Intestinal microbiome of poultry and its interaction with host and diet

Effects of bacitracin methylene disalicylate and diet change on gastrointestinal integrity and endotoxin permeability in the duodenum of broiler chicken

Objective

To determine the effect of bacitracin methylene disalicylate (BMD) and feed changes on gastrointestinal integrity, endotoxin permeability, and morphometric parameters in the duodenum of broilers.

Results

Birds were raised on a starter diet without growth promoting antibiotics for 31 days then switched to a grower diet. Four of the pens including 50 g/ton of BMD while 4 pens remained antibiotic free. Eight birds per treatment were sampled prior to the feed change and at 3 and 7 days following the feed change. Gastrointestinal integrity and endotoxin permeability in the duodenum were determined using a modified Ussing Chamber and an adjacent section fixed in 10% formalin for morphometric analysis. Data were analyzed using Proc Glimmix of SAS with the model fitting BMD treatment, time, and the interaction of BMD treatment and time as fixed effects. Intestinal integrity increased at d 3 and 7 compared to prior to the feed change and addition of BMD (P > 0.001) and villus height was decreased with BMD supplementation (P = 0.049). All other tested effects similar (P > 0.1). In conclusion, the practice of changing feed had a greater effect on intestinal health than addition of BMD. However, the factors driving these differences 42 are unclear.

Electronic supplementary material

The online version of this article (doi:10.1186/s13104-017-2781-8) contains supplementary material, which is available to authorized users.

Beneficial microbial signals from alternative feed ingredients: a way to improve sustainability of broiler production?

More sustainable broiler meat production can be facilitated by the increased use of cheap by‐products and local crops as feed ingredients, while not affecting animal performance and intestinal health, or even improving intestinal health, so that antibiotic usage is further reduced. To achieve this, knowledge of the relationship between the taxonomic and functional microbiota composition and intestinal health is required. In addition, the relationship between the novel feed sources, the substrates present in these feed sources, and the breakdown by enzymes and microbial networks can be crucial, because this can form the basis for development of tailored feed‐type specific solutions for optimal digestion and animal performance.

In vitro characteristics of Lactobacillus spp. strains isolated from the chicken digestive tract and their role in the inhibition of Campylobacter colonization

Campylobacter jejuni/coli infections are the leading cause of bacterial diarrheal illnesses in humans. Many epidemiological studies indicate that improperly prepared meat from chickens that carry a high load of Campylobacter in their intestinal tracts is the key source of human infections. LAB, mainly members of the Lactococcus and Lactobacillus genera, increasingly have been tested as vehicles for the delivery of heterologous bacterial or viral antigens to animal mucosal immune systems. Thus, the objective of this study was to isolate, identify, and characterize Lactobacillus spp. strains isolated from chickens bred in Poland. Their ability to decrease the level of bird gut colonization by C. jejuni strain was also analyzed. First, the influence of the different chicken rearing systems was evaluated, especially the effect of diets on the Lactobacillus species that colonize the gut of chickens. Next, selected strains were analyzed in terms of their anti‐Campylobacter activity in vitro; potential probiotic traits such as adhesion properties, bile and low pH tolerance; and their ability to grow on a defined carbon source. Given that improperly prepared chicken meat is the main source of human infection by Campylobacter, the selected strains were also assessed for their ability to inhibit Campylobacter colonization in the bird's intestine. These experiments revealed enormous physiological diversity among the Lactobacillus genus strains. Altogether, our results showed that L. plantarum strains isolated from the digestive tracts of chickens bred in Poland displayed some probiotic attributes in vitro and were able to decrease the level of bird gut colonization by C. jejuni strain. This suggests that they can be employed as vectors to deliver Campylobacter immunodominant proteins to the bird's immune system to strengthen the efficacy of in ovo vaccination.

Age-Related Variations in Intestinal Microflora of Free-Range and Caged Hens

Free range feeding pattern puts the chicken in a mixture of growth materials and enteric bacteria excreted by nature, while it is typically unique condition materials and enteric bacteria in commercial caged hens production. Thus, the gastrointestinal microflora in two feeding patterns could be various. However, it remains poorly understood how feeding patterns affect development and composition of layer hens’ intestinal microflora. In this study, the effect of feeding patterns on the bacteria community in layer hens’ gut was investigated using free range and caged feeding form. Samples of whole small intestines and cecal digesta were collected from young hens (8-weeks) and mature laying hens (30-weeks). Based on analysis using polymerase chain reaction-denaturing gradient gel electrophoresis and sequencing of bacterial 16S rDNA gene amplicons, the microflora of all intestinal contents were affected by both feeding patterns and age of hens. Firmicutes, Bacteroidetes, Actinobacteria, Proteobacteria, and Fusobacteria were the main components. Additionally, uncultured environmental samples were found too. There were large differences between young hens and adult laying hens, the latter had more Firmicutes and Bacteroidetes, and bacterial community is more abundant in 30-weeks laying hens of all six phyla than 8-weeks young hens of only two phyla. In addition, the differences were also observed between free range and caged hens. Free range hens had richer Actinobacteria, Bacteroidetes, and Proteobacteria. Most of strains found were detected more abundant in small intestines than in cecum. Also the selected Lactic acid bacteria from hens gut were applied in feed and they had beneficial effects on growth performance and jejunal villus growth of young broilers. This study suggested that feeding patterns have an importance effect on the microflora composition of hens, which may impact the host nutritional status and intestinal health.

Performance, gut morphology and microbiology effects of a Bacillus probiotic, avilamycin and their combination in mixed grain broiler diets

1. This study aimed to determine the effect of avilamycin (AGP) and a multi-strain Bacillus probiotic (DFM) on the performance, gut histology and microbiology of broilers fed on a mixed grain diet. 2. A total of 800 chicks were allocated to four treatments: a control diet, control+AGP, control+DFM, or control+AGP+DFM. Bodyweight, feed intake and FCR were measured at d 0, 21 and 42. Samples were taken at d42 to determine villus height (VH), crypt depth (CD) and ratio (VH:CD). Mucosal E. coli and Lactobacilli counts were measured at d42. 3. At d42, DFM and AGP+DFM significantly increased weight over the control, with AGP returning an intermediate value. FCR followed a similar pattern. DFM and AGP+DFM significantly increased VH and CD in all gut sections compared to the control. 4. DFM and AGP+DFM reduced E. coli counts compared to control, with AGP reducing caecal counts only, while Lactobacilli counts were increased. 5. Divergent histology and microbiology between treatments highlight the different modes of action of AGP and DFM for improving broiler growth and feed efficiency.

Zinc Oxide Nanoparticles Influence Microflora in Ileal Digesta and Correlate Well with Blood Metabolites

Zinc oxide nanoparticles (ZnO NPs) are used widely in consumer and industrial products, however, their influence on gut microbiota and metabolism and their mutual interactions are not fully understood. In this study, the effects of ZnO NPs on ileal bacterial communities, plasma metabolites, and correlations between them were investigated. Hens were fed with different concentrations of ZnO NPs [based on Zn; 0 mg/kg (control), 25 mg/kg, 50 mg/kg, and 100 mg/kg] for 9 weeks. Subsequently, ileal digesta and blood plasma were collected for analysis of microflora and metabolites, respectively. The V3-V4 region of the 16S rRNA gene of ileal digesta microbiota was sequenced using the Illumina HiSeq 2500 platform. The predominant bacterial community in the ileum belongs to the phylum Firmicutes. The richness of the bacterial community was negatively correlated with increasing amounts of ZnO NPs (r = -0.636, P < 0.01); when ZnO NP levels were at 100 mg/kg, microbiota diversity was significantly decreased (P < 0.05). The community structure determined by LEfSe analysis indicated that Bacilli, Fusobacteria, and Proteobacteria were changed, and Lactobacillus was reduced by ZnO NPs. Moreover, metabolism as analyzed by nuclear magnetic resonance (NMR) indicated that glucose, some amino acids, and other metabolites were changed by ZnO NPs. Choline, lactate, and methionine were positively correlated with bacterial richness. In summary, ZnO NPs could influence the levels of microflora in ileal digesta, particularly Lactobacillus. Furthermore, the richness of the microbiota was related to changes in choline, lactate, and methionine metabolism.

The effect of Boswellia serrata resin diet supplementation on production, hematological, biochemical and immunological parameters in broiler chickens

Boswellia serrata resin (BSR), exhibiting a variety of therapeutic properties, is applied in Asian traditional medicine. These properties can be used in poultry production as well. Application of the resin as a phytobiotic in broiler chicken rearing can increase the productivity and improve meat quality. However, the optimum and maximum levels of BSR in broiler diets need to be assessed. The study determined the effect of different levels of supplementation of BSR (directly derived, unprocessed) in diets for broiler chickens on the production traits, selected slaughter analysis parameters, nutrient digestibility and selected hematological, biochemical and immunological parameters. In total, 200 1-day-old broiler chickens were assigned randomly to four treatments with five replicate cages of 10 broiler chickens/cage (five females and five males). The experiment lasted 6 weeks, and the broiler chickens were fed diets containing 0% (control), 3% (BSR3), 4% (BSR4) or 5% (BSR5). In the broiler chickens receiving diets with addition of resin BSR3 and BSR4, there was an increase in (P<0.05) BW gain, ether extract, ADF, organic matter and energy digestibility of the diets. Moreover, the best carcass quality with a high proportion of muscles and low abdominal fat content (P<0.05) was noted in these groups. The content of uric acid (P<0.01) and the activity of aspartate aminotransferase (P<0.001) and alkaline phosphatase (P<0.05) in blood plasma decreased upon the BSR supplementation. Globulin content increased in blood plasma (P<0.05) along the increasing level of BSR. The blood immunoglobulin A concentration was only affected by the BSR treatments (P<0.05). It may be concluded that BSR can be regarded as a safe and effective dietary additive for broiler chicken.

Multicausal etiology of the enteric syndrome in rabbits from Mexico

Enteropathies in rabbits are difficult to diagnose; their etiology involves pathogens that act synergistically, causing damage to the intestine. The aim of the present study was isolate enteric pathogens from rabbits in Mexico. Using parasitological, bacteriological and molecular analyses, we screened 58 samples of the intestinal content of rabbits having a clinical history of enteric disease from the southeastern part of the State of Mexico. Out of the 58 samples analyzed, a total of 86 identifications were made, Eimeria spp. were found in 77.5%, followed by Aeromonas spp. in 15.5% and Escherichia coli in 8.6%, which were identified as enteropathogenic E. coli (EPEC), and the presence of the following agents was also confirmed: Salmonella spp., Klebsiella spp., Streptococcus spp., Staphylococcus aureus, Enterococcus spp., Mannheimia spp. and Rotavirus. The concurrent presence of Eimeria spp. with Aeromonas was frequent (15.5%); there was statistical significance for the presence of an association between the clinical profiles and Eimeria spp. (p=0.000), Mannheimia spp. (p=0.001), Salmonella spp., Klebsiella spp., Streptococcus spp. and Enterococcus spp. (p=0.006).

Synbiotics for Broiler Chickens-In Vitro Design and Evaluation of the Influence on Host and Selected Microbiota Populations following In Ovo Delivery

Synbiotics are synergistic combinations of prebiotics and probiotics. In chickens, synbiotics can be delivered in ovo to expedite colonization of the gut by beneficial bacteria. We therefore aimed to design synbiotics in vitro and validate them in broiler chickens upon in ovo delivery. The probiotic components of the synbiotics were Lactobacillus salivarius and Lactobacillus plantarum. Their growth was assessed in MRS medium supplemented with different prebiotics. Based on in vitro results (hatchability and growth curve), two synbiotics were designed: S1 –Lactobacillus salivarius with galactooligosaccarides (GOS) and S2 –Lactobacillus plantarum with raffinose family oligosaccharides (RFO). These synbiotics were delivered to Cobb broiler chicken embryos on day 12 of incubation at optimized doses (10⁵ cfu egg^-1 of probiotic, 2 mg egg^-1 of prebiotic). Post hatching, 2,400 roosters were reared (600 individuals group^-1 divided into eight replicate pens). Microbial communities were analyzed in ileal and cecal digesta on day 21 using FISH. Gene expression analysis (IL1β, IL4, IL6, IL8, IL12, IL18, IFNβ, and IFNγ) was performed on days 7, 14, 21, and 42 for the spleen and cecal tonsils with RT-qPCR. Body weight and feed intake of the roosters did not differ by the treatments. Microbial populations of Lactobacillus spp. and Enterococcus spp. in the ileum were higher in S1 and S2 than in the control. In the cecum, the control had the highest bacterial counts. S1 caused significant up-regulation of IL6, IL18, IL1β, IFNγ, and IFNβ in the spleen on day 21 and IL1β on day 7 (P < 0.05). In cecal tonsils, S1 caused significant down-regulation of IL12, IL8, and IL1β on day 42 and IFNβ on day 14 (P < 0.05). S2 did not elicit such patterns in any tissues investigated. Thus, we demonstrate that divergent effects of synbiotics in broiler chickens were reflected in in vitro tests.

Managing gut health without reliance on antimicrobials in poultry

It is well established that antimicrobials in animal feed enhance feed efficiency, promote animal growth and improve the quality of animal products. However, resistance development in bacterial populations, and hence consumer demand for products free of antimicrobial residues, has prompted efforts to develop alternatives that can replace antimicrobials without causing loss of productivity or product quality. One of the key barriers to complete withdrawal from antimicrobial use is microbial infection, for example, necrotic enteritis. There is much interest in using in-feed nutraceuticals such as prebiotics, probiotics, organic acids and plant extracts as alternatives to antimicrobials to create a healthy gastrointestinal environment and to prevent and treat enteric infections. Enzymes are generally used to alleviate anti-nutritional factors in feed, but there is growing awareness of their beneficial effects on the gastrointestinal environment, and consequently on gut health. An example of this is production of prebiotic xylo-oligosaccharides when xylanase is added to feed. This review discusses developments in alternatives to antimicrobials that can aid in managing gut health in a post-antimicrobial era, with particular reference to recent nutritional strategies.

An update on direct-fed microbials in broiler chickens in post-antibiotic era

In a post-antibiotic era, applying dietary alternatives to antibiotics into diets of chickens has become a common practice to improve the productivity and health status of chickens. It is generally accepted that direct-fed microbials (DFMs), defined as a source of viable, naturally occurring microorganisms, as an alternative to antibiotics, have a long history for their safe use and health benefit and are generally regarded for therapeutic, prophylactic and growth-promotion uses in poultry industry. It has been suggested that two primary modes of action by DFMs are balancing gut microbiota and modulating host immunity. Recent findings have suggested that gut microbiota plays an important role in developing immune system and maintaining the homeostasis of mature immune system in mammals and chickens. With the help of molecular and bioinformatics tools, it is now scientifically proven that gut microbiota is diverse, dynamic, and varies according to age, breed, diet composition, environment and feed additives. Broiler chickens are commonly raised on the floor with bedding materials, which facilitates the acquisition of microorganisms present in the bedding materials. Thus, it is expected that environmental factors, including the type of litter, influence host immunity in a positive or negative way. In this regard, adding DFMs into diets of chickens will affect host–microbe interaction, shaping host immunity towards increasing resistance of chickens to enteric diseases.

Comprehensive Molecular Characterization of Bacterial Communities in Feces of Pet Birds Using 16S Marker Sequencing

Birds and other animals live and evolve in close contact with millions of microorganisms (microbiota). While the avian microbiota has been well characterized in domestic poultry, the microbiota of other bird species has been less investigated. The aim of this study was to describe the fecal bacterial communities of pet birds. Pooled fecal samples from 22 flocks representing over 150 individual birds of three different species (Melopsittacus undulatus or budgerigars, Nymphicus hollandicus or cockatiels, and Serinus canaria or domestic canaries) were used for analysis using the 16S rRNA gene sequencing in the MiSeq platform (Illumina). Firmicutes was the most abundant phylum (median 88.4 %; range 12.9-98.4 %) followed by other low-abundant phyla such as Proteobacteria (median 2.3 %; 0.1-85.3 %) and Actinobacteria (median 1.7 %; 0-18.3 %). Lactobacillaceae (mostly Lactobacillus spp.) was the most abundant family (median 78.1 %; 1.4-97.5 %), especially in budgerigars and canaries, and it deserves attention because of the ascribed beneficial properties of lactic acid bacteria. Importantly, feces from birds contain intestinal, urinary, and reproductive-associated microbiota thus posing a serious problem to study one anatomical region at a time. Other groups of interest include the family Clostridiaceae that showed very low abundance (overall median <0.1 %) with the exception of two samples from cockatiels (14 and 45.9 %) and one sample from budgerigars (19.9 %). Analysis of UniFrac metrics showed that overall, the microbial communities from the 22 flocks tended to cluster together for each bird species, meaning each species shed distinctive bacterial communities in feces. This descriptive analysis provides insight into the fecal microbiota of pet birds.

The Bacteriomes of Ileal Mucosa and Cecal Content of Broiler Chickens and Turkeys as Revealed by Metagenomic Analysis

The gastrointestinal (GI) bacteriome of poultry is important in host nutrition and health, but its diversity and composition remain poorly characterized. In this study we phylogenetically characterized the bacteriome in the cecal contents and ileal mucosa of chickens and turkeys using metagenomics empowered by pyrosequencing technique. >95% coverage of bacterial diversity was achieved except for the turkey ileal mucosa. Collectively, 3,401 and 125 operational taxonomy units (OTU, defined at a 0.03 phylogenetic distance) in chicken, and 1,687 and 16 OTUs in turkey were identified from the cecal content and the ileal mucosa, respectively. Besides those previously reported, 39 and 50 additional genera of bacteria were identified in the chicken and turkey cecal bacteriome, respectively. Although the GI bacteriomes of the same region in both species exhibited greater similarity than the bacteriomes of different regions within each species, broiler chickens and turkeys harbor a distinct intestinal bacteriome. Such difference may suggest different dietary interventions for bacteriome modulation for enhanced nutrient utilization and gut health. The results may also be useful in developing prebiotics, probiotics, and analytical tools (e.g., phylochips). We also determined the variation in the number of OTUs and variability between two independent pyrosequencing runs and two data processing pipelines.

Long-Term Transcriptomic Effects of Prebiotics and Synbiotics Delivered In Ovo in Broiler Chickens

In ovo delivery of prebiotics and synbiotics in chickens allows for the development of intestinal microflora prior to hatching, which boosts their robustness. The goal of this study was to determine the transcriptomic profile of the spleen (S), cecal tonsils (CT), and large intestine (LI) of adult chickens injected with prebiotics and synbiotics in ovo. On day 12 of embryo development, incubating eggs were injected with prebiotics: inulin alone (P1) or in combination with Lactococcus lactis subsp. lactis IBB2955 (S1), galactooligosaccharides (GOS) alone (P2) or in combination with Lactococcus lactis subsp. cremoris IBB477 (S2); control group (C) was mock injected with physiological saline. Gene expression analysis was conducted using an Affymetrix Chicken Gene 1.1 ST Array Strip. Most of the differentially expressed genes (DEG) were detected in the cecal tonsils of P2 (378 DEG), and were assigned to gene ontology categories: lymphocyte proliferation, activation and differentiation, and cytokine production. Ingenuity pathway analysis of the DEG (CT of P2) indicated the inhibition of humoral and cellular immune responses, e.g., role of NFAT in regulation of immune responses, phagocytosis, production of nitric oxide, NF-κB, IL-8, and CXCR4 signaling. The DEG with the highest up-regulation from S1 and P2 were involved in gene expression (PAPOLA, RPL27A, RPLP1, and RPS29) from P1 and P2 in transport (BEST4, SLC9A3, and SLC13A2), metabolism (OGT, ALPP, CA4, and CA7), signaling (FGG, G3BP2, UBB, G3BP2, CACNA1G, and ATP6V0A4), and immune responses (MSMB, LGALS3, CABIN1, CXCR5, PAX5, and TNFRSF14). Two DEG influencing the complement system (SERPING1 and MIR1674) were down-regulated in P2 and S1. In conclusion, GOS injected in ovo provided the most potent stimulation of the host transcriptome. This is likely due to its strong bifidogenic effect, which triggers proliferation of indigenous embryonic microflora in ovo, and indirectly influences gene expression regulation in host tissues, especially cecal tonsils.

Metagenomic profiling of gut microbial communities in both wild and artificially reared Bar-headed goose (Anser indicus)

Bar-headed goose (Anser indicus), a species endemic to Asia, has become one of the most popular species in recent years for rare bird breeding industries in several provinces of China. There has been no information on the gut metagenome configuration in both wild and artificially reared Bar-headed geese, even though the importance of gut microbiome in vertebrate nutrient and energy metabolism, immune homeostasis and reproduction is widely acknowledged. In this study, metagenomic methods have been used to describe the microbial community structure and composition of functional genes associated with both wild and artificially reared Bar-headed goose. Taxonomic analyses revealed that Firmicutes, Proteobacteria, Actinobacteria and Bacteroidetes were the four most abundant phyla in the gut of Bar-headed geese. Bacteroidetes were significantly abundant in the artificially reared group compared to wild group. Through functional profiling, we found that artificially reared Bar-headed geese had higher bacterial gene content related to carbohydrate transport and metabolism, energy metabolism and coenzyme transport, and metabolism. A comprehensive gene catalog of Bar-headed geese metagenome was built, and the metabolism of carbohydrate, amino acid, nucleotide, and energy were found to be the four most abundant categories. These results create a baseline for future Bar-headed goose microbiology research, and make an original contribution to the artificial rearing of this bird.

Feed supplementation with avian Propionibacterium acidipropionici contributes to mucosa development in early stages of rearing broiler chickens

Different studies in animal rearing claim the probiotic potential of species of the genus Propionibacterium. The effects of strains of Propionibacterium acidipropionici isolated from poultry intestine on microbiota activity and intestinal mucosa development were investigated in the early stage of rearing chicks and the safety of the dose used was investigated. The strains P. acidipropionici LET105 and LET107, administered as monoculture to chicks from the 1st to 14th day of life in a daily dose of 106 cfu/ml administered in the drinking water resulted harmless. The animals arrived at the expected weight for age and no differences were observed with respect to the food intake and water consumption related to control without bacteria administration. The analysis of microbiota composition revealed the presence of propionibacteria at the middle and end of the trial only in treated groups. Normal development of lactic acid bacteria and bifidobacteria, and slow colonisation by Bacteroides at the 7th day of the study was observed in the same groups. Analysis of the organic acids concentrations in the caecal content of birds revealed higher lactic acid and lower butyric acid production. Lower short chain fatty acids total concentration than expected during treatment was related to a better development of the gut mucosa. Increase in length of villus-crypt units, goblet cells counts and neutral mucins production were evidenced. Higher mucus secretion produced by dietary supplementation with propionibacteria could provide increased protection against pathogens.

Age-Related Differences in the Luminal and Mucosa-Associated Gut Microbiome of Broiler Chickens and Shifts Associated with Campylobacter jejuni Infection

Despite the importance of gut microbiota for broiler performance and health little is known about the composition of this ecosystem, its development and response towards bacterial infections. Therefore, the current study was conducted to address the composition and structure of the microbial community in broiler chickens in a longitudinal study from day 1 to day 28 of age in the gut content and on the mucosa. Additionally, the consequences of a Campylobacter (C.) jejuni infection on the microbial community were assessed. The composition of the gut microbiota was analyzed with 16S rRNA gene targeted Illumina MiSeq sequencing. Sequencing of 130 samples yielded 51,825,306 quality-controlled sequences, which clustered into 8285 operational taxonomic units (OTUs; 0.03 distance level) representing 24 phyla. Firmicutes, Proteobacteria, Bacteroidetes, Actinobacteria, and Tenericutes were the main components of the gut microbiota, with Proteobacteria and Firmicutes being the most abundant phyla (between 95.0 and 99.7% of all sequences) at all gut sites. Microbial communities changed in an age-dependent manner. Whereas, young birds had more Proteobacteria, Firmicutes, and Tenericutes dominated in older birds (>14 days old). In addition, 28 day old birds had more diverse bacterial communities than young birds. Furthermore, numerous significant differences in microbial profiles between the mucosa and luminal content of the small and large intestine were detected, with some species being strongly associated with the mucosa whereas others remained within the luminal content of the gut. Following oral infection of 14 day old broiler chickens with 1 × 10⁸ CFU of C. jejuni NCTC 12744, it was found that C. jejuni heavily colonized throughout the small and large intestine. Moreover, C. jejuni colonization was associated with an alteration of the gut microbiota with infected birds having a significantly lower abundance of Escherichia (E.) coli at different gut sites. On the contrary, the level of Clostridium spp. was higher in infected birds compared with birds from the negative controls. In conclusion, the obtained results demonstrate how the bacterial microbiome composition changed within the early life of broiler chickens in the gut lumen and on the mucosal surface. Furthermore, our findings confirmed that the Campylobacter carrier state in chicken is characterized by multiple changes in the intestinal ecology within the host.

The use of Lactobacillus as an alternative of antibiotic growth promoters in pigs: A review

Antibiotics, often supplemented in feed, used as a growth promoter, may cause their residual effect in animal produce and also trigger antibiotic resistance in bacteria, which is of serious concern among swine farming entrepreneurs. As an alternative, supplementing probiotics gained interest in recent years. Lactobacillus being the most commonly used probiotic agent improves growth performance, feed conversion efficiency, nutrient utilization, intestinal microbiota, gut health and regulates immune system in pigs. The characteristics of Lactobacillus spp. and their probiotic effects in swine production are reviewed here under.

Heterogeneous size datasets of broiler intestinal microbial communities can be analyzed without normalization

Next-generation sequencing technologies have become a powerful tool for the analysis of microbial communities. Sequencing of the hypervariable regions of the 16S ribosomal RNA gene following the amplitag amplification process has allowed the study of the diversity of samples of diverse origin. According to previous reports, the number of sequences required for the correct determination of the composition of a given sample may vary with the degree of diversity of that sample. In this paper, we investigate the correctness of comparing heterogeneous size datasets of bird intestinal microbial communities obtained from pyrosequencing data (Roche 454 technology) without prior normalization. We conclude that the differences observed between samples are due mainly to individual differences, not to differences in the number of readings in each sample, which makes data normalization unnecessary with the conditions described here.

Effects of captivity and artificial breeding on microbiota in feces of the red-crowned crane (Grus japonensis)

Reintroduction of the threatened red-crowned crane has been unsuccessful. Although gut microbiota correlates with host health, there is little information on gut microbiota of cranes under different conservation strategies. The study examined effects of captivity, artificial breeding and life stage on gut microbiota of red-crown cranes. The gut microbiotas of wild, captive adolescent, captive adult, artificially bred adolescent and artificially bred adult cranes were characterized by next-generation sequencing of 16S rRNA gene amplicons. The gut microbiotas were dominated by three phyla: Firmicutes (62.9%), Proteobacteria (29.9%) and Fusobacteria (9.6%). Bacilli dominated the 'core' community consisting of 198 operational taxonomic units (OTUs). Both captivity and artificial breeding influenced the structures and diversities microbiota of the gut. Especially, wild cranes had distinct compositions of gut microbiota from captive and artificially bred cranes. The greatest alpha diversity was found in captive cranes, while wild cranes had the least. According to the results of ordination analysis, influences of captivity and artificial breeding were greater than that of life stage. Overall, captivity and artificial breeding influenced the gut microbiota, potentially due to changes in diet, vaccination, antibiotics and living conditions. Metagenomics can serve as a supplementary non-invasive screening tool for disease control.

Applications of In Ovo Technique for the Optimal Development of the Gastrointestinal Tract and the Potential Influence on the Establishment of Its Microbiome in Poultry

As the current poultry production system stands, there is a period of time when newly hatched chicks are prevented from access to feed for approximately 48-72 h. Research has indicated that this delay in feeding may result in decreased growth performance when compared to chicks that are fed immediately post-hatch. To remedy this issue, in ovo methodology may be applied in order to supply the embryo with additional nutrients prior to hatching and those nutrients will continue to be utilized by the chick post-hatch during the fasting period. Furthermore, in ovo injection of various biologics have been researched based on the ability of not only supplying the chick embryo with additional nutrients that would promote improved growth but also compounds that may benefit the future health of the chicken host. Such compounds include various immunostimulants, live beneficial bacteria, prebiotics, and synbiotics. However, it is important to determine the site and age of the in ovo injection for the most productive effects. The primary focus of the current review is to address these two issues [the most effective site(s) and age(s) of in ovo injection] as well as provide the framework for the development of the gastrointestinal tract (GIT) of the chick embryo. Additionally, recent research suggests the colonization of the microbiota in the developing chick may occur during the late stages of embryogenesis. Therefore, we will also discuss the potentials of the in ovo injection method in establishing a healthy and diverse community of microorganisms to colonize the developing GIT that will provide both protection from pathogen invasion and improvement in growth performance to developing chicks.

Chicken Anti-Campylobacter Vaccine - Comparison of Various Carriers and Routes of Immunization

Campylobacter spp, especially the species Campylobacter jejuni, are important human enteropathogens responsible for millions of cases of gastro-intestinal disease worldwide every year. C. jejuni is a zoonotic pathogen, and poultry meat that has been contaminated by microorganisms is recognized as a key source of human infections. Although numerous strategies have been developed and experimentally checked to generate chicken vaccines, the results have so far had limited success. In this study, we explored the potential use of non-live carriers of Campylobacter antigen to combat Campylobacter in poultry. First, we assessed the effectiveness of immunization with orally or subcutaneously delivered Gram-positive Enhancer Matrix (GEM) particles carrying two Campylobacter antigens: CjaA and CjaD. These two immunization routes using GEMs as the vector did not protect against Campylobacter colonization. Thus, we next assessed the efficacy of in ovo immunization using various delivery systems: GEM particles and liposomes. The hybrid protein rCjaAD, which is CjaA presenting CjaD epitopes on its surface, was employed as a model antigen. We found that rCjaAD administered in ovo at embryonic development day 18 by both delivery systems resulted in significant levels of protection after challenge with a heterologous C. jejuni strain. In practice, in ovo chicken vaccination is used by the poultry industry to protect birds against several viral diseases. Our work showed that this means of delivery is also efficacious with respect to commensal bacteria such as Campylobacter. In this study, we evaluated the protection after one dose of vaccine given in ovo. We speculate that the level of protection may be increased by a post-hatch booster of orally delivered antigens.

Intestinal Microbiota of Broiler Chickens As Affected by Litter Management Regimens

Poultry litter is a mixture of bedding materials and enteric bacteria excreted by chickens, and it is typically reused for multiple growth cycles in commercial broiler production. Thus, bacteria can be transmitted from one growth cycle to the next via litter. However, it remains poorly understood how litter reuse affects development and composition of chicken gut microbiota. In this study, the effect of litter reuse on the microbiota in litter and in chicken gut was investigated using 2 litter management regimens: fresh vs. reused litter. Samples of ileal mucosa and cecal digesta were collected from young chicks (10 days of age) and mature birds (35 days of age). Based on analysis using DGGE and pyrosequencing of bacterial 16S rRNA gene amplicons, the microbiota of both the ileal mucosa and the cecal contents was affected by both litter management regimen and age of birds. Faecalibacterium, Oscillospira, Butyricicoccus, and one unclassified candidate genus closely related to Ruminococcus were most predominant in the cecal samples, while Lactobacillus was predominant in the ileal samples at both ages and in the cecal samples collected at day 10. At days 10 and 35, 8 and 3 genera, respectively, in the cecal luminal microbiota differed significantly in relative abundance between the 2 litter management regimens. Compared to the fresh litter, reused litter increased predominance of halotolerant/alkaliphilic bacteria and Faecalibacterium prausnitzii, a butyrate-producing gut bacterium. This study suggests that litter management regimens affect the chicken GI microbiota, which may impact the host nutritional status and intestinal health.

The gastrointestinal tract microbiota of the Japanese quail, Coturnix japonica

Microbiota in the gastrointestinal tract (GIT) plays an essential role in the health and well-being of the host. With the exception of chickens, this area has been poorly studied within birds. The avian GIT harbours unique microbial communities. Birds require rapid energy bursts to enable energy-intensive flying. The passage time of feed through the avian GIT is only 2-3.5 h, and thus requires the presence of microbiota that is extremely efficient in energy extraction. This investigation has used high-throughput 16S rRNA gene sequencing to explore the GIT microbiota of the flighted bird, the Japanese quail (Coturnix japonica). We are reporting, for the first time, the diversity of bacterial phylotypes inhabiting all major sections of the quail GIT including mouth, esophagus, crop, proventriculus, gizzard, duodenum, ileum, cecum, large intestine and feces. Nine phyla of bacteria were found in the quail GIT; however, their distribution varied significantly between GIT sections. Cecal microbiota was the most highly differentiated from all the other communities and showed highest richness at an OTU level but lowest richness at all other taxonomic levels being comprised of only 15 of total 57 families in the quail GIT. Differences were observed in the presence and absence of specific phylotypes between sexes in most sections.

Effect of doxycycline and Lactobacillus probiotics on mRNA expression of ABCC2 in small intestines of chickens

Probiotics and antibiotics are widely used in poultry and may alter drug bioavailability by affecting the expression of intestinal ATP-binding cassette (ABC) efflux transporters. Therefore the aim of the present investigation was to evaluate the effect of Lactobacilli probiotics, administered alone or in combination with doxycycline, on the expression of ABCB1 (gene, encoding P-glycoprotein), ABCC2 (gene, encoding multidrug resistance protein 2, MRP2) and ABCG2 (gene, encoding breast cancer resistance protein) mRNAs in chicken using RT-PCR. Duc one-day-old chicks (n=24) were divided equally in four groups: untreated control, probiotics supplemented group, probiotics plus doxycycline treated chickens and antibiotic administered group. Expression of ABCC2 mRNA was affected by doxycycline or by combination of Lactobacillus plantarum, L. brevis and L. bulgaricus and the antibiotic in the intestines. These results can be used as a basis for further functional studies to prove the beneficial effect on limitation of the absorption of toxins and improvement of efflux of endogenous substances and xenobiotics when the combination of doxycycline and Lactobacillus spp. probiotics are administered to poultry.

Alternatives to Antibiotics to Prevent Necrotic Enteritis in Broiler Chickens: A Microbiologist's Perspective

Since the 2006 European ban on the use of antibiotics as growth promoters in animal feed, numerous studies have been published describing alternative strategies to prevent diseases in animals. A particular focus has been on prevention of necrotic enteritis in poultry caused by Clostridium perfringens by the use of microbes or microbe-derived products. Microbes produce a plethora of molecules with antimicrobial properties and they can also have beneficial effects through interactions with their host. Here we review recent developments in novel preventive treatments against C. perfringens-induced necrotic enteritis in broiler chickens that employ yeasts, bacteria and bacteriophages or secondary metabolites and other microbial products in disease control.

The Role of Direct-Fed Microbials in Conventional Livestock Production

Supplementation of direct-fed microbials (DFM) as a means to improve the health and performance of livestock has generated significant interest over the past 15+ years. A driving force for this increased interest in DFM is to reduce or eliminate the use of low-dose antibiotics in livestock production. This increased attention toward DFM supplementation has generated an extensive body of research. This effort has resulted in conflicting reports. Although there has been considerable variation in the design of these studies, one of the main causes for this lack of consistency may be attributed to the variation in the experimental immune challenge incorporated to evaluate DFM supplementation. Taking into account the experimental immune challenge, there is strong evidence to suggest that DFM supplementation may have an impact on the immune response, overall health, and performance of livestock.

Differences in major bacterial populations in the intestines of mature broilers after feeding virginiamycin or bacitracin methylene disalicylate

AIMS

The purpose of this study was to compare the effects of feeding virginiamycin or bacitracin methylene disalicylate (BMD), two in-feed antibiotics typically used by commercial poultry producers in the United States, on the chicken gastrointestinal microbiota.

METHODS AND RESULTS

454 pyrosequencing of the V6-V8 region of the 16S rRNA gene and quantitative PCR were employed to examine the bacterial microbiota and Clostridium perfringens, respectively, in the jejunum and caecum of market-age broiler chickens over four replicate grow-outs.

CONCLUSIONS

Our results suggest that virginiamycin has a more pronounced impact on broiler gastrointestinal tract bacterial communities, relative to BMD, manifested primarily through significant enrichments in the genus Faecalibacterium in the caecum and a distinct population of Lactobacillus, OTU_02, in both the jejunum and caecum. No evidence for a difference among the diets in Cl. perfringens levels in the jejunum or caecum was observed.

SIGNIFICANCE AND IMPACT OF THE STUDY

This work represents the highest resolution comparison to date of the jejunum and caecum microbiota in broilers fed either virginiamycin or BMD, and provides evidence for specific bacterial OTUs potentially involved in the health and performance benefits typically attributed to these in-feed antibiotics.

An Introduction to the Avian Gut Microbiota and the Effects of Yeast-Based Prebiotic-Type Compounds as Potential Feed Additives

The poultry industry has been searching for a replacement for antibiotic growth promoters in poultry feed as public concerns over the use of antibiotics and the appearance of antibiotic resistance has become more intense. An ideal replacement would be feed amendments that could eliminate pathogens and disease while retaining economic value via improvements on body weight and feed conversion ratios. Establishing a healthy gut microbiota can have a positive impact on growth and development of both body weight and the immune system of poultry while reducing pathogen invasion and disease. The addition of prebiotics to poultry feed represents one such recognized way to establish a healthy gut microbiota. Prebiotics are feed additives, mainly in the form of specific types of carbohydrates that are indigestible to the host while serving as substrates to select beneficial bacteria and altering the gut microbiota. Beneficial bacteria in the ceca easily ferment commonly studied prebiotics, producing short-chain fatty acids, while pathogenic bacteria and the host are unable to digest their molecular bonds. Prebiotic-like substances are less commonly studied, but show promise in their effects on the prevention of pathogen colonization, improvements on the immune system, and host growth. Inclusion of yeast and yeast derivatives as probiotic and prebiotic-like substances, respectively, in animal feed has demonstrated positive associations with growth performance and modification of gut morphology. This review will aim to link together how such prebiotics and prebiotic-like substances function to influence the native and beneficial microorganisms that result in a diverse and well-developed gut microbiota.

Dietary Capsicum and Curcuma longa oleoresins increase intestinal microbiome and necrotic enteritis in three commercial broiler breeds

Three commercial broiler breeds were fed from hatch with a diet supplemented with Capsicum and Curcuma longa oleoresins, and co-infected with Eimeria maxima and Clostridium perfringens to induce necrotic enteritis (NE). Pyrotag deep sequencing of bacterial 16S rRNA showed that gut microbiota compositions were quite distinct depending on the broiler breed type. In the absence of oleoresin diet, the number of operational taxonomic units (OTUs), was decreased in infected Cobb, and increased in Ross and Hubbard, compared with the uninfected. In the absence of oleoresin diet, all chicken breeds had a decreased Candidatus Arthromitus, while the proportion of Lactobacillus was increased in Cobb, but decreased in Hubbard and Ross. Oleoresin supplementation of infected chickens increased OTUs in Cobb and Ross, but decreased OTUs in Hubbard, compared with unsupplemented/infected controls. Oleoresin supplementation of infected Cobb and Hubbard was associated with an increased percentage of gut Lactobacillus and decreased Selenihalanaerobacter, while Ross had a decreased fraction of Lactobacillus and increased Selenihalanaerobacter, Clostridium, Calothrix, and Geitlerinema. These results suggest that dietary Capsicum/Curcuma oleoresins reduced the negative consequences of NE on body weight and intestinal lesion, in part, through alteration of the gut microbiome in 3 commercial broiler breeds.

The chicken gastrointestinal microbiome

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

Harnessing microbiome and probiotic research in sub-Saharan Africa: recommendations from an African workshop

To augment capacity-building for microbiome and probiotic research in Africa, a workshop was held in Nairobi, Kenya, at which researchers discussed human, animal, insect, and agricultural microbiome and probiotics/prebiotics topics. Five recommendations were made to promote future basic and translational research that benefits Africans.