Effects of feed additives on the development on the ileal bacterial community of the broiler chicken

Effect of orally administered B. subtilis-cNK-2 on growth performance, immunity, gut health, and gut microbiome in chickens infected with Eimeria acervulina and its potential as an alternative to antibiotics

This study investigated the best oral delivery strategy (gavage or feed) for the B. subtilis expressing the chicken anti-microbial peptide cNK-2 (B. subtilis-cNK-2) in comparison to monensin, in chickens challenged with Eimeria acervulina (E. acervulina). A total of 120 broiler chickens were randomly allocated into 5 treatment groups in a completely randomized design: 1) uninfected chickens fed with basal diet (NC), 2) E. acervulina-infected chickens fed a basal diet (PC), 3) E. acervulina-infected chickens fed a basal diet supplemented with 90 mg monensin/kg feed (MO), 4) E. acervulina-infected chickens fed a basal diet and orally gavaged with B. subtilis-cNK-2 at 1 × 1010 cfu/d (CNK-O), and 5) E. acervulina-infected chickens fed a basal diet mixed with B. subtilis-cNK-2 at 1 × 1010 cfu/kg feed (CNK-F). The challenge consisted of 5,000 sporulated E. acervulina oocysts through oral gavage on d 15. Body weights were measured on d 7, 14, 21, and 23. Duodenal tissue and digesta samples were collected at 6 d postinfection (dpi) to assess the gut integrity, oxidative stress, mucosal immunity, and the gut microbiome. Fecal samples were collected from 6 to 8 dpi to enumerate the oocyst shedding. Chickens in the CNK-O group showed improved (P < 0.05) growth performance, gut integrity, and mucosal immunity compared to PC, comparable to chickens in the MO group. Chickens in the MO, CNK-F, and CNK-O treatment groups all showed lower (P < 0.05) oocyst shedding compared to PC chickens. Moreover, distinct cytokine profile, oxidative stress measures, tight junction proteins, and shifts in the gut microbiome with associated functional changes were observed in all challenge groups. In conclusion, we showed that the oral administration of B. subtilis-cNK-2 improved growth performance, enhanced local protective immunity, and reduced fecal oocyst shedding in broiler chickens infected with E. acervulina, demonstrating potential use of B. subtilis-cNK-2 as an alternative to antibiotics to protect chickens against coccidiosis.

Unraveling frontiers in poultry health (part 1) - Mitigating economically important viral and bacterial diseases in commercial Chicken and Turkey production

This symposium offered up-to-date perspectives on field experiences and the latest research on significant viral and bacterial diseases affecting poultry. A highlight was the discussion on the use of enteroids as advanced in vitro models for exploring disease pathogenesis. Outcomes of this symposium included identifying the urgent need to improve the prevention and control of avian influenza by focusing research on vaccine effectiveness. In this regard, efforts should focus on enhancing the relatedness of vaccine antigen to the field (challenge) virus strain and improving immunogenicity. It was also revealed that gangrenous dermatitis could be controlled through withholding or restricting the administration of ionophores during broiler life cycle, and that administration of microscopic polymer beads (gel) based-live coccidia vaccines to chicks could be used to reduce necrotic enteritis-induced mortality. It was emphasized that effective diagnosis of re-emerging Turkey diseases (such as blackhead, fowl cholera, and coccidiosis) and emerging Turkey diseases such as reoviral hepatitis, reoviral arthritis, Ornithobacterium rhinotracheale infection, and strepticemia require complementarity between investigative research approaches and production Veterinarian field approaches. Lastly, it was determined that the development of a variety of functionally-specific enteroids would expedite the delineation of enteric pathogen mechanisms and the identification of novel vaccine adjuvants.

Pioneer colonizers: Bacteria that alter the chicken intestinal morphology and development of the microbiota

Microbes commonly administered to chickens facilitate development of a beneficial microbiome that improves gut function, feed conversion and reduces pathogen colonization. Competitive exclusion products, derived from the cecal contents of hens and shown to reduce Salmonella colonization in chicks, possess important pioneer-colonizing bacteria needed for proper intestinal development and animal growth. We hypothesized that inoculation of these pioneer-colonizing bacteria to day of hatch chicks would enhance the development of their intestinal anatomy and microbiome. A competitive exclusion product was administered to broiler chickens, in their drinking water, at day of hatch, and its impact on intestinal morphometrics, intestinal microbiome, and production parameters, was assessed relative to a control, no treatment group. 16S rRNA gene, terminal restriction fragment length polymorphism (T-RFLP) was used to assess ileal community composition. The competitive exclusion product, administered on day of hatch, increased villus height, villus height/width ratio and goblet cell production ∼1.25-fold and expression of enterocyte sugar transporters 1.25 to 1.5-fold in chickens at 3 days of age, compared to the control group. As a next step, chicks were inoculated with a defined formulation, containing Bacteroidia and Clostridia representing pioneer-colonizing bacteria of the two major bacterial phyla present in the competitive exclusion product. The defined formulation, containing both groups of bacteria, were shown, dependent on age, to improve villus height (jejunum: 1.14 to 1.46-fold; ileum: 1.17-fold), goblet cell numbers (ileum 1.32 to 2.51-fold), and feed efficiency (1.18-fold, day 1) while decreasing Lactobacillus ileal abundance by one-third to half in birds at 16 and 42 days of age, respectively; compared to the phosphate buffered saline treatment group. Therefore, specific probiotic formulations containing pioneer colonizing species can provide benefits in intestinal development, feed efficiency and body weight gain.

Systematic profiling of the chicken gut microbiome reveals dietary supplementation with antibiotics alters expression of multiple microbial pathways with minimal impact on community structure

BACKGROUND

The emergence of antimicrobial resistance is a major threat to global health and has placed pressure on the livestock industry to eliminate the use of antibiotic growth promotants (AGPs) as feed additives. To mitigate their removal, efficacious alternatives are required. AGPs are thought to operate through modulating the gut microbiome to limit opportunities for colonization by pathogens, increase nutrient utilization, and reduce inflammation. However, little is known concerning the underlying mechanisms. Previous studies investigating the effects of AGPs on the poultry gut microbiome have largely focused on 16S rDNA surveys based on a single gastrointestinal (GI) site, diet, and/or timepoint, resulting in an inconsistent view of their impact on community composition.

METHODS

In this study, we perform a systematic investigation of both the composition and function of the chicken gut microbiome, in response to AGPs. Birds were raised under two different diets and AGP treatments, and 16S rDNA surveys applied to six GI sites sampled at three key timepoints of the poultry life cycle. Functional investigations were performed through metatranscriptomics analyses and metabolomics.

RESULTS

Our study reveals a more nuanced view of the impact of AGPs, dependent on age of bird, diet, and intestinal site sampled. Although AGPs have a limited impact on taxonomic abundances, they do appear to redefine influential taxa that may promote the exclusion of other taxa. Microbiome expression profiles further reveal a complex landscape in both the expression and taxonomic representation of multiple pathways including cell wall biogenesis, antimicrobial resistance, and several involved in energy, amino acid, and nucleotide metabolism. Many AGP-induced changes in metabolic enzyme expression likely serve to redirect metabolic flux with the potential to regulate bacterial growth or produce metabolites that impact the host.

CONCLUSIONS

As alternative feed additives are developed to mimic the action of AGPs, our study highlights the need to ensure such alternatives result in functional changes that are consistent with site-, age-, and diet-associated taxa. The genes and pathways identified in this study are therefore expected to drive future studies, applying tools such as community-based metabolic modeling, focusing on the mechanistic impact of different dietary regimes on the microbiome. Consequently, the data generated in this study will be crucial for the development of next-generation feed additives targeting gut health and poultry production. Video Abstract.

Effects of dietary bacitracin or Bacillus subtilis on the woody breast myopathy-associated gut microbiome of Eimeria spp. challenged and unchallenged broilers

Study suggested that dysbiosis of the gut microbiota may affect the etiology of woody breast (WB). In the current study, the cecal microbiota and WB in chickens fed three different diets were investigated. A total of 504 male chicks were used in a randomized complete block design with a 3 (Diet) × 2 (Challenge) factorial arrangement of treatments with 6 replicates per treatment, 6 treatments per block, and 14 birds per treatment. The experimental diets were a control diet (corn-soybean meal basal diet), an antibiotic diet (basal diet + 6.075 mg bacitracin/kg feed), and a probiotic diet (basal diet + 2.2 × 10⁸ CFU Bacillus subtilis PB6/kg feed). On d 14, birds that were assigned to the challenge treatment received a 20 × live cocci vaccine. On d 41, breast muscle hardness in live birds was palpated and grouped into normal (NB) and WB phenotypes. Cecal contents were collected and their bacterial compositions were analyzed and compared. The genomic DNA of the cecal contents was extracted and the V3 and V4 regions of 16S rRNA gene were amplified and sequenced via an Illumina MiSeq platform. There were no differences (P > 0.05) in Shannon and Chao 1 indexes between the challenges, diets, and phenotypes (NB vs. WB). However, there was a difference (P = 0.001) in the beta diversity of the samples between the challenged and nonchallenged groups. Relative bacterial abundance differed (false discovery rate, FDR < 0.05) between the challenge treatments, but there were no significant differences (FDR > 0.05) among the three diets or two phenotypes. Predicted energy metabolism, nucleotide metabolism, and amino acid and coenzyme biosynthesis activities only differed (q-value < 0.05) between challenged and nonchallenged groups. The cocci challenge altered the gut microbial composition on Butyricicoccus pullicaecorum, Sporobacter termitidis, and Subdoligranulum variabile, but the dietary antibiotic and probiotic treatments did not impact gut microbial composition. No strong association was found between WB myopathy and gut microbial composition in this study.

Gut microbiota and age shape susceptibility to clostridial enteritis in lorikeets under human care

Background

Enteritis is a common cause of morbidity and mortality in lorikeets that can be challenging to diagnose and treat. In this study, we examine gut microbiota in two lorikeet flocks with enteritis (Columbus Zoo and Aquarium—CZA; Denver Zoo—DZ). Since 2012, the CZA flock has experienced repeated outbreaks of enteritis despite extensive diet, husbandry, and clinical modifications. In 2018, both CZA and DZ observed a spike in enteritis. Recent research has revealed that the gut microbiota can influence susceptibility to enteropathogens. We hypothesized that a dysbiosis, or alteration in the gut microbial community, was making some lorikeets more susceptible to enteritis, and our goal was to characterize this dysbiosis and determine the features that predicted susceptibility.

Results

We employed 16S rRNA sequencing to characterize the cloacal microbiota in lorikeets (CZA n = 67, DZ n = 24) over time. We compared the microbiota of healthy lorikeets, to lorikeets with enteritis, and lorikeets susceptible to enteritis, with “susceptible” being defined as healthy birds that subsequently developed enteritis. Based on sequencing data, culture, and toxin gene detection in intestinal contents, we identified Clostridium perfringens type A (CZA and DZ) and C. colinum (CZA only) at increased relative abundances in birds with enteritis. Histopathology and immunohistochemistry further identified the presence of gram-positive bacilli and C. perfringens, respectively, in the necrotizing intestinal lesions. Finally, using Random Forests and LASSO models, we identified several features (young age and the presence of Rhodococcus fascians and Pseudomonas umsongensis) associated with susceptibility to clostridial enteritis.

Conclusions

We identified C. perfringens type A and C. colinum associated with lorikeet necrohemorrhagic enteritis at CZA and DZ. Susceptibility testing of isolates lead to an updated clinical treatment plan which ultimately resolved the outbreaks at both institutions. This work provides a foundation for understanding gut microbiota features that are permissive to clostridial colonization and host factors (e.g. age, prior infection) that shape responses to infection.

Supplementary Information

The online version contains supplementary material available at 10.1186/s42523-021-00148-7.

Dietary encapsulated Bifidobacterium animalis and Agave fructans improve growth performance, health parameters, and immune response in broiler chickens

Objective

The present study was conducted to evaluate the effects of dietary supplementation with Bifidobacterium animalis, Agave fructans, and symbiotic of both encapsulated on growth performance, feed efficiency, blood parameters, and immune status in broiler chickens, and to compare these with diets including antibiotic growth promoters and without additives.

Methods

A comparative experimental study was carried out with 135 male Ross 308 broiler chickens. Each trial was divided into 5 equal groups. Control group (CON) received a standard diet without growth promoter; GPA: a standard diet with colistin sulfate and zinc bacitracin (0.25 g/kg of feed); PRE: a standard diet with 1% Agave fructans; PRO: a standard diet with Bifidobacterium animalis (11.14±0.70 log CFU/g); SYM: a standard diet with B. animalis and Agave fructans.

Results

A significant decrease in food consumption was found for the GPA, PRE, and SYM, compared to the CON group. The results show a better feed conversion index in PRE and GPA with respect to the CON group with the highest conversion index. Interestingly, the weight of the gastrointestinal tract shows a statistically significant difference between GPA and PRE groups. Moreover, the length of the gastrointestinal tract of the GPA group was less than the PRE group. In the total leukocyte count, there was a statistically significant increase in the GPA group compared to the CON, PRE, and PRO groups, and the H:L index was lower in PRO. Regarding the cytokines, IL-10 decreased in PRO compared to CON and PRE, while IL-1β increased in the SYM group.

Conclusion

Alternative treatments were shown to achieve similar productive results as growth-promoting antibiotics and showed improvement over diet without additives; however, they have immunomodulatory properties and improved the development of the gastrointestinal tract compared to the treatment of growth-promoting antibiotics.

Effects of Bacillus subtilis and coccidial vaccination on cecal microbial diversity and composition of Eimeria-challenged male broilers

In a companion study, the effects of dietary antibiotic alternative and coccidial vaccination on the growth performance of male broilers have been reported. In this paper, the effects of dietary probiotics and coccidial vaccination on diversity and composition of cecal microbiota were investigated using a 3 (diets) × 2 (vaccinated or non-vaccinated) factorial setting of treatments. Three diets, including a corn and soybean-meal control diet, an antibiotic diet (a control diet supplemented with bacitracin and salinomycin), and a probiotic diet (a control diet supplemented with Bacillus subtilis) were provided to broiler chicken from day 0 to 42. To simulate an Eimeria challenge in the field, all chicks were gavaged with a 20× dose of commercial coccidial vaccine containing live Eimeria oocysts on day 14. Cecal contents were collected on day 42. High-throughput sequencing of the 16S rRNA gene was used to determine microbial diversity and composition. Coccidial vaccination to broilers reduced bacterial diversity (Shannon index) of the cecal microbiota. There was a significant interaction between the dietary additive and coccidial vaccination on the observed bacterial species number. Diets supplemented with B. subtilis increased bacterial species of non-vaccinated broilers but decreased bacterial species of vaccinated broilers. In contrast, diets supplemented with antibiotics reduced bacterial species of broilers from both groups. Interactions between dietary additive and coccidial vaccination were also observed on microbial composition. Vaccinated broilers fed the B. subtilis diet exhibited the lowest Firmicutes percentage and highest Bacteroidetes percentage within the microbial community. In addition, vaccinated broilers fed the B. subtilis diet exhibited the highest Rikenella microfusus percentage. From this study, the coccidial vaccination on the day of hatch reduced the microbial diversity of broilers at a later age. The inclusion of B. subtilis-probiotics in the feed of vaccinated broilers may reduce microbial diversity in cecal content by increasing the proportion of a predominant bacterial species, R. microfusus, in the microbial community.

Synbiotic supplementation to decrease Salmonella colonization in the intestine and carcass contamination in broiler birds

In vitro and in vivo experiments were conducted to study the effects of synbiotic supplementation on Salmonella enterica ser. Enteritidis (SE) proliferation, cecal content load, and broiler carcass contamination. Lactobacillus reuteri, Enterococcus faecium, Bifidobacterium animalis, and Pediococcus acidilactici culture supernatants decreased (P < 0.05) the in vitro proliferation of SE at 1:1 supernatant: pathogen dilution. A total of 240 Cobb-500 broiler chicks were randomly allotted to three treatment groups (8 replicates/group with 10 birds/replicate): control (basal diet), antibiotic (Virginiamycin at 20 mg/kg feed), synbiotic (PoultryStar® ME at 0.5 g/kg feed containing L. reuteri, E. faecium, B. animalis, P. acidilactici and a Fructooligosaccharide) from day of hatch. At 21 d of age, all birds in experimental groups were orally inoculated with 250 μl of 1 X 109 CFU SE. Antibiotic supplementation increased (P < 0.05) body weight and feed consumption, compared to the control group. Birds in the synbiotic supplementation had intermediate body weight and feed consumption that were not significantly different from both the control and antibiotic group at 42 d of age in SE infected birds. No significant effects were observed in feed efficiency at 42 d of age among the groups. Antibiotic and synbiotic supplementation decreased (P < 0.05) SE load in cecal contents by 0.90 and 0.85 log units/ g and carcass SE load by 1.4 and 1.5 log units/mL of rinsate compared to the control group at 42 d of age (21 dpi). The relative abundance of IL-10, IL-1, TLR-4, and IFNγ mRNA was decreased (P < 0.05) in the antibiotic and synbiotic supplementation groups compared to the control birds at 42 d of age (21 dpi). It can be concluded that synbiotic supplementation decreased SE proliferation in vitro and decreased SE load in the cecal contents and broiler carcass.

Differential Impact of Subtherapeutic Antibiotics and Ionophores on Intestinal Microbiota of Broilers

Antimicrobial growth promoters (AGPs) are commonly used in the livestock industry at subtherapeutic levels to improve production efficiency, which is achieved mainly through modulation of the intestinal microbiota. However, how different classes of AGPs, particularly ionophores, regulate the gut microbiota remains unclear. In this study, male Cobb broiler chickens were supplemented for 14 days with or without one of five commonly used AGPs including three classical antibiotics (bacitracin methylene disalicylate, tylosin, and virginiamycin) and two ionophores (monensin and salinomycin) that differ in antimicrobial spectrum and mechanisms. Deep sequencing of the V3-V4 region of the bacterial 16S rRNA gene revealed that two ionophores drastically reduced a number of rare bacteria resulting in a significant decrease in richness and a concomitant increase in evenness of the cecal microbiota, whereas three antibiotics had no obvious impact. Although each AGP modulated the gut microbiota differently, the closer the antibacterial spectrum of AGPs, the more similarly the microbiota was regulated. Importantly, all AGPs had a strong tendency to enrich butyrate- and lactic acid-producing bacteria, while reducing bile salt hydrolase-producing bacteria, suggestive of enhanced metabolism and utilization of dietary carbohydrates and lipids and improved energy harvest, which may collectively be responsible for the growth-promoting effect of AGPs.

Differential Effects of Bacitracin Methylene Disalicylate (BMD) on the Distal Colon and Cecal Microbiota of Young Broiler Chickens

Antibiotics have been used extensively for growth promotion in poultry, along with other food production animals, as well as therapeutically to treat infectious diseases. However, with concerns over selection for drug antibiotic resistant bacteria the practice of using subtherapeutic doses of antibiotics is under increased scrutiny. Consequently, we assessed the impact of the commonly used antibiotic bacitracin methylene disalicylate (BMD) on the gastrointestinal microbiota of chickens. For this we administered therapeutic doses of BMD as a feed additive and 16s rRNA gene amplicon sequencing to measure changes in taxonomic abundance on the distal colon and cecal microbiota of young broiler chickens. While BMD treatment was found to impact the abundance of selected taxa and overall beta diversity, significant changes were, in general, limited to the colon of the treated birds. Selected taxa at the phylum, class, and genus levels that were most impacted were identified. The composition of the cecum remained relatively stable in BMD-treated animals. As poultry production practices seek alternatives to growth promoting antibiotic feed additives, manipulation of the gastrointestinal microbiota holds promise. These results suggest that targeting the cecum may offer a means to promote changes to the microbiota that maximize the benefits for the hosts.

An optimist's view on limiting necrotic enteritis and maintaining broiler gut health and performance in today's marketing, food safety, and regulatory climate

The future poultry nutritionist, veterinarian, and husbandryman will have many new regulatory requirements and consumer preferences to navigate in addition to their normal responsibility of raising birds in a cost-efficient and wholesome manner. New challenges include changes to antibiotic use, increased food safety regulations, and more concern over how birds are raised and how to dispose of poultry house waste. All of these new programs and new regulations will alter how we have been raising birds for the last 60 years since the inception of the integrated poultry industry. The most significant change may be the voluntary or regulatory withdrawal of the use of antibiotics in poultry production. In North America, this withdrawal of antibiotic use includes removal of in-ovo antibiotics, performance-improving antibiotics or antibiotic growth promotors (AGP), and the polyether ionophore antibiotics (ionophore anticoccidials).The removal of antibiotics in poultry production may result in welfare concerns due to elevated mortality and less efficient feed conversion, resulting in greater environmental impacts from increased manure production and more use of grain per unit of meat produced. There also may be concerns with greater intestinal disease in the birds resulting in increased numbers of foodborne illness-causing bacteria such as Salmonella sp. or Campylobacter sp. on the carcass. A major impact will be the disease necrotic enteritis (NE). This review will focus on the pathophysiology of NE, the management of the disease, and the additional effects on growth rate, feed efficiency, and body weight that may be associated with NE.

Immunomodulation and effects on microbiota after in ovo administration of chicken cathelicidin-2

Host Defense Peptides (HDPs) such as cathelicidins are multifunctional effectors of the innate immune system with both antimicrobial and pleiotropic immunomodulatory functions. Chicken cathelicidin-2 (CATH-2) has multiple immunomodulatory effects in vitro and the D-amino acid analog of this peptide has been shown to partially protect young chicks from a bacterial infection. However, the mechanisms responsible for CATH-2 mediated in vivo protection have not been investigated so far. In this study, D-CATH-2 was administered in ovo and the immune status and microbiota of the chicks were investigated at 7 days posthatch to elucidate the in vivo mechanisms of the peptide. In three consecutive studies, no effects on numbers and functions of immune cells were found and only small changes were seen in gene expression of Peripheral Blood Mononuclear Cells (PBMCs). In two studies, intestinal microbiota composition was determined which was highly variable, suggesting that it was strongly influenced by environmental factors. In both studies, in ovo D-CATH-2 treatment caused significant reduction of Ruminococcaceae and Butyricicoccus in the cecum and Escherichia/Shigella in both ileum and cecum. In conclusion, this study shows that, in the absence of an infectious stimulus, in ovo administration of a CATH-2 analog alters the microbiota composition but does not affect the chicks' immune system posthatch.

Sodium butyrate improved performance while modulating the cecal microbiota and regulating the expression of intestinal immune-related genes of broiler chickens

This study evaluated the effect of sodium butyrate (SB) on performance, expression of immune-related genes in the cecal tonsils, and cecal microbiota of broiler chickens when dietary energy and amino acids concentrations were reduced. Day-old male Ross 708 broiler chicks were fed dietary treatments in a 3 × 2 factorial design (8 pens per treatment) with 3 dietary formulations (control diet; reduction of 2.3% of amino acids and 60 kcal/kg; and reduction of 4.6% of amino acids and 120 kcal/kg) with or without the inclusion of 0.1% of SB. Feed intake (FI), body weight gain (BW gain), and feed conversion ratio (FCR) were recorded until 28 d of age. From 14 to 28 d, there was an interaction of nutrient density by SB (P = 0.003) wherein BW gain of birds fed SB was impaired less by the energy/amino acids reduction than unsupplemented birds. A similar result was obtained from 1 to 28 d (P = 0.004). No interaction (P < 0.05) between nutrient density by SB was observed for FCR. Nutritional density of the diets and SB modified the structure, composition, and predicted function of the cecal microbiota. The nutritionally reduced diet altered the imputed function performed by the microbiota and the SB supplementation reduced these variations, keeping the microbial function similar to that observed in chickens fed a control diet. The frequency of bacterial species presenting the butyryl-CoA: acetate CoA-transferase gene increased in the microbiota of chickens fed a nutritionally reduced diet without SB supplementation, and was not changed by nutrient density of the diet when supplemented with SB (interaction; P = 0.01). SB modulated the expression of immune related genes in the cecal tonsils; wherein SB upregulated the expression of A20 in broilers fed control diets (P < 0.05) and increased IL-6 expression (P < 0.05). These results show that SB had positive effects on the productive performance of broilers fed nutritionally reduced diets, partially by modulating the cecal microbiota and exerting immune-modulatory effects.

The sub-inhibitory theory for antibiotic growth promoters

Antibiotics have played a critical role in the prevention, control, and treatment of bacterial diseases in humans and animals, and as growth promoters (AGPs) when used at sub-therapeutic concentrations in animal production. Numerous hypotheses have been proposed for the effectiveness of AGPs, which have largely centered on the beneficial modulation of the intestinal microbiota. However, these hypotheses have been doubted by some researchers, as AGPs are fed at concentrations that would typically be below minimum inhibitory concentrations (sub-MIC) for the antibiotic used. More recently, pro-inflammatory immune responses have been associated with poor growth performance, and this, along with reported direct, anti-inflammatory effects of some antibiotics, have led to suggestions that reducing the nutrient cost of (intestinal) inflammation may explain the growth promoting or permitting effect of AGPs. However, doubts about antibacterial effects of AGPs, and the search for alternative explanations, overlook the sub-MIC effects of antibiotics. This paper summarizes some of the reported sub-MIC effects of antibiotics and considers these in the context of helping to explain the mode of action of AGPs and effects seen in studies in vivo. This leads to suggestions for the features that alternatives to AGPs could exhibit to achieve similar performance efficacy as AGPs.

Probiotics Strains Modulate Gut Microbiota and Lipid Metabolism in Mule Ducks

Background:

Livestock production should respond to societal, environmental and economic changes. Since 2006 and the ban on antibiotics as growth factors in European Union, the use of probiotics has become widespread and has demonstrated the effect of intestinal microbiota on the performance of farm animals.

Objective:

The aim of this study was to investigate the effect of supplementation with Lactobacillus salivarius (as a probiotics strain or combined with other strains) on zootechnical performance, metabolic and immune gene expression and intestinal microbiota diversity in mule ducks using high-throughput sequencing and real-time PCR.

Method:

The mule ducks were reared for 79 days and overfed for 12 days with or without probiotics. Samples were collected at 14 (starting period) and 91 days (end of overfeeding period), 3 hours post feeding.

Results:

Irrespective of digestive content, age, level of feed intake or supplementation with probiotics, Firmicutes, Proteobacteria and Bacteroidetes were the dominant phyla in the bacterial community in mule ducks. At 14 days, both the ileal and cecal samples were dominated by Firmicutes (in particular the Clostridiales order). Overfeeding induced a shift between Clostridiales and Lactobacillales in the ileal samples whereas in the cecal samples, the relative abundance of Firmicutes decreased. Overfeeding also induced hepatic over-expression of Fatty Acid Synthase (FAS) and of the lipid transporter gene Fatty Acid Binding Protein 4 (FABP4). This increase in lipid metabolism genes is associated with a decrease in inflammatory response.

Conclusion:

Finally, probiotic supplementation had only a slight impact on gene expression and microbiota diversity, both at 14 days and after overfeeding.

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

Although dietary antibiotic growth promoters have long been used to increase growth performance in commercial food animal production, the biochemical details associated with these effects remain poorly defined. A metabolomics approach was used to characterize and identify the biochemical compounds present in the intestine of broiler chickens fed a standard, unsupplemented diet or a diet supplemented with the antibiotic growth promoters, virginiamycin or bacitracin methylene disalicylate. Compared with unsupplemented controls, the levels of 218 biochemicals were altered (156 increased, 62 decreased) in chickens given the virginiamycin-supplemented diet, while 119 were altered (96 increased, 23 decreased) with the bacitracin-supplemented diet. When compared between antibiotic-supplemented groups, 79 chemicals were altered (43 increased, 36 decreased) in virginiamycin- vs. bacitracin-supplemented chickens. The changes in the levels of intestinal biochemicals provided a distinctive biochemical signature unique to each antibiotic-supplemented group. These biochemical signatures were characterized by increases in the levels of metabolites of amino acids (e.g. 5-hydroxylysine, 2-aminoadipate, 5-hydroxyindoleaceate, 7-hydroxyindole sulfate), fatty acids (e.g. oleate/vaccenate, eicosapentaenoate, 16-hydroxypalmitate, stearate), nucleosides (e.g. inosine, N⁶-methyladenosine), and vitamins (e.g. nicotinamide). These results provide the framework for future studies to identify natural chemical compounds to improve poultry growth performance without the use of in-feed antibiotics.

Tannins and Bacitracin Differentially Modulate Gut Microbiota of Broiler Chickens

Antibiotic growth promoters have been used for decades in poultry farming as a tool to maintain bird health and improve growth performance. Global concern about the recurrent emergence and spreading of antimicrobial resistance is challenging the livestock producers to search for alternatives to feed added antibiotics. The use of phytogenic compounds appears as a feasible option due to their ability to emulate the bioactive properties of antibiotics. However, detailed description about the effects of in-feed antibiotics and alternative natural products on chicken intestinal microbiota is lacking. High-throughput sequencing of 16S rRNA gene was used to study composition of cecal microbiota in broiler chickens supplemented with either bacitracin or a blend of chestnut and quebracho tannins over a 30-day grow-out period. Both tannins and bacitracin had a significant impact on diversity of cecal microbiota. Bacitracin consistently decreased Bifidobacterium while other bacterial groups were affected only at certain times. Tannins-fed chickens showed a drastic decrease in genus Bacteroides while certain members of order Clostridiales mainly belonging to the families Ruminococcaceae and Lachnospiraceae were increased. Different members of these groups have been associated with an improvement of intestinal health and feed efficiency in poultry, suggesting that these bacteria could be associated with productive performance of birds.

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.

Diversity of Antimicrobial Resistance Phenotypes in Salmonella Isolated from Commercial Poultry Farms

Salmonella remains the leading cause of foodborne illness in the United States, and the dissemination of drug-resistant Salmonellae through the food chain has important implications for treatment failure of salmonellosis. We investigated the ecology of Salmonella in integrated broiler production in order to understand the flow of antibiotic susceptible and resistant strains within this system. Data were analyzed from a retrospective study focused on antimicrobial resistant Salmonella recovered from commercial broiler chicken farms conducted during the initial years of the US FDA's foray into retail meat surveillance by the National Antimicrobial Resistance Monitoring System (NARMS). Sixty-three percentage of Salmonella were pan-susceptible to a panel of 19 antimicrobials used by the NARMS program. Twenty-five antimicrobial resistance phenotypes were observed in Salmonella isolated from two broiler chicken farms. However, Salmonella displaying resistance to streptomycin, alone, and in combination with other antibiotics was the most prevalent (36.3%) antimicrobial resistance phenotype observed. Resistance to streptomycin and sulfadimethoxine appeared to be linked to the transposon, Tn21. Combinations of resistance against streptomycin, gentamicin, sulfadimethoxine, trimethoprim, and tetracycline were observed for a variety of Salmonella enterica serovars and genetic types as defined by pulsed-field gel electrophoresis. There were within and between farm differences in the antibiotic susceptibilities of Salmonella and some of these differences were linked to specific serovars. However, farm differences were not linked to antibiotic usage. Analysis of the temporal and spatial distribution of the endemic Salmonella serovars on these farms suggests that preventing vertical transmission of antibiotic-resistant Salmonella would reduce carcass contamination with antibiotic-resistant Salmonella and subsequently human risk exposure.

Different antibiotic growth promoters induce specific changes in the cecal microbiota membership of broiler chicken

Antimicrobials are sometimes given to food animals at low doses in order to promote faster growth. However, the mechanisms by which those drugs improve performance are not fully understood. This study aimed to investigate the impact of zinc bacitracin (55g/ton), enramycin (10g/ton); halquinol^® (30g/ton); virginiamycin (16,5g/ton) and avilamycin (10g/ton) on the cecal microbiota of broiler chicken, compared to a control group. Six hundred and twenty four chicks (Cobb 500) arriving to an experimental unit were randomly assigned into each treatment with four repetitions per treatment. The cecal content of 16 animals per treatment (n = 96) was used for DNA extraction and sequencing of the V4 region of the 16S rRNA gene using Illumina technology. The use of antimicrobials induced significant changes in membership but not in structure of the cecal microbiota compared to the control group, suggesting a greater impact on the less abundant species of bacteria present in that environment. Halquinol was the only drug that did not affect microbial membership. Firmicutes comprised the major bacterial phylum present in the cecum of all groups. There was no statistical difference in relative abundances of the main phyla between treated animals and the control group (all P>0.05). Treatment with enramycin was associated with decreased richness and with lower relative abundance of unclassified Firmicutes, Clostridium XI, unclassified Peptostreptococcaceae (all P<0.001) and greater abundance of Clostridium XIVb (P = 0.004) and Anaerosporobacter spp. (P = 0.015), and treatment with bacitracin with greater relative abundance of Bilophila spp. (P = 0.004). Several bacterial genera were identified as representative of usage of each drug. This study used high throughput sequencing to characterize the impact of several antimicrobials in broiler chicken under controlled conditions and add new insights to the current knowledge on how AGPs affect the cecal microbiota of chicken.

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

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

Organic trace mineral supplementation enhances local and systemic innate immune responses and modulates oxidative stress in broiler chickens

The effect of organic trace mineral supplementation on performance, intestinal morphology, immune organ weights (bursa of Fabricius and spleen), expression of innate immune response related genes, blood heterophils/lymphocytes ratio, chemical metabolic panel, natural antibodies (IgG), and oxidative stress of broiler chickens was studied. A total of 1,080 day-old male broilers were assigned to 1 of 3 dietary treatments, which included basal diet with Monensin (control), control diet supplemented with bacitracin methylene disalicylate (BMD), and BMD diet supplemented with organic trace minerals (OTM). No difference in feed conversion ratio was observed among treatments; ileum histomorphological analysis showed a lower crypt depth, higher villi height/crypt depth ratio, and lower villi width in the OTM treatment compared to control. Furthermore, OTM treatment resulted in higher uric acid and lower plasma malondehaldehyde (MDA), indicating lower oxidative stress. Gene expression analysis showed that OTM treatment resulted in up-regulations of TLR2 bin the ileum, and TLR2b, TLR4, and IL-12p35 in the bursa of Fabricius, and down-regulation of TLR2b and TLR4 in the cecal tonsils. In the spleen, OTM treatment resulted in up-regulation of IL-10. In conclusion, OTM supplementation to broiler diets may have beneficial effects on intestinal development, immune system status, and survival by improving ileum histomorphological parameters, modulation of Toll-like receptors and anti-inflammatory cytokines, and decreasing level of MDA, which in conjunction could enhance health status.

Temporal Relationships Exist Between Cecum, Ileum, and Litter Bacterial Microbiomes in a Commercial Turkey Flock, and Subtherapeutic Penicillin Treatment Impacts Ileum Bacterial Community Establishment

Gut health is paramount for commercial poultry production, and improved methods to assess gut health are critically needed to better understand how the avian gastrointestinal tract matures over time. One important aspect of gut health is the totality of bacterial populations inhabiting different sites of the avian gastrointestinal tract, and associations of these populations with the poultry farm environment, since these bacteria are thought to drive metabolism and prime the developing host immune system. In this study, a single flock of commercial turkeys was followed over the course of 12 weeks to examine bacterial microbiome inhabiting the ceca, ileum, and corresponding poultry litter. Furthermore, the effects of low-dose, growth-promoting penicillin treatment (50 g/ton) in feed on the ileum bacterial microbiome were also examined during the early brood period. The cecum and ileum bacterial communities of turkeys were distinct, yet shifted in parallel to one another over time during bird maturation. Corresponding poultry litter was also distinct yet more closely represented the ileal bacterial populations than cecal bacterial populations, and also changed parallel to ileum bacterial populations over time. Penicillin applied at low dose in feed significantly enhanced early weight gain in commercial poults, and this correlated with predictable shifts in the ileum bacterial populations in control versus treatment groups. Overall, this study identified the dynamics of the turkey gastrointestinal microbiome during development, correlations between bacterial populations in the gastrointestinal tract and the litter environment, and the impact of low-dose penicillin on modulation of bacterial communities in the ileum. Such modulations provide a target for alternatives to low-dose antibiotics.

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.

Effect of dietary antimicrobials on immune status in broiler chickens

This study evaluated the effects of dietary anticoccidial drugs plus antibiotic growth promoters (AGPs) on parameters of immunity in commercial broiler chickens. Day-old chicks were raised on used litter from a farm with endemic gangrenous dermatitis to simulate natural pathogen exposure and provided with diets containing decoquinate (DECX) or monensin (COBN) as anticoccidials plus bacitracin methylene disalicylate and roxarsone as AGPs. As a negative control, the chickens were fed with a non-supplemented diet. Immune parameters examined were concanavalin A (ConA)-stimulated spleen cell proliferation, intestine intraepithelial lymphocyte (IEL) and spleen cell subpopulations, and cytokine/chemokine mRNA levels in IELs and spleen cells. ConA-induced proliferation was decreased at 14 d post-hatch in DECX-treated chickens, and increased at 25 and 43 d in COBN-treated animals, compared with untreated controls. In DECX-treated birds, increased percentages of MHC2(+) and CD4(+) IELS were detected at 14 d, but decreased percentages of these cells were seen at 43 d, compared with untreated controls, while increased TCR2(+) IELs were evident at the latter time. Dietary COBN was associated with decreased fractions of MHC2(+) and CD4(+) IELs and reduced percentages of MHC2(+), BU1(+), and TCR1(+) spleen cells compared with controls. The levels of transcripts for interleukin-4 (IL-4), IL-6, IL-17F, IL-13, CXCLi2, interferon-γ (IFN-γ), and transforming growth factorβ4 were elevated in IELs, and those for IL-13, IL-17D, CXCLi2, and IFN-γ were increased in spleen cells, of DECX- and/or COBN-treated chickens compared with untreated controls. By contrast, IL-2 and IL-12 mRNAs in IELs, and IL-4, IL-12, and IL-17F transcripts in spleen cells, were decreased in DECX- and/or COBN-treated chickens compared with controls. These results suggest that DECX or COBN, in combination with bacitracin and roxarsone, modulate the development of the chicken post-hatch immune system.

Lactobacillus sakei modulates mule duck microbiota in ileum and ceca during overfeeding

The supplementation with Lactobacillus sakei as probiotic on the ileal and cecal microbiota of mule ducks during overfeeding was investigated using high-throughput 16S rRNA gene-based pyrosequencing and real-time PCR. The ducks were overfed with or without L. sakei for 12 d with 56% ground corn and 42% whole corn. Samples were collected before the overfeeding period (at 12 wk), at 13 wk (meal 12 of overfeeding), and at 14 wk (meal 24), 3 h postfeeding. Whatever the digestive segment and the level of intake, Firmicutes, Bacteroidetes, and Proteobacteria were the dominant phyla in the bacterial community of mule ducks (at least 90%). Before overfeeding, ileal samples were dominated by Clostridia, Bacteroidia, and Gammaproteobacteria (80% and up), and cecal samples by Bacteroidia and Clostridia (around 85%). The richness and diversity decreased in the ileum and increased in the ceca after overfeeding. Overfeeding increased the relative abundance of Firmicutes and especially the Lactobacillus group in ileal samples. Nonmetric multidimensional scaling profiles separated the bacterial communities with respect to overfeeding only in cecal samples. Richness indicators decreased after L. sakei has been added at mid-overfeeding only in the ileum. In the ceca, the decrease of these indexes only occurred at the end of overfeeding. The addition of L. sakei triggers major changes in the ileum, whereas the ceca are not affected. Lactobacillus sakei decreased the relative abundance of Bacteroides at mid-overfeeding and the relative abundance of Enterobacteria at the end of overfeeding in the ileum.

Microbiota of the chicken gastrointestinal tract: influence on health, productivity and disease

Recent advances in the technology available for culture-independent methods for identification and enumeration of environmental bacteria have invigorated interest in the study of the role of chicken intestinal microbiota in health and productivity. Chickens harbour unique and diverse bacterial communities that include human and animal pathogens. Increasing public concern about the use of antibiotics in the poultry industry has influenced the ways in which poultry producers are working towards improving birds' intestinal health. Effective means of antibiotic-independent pathogen control through competitive exclusion and promotion of good protective microbiota are being actively investigated. With the realisation that just about any change in environment influences the highly responsive microbial communities and with the abandonment of the notion that we can isolate and investigate a single species of interest outside of the community, came a flood of studies that have attempted to profile the intestinal microbiota of chickens under numerous conditions. This review aims to address the main issues in investigating chicken microbiota and to summarise the data acquired to date.

Overfeeding and genetics affect the composition of intestinal microbiota in Anas platyrhynchos (Pekin) and Cairina moschata (Muscovy) ducks

To investigate the effect of overfeeding on the ileal and cecal microbiota of two genotypes of ducks (Pekin and Muscovy), high-throughput 16S rRNA gene-based pyrosequencing was used. The ducks were overfed for 12 days with 58% maize flour and 42% maize grain. Samples were collected before the overfeeding period (at 12 weeks), at 13 weeks, at 14 weeks, and 3 h after feeding. In parallel, ducks fed ad libitum were killed at the same ages. Whatever the digestive segment, the genotype, and the level of intake, Firmicutes and Bacteroidetes are the dominant phyla in the bacterial community of ducks (at least 80%). Before overfeeding, ileal samples were dominated by Bacilli, Clostridia, and Bacteroidia classes (≥ 70%), and cecal samples, by Bacteroidia and Clostridia classes (around 90%) in both Pekin and Muscovy ducks. The richness and diversity decreased in the ileum and increased in the ceca after overfeeding. Overfeeding triggers major changes in the ileum, whereas the ceca are less affected. Overfeeding increased the relative abundance of Clostridiaceae, Lactobacillaceae, Streptococcaceae, and Enterococcaceae families in the ileum, whereas genotype affects particularly three families: Lachnospiraceae, Bacteroidaceae, and Desulfovibrionaceae in the ceca.

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

Food animal production systems have become more consolidated and integrated, producing large, concentrated animal populations and significant amounts of fecal waste. Increasing use of manure and litter as a more "natural" and affordable source of fertilizer may be contributing to contamination of fruits and vegetables with foodborne pathogens. In addition, human and animal manure have been identified as a significant source of antibiotic resistance genes thereby serving as a disseminator of resistance to soil and waterways. Therefore, identifying methods to remediate human and animal waste is critical in developing strategies to improve food safety and minimize the dissemination of antibiotic resistant bacteria. In this study, we sought to determine whether withdrawing antibiotic growth promoters or using alternatives to antibiotics would reduce the abundance of antibiotic resistance genes or prevalence of pathogens in poultry litter. Terminal restriction fragment length polymorphism (T-RFLP) paired with high throughput sequencing was used to evaluate the bacterial community composition of litter from broiler chickens that were treated with streptogramin growth-promoting antibiotics, probiotics, or prebiotics. The prevalence of resistance genes and pathogens was determined from sequencing results or PCR screens of litter community DNA. Streptogramin antibiotic usage did not elicit statistically significant differences in Shannon diversity indices or correlation coefficients among the flocks. However, T-RFLP revealed that there were inter-farm differences in the litter composition that was independent of antibiotic usage. The litter from all farms, regardless of antibiotic usage, contained streptogramin resistance genes (vatA, vatB, and vatE), macrolide-lincosamide-streptogramin B resistance genes (ermA and ermB), the tetracycline resistance gene tetM and class 1 integrons. There was inter-farm variability in the distribution of vatA and vatE with no statistically significant differences with regards to usage. Bacterial diversity was higher in litter when probiotics or prebiotics were administered to flocks but as the litter aged, diversity decreased. No statistically significant differences were detected in the abundance of class 1 integrons where 3%-5% of the community was estimated to harbor a copy. Abundance of pathogenic Clostridium species increased in aging litter despite the treatment while the abundance of tetracycline-resistant coliforms was unaffected by treatment. However some treatments decreased the prevalence of Salmonella. These findings suggest that withdrawing antibiotics or administering alternatives to antibiotics can change the litter bacterial community and reduce the prevalence of some pathogenic bacteria, but may not immediately impact the prevalence of antibiotic resistance.

Dietary plant bioactives for poultry health and productivity

1. Plants and their biologically active chemical constituents, sometimes called secondary metabolites or bioactives, present numerous opportunities for the improvement of livestock production by inclusion in the diet. 2. Many such plant derived materials have well established therapeutic values in man; however, their potential as feed additives in animal production, particularly of poultry, remains largely unexploited. 3. There is increasing evidence indicating that they can be efficient in controlling diseases, and plant bioactives may also influence production parameters such as feed efficiency and product quality. 4. It has been reported that they may even replicate some of the effects of antibiotic growth promoters, which were banned from use in Europe from 2006. 5. This review assesses the status of plant bioactives in poultry production and their mode of action on avian physiology, particularly in the digestive tract.