groups, compared with the antibiotic-free diet. LPS-challenged chickens fed the unsupplemented diet had increased expression levels of intestinal tight junction proteins (ZO1, JAM2), MUC2 gel-forming mucin, and inflammatory cytokines (IL-1β, IL-2, IL-6, IL-8, IL-17A) at 24 h post-challenge, compared with unsupplemented chickens given the PBS control. However, LPS-challenged chickens fed the antibiotic-supplemented diets had decreased levels of intestinal inflammatory cytokine transcripts, compared with LPS-challenged chickens given the unsupplemented basal diet. In experiment 2, E. maxima/C. perfringens-co-infected chickens fed the antibiotic-supplemented diets had increased body weight gains, decreased intestinal pathology, and greater intestinal crypt depth, compared with co-infected chickens given the unsupplemented diet. Further, similar to LPS challenge, E. maxima/C. perfringens-co-infection of chickens fed the antibiotic-supplemented diets decreased expression levels of intestinal inflammatory cytokines, compared with co-infected chickens given the unsupplemented diet. These results support the hypothesis that dietary antibiotic growth promoters might increase poultry growth, in part, through down-regulation of pathogen-induced inflammatory responses.

Untargeted Metabolite Profiling for Screening Bioactive Compounds in Digestate of Manure under Anaerobic Digestion

Untargeted metabolite profiling was performed on chicken manure (CHM), swine manure (SM), cattle manure (CM), and their respective digestate by XCMS coupled with MetaboAnalyst programs. Through global chemical profiling, the chemical characteristics of different digestates and types of manure were displayed during the anaerobic digestion (AD) process. As the feed for AD, CM had less easily-degradable organics, SM contained the least O-alkyls and anomerics of carbohydrates, and CHM exhibited relatively lower bio-stability. The derived metabolite pathways of different manure during the AD process were identified by MetaboAnalyst. Twelve, 8, and 5 metabolic pathways were affected by the AD process in CHM, SM, and CM, respectively. Furthermore, bioactive compounds of digestate were detected, such as amino acids (L-arginine, L-ornithine, L-cysteine, and L-aspartate), hormones (L-adrenaline, 19-hydroxy androstenedione, and estrone), alkaloids (tryptamine and N-methyltyramine), and vitamin B5, in different types of manure and their digestates. The combination of XCMS and MetaboAnalyst programs can be an effective strategy for metabolite profiling of manure and its anaerobic digestate under different situations.

The Microbial Pecking Order: Utilization of Intestinal Microbiota for Poultry Health

The loss of antibiotics as a tool to improve feed efficiency in poultry production has increased the urgency to understand how the microbiota interacts with animals to impact productivity and health. Modulating and harnessing microbiota-host interactions is a promising way to promote poultry health and production efficiencies without antibiotics. In poultry, the microbiome is influenced by many host and external factors including host species, age, gut compartment, diet, and environmental exposure to microbes. Because so many factors contribute to the microbiota composition, specific knowledge is needed to predict how the microbiome will respond to interventions. The effects of antibiotics on microbiomes have been well documented, with different classes of antibiotics having distinctive, specific outcomes on bacterial functions and membership. Non-antibiotic interventions, such as probiotics and prebiotics, target specific bacterial taxa or function to enhance beneficial properties of microbes in the gut. Beneficial bacteria provide a benefit by displacing pathogens and/or producing metabolites (e.g., short chain fatty acids or tryptophan metabolites) that promote poultry health by improving mucosal barrier function or immune function. Microbiota modulation has been used as a tool to reduce pathogen carriage, improve growth, and modulate the immune system. An increased understanding of how the microbiota interacts with animal hosts will improve microbiome intervention strategies to mitigate production losses without the need for antibiotics.

Microbiota, Gut Health and Chicken Productivity: What Is the Connection?

Gut microbiota and its relationship to animal health and productivity in commercial broiler chickens has been difficult to establish due to high variability between flocks, which derives from plenty of environmental, nutritional, and host factors that influence the load of commensal and pathogenic microbes surrounding birds during their growth cycle in the farms. Chicken gut microbiota plays a key role in the maintenance of intestinal health through its ability to modulate host physiological functions required to maintain intestinal homeostasis, mainly through competitive exclusion of detrimental microorganisms and pathogens, preventing colonization and therefore decreasing the expense of energy that birds normally invest in keeping the immune system active against these pathogens. Therefore, a “healthy” intestinal microbiota implies energy saving for the host which translates into an improvement in productive performance of the birds. This review compiles information about the main factors that shape the process of gut microbiota acquisition and maturation, their interactions with chicken immune homeostasis, and the outcome of these interactions on intestinal health and productivity.

In-feed bacitracin methylene disalicylate modulates the turkey microbiota and metabolome in a dose-dependent manner

Beginning in 2017, the subtherapeutic use of most antibiotic compounds for growth promotion in food producing animals in the US was prohibited, highlighting the need to discover alternative growth promotants. Identifying the mechanism of action of growth promoting antibiotics may aid in the discovery of antibiotic alternatives. We describe the effects of feeding a subtherapeutic (50 g/ton of feed) and therapeutic (200 g/ton) concentration of bacitracin methylene disalicylate (BMD) to commercial turkeys for 14 weeks, and its effect on turkey intestinal microbial communities and cecal metabolomes. Both BMD concentrations had an immediate and lasting impact on the microbiota structure, and reduced bacterial richness through the end of the study (12 weeks). Metabolomic analysis identified 712 biochemicals, and 69% of metabolites were differentially present in BMD treated turkeys for at least one time point (q < 0.1). Amino acids, carbohydrates, nucleotides, peptides, and lipids were decreased in the turkey ceca early after BMD administration. Long-term metabolome alterations continued even after withdrawal of BMD. The microbial composition, determined by 16S rRNA gene sequencing, was predictive of the metabolome, indicating a connection between the microbiome and metabolome. In-feed BMD may cause bacterial metabolic shifts, leading to beneficial traits that can be targeted to improve animal health and production.

Egg Production in Poultry Farming Is Improved by Probiotic Bacteria

Antimicrobial resistance (AMR) is one of the most serious threats for human health in the near future. Livestock has played an important role in the appearance of antibiotic-resistant bacteria, intestinal dysbiosis in farming animals, or the spread of AMR among pathogenic bacteria of human concern. The development of alternatives like probiotics is focused on maintaining or improving production levels while diminishing these negative effects of antibiotics. To this end, we supplied the potential probiotic Enterococcus faecalis UGRA10 in the diet of laying hens at a final concentration of 10⁸ Colony Forming Units per gram (CFU/g) of fodder. Its effects have been analyzed by: (i) investigating the response of the ileum and caecum microbiome; and (ii) analyzing the outcome on eggs production. During the second half of the experimental period (40 to 76 days), hens fed E. faecalis UGRA10 maintained egg production, while control animals dropped egg production. Supplementation diet with E. faecalis UGRA10 significantly increased ileum and caecum bacterial diversity (higher bacterial operational taxonomic unit richness and Faith’s diversity index) of laying hens, with animals fed the same diet showing a higher similarity in microbial composition. These results point out to the beneficial effects of E. faecalis UGRA10 in egg production. Future experiments are necessary to unveil the underlying mechanisms that mediate the positive response of animals to this treatment.

Benefits of probiotics and/or prebiotics for antibiotic-reduced poultry

Antibiotics have been used for many years as growth promoters. They contribute to build the immunocompetence (i.e. ability of the body to produce a normal immune response following exposure to an antigen) of birds against infectious diseases and as growth promoters. Antibiotics have been widely used as growth promoters in the field of animal production since 1940s. There is a hypothesis that is effect is brought about by dynamic biological interaction with the micro-flora in the intestine. In 1951, the United States Food and Drug Administration approved the use of antibiotics as animal additives to prevent disease in general and, in some cases, to improve efficiency without veterinary prescription. In the 1950s and 1960s, each European state approved its own national regulations about the use of antibiotics in animal feeds. However, using antibiotics may develop bacteria resistant to these drugs. Accordingly, the use of antibiotics has been minimized and replaced by effective dietary supplements such as probiotics and/or prebiotics that are claimed to enhance growth and positively modulate the immune response. The current review paper sheds light on the benefits of using probiotics and/or prebiotics in poultry feed versus the risk of using antibiotics and the mechanisms by which they exert their effects, as well as the economic analysis of using these beneficial additives in poultry feed.