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

Metagenomic analysis reveals the microbiome and antibiotic resistance genes in indigenous Chinese yellow-feathered chickens

Yellow-feathered chickens have great nutritional value and are widely and traditionally used in China, on an industrial scale as broilers. The presence of intestinal microbes has been shown to correlate with poultry performance and serves as an essential reservoir of antibiotic resistance genes (ARGs). Antibiotic resistance is a major public health concern. Here, we investigated functional characteristics of the gut microbiome of indigenous Chinese yellow-feathered chickens (the Huiyang Bearded, Xinghua, Huaixiang, Zhongshan Shanlan, Qingyuan Partridge, and Yangshan chickens) through metagenomic sequencing and reconstructed 409 draft genomes, including 60 novel species and 6 novel genera. Furthermore, we assessed the functions of the intestinal microbial communities and examined the ARGs within them. The results showed that the microbial populations of yellow-feathered broilers were primarily dominated by Bacteroidetes and Firmicutes at the phylum level and Bacteroides at the genus level. Furthermore, the Qingyuan Partridge chicken showed a significantly higher abundance of Prevotella than the other five breeds of chicken. Principal coordinates analysis indicated significant differences in the structures of microbial communities and ARGs, based on the binary Jaccard distance, among the six chicken breeds. Moreover, 989 ARGs conferring tetracycline, multidrug, and aminoglycoside resistance were identified, which represented more than 80% of the faecal resistomes; the most abundant gene in the yellow-feathered chickens was tet(Q). In addition, we found the greatest abundance of resistance genes in Xinghua chickens, indicating that Xinghua chickens are highly resistant to antibiotics. Overall, our findings revealed differences in the gut microbial community structure of indigenous Chinese yellow-feathered broiler breeds and the composition and characteristics of ARGs and antibiotic resistance that enabled us to reconstruct the yellow-feathered chicken gut microbial community genomes. The current data significantly improves our knowledge of the gut microbiome and antibiotic resistance of popular broiler breeds in China.

Novel strategies to improve chicken performance and welfare by unveiling host-microbiota interactions through hologenomics

Fast optimisation of farming practices is essential to meet environmental sustainability challenges. Hologenomics, the joint study of the genomic features of animals and the microbial communities associated with them, opens new avenues to obtain in-depth knowledge on how host-microbiota interactions affect animal performance and welfare, and in doing so, improve the quality and sustainability of animal production. Here, we introduce the animal trials conducted with broiler chickens in the H2020 project HoloFood, and our strategy to implement hologenomic analyses in light of the initial results, which despite yielding negligible effects of tested feed additives, provide relevant information to understand how host genomic features, microbiota development dynamics and host-microbiota interactions shape animal welfare and performance. We report the most relevant results, propose hypotheses to explain the observed patterns, and outline how these questions will be addressed through the generation and analysis of animal-microbiota multi-omic data during the HoloFood project.

Application of Organic Acids and Essential Oils as Alternatives to Antibiotic Growth Promoters in Broiler Chickens

This study was conducted to evaluate the effects of OAs and EOs on growth performance, serum biochemistry, antioxidant enzyme activities, intestinal morphology, and digestive enzyme activities to replace AGP in broilers. Six hundred one-day-old broilers were allotted to five treatments with six replicates: (1) negative control (NC; basal diet); (2) positive control (PC; NC + 50 mg/kg bacitracin methylene disalicylate); (3) organic acids (OA; NC + 2000 mg/kg OA); (4) essential oils (EO; NC + 300 mg/kg EO); and (5) OA + EO (NC + 2000 mg/kg OA + 300 mg/kg EO). In the starter phase, the PC, EO, and OA + EO groups had a significantly lower feed conversion ratio (FCR) compared to the NC group. While the final body weight (BW) of broilers fed OAs was similar compared to broilers fed PC (p > 0.1), the FCR of the OA group tended to be lower than the PC group on D 42 (p = 0.074). The OA group had the higher serum GLOB:ALB (albumin) and ileal villus height and crypt depth (VH:CD) ratios compared to the EO group. Thus, the supplementation of EOs and OAs could substitute AGP in the starter and finisher phase, respectively.

Recent developments in antimicrobial growth promoters in chicken health: Opportunities and challenges

With a continuously increasing human population is an increasing global demand for food. People in countries with a higher socioeconomic status tend to switch their preferences from grains to meat and high-value foods. Their preference for chicken as a source of protein has grown by 70% over the last three decades. Many studies have shown the role of feed in regulating the animal gut microbiome and its impact on host health. The microbiome absorbs nutrients, digests foods, induces a mucosal immune response, maintains homeostasis, and regulates bioactive metabolites. These metabolic activities are influenced by the microbiota and diet. An imbalance in microbiota affects host physiology and progressively causes disorders and diseases. With the use of antibiotics, a shift from dysbiosis with a higher density of pathogens to homeostasis can occur. However, the progressive use of higher doses of antibiotics proved harmful and resulted in the emergence of multidrug-resistant microbes. As a result, the use of antibiotics as feed additives has been banned. Researchers, regulatory authorities, and managers in the poultry industry have assessed the challenges associated with these restrictions. Research has sought to identify alternatives to antibiotic growth promoters for poultry that do not have any adverse effects. Modulating the host intestinal microbiome by regulating dietary factors is much easier than manipulating host genetics. Research efforts have led to the identification of feed additives, including bacteriocins, immunostimulants, organic acids, phytogenics, prebiotics, probiotics, phytoncides, and bacteriophages. In contrast to focusing on one or more of these alternative bioadditives, an improved feed conversion ratio with enhanced poultry products is possible by employing a combination of feed additives. This article may be helpful in future research towards developing a sustainable poultry industry through the use of the proposed alternatives.

Chicken jejunal microbiota improves growth performance by mitigating intestinal inflammation

Background

Intestinal inflammation is prevalent in chicken, which results in decreased growth performance and considerable economic losses. Accumulated findings established the close relationship between gut microbiota and chicken growth performance. However, whether gut microbiota impacts chicken growth performance by lessening intestinal inflammation remains elusive.

Results

Seven-weeks-old male and female chickens with the highest or lowest body weights were significantly different in breast and leg muscle indices and average cross-sectional area of muscle cells. 16S rRNA gene sequencing indicated Gram-positive bacteria, such as Lactobacilli, were the predominant species in high body weight chickens. Conversely, Gram-negative bacteria, such as Comamonas, Acinetobacter, Brucella, Escherichia-Shigella, Thermus, Undibacterium, and Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium were significantly abundant in low body weight chickens. Serum lipopolysaccharide (LPS) level was significantly higher in low body weight chickens (101.58 ± 5.78 ng/mL) compared with high body weight chickens (85.12 ± 4.79 ng/mL). The expression of TLR4, NF-κB, MyD88, and related inflammatory cytokines in the jejunum was significantly upregulated in low body weight chickens, which led to the damage of gut barrier integrity. Furthermore, transferring fecal microbiota from adult chickens with high body weight into 1-day-old chicks reshaped the jejunal microbiota, mitigated inflammatory response, and improved chicken growth performance.

Conclusions

Our findings suggested that jejunal microbiota could affect chicken growth performance by mitigating intestinal inflammation.

Effect of Raw Chickpea in the Broiler Chicken Diet on Intestinal Histomorphology and Intestinal Microbial Populations

The aim of the study was to determine the effect of partial replacement of SBM protein with CPR-derived protein in the broiler rearing period from 22 to 42 days of age on the intestinal histomorphology and the composition of the intestinal microbial population. Male broiler chicks aged 1 day were assigned to two groups with different nutrition schemes (n = 100 in each, 5 cages of 20 chicks in each). The chickens were reared for 42 days. All birds were fed isonitrogenous and isoenergetic diets: starter (1 to 21 d), grower (22 to 35 d), and finisher (36 to 42 d). From rearing day 22, different diets were provided to the birds: the SBM group received feed with 100% soybean meal protein, and the diet of the CPR group the protein originated from soybean meal was replaced by 50% chickpea protein. The study results indicated a significant impact of the inclusion of CPR in the diet on the basic intestinal structures (thickness of myenteron: submucosa, jejunum and duodenum mucosa, and jejunum transversal lamina). The addition of CPR led to shortening of intestinal villi, an increase in villus thickness, and reduced intestine absorptive surface in the duodenum and jejunum. The CPR group exhibited a significantly lower villus length-to-crypt depth ratio in the jejunum (p < 0.001). The inclusion of chickpeas in the diet increased the total count of mesophilic bacteria and coliforms in the intestinal contents (p < 0.05). In summary, it has been demonstrated that the inclusion of CPR in the diet induced considerable disturbances in metabolism and intestinal structure. Although CPR is a cheap protein source, its use in poultry diet does not ensure development of the intestinal structure comparable to that in the case of an SBM-only diet.

The Growth Performance, Nutrient Digestibility, Gut Bacteria and Bone Strength of Broilers Offered Alternative, Sustainable Diets Varying in Nutrient Specification and Phytase Dose

This study assessed the use of locally sourced sustainable feed ingredients, rapeseed meal (RSM) and maize dried distiller grains with solubles (DDGS) in diets over traditional ingredients on the growth performance, bone strength and nutrient digestibility of broilers. This work also investigated the effects of supplementing exogenous phytase in two doses (500 vs. 1500 FTU/kg). Using male Ross 308 chicks (n = 320) assigned to receive one of four experimental diets: (1) Positive control diet 1 (PC1), a wheat, soya-based diet + 500 FTU/kg phytase. (2) Positive control diet 2, RSM/DDGS diet + 500 FTU/kg phytase (PC2). (3) Negative control (NC) reduced nutrient RSM/DDGS diet, no phytase. (4) The NC diet plus 1500 FTU/kg phytase (NC+). PC1 birds displayed higher feed intake and body weight gain consistently throughout the trial (p < 0.001) as well as increased body weight by 28 d and 42 d (p < 0.001). Whole-body dual emission X-ray absorptiometry (DXA) analysis revealed PC1 birds also had higher bone mineral density (BMD), bone mineral content (BMC), total bone mass, total lean mass and total fat mass than birds offered other treatments (p < 0.01). Diet had no significant effect on bone strength. Phytase superdosing improved the digestibility of dry matter (DM), neutral detergent fibre (NDF), gross energy (GE), calcium (Ca), potassium (K) and magnesium (Mg) compared to birds in other treatment groups. The phytase superdose also improved performance in comparison to birds offered the NC diet. Phytase superdosing increased the IP6 and IP5 degradation and increased the ileal inositol concentration of the birds. N excretion was lower for birds offered the traditional wheat−soya diet and highest for those offered the high-specification RSM/DDGS diet with a commercial dose of phytase. The addition of a phytase superdose to the negative control diet (NC+) reduced P excretion of birds by 15% compared to birds offered NC.

Cecal Microbial Hydrogen Cycling Potential Is Linked to Feed Efficiency Phenotypes in Chickens

In chickens, early life exposure to environmental microbes has long-lasting impacts on gastrointestinal (GI) microbiome development and host health and growth, via mechanisms that remain uncharacterized. In this study, we demonstrated that administrating a fecal microbiome transplant (FMT) from adults to day-of-hatch chicks results in significantly higher body mass of birds and decreased residual feed intake (RFI), implying enhanced feed efficiency, at 6 weeks of age. To assess the potential mechanisms through which FMT affects adult bird phenotype, we combined 16 S rRNA gene amplification, metagenomic, and comparative genomic approaches to survey the composition and predicted activities of the resident microbiome of various GI tract segments. Early life FMT exposure had a long-lasting significant effect on the microbial community composition and function of the ceca but not on other GI segments. Within the ceca of 6-week-old FMT birds, hydrogenotrophic microbial lineages and genes were most differentially enriched. The results suggest that thermodynamic regulation in the cecum, in this case via hydrogenotrophic methanogenic and sulfur-cycling lineages, potentially serving as hydrogen sinks, may enhance fermentative efficiency and dietary energy harvest capacity. Our study provides a specific mechanism of action through which early-life microbiome transplants modulate market-relevant phenotypes in poultry and, thereby, may represent a significant advance toward microbiome-focused sustainable agriculture.

Comparative Efficacy of Fish Meal Replacement With Enzymatically Treated Soybean Meal on Growth Performance, Immunity, Oxidative Capacity and Fecal Microbiota in Weaned Pigs

This study investigated the growth performance, immunity, antioxidant capacity and fecal microbiota of weaned pigs by partially or completely replacing dietary fish meal with enzymatically treated soybean meal. A total of 144 piglets (initial body weight of 7.19 ± 0.11 kg) weaned at 28 d were allotted to 3 dietary treatments (6 replicates per treatment): 4% fish meal diet (FM); 2% fishmeal plus 6% enzymatically treated soybean meal (ESBM1); and 6% enzymatically treated soybean meal without fish meal (ESBM2). The experimental period was 28 d, serum was collected at day 14 and day 28 for biochemical parameters analysis, feces was obtained for microbiota analysis at 28d. The body weight, average daily gain and average daily feed intake of piglets in the ESBM2 group were significantly increased compared with those in the FM and ESBM1 groups from 0 to 28 d, respectively (P < 0.05). The diets with enzymatically treated soybean meal in ESBM1 and ESBM2 groups decreased the diarrhea rate (P < 0.05). Compared with FM, ESBM1 and ESBM2 decreased 5-hydroxytryptamine (5-HT) (P < 0.05). ESBM1 decreased diamine oxidase (DAO) and Interleukin 6 (IL-6) compared with FM and ESBM2 (P < 0.05). ESBM1 decreased serum Interleukin 1β (IL-1β) compared with FM at d 14 (P < 0.05). The serum Immunoglobulin E (IgE), secretory curl associated protein 5 (sFRP-5) were higher in ESBM1 compared with FM and ESBM2 (P < 0.05). ESBM2 increased super oxidase dismutase (SOD) level and decreased malondialdehyde (MDA) content compared with FM and ESBM1, the concentration of SOD in ESBM1was higher than that in FM (P < 0.05). ESBM1 decreased cortisol and caspase 3 (Casp-3) (P < 0.05). FM showed a higher content of tri-iodothyronine (T3) (P < 0.05) and a lower thyroxine/ tri-iodothyronine ratio compared with those in the other two groups (P < 0.05). The concentration of leptin was lower in ESBM2 (P < 0.05). ESBM1 had a higher α-diversity than ESBM2 (P < 0.05). The microbiota composition was different among three treatments (difference between FM and ESBM1, p = 0.005; FM and ESBM2, p = 0.009; ESBM1 and ESBM2, p = 0.004). ESBM2 tend to increase the abundance of Firmicutes (P = 0.070) and decrease Bacteroidetes (P = 0.069). ESBM2 decreased the abundance of Parabacteroides and increased SMB53 compared with FM (P < 0.05). The spearman correlation analysis revealed that the abundance of Parabacteroides enriched in FM group was negatively correlated with SOD, Megasphaera enriched in ESBM2 group were positively correlated with SOD. The abundance of Lachnospira enriched in ESBM2 group were negatively correlated with serum concentration of D-lactate, DAO, IL-6, and NO. In conclusion, under the conditions of this study, diet with only ESBM demonstrate the beneficial impact on intestinal microbiota developments, antioxidant capacity as well as growth performance for weaned pigs.

Caecal microbiota composition of experimental inbred MHC-B lines infected with IBV differs according to genetics and vaccination

Interactions between the gut microbiota and the immune system may be involved in vaccine and infection responses. In the present study, we studied the interactions between caecal microbiota composition and parameters describing the immune response in six experimental inbred chicken lines harboring different MHC haplotypes. Animals were challenge-infected with the infectious bronchitis virus (IBV), and half of them were previously vaccinated against this pathogen. We explored to what extent the gut microbiota composition and the genetic line could be related to the immune response, evaluated through flow cytometry. To do so, we characterized the caecal bacterial communities with a 16S rRNA gene amplicon sequencing approach performed one week after the IBV infectious challenge. We observed significant effects of both the vaccination and the genetic line on the microbiota after the challenge infection with IBV, with a lower bacterial richness in vaccinated chickens. We also observed dissimilar caecal community profiles among the different lines, and between the vaccinated and non-vaccinated animals. The effect of vaccination was similar in all the lines, with a reduced abundance of OTU from the Ruminococcacea UCG-014 and Faecalibacterium genera, and an increased abundance of OTU from the Eisenbergiella genus. The main association between the caecal microbiota and the immune phenotypes involved TCR_ϒδ expression on TCR_ϒδ⁺ T cells. This phenotype was negatively associated with OTU from the Escherichia-Shigella genus that were also less abundant in the lines with the highest responses to the vaccine. We proved that the caecal microbiota composition is associated with the IBV vaccine response level in inbred chicken lines, and that the TCR_ϒδ⁺ T cells (judged by TCR_ϒδ expression) may be an important component involved in this interaction, especially with bacteria from the Escherichia-Shigella genus. We hypothesized that bacteria from the Escherichia-Shigella genus increased the systemic level of bacterial lipid antigens, which subsequently mitigated poultry γδ T cells.

Altitude-adaption of gut microbiota in Tibetan chicken

Low oxygen levels and extremely cold weather in high-altitude environments requires more energy intake to maintain body temperature in animals. However, little is known about the characteristics of cecal and ileac microbiota in Tibetan chicken and how the high and low altitude environments affect the gut microbiota communities in Tibetan chicken. In the present study, In the present study, Tibetan chickens (Group HA, 3572 m, 578.5 Pa) and their introduced flatland counterparts (Group LA, 580 m, 894.6 Pa) in the cecum and ileum to identify the possible bacterial species that are helpful for their host in environmental adaption. High-throughput sequencing was used to sequence the V3 to V4 hypervariable regions of the bacterial 16S rRNA gene. By comparing the gut microbial diversity of HA chicken with that of LA, the results indicated that the microbial diversity of the cecum and ileum in group HA was significantly lower (P < 0.05) than those in group LA. The cecum microbiome maintained higher population diversity and richness than the ileum (P < 0.05). Four phyla Firmicutes, Bacterioidetes, Actinobacteria, and Proteobacteria were dominant in two groups. Interestingly, there were significant differences in abundance ratio among the four groups (P < 0.05). The predominant bacteria in HA and LA ileum belong to Proteobacteria and Firmicutes, whereas in cecum, Bacterioidetes and Actinobacteria were predominant in both groups (P < 0.05). Correlation analysis showed that Sporosarcina, Enterococcus, and Lactococcus were strongly related to air pressure, and Peptoclostridium and Ruminococcaceae_UCG-014 are related to altitude and gut microbiota of LA group was influenced by altitude, while HA group affected by air pressure. Meanwhile, the Ruminococcus-torques-group was negatively correlated with the relative abundance of Paenibacillus, and positive correlated with those of other microorganisms. Furthermore, HA has higher abundance of microbiota involved in energy and glycan biosynthesis metabolism pathway, while LA has higher abundance of microbiota involved in membrane transport, signal transduction, and xenobiotics biodegradation and metabolism. Generally, our results suggested that the composition and diversity of gut microbes changed after Tibetan chickens were introduced to the plain. Tibetan chicken may adapt to new environment via reshaping the gut microbiota. Gut microbes may contribute to the host adaption to high altitude environments by increasing host energy and glycan biosynthesis.

The Microbial Community of the Respiratory Tract of Commercial Chickens and Turkeys

Respiratory tract health critically affects the performance of commercial poultry. This report presents data on the microbial community in these organs from a comprehensive study of laying chickens and turkey breeders. The main objective was to characterize and compare the compositions of the respiratory system bacteria isolated from birds of different ages and geographical locations in Poland. Using samples from 28 turkey and 26 chicken flocks, the microbial community was determined by 16S ribosomal RNA sequencing. There was great variability between flocks. The diversity and abundance of upper respiratory tract (URT) bacteria was greater in chickens than in turkeys. At the phyla level, the URT of the chickens was heavily colonized by Proteobacteria, which represented 66.4% of the total microbiota, while in turkeys, this phylum constituted 42.6% of all bacteria. Firmicutes bacteria were more abundant in turkeys (43.2%) than in chickens (24.1%). The comparison of the respiratory tracts at the family and genus levels showed the diversity and abundance of amplicon sequence variants (ASV) differing markedly between the species. Potentially pathogenic bacteria ASV were identified in the respiratory tract, which are not always associated with clinical signs, but may affect bird productivity and performance. The data obtained, including characterization of the bacterial composition found in the respiratory system, may be useful for developing effective interventions strategies to improve production performance and prevent and control disease in commercial laying chickens and turkeys.

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.

A Complex Competitive Exclusion Culture Reduces Campylobacter jejuni Colonization in Broiler Chickens at Slaughter Age In Vivo

Diminishing Campylobacter prevalence in poultry flocks has proven to be extremely challenging. To date, efficacious control measures to reduce Campylobacter prevalence are still missing. A potential approach to control Campylobacter in modern poultry productions is to occupy its niche in the mucosal layer by administering live intestinal microbiota from adult chickens to dayold-chicks (competitive exclusion (CE)). Therefore, this in vivo study investigates the efficacy of a complex CE culture to reduce Campylobacter (C.) jejuni colonization in broiler chickens. For this purpose, the complex CE culture was applied twice: once by spray application to day-old chicks immediately after hatching (on the 1st day of life) and subsequently by an additional application via drinking water on the 25th day of life. We observed a consistent and statistically significant reduction of C. jejuni counts in cloacal swabs throughout the entire fattening period. At the end of the trial after necropsy (at 33 days of age), C. jejuni cecal counts also showed a statistically significant decrease of 1 log₁₀ MPN/g compared to the control group. Likewise, colon counts were reduced by 2.0 log₁₀ MPN/g. These results suggest that CE cultures can be considered a practically relevant control strategy to reduce C. jejuni colonization in broiler chickens on poultry farms.

Ileal Microbiota Alters the Immunity Statues to Affect Body Weight in Muscovy Ducks

The ileum is mainly responsible for food absorption and nutrients transportation. The microbes in its intestinal lumen play an essential role in the growth and health of the host. However, it is still unknown how the ileal microbes affect the body weight of the host. In this study, we used Muscovy ducks as an animal model to investigate the relationship between the ileal microbes and body weight and further explore the potential mechanism. The ileum tissue and ileal contents of 200 Muscovy ducks were collected for mRNA extraction and real-time quantitative PCR, as well as DNA separation and 16S rRNA gene sequencing. With body weight being ranked, the bottom 20% (n = 40) and top 20% (n = 40) were set as the low and high groups, respectively. Our results showed that in the ileum of Muscovy ducks, the Bacteroides, Firmicutes, and Proteobacteria were the predominant phyla with the 10 most abundant genera, namely Candidatus Arthromitus, Bacteroides, Streptococcus, Vibrio, Romboutsia, Cetobacterium, Clostridium sensu stricto 1, Terrisporobacter, Escherichia-Shigella, and Lactobacillus. We identified Streptococcus, Escherichia-Shigella, Candidatus Arthromitus, Bacteroides, Faecalibacterium, and Oscillospira were closely correlated to the growth of Muscovy ducks. Streptococcus and Escherichia-Shigella were negatively related to body weight (BW), while Candidatus Arthromitus, Bacteroides, Faecalibacterium, and Oscillospira were positively associated with BW. In addition, we found that the relative expression levels of tight junction proteins (Claudin 1, Claudin 2, ZO-1 and ZO-2) in the high group showed an upward trend, although this trend was not significant (P > 0.05). The expression of pro-inflammatory factors (IL-1β, IL-2 and TNF-α) decreased in the high group, while the anti-inflammatory factor IL-10 increased. Of course, except IL-2, these differences were not significant (P > 0.05). Finally, the correlation analysis showed that Escherichia-Shigella was significantly positively correlated with IL-1β (P < 0.05). These findings may provide fundamental data for the development of next-generation probiotics and assist the development of strategies for changing the gut microbiota to promote the growth performance in the duck industry.

Multi-Omics Reveals Different Strategies in the Immune and Metabolic Systems of High-Yielding Strains of Laying Hens

Lohmann Brown (LB) and Lohmann Selected Leghorn (LSL) are two commercially important laying hen strains due to their high egg production and excellent commercial suitability. The present study integrated multiple data sets along the genotype-phenotype map to better understand how the genetic background of the two strains influences their molecular pathways. In total, 71 individuals were analyzed (LB, n = 36; LSL, n = 35). Data sets include gut miRNA and mRNA transcriptome data, microbiota composition, immune cells, inositol phosphate metabolites, minerals, and hormones from different organs of the two hen strains. All complex data sets were pre-processed, normalized, and compatible with the mixOmics platform. The most discriminant features between two laying strains included 20 miRNAs, 20 mRNAs, 16 immune cells, 10 microbes, 11 phenotypic traits, and 16 metabolites. The expression of specific miRNAs and the abundance of immune cell types were related to the enrichment of immune pathways in the LSL strain. In contrast, more microbial taxa specific to the LB strain were identified, and the abundance of certain microbes strongly correlated with host gut transcripts enriched in immunological and metabolic pathways. Our findings indicate that both strains employ distinct inherent strategies to acquire and maintain their immune and metabolic systems under high-performance conditions. In addition, the study provides a new perspective on a view of the functional biodiversity that emerges during strain selection and contributes to the understanding of the role of host–gut interaction, including immune phenotype, microbiota, gut transcriptome, and metabolome.

Dietary Probiotic Supplementation Suppresses Subclinical Necrotic Enteritis in Broiler Chickens in a Microbiota-Dependent Manner

Background

Chicken meat is one of the most consumed meats worldwide and poultry production is increasing at an exponential rate. Reducing antibiotic usage has resulted in the recurrence of subclinical necrotic enteritis again and influenced global poultry production. Probiotics are potential antibiotic substitutes that can be used to prevent subclinical necrotic enteriti. However, the precise mechanism of action of probiotics and information on which gut microbes confer this efficacy remain elusive.

Methods and results

The subclinical necrotic enteritis animal model was used to reveal the mechanism underlying the effect of probiotics on intestinal health through RNA sequencing and 16S rDNA amplicon sequencing. Bacillus licheniformis H2 feeding significantly reduced the relative abundance of Clostridium perfringens in the ileum and markedly ameliorated the pathological damage in the ileum and liver. In addition, oral administration of B. licheniformis H2 contributed to the enhancement of the intestinal barrier function and epithelial renewal, reducing energy consumption, and improving enteral nutrition absorption. Probiotic B. licheniformis H2 also ameliorated the inflammatory response and increased the immunity of subclinical necrotic enteritis infected broilers. Finally, B. licheniformis H2 feeding regulated liver gene expression to suppress immune response and promoted growth and metabolism depending on the gut microbiota.

Conclusions

These results indicated the mechanism of probiotic action of B. licheniformis H2 in maintaining intestinal health and thus promoting growth and B. licheniformis H2 may serve as an antibiotic substitute to prevent subclinical necrotic enteritis in poultry farming.

A carvacrol‐based product reduces Campylobacter jejuni load and alters microbiota composition in the caeca of chickens

Aim

This study was conducted to test the ability of a carvacrol‐based formulation (Phodé, France) to decrease the C. jejuni caecal load in inoculated broiler chickens and to study the impact of the C. jejuni inoculation alone or combined with the product, on the caecal microbiota.

Methods and Results

On day 1, chickens were either fed a control feed or the same diet supplemented with a carvacrol‐based product. On day 21, the carvacrol‐supplemented chickens and half of the non‐supplemented chickens were inoculated with C. jejuni (10⁸ CFU). Quantitative PCR was used to quantify C. jejuni in chicken caecal samples and 16S rRNA gene sequencing was carried out at 25, 31 and 35 days of age. A significant decrease of 1.4 log of the C. jejuni caecal load was observed in 35‐day‐old chickens supplemented with the product, compared to the inoculated and unsupplemented group (p < 0.05). The inoculation with C. jejuni significantly increased the population richness, Shannon and Simpson diversity and altered beta‐diversity. Compared to the control group, the C. jejuni inoculation causes significant changes in the microbiota. The carvacrol‐based product associated with C. jejuni inoculation increased the diversity and strongly modified the structure of the microbial community. Functional analysis by 16S rRNA gene‐based predictions further revealed that the product up‐regulated the pathways involved in the antimicrobial synthesis, which could explain its shaping effect on the caecal microbiota.

Conclusions

Our study confirmed the impairment of the caecal bacterial community after inoculation and demonstrated the ability of the product to reduce the C. jejuni load in chickens. Further investigations are needed to better understand the mode of action of this product to promote the installation of a beneficial microbiota to its host.

Significance and Impact of the Study

Results suggested that this product could be promising to control C. jejuni contamination of broilers.

Role of diet-microbiota interactions in precision nutrition of the chicken: facts, gaps, and new concepts

In the intestine, host-derived factors are genetically hardwired and difficult to modulate. However, the intestinal microbiome is more plastic and can be readily modulated by dietary factors. Further, it is becoming more apparent that the microbiome can potentially impact poultry physiology by participating in digestion, the absorption of nutrients, shaping of the mucosal immune response, energy homeostasis, and the synthesis or modulation of several potential bioactive metabolites. These activities are dependent on the quantity and quality of the microbiota alongside its metabolic potential, which are dictated in large part by diet. Thus, diet-induced microbiota alterations may be harnessed to induce changes in host physiology, including disease development and progression. In this regard, the gut microbiome is malleable and renders the gut microbiome a candidate 'organ' for the possibility of precision nutrition to induce precision microbiomics-the use of the gut microbiome as a biomarker to predict responsiveness to specific dietary constituents to generate precision diets and interventions for optimal poultry performance and health. However, it is vital to identify the causal relationships and mechanisms by which dietary components and additives affect the gut microbiome which then ultimately influence avian physiology. Further, an improved understanding of the spatial and functional relationships between the different sections of the avian gut and their regional microbiota will provide a better understanding of the role of the diet in regulating the intestinal microbiome.

A Probabilistic Structural Equation Model to Evaluate Links between Gut Microbiota and Body Weights of Chicken Fed or Not Fed Insect Larvae

Simple Summary

Feeding poultry with insects could reduce production costs, but the impact of this diet on their gut microbiota and growth is little known because the network of relationships between their weights, the composition of their microbiota and their diet is complex and potentially biased by confounding factors (such as the gut compartment, age and sex of the birds). In this study, we were able to unravel these relationships in local breed chickens fed or not fed with black soldier fly larvae thanks to a technique of artificial intelligence (the probabilistic structural equation model). Bacteria were grouped into few entities with distinctive metabolic attributes and were probably linked nutritionally. Birds’ age influenced body weights and bacterial composition. The proposed methodology was thus able to simplify the complex dependencies among bacteria present in the gut and to highlight links potentially important in the response of chicken to insect feed.

Abstract

Feeding chicken with black soldier fly larvae (BSF) may influence their rates of growth via effects on the composition of their gut microbiota. To verify this hypothesis, we aim to evaluate a probabilistic structural equation model because it can unravel the complex web of relationships that exist between the bacteria involved in digestion and evaluate whether these influence bird growth. We followed 90 chickens fed diets supplemented with 0%, 5% or 10% BSF and measured the strength of the relationship between their weight and the relative abundance of bacteria (OTU) present in their cecum or cloaca at 16, 28, 39, 67 or 73 days of age, while adjusting for potential confounding effects of their age and sex. Results showed that OTUs (62 genera) could be combined into ten latent constructs with distinctive metabolic attributes. Links were discovered between these constructs that suggest nutritional relationships. Age directly influenced weights and microbiotal composition, and three constructs indirectly influenced weights via their dependencies on age. The proposed methodology was able to simplify dependencies among OTUs into knowledgeable constructs and to highlight links potentially important to understand the role of insect feed and of microbiota in chicken growth.

Cecal Microbiota of Free-Range Hens Varied With Different Rearing Enrichments and Ranging Patterns

Free-range pullets are reared indoors but the adult hens can go outside which is a mismatch that may reduce adaptation in the laying environment. Rearing enrichments might enhance pullet development and adaptations to subsequent free-range housing with impact on behavior and health measures including gut microbiota. Adult free-range hens vary in range use which may also be associated with microbiota composition. A total of 1,700 Hy-Line Brown^® chicks were reared indoors across 16 weeks with three enrichment treatment groups: “control” with standard litter housing, “novelty” with weekly changed novel objects, and “structural” with custom-designed perching structures in the pens. At 15 weeks, 45 pullet cecal contents were sampled before moving 1,386 pullets to the free-range housing system. At 25 weeks, range access commenced, and movements were tracked via radio-frequency identification technology. At 65 weeks, 91 hens were selected based on range use patterns (“indoor”: no ranging; “high outdoor”: daily ranging) across all rearing enrichment groups and cecal contents were collected for microbiota analysis via 16S rRNA amplicon sequencing at V3-V4 regions. The most common bacteria in pullets were unclassified Barnesiellaceae, Prevotella, Blautia and Clostridium and in hens Unclassified, Ruminococcus, unclassified Lachnospiraceae, unclassified Bacteroidales, unclassified Paraprevotellaceae YRC22, and Blautia. The microbial alpha diversity was not significant within the enrichment/ranging groups (pullets: P ≥ 0.17, hen rearing enrichment groups: P ≥ 0.06, hen ranging groups: P ≥ 0.54), but beta diversity significantly varied between these groups (pullets: P ≤ 0.002, hen rearing enrichment groups: P ≤ 0.001, hen ranging groups: P ≤ 0.008). Among the short-chain fatty acids (SCFAs), the propionic acid content was higher (P = 0.03) in the novelty group of pullets than the control group. There were no other significant differences in the SCFA contents between the rearing enrichment groups (all P ≥ 0.10), and the ranging groups (all P ≥ 0.17). Most of the genera identified were more abundant in the indoor than high outdoor hens. Overall, rearing enrichments affected the cecal microbiota diversity of both pullets and adult hens and was able to distinguish hens that remained inside compared with hens that ranging daily for several hours.

Probiotics, Prebiotics, and Phytogenic Substances for Optimizing Gut Health in Poultry

The gut microbiota has been designated as a hidden metabolic ‘organ’ because of its enormous impact on host metabolism, physiology, nutrition, and immune function. The connection between the intestinal microbiota and their respective host animals is dynamic and, in general, mutually beneficial. This complicated interaction is seen as a determinant of health and disease; thus, intestinal dysbiosis is linked with several metabolic diseases. Therefore, tractable strategies targeting the regulation of intestinal microbiota can control several diseases that are closely related to inflammatory and metabolic disorders. As a result, animal health and performance are improved. One of these strategies is related to dietary supplementation with prebiotics, probiotics, and phytogenic substances. These supplements exert their effects indirectly through manipulation of gut microbiota quality and improvement in intestinal epithelial barrier. Several phytogenic substances, such as berberine, resveratrol, curcumin, carvacrol, thymol, isoflavones and hydrolyzed fibers, have been identified as potential supplements that may also act as welcome means to reduce the usage of antibiotics in feedstock, including poultry farming, through manipulation of the gut microbiome. In addition, these compounds may improve the integrity of tight junctions by controlling tight junction-related proteins and inflammatory signaling pathways in the host animals. In this review, we discuss the role of probiotics, prebiotics, and phytogenic substances in optimizing gut function in poultry.

Coccidiosis: Recent Progress in Host Immunity and Alternatives to Antibiotic Strategies

Coccidiosis is an avian intestinal disease caused by several distinct species of Eimeria parasites that damage the host’s intestinal system, resulting in poor nutrition absorption, reduced growth, and often death. Increasing evidence from recent studies indicates that immune-based strategies such as the use of recombinant vaccines and various dietary immunomodulating feed additives can improve host defense against intracellular parasitism and reduce intestinal damage due to inflammatory responses induced by parasites. Therefore, a comprehensive understanding of the complex interactions between the host immune system, gut microbiota, enteroendocrine system, and parasites that contribute to the outcome of coccidiosis is necessary to develop logical strategies to control coccidiosis in the post-antibiotic era. Most important for vaccine development is the need to understand the protective role of the local intestinal immune response and the identification of various effector molecules which mediate anti-coccidial activity against intracellular parasites. This review summarizes the current understanding of the host immune response to coccidiosis in poultry and discusses various non-antibiotic strategies which are being developed for coccidiosis control. A better understanding of the basic immunobiology of pertinent host–parasite interactions in avian coccidiosis will facilitate the development of effective anti-Eimeria strategies to mitigate the negative effects of coccidiosis.

Blue Light Alters the Composition of the Jejunal Microbiota and Promotes the Development of the Small Intestine by Reducing Oxidative Stress

Environmental light has an important impact on the growth, development and oxidative stress of chicks. Thus, we investigated the effects of colored lights on microbes and explored the molecular mechanism by which external color light information alters the gut microbiota and induces the cell response in vivo. We raised 96 chicks under 400-700 nm white (WL), 660 nm red (RL), 560 nm green (GL) or 480 nm blue light (BL) for 42 days. We used 16S rRNA high-throughput pyrosequencing and gas chromatography to explore the effect of different monochromatic lights on the jejunal microbiota. We used qRT-PCR, western blotting, immunohistochemistry and Elisa to determine the effect of different monochromatic lights on small intestine development and oxidative stress levels. With consistency in the upregulation of antioxidant enzyme ability and anti-inflammatory cytokine level, the 16S rRNA and gas chromatography results showed that BL significantly increased the diversity and richness of the jejunal microbiota and improved the relative abundances of Faecalibacterium, Ruminiclostridium_9 and metabolite butyrate content compared with WL, RL and GL (p < 0.05). In addition, we observed that BL increased the goblet cell numbers, PCNA cell numbers, villus-length-to-crypt-depth (V/C) ratios, ZO-1, Occludin, and Claudin-1 protein expression; decreased permeability; and enhanced the digestion and absorption capacity in the jejunum (p < 0.05). In the in vitro experiment, we found that butyrate promoted chick small intestinal epithelial cell (CIEC) proliferation and inhibited apoptosis (p < 0.05). These responses were abrogated by the Gi inhibitor, PI3K inhibitor or AKT inhibitor, but were mimicked by GPR43 agonists or the GSK-3β inhibitor (p < 0.05). Overall, these findings suggested that BL increased the relative abundance of Faecalibacterium, Ruminiclostridium_9 and butyrate production. Butyrate may act as one of the signals to mediate blue-light-induced small intestinal development and mucosal barrier integrity enhancement and promote cell proliferation via the GPR43/Gi/PI3K/AKT/p-GSK-3β/β-catenin pathway.

Characteristics of Essential Oils of Apiaceae Family: Their Chemical Compositions, in vitro Properties and Effects on Broiler Production

There has been an upsurge of interest in the phytobiotics coincident with the onset of the potential ban on the use of antibiotic growth promoters (AGPs) in the broiler industry and because many kinds of nutraceuticals play an important role in improving growth performance, feed efficiency, and gut health of broilers. In the previous years, significant biological activities of essential oils (EOs) belonging to phytobiotics were observed, including anti-bacterial, antifungal, antiviral, and antioxidant properties. We found new perspectives on the roles of EOs, particularly extracts from the Apiaceae family, which is one of the largest plant families, in potential replacement of AGPs, and on the chemical composition involved in regulating microorganism activity and oxidative damage. Furthermore, the positive effects of EOs on broiler production and the possible mechanisms inducing the involvement of gut health and growth performance have been studied.

Effects of a blend of chestnut and quebracho tannins on gut health and performance of broiler chickens

Antimicrobial restrictions prompted the search for cost and biologically effective alternatives to replace antimicrobial growth promoters (AGPs) in food-producing animals. In addition, the efficacy of this alternatives needs to be contrasted in field/commercial trials under different challenge conditions. However only a few studies describing the impact of tannins or others AGP-alternatives in commercial poultry production conditions are actually available. The aim of the present work is to study how the inclusion of a blend of chestnut and quebracho tannins can affect broiler productive performance and health under commercial conditions. Three experiments with different approaches were conducted: (1) a trial comparing the effects of both additives (tannins vs AGP) on different commercial farms at the same time; (2) the follow-up of one farm during an entire productive year; and (3) an experimental trial using a C. perfringens challenge model in broiler chickens. Although productive results from field trials were similar among treatments, evaluations of gut health indicators showed improvements in the tannins treated flocks. Frequency and severity of intestinal gross lesions were reduced in jejunum (42% vs 23%; p<0.05-1.37 vs. 0.73; p<0.01, respectively) and ileum (25% vs. 10%; p<0.0.5-1.05 vs. 0.58; p<0.01) in tannins treated birds. Results from 16S studies, show that cecal microbiota diversity was not differentially affected by AGPs or tannins, but changes in the relative abundance of certain taxa were described, including Lactobacillus and Bifidobacterium groups. Results from experimental C. perfringens necrotic enteritis showed that tannins treated birds had reduced incidence of gross lesions in jejunum (43.75 vs. 74.19%; p<0.01) and ileum (18.75% vs. 45.16%; p<0.05) compared with control. These results suggest that AGPs can be replaced by tannins feed additives, and contribute in the implementation of antimicrobial-free programs in broilers without affecting health or performance.

Impact of Dietary Sodium Butyrate and Salinomycin on Performance and Intestinal Microbiota in a Broiler Gut Leakage Model

Unfavorable alterations of the commensal gut microbiota and dysbacteriosis is a major health problem in the poultry industry. Understanding how dietary intervention alters the microbial ecology of broiler chickens is important for prevention strategies. A trial was conducted with 672 Ross 308 day-old male broilers fed a basic diet (no additives, control) or the basic diet supplemented with 500 mg/kg encapsulated butyrate or 68 mg/kg salinomycin. Enteric challenge was induced by inclusion of 50 g/kg rye in a grower diet and oral gavage of a 10 times overdose of a vaccine against coccidiosis. Compared to control and butyrate-supplemented birds, salinomycin supplementation alleviated growth depression. Compared to butyrate and non-supplemented control, salinomycin increased potentially beneficial Ruminococcaceae and reduced potentially pathogenic Enterobacteriaceae and counts of Lactobacillus salivarius and Clostridium perfringens. Further, salinomycin supplementation was accompanied by a pH decrease and succinic acid increase in ceca, while coated butyrate (0.5 g/kg) showed no or limited effects. Salinomycin alleviated growth depression and maintained intestinal homeostasis in the challenged broilers, while butyrate in the tested concentration showed limited effects. Thus, further investigations are required to identify optimal dietary inclusion rates for butyrate used as alternative to ionophore coccidiostats in broiler production.

Bacillus amyloliquefaciens and Saccharomyces cerevisiae feed supplements improve growth performance and gut mucosal architecture with modulations on cecal microbiota in red-feathered native chickens

Objective

The aim of study was to investigate the effects of in-feed supplementation of Bacillus amyloliquefaciens (BA) and Saccharomyces cerevisiae (SC) on growth performance, gut integrity, and microbiota modulations in red-feathered native chickens (RFCs).

Methods

A total of 18,000 RFCs in a commercial farm were evenly assigned into two dietary treatments (control diet; 0.05% BA and 0.05% SC) by randomization and raised for 11 weeks in two separate houses. Fifty RFCs in each group were randomly selected and raised in the original house with the partition for performance evaluations at the age of 9 and 11 weeks. Six non-partitioned RFCs per group were randomly selected for analyses of intestinal architecture and 16S rRNA metagenomics.

Results

Feeding BA and SC increased the body weight and body weight gain, significantly at the age of 11 weeks (p<0.05). The villus height/crypt ratio in the small intestines and Firmicutes to Bacteroidetes ratio were also notably increased (p<0.05). The supplementation did not disturb the microbial community structure but promote the featured microbial shifts characterized by the significant increments of Bernesiella, Prevotellaceae_NK3B31_group, and Butyrucimonas, following remarkable decrements of Bacteroides, Rikenellaceae_RC9_gut_group, and Succinatimonas in RFCs with growth benefits. Besides, functional pathways of peptidoglycan biosynthesis, nucleotide excision repair, glycolysis/gluconeogenesis, and aminoacyl transfer ribonucleic acid (tRNA) biosynthesis were significantly promoted (p<0.05).

Conclusion

In-feed supplementation of BA and SC enhanced the growth performance, improved mucosal architectures in small intestines, and modulated the cecal microbiota and metabolic pathways in RFCs.

<i>Bacillus subtilis-</i>Fermented Products Ameliorate the Growth Performance, Alleviate Intestinal Inflammatory Gene Expression, and Modulate Cecal Microbiota Community in Broilers during the Starter Phase under Dextran Sulfate Sodium Challenge

The aim of this study was to evaluate the effects of B. subtilis-fermented products (BSFP) on growth performance, intestinal inflammatory gene expression, and cecal microbiota community in broilers challenged with dextran sulfate sodium (DSS) in a 14-day experiment. A total of 32, 1-day-old male broiler chickens (Ross 308), were randomly divided into four groups of eight birds per group and reared individually (n=8). The treatments consisted of a control diet without supplementation and DSS challenge, control diet plus 1.5% DSS, control diet plus 1 g/kg BSFP in combination with 1.5% DSS, and control diet plus 3 g/kg of BSFP in combination with 1.5% DSS. The results showed that BSFP supplementation (1 and 3 g/kg) partially improved body weight and average daily gain in broilers under DSS challenge. Relative to DSS treatment alone, BSFP supplementation dose-dependently increased the body weight of broilers at 7 days of age, with the average daily gain being at 1 to 7 days of age. BSFP supplementation (1 and 3 g/kg) alleviated intestinal inflammatory gene expression in broilers under DSS challenge. The richness and evenness of bacterial species in cecal digesta increased in a dose-dependent manner in the groups treated with BSFP (1 and 3 g/kg) in combination with DSS challenge, compared with the control group. Unweighted principal coordinate analysis indicated distinct clusters separating the group treated with 3 g/kg of BSFP in combination with DSS challenge from the other three groups. The abundance of short-chain fatty acid-producing bacteria (genus Ruminococcaceae_unclassified) increased and that of mucindegrading bacteria (genus Ruminococcus torques group) decreased in the cecal digesta of broilers fed 3 g/kg of BSFP, compared with the control group. In conclusion, BSFP supplementation dose-dependently improved growth performance, reduced gut inflammation, and regulated the cecal microbiota of broilers exposed to DSS challenge during the starter phase.

Effect of feed restriction on the intestinal microbial community structure of growing ducks

In poultry, feed restriction is common feeding management to limit poultry nutrients intake so that poultry only intake the essential energy, meeting the basic need of growth and development. Our study investigated whether feeding restriction affects the diversity of the intestinal microbiota of growing breeding ducks. In this research, the 60-120-day-old ducks were raised in restricted and free-feeding groups. After slaughtering, the carcass traits and the cecal contents were collected for 16S rRNA sequencing analysis. After feeding restriction, the growth rate of ducks was limited, the weight and rate of abdominal fat decreased, and the rate of chest and leg muscles increased. In addition, feeding restriction can also change the diversity of intestinal microorganisms in breeding ducks, such as the increase of Firmicutes abundance and the decrease of Bacteroidetes abundance. After analyzing of correlation, significant correlations between gut microbiota and carcass phenotypes were found. The results indicated that gut microbiota might be involved in the life activities associated with phenotypic changes. This study proved the effect of feeding methods on the intestinal microbiota of ducks, providing a theoretical basis of the microbial angle for raising ducks in a feeding-restricted period.

The Efficiency of Probiotics Administrated via Different Routes and Doses in Enhancing Production Performance, Meat Quality, Gut Morphology, and Microbial Profile of Broiler Chickens

Simple Summary

Antimicrobial growth promoters (AGPs) have been used in the animal production industry around the world for decades, with the consequence of a high potential of antibiotic-resistant bacteria transfer to humans. Efficiently raising broiler chickens in an antibiotic-free production system is a challenge, and identifying an effective nutritional alternative to support growth performance, gut health, and functionality without administrating AGPs is of essence. Several antimicrobial alternative options that are commercially available include herbal essential oils, exogenous enzymes, organic acids, plant secondary metabolites, probiotics, and prebiotics. Probiotics in animal feed is projected to attain a massive global growth, reaching USD 6.24 billion by 2026. This study tested the efficiency of probiotics when supplemented via different administration routes (feed or water) and doses, or in combination with prebiotics, on growth performance, meat quality, gut morphology, and microbial profile of broiler chickens. The outcomes revealed that probiotics enhance production performance, and compared to AGPs, do not reduce the beta-diversity of the gut microbial community. Water-soluble probiotics seemed to be more effective in improving growth performance.

Abstract

To study the efficiency of Bacillus spp. probiotics administered via different routes and doses, a 6-week grow-out trial was conducted using a total of 378 day-old mixed-sex ROSS308 broiler chickens in a completely randomized block design. Six experimental diets included probiotics added at two different inclusion rates into the feed (250 g/ton; PRO250, or 500 g/ton; PRO500), or in the drinking water (25 g/L; PRO-WS), or as a feed synbiotic (250 g probiotic + 250 g/ton prebiotic; SYN), compared to a negative (NC; without additives) and positive control (PC; with antibiotics) diets. The PRO-WS enhanced feed intake (p < 0.05) and tended to improve average daily gain and final body weight (p = 0.14). Broiler gut morphology in the duodenum including the villus height (p = 0.04), villus width (p = 0.05) and crypt depth (p = 0.02) were improved by PRO500. Firmicutes was the most abundant phylum, followed by Bacteroidetes. Streptococcaceae, Lachnoospiraceae, Peptostreptococcaceae, Ruminococcaceae, and Erysipe-lotrichaceae were the top five most abundant families. Antibiotic inclusion in PC reduced microbial beta-diversity and increased similarity compared to probiotic inclusion (p = 0.05). Probiotic inclusion reduced the relative abundance of Bacteroides fragilis, which is a commonly isolated pathogen and is considered as a marker for antimicrobial resistance. Overall, probiotic supplementation via feed or water may potentially improve the production performance of the broiler chickens, and water-soluble probiotics are potentially more effective. Probiotics, especially when added to water, suggest a promising feed additive to support gut microbial maturation and diversity, and may reduce resistant bacteria in broiler chickens. However, it is suggested that the best route for the administration of probiotics be further examined under commercial conditions to find the most effective and practical application method that yields the most consistent results.

The Emerging Biotherapeutic Agent: Akkermansia

The human gastrointestinal tract (GIT) is a well-recognized hub of microbial activities. The microbiota harboring the mucus layer of the GIT act as a defense against noxious substances, and pathogens including Clostridium difficile, Enterococcus faecium, Escherichia coli, Salmonella Typhimurium. Toxins, pathogens, and antibiotics perturb the commensal floral composition within the GIT. Imbalanced gut microbiota leads to dysbiosis, manifested as diseases ranging from obesity, diabetes, and cancer to reduced lifespan. Among the bacteria present in the gut microbiome, the most beneficial are those representing Firmicutes and Bacteroidetes. Recent studies have revealed the emergence of a novel biotherapeutic agent, Akkermansia, which is instrumental in regaining eubiosis and conferring various health benefits.

Centennial Review: Factors affecting the chicken gastrointestinal microbial composition and their association with gut health and productive performance

Maintenance of "gut health" is considered a priority in commercial chicken farms, although a precise definition of what constitutes gut health and how to evaluate it is still lacking. In research settings, monitoring of gut microbiota has gained great attention as shifts in microbial community composition have been associated with gut health and productive performance. However, microbial signatures associated with productivity remain elusive because of the high variability of the microbiota of individual birds resulting in multiple and sometimes contradictory profiles associated with poor or high performance. The high costs associated with the testing and the need for the terminal sampling of a large number of birds for the collection of gut contents also make this tool of limited use in commercial settings. This review highlights the existing literature on the chicken digestive system and associated microbiota; factors affecting the gut microbiota and emergence of the major chicken enteric diseases coccidiosis and necrotic enteritis; methods to evaluate gut health and their association with performance; main issues in investigating chicken microbial populations; and the relationship of microbial profiles and production outcomes. Emphasis is given to emerging noninvasive and easy-to-collect sampling methods that could be used to monitor gut health and microbiological changes in commercial flocks.

Managing Gut Microbiota through In Ovo Nutrition Influences Early-Life Programming in Broiler Chickens

The chicken gut is the habitat to trillions of microorganisms that affect physiological functions and immune status through metabolic activities and host interaction. Gut microbiota research previously focused on inflammation; however, it is now clear that these microbial communities play an essential role in maintaining normal homeostatic conditions by regulating the immune system. In addition, the microbiota helps reduce and prevent pathogen colonization of the gut via the mechanism of competitive exclusion and the synthesis of bactericidal molecules. Under commercial conditions, newly hatched chicks have access to feed after 36-72 h of hatching due to the hatch window and routine hatchery practices. This delay adversely affects the potential inoculation of the healthy microbiota and impairs the development and maturation of muscle, the immune system, and the gastrointestinal tract (GIT). Modulating the gut microbiota has been proposed as a potential strategy for improving host health and productivity and avoiding undesirable effects on gut health and the immune system. Using early-life programming via in ovo stimulation with probiotics and prebiotics, it may be possible to avoid selected metabolic disorders, poor immunity, and pathogen resistance, which the broiler industry now faces due to commercial hatching and selection pressures imposed by an increasingly demanding market.

Effect of Oils in Feed on the Production Performance and Egg Quality of Laying Hens

With the development of a large-scale and intensive production industry, the number of laying hens in China is rapidly increasing. Oils, as an important source of essential fatty acids, can be added to the diet to effectively improve the production performance and absorption of other nutrients. The present review discusses the practical application of different types and qualities of oils in poultry diets and studies the critical effects of these oils on production performance, such as the egg weight, feed intake, feed conversion ratio (FCR), and various egg quality parameters, including the albumen height, Haugh units, yolk color, and saturated/unsaturated fatty acids. This article reviews the effects of different dietary oil sources on the production performance and egg quality of laying hens and their potential functional mechanisms and provides a reference for the selection of different sources of oils to include in the diet with the aim of improving egg production. This review thus provides a reference for the application of oils to the diets of laying hens. Future studies are needed to determine how poultry products can be produced with the appropriate proper oils in the diet and without negative effects on production performance and egg quality.

Bacitracin, Bacillus subtilis, and Eimeria spp. challenge exacerbates woody breast incidence and severity in broilers

Woody breast (WB) is a myopathy that is related to the increasing growth rate. Understanding the influence of management factors on WB formation and development is important to minimize WB. This study was conducted to define how management factors affect broiler growth performance, processing yield, and WB incidence. Ross × Ross 708 chicks were randomly assigned to a 3 (diet) × 2 (cocci challenge) × 2 (sex) factorial arrangement of treatments. The 3 dietary treatments were: control diet (corn-soybean meal basal diet), antibiotic diet (basal diet + 6.075 mg bacitracin /kg feed), and probiotic diet (basal diet + 2.2 × 10⁸ CFU Bacillus subtilis PB6/kg feed). Birds in cocci challenge treatments received 20 × live cocci vaccine on d 14. The hardness of breast muscle in live birds was determined by palpation and grouped into Normal, Slight, Moderate, and Severe categories. Across diet and sex treatments, the cocci challenge resulted in decreases in body weight (BW) on d 29 and 35 (P < 0.0001 and = 0.032) in body weight gain (BWG) from d 14 to 29 (P < 0.0001). However, an increase of BW occurred on d 35 (P = 0.032) and an increase of BWG occurred from d 29 to 35 and d 35 to 43 (P = 0.0001 and 0.002), and the cocci challenge increased WB incidence on d 29 (P = 0.043) and d 43 (P = 0.013). Across challenge and sex treatments, birds fed the antibiotic diet exhibited a higher growth rate (GR) than those fed the control or probiotic diet from d 0 to 14 (P = 0.016), but not after d 14 (P > 0.05). Across sex, the antibiotic and probiotic diets increased WB incidence for those birds that did not receive a cocci challenge on d 43 (P = 0.040). Across challenge and diet treatments, males exhibited a higher BW, BWG, and GR throughout all growth phases, and males showed a higher WB incidence on d 29, 35, and 43 (P = 0.002, P < 0.0001, and P = 0.0002, respectively). In conclusion, bacitracin and Eimeria spp. increased WB incidence, BW, and GR. However, Bacillus subtilis increased WB incidence in male broilers without affecting BW and GR.

Metagenome-assembled genomes and gene catalog from the chicken gut microbiome aid in deciphering antibiotic resistomes

Gut microbial reference genomes and gene catalogs are necessary for understanding the chicken gut microbiome. Here, we assembled 12,339 microbial genomes and constructed a gene catalog consisting of ~16.6 million genes by integrating 799 public chicken gut microbiome samples from ten countries. We found that 893 and 38 metagenome-assembled genomes (MAGs) in our dataset were putative novel species and genera, respectively. In the chicken gut, Lactobacillus aviarius and Lactobacillus crispatus were the most common lactic acid bacteria, and glycoside hydrolases were the most abundant carbohydrate-active enzymes (CAZymes). Antibiotic resistome profiling results indicated that Chinese chicken samples harbored a higher relative abundance but less diversity of antimicrobial resistance genes (ARGs) than European samples. We also proposed the effects of geography and host species on the gut resistome. Our study provides the largest integrated metagenomic dataset from the chicken gut to date and demonstrates its value in exploring chicken gut microbial genes.

Feng et al. include genome recovery and data analysis of large number of chicken gut metagenomic datasets which significantly expands the reference genomes available from the chicken gut microbial communities, and catalog the genes prevalent in the gut systems. They further depict the countryspecific chicken gut antibiotic resistomes and the effects of geography and host species on the gut resistome.

Effect of dietary folic acid and energy density on immune response, gut morphology, and oxidative status in blood and breast muscle of broiler chickens

Folic acid (FA) plays essential roles in many metabolic functions and has been reported to have antioxidant effects. Therefore, dietary supplementation with high levels of FA may improve gut health and prevent potential oxidative stress caused by feeding a high energy density diet to broiler chickens. Broiler chickens were assigned into eight treatments, consisting of either a normal energy (NE) or high energy (HE) density diet, and four FA levels (2.2, 5, 10, and 15 ppm). Data were analyzed by SAS 16 GLM procedure. Birds-fed HE diets had increased (P < 0.05) plasma concentrations of calcium and albumin but reduced (P < 0.005) weights of ceca and bursa compared with those fed NE diets. Dietary supplementation with 10 ppm FA significantly increased (P < 0.05) birds’ heart weight and bile acid concentration. Folic acid and energy density interactions were significant for jejunal villus height (VH; P = 0.0226), villus width (VW; P < 0.0001), and crypt depth (CD; P = 0.0332). Among the NE group, birds fed 5–15 ppm FA had reduced (P < .0001) VW, while in the HE groups, 15 ppm FA supplementation resulted in an increased jejunal VH (P = 0.0317) compared with other treatments. In conclusion, dietary supplementation with increased levels of FA in HE diets could be beneficial for the intestinal health of broiler chickens.

Effect of Insect Live Larvae as Environmental Enrichment on Poultry Gut Health: Gut Mucin Composition, Microbiota and Local Immune Response Evaluation

The aim of this study was to evaluate the effect of Hermetia illucens (HI) and Tenebrio molitor (TM) live larvae as environmental enrichment on the mucin composition, local immune response and microbiota of broilers. A total of 180 four-day-old male broiler chickens (Ross 308) were randomly allotted to three dietary treatments (six replicates/treatment; ten animals/replicate): (i) control (C); (ii) C+HI; (iii) C+TM. Live larvae were distributed based on 5% of the expected daily feed intake. At slaughter (39 days of age), samples of duodenum, jejunum and ileum (twelve animals/diet) were submitted to mucin histochemical evaluation. Expression of MUC-2 and cytokines was evaluated by rt-qPCR in jejunum. Mucin staining intensity was not influenced by diet (p > 0.05); however, this varied depending on the intestinal segment (p < 0.001). No significant differences were recorded for IL-4, IL-6 TNF-α, MUC-2 and INF-γ gene expression in jejunum, while IL-2 was lower in the TM group compared to HI and C (p = 0.044). Caecal microbiota showed higher abundance of Clostridium, Saccharibacteria and Victivallaceae in the HI group, while Collinsella was higher in the TM group. The results suggested that live insect larvae did not impair mucin composition or local immune response, and can slightly improve caecal microbiota by enhancing a minor fraction of short chain fatty acid-producing taxa.

Animal Welfare Assessment in Antibiotic-Free and Conventional Broiler Chicken

Simple Summary

Antibiotic resistance in the veterinary field, other than making the control of infectious diseases in farm animals progressively more difficult, can increase the risk that resistant microorganisms are transferred from animals to humans either directly—by contact or from food of animal origin—or indirectly due to environmental contamination. The poultry sector is now moving towards antibiotic-free production in order to meet the rising market demand, but this could affect the health and welfare of chickens. In this study, we compared the welfare of broiler chickens raised with and without the use antibiotics on a commercial scale. We found no correlation between the absence of antibiotics and poor animal health. There is no necessary correlation between the absence of antibiotics at farms and poor health of the animals, given that adequate animal-welfare-friendly management tools and methodologies are in place. These should be, however, adequately standardised in specific guidelines. In this way, it will be possible to reduce the dependence of the livestock sector on antimicrobials with regard to animal welfare and human health.

Abstract

The poultry sector is moving towards antibiotic-free production, both to challenge the increasing spread of the antibiotic resistance phenomenon and to meet market demands. This could negatively impact the health and welfare of the animals. In this study, the welfare of 14 batches of 41–47-day-old broilers raised by the same integrated company with and without antibiotics was assessed using the Welfare Quality^® protocol. The total welfare score did not significantly differ between the two systems: the good-feeding principle was, on average, higher in the conventional batches, with statistical significance (t = −2.45; p = 0.024), while the other welfare principles (good housing, good health and appropriate behaviour) were slightly better in the antibiotic-free batches. Despite stocking densities averagely higher in the antibiotic-free batches, the absence of antibiotics did not seem to impact the good-health principle; in particular, hock burns, foot pad dermatitis and lameness were significantly less severe in the antibiotic-free batches (p < 0.0001, p = 0.018, p < 0.0001, respectively), which showed also a lower death rate (2.34% vs. 2.50%). Better management of antibiotic-free batches was reported, particularly concerning litter conditions. Further studies would be required to identify and standardise a set of managerial methodologies in order to improve the health of broilers raised without antibiotics.

Butyric and Citric Acids and Their Salts in Poultry Nutrition: Effects on Gut Health and Intestinal Microbiota

Intestinal dysfunction of farm animals, such as intestinal inflammation and altered gut microbiota, is the critical problem affecting animal welfare, performance and farm profitability. China has prohibited the use of antibiotics to improve feed efficiency and growth performance for farm animals, including poultry, in 2020. With the advantages of maintaining gut homeostasis, enhancing digestion, and absorption and modulating gut microbiota, organic acids are regarded as promising antibiotic alternatives. Butyric and citric acids as presentative organic acids positively impact growth performance, welfare, and intestinal health of livestock mainly by reducing pathogenic bacteria and maintaining the gastrointestinal tract (GIT) pH. This review summarizes the discovery of butyric acid (BA), citric acid (CA) and their salt forms, molecular structure and properties, metabolism, biological functions and their applications in poultry nutrition. The research findings about BA, CA and their salts on rats, pigs and humans are also briefly reviewed. Therefore, this review will fill the knowledge gaps of the scientific community and may be of great interest for poultry nutritionists, researchers and feed manufacturers about these two weak organic acids and their effects on intestinal health and gut microbiota community, with the hope of providing safe, healthy and nutrient-rich poultry products to consumers.

The Spatial and Temporal Characterization of Gut Microbiota in Broilers

The gut microbiota of chickens plays an important role in host physiology. However, the colonization and prevalence of gut microbiota have not been well-characterized. Here, we performed 16S rRNA gene sequencing on the duodenal, cecal and fecal microbiota of broilers at 1, 7, 21, and 35 days of age and characterized the dynamic succession of microbiota across the intestinal tract. Our results showed that Firmicutes was the most abundant phylum detected in each gut site at various ages, while the microbial diversity and composition varied among the duodenum, cecum, and feces at different ages. The microbial diversity and complexity of the cecal microbiota increased with age, gradually achieving stability at 21 days of age. As a specific genus in the cecum, Clostridium_sensu_stricto_1 accounted for 83.50% of the total abundance at 1 day of age, but its relative abundance diminished with age. Regarding the feces, the highest alpha diversity was observed at 1 day of age, significantly separated from the alpha diversity of other ages. In addition, no significant differences were observed in the alpha diversity of duodenal samples among 7, 21, and 35 days of age. The predominant bacterium, Lactobacillus, was relatively low (0.68–6.04%) in the intestinal tract of 1-day-old chicks, whereas its abundance increased substantially at 7 days of age and was higher in the duodenum and feces. Escherichia-Shigella, another predominant bacterium in the chicken intestinal tract, was also found to be highly abundant in fecal samples, and the age-associated dynamic trend coincided with that of Lactobacillus. In addition, several genera, including Blautia, Ruminiclostridium_5, Ruminococcaceae_UCG-014, and [Ruminococcus]_torques_group, which are related to the production of short-chain fatty acids, were identified as biomarker bacteria of the cecum after 21 days of age. These findings shed direct light on the temporal and spatial dynamics of intestinal microbiota and provide new opportunities for the improvement of poultry health and production.

Polysaccharides from Premna microphylla turcz ameliorate inflammation via the enhancement of intestinal resistance in host

ETHNOPHARMACOLOGICAL RELEVANCE

Premna microphylla turcz is traditionally used as a folk remedy. Its roots, stems and leaves can be invoked as medicines, which have the functions of detoxification, swelling and hemostasis. It belongs to the Premna in the Verbenaceae and is mainly distributed in the mountains of southeastern China. However, there are few reports of in-depth studies on the anti-inflammatory effects of polysaccharide, which was the main component in Premna microphylla turcz.

MATERIALS AND METHODS

The flies were fed with standard corn flour-yeast medium to cause inflammation by sodium lauryl sulfate (SDS). The treatment group contained Premna microphylla turcz polysaccharide (pPMTLs) extract. The survival rate was obtained by feeding a vial containing five layers of filter paper, which was infiltrated with the 5% sucrose solution contaminated with SDS or SDS polysaccharide. The microvilli and nucleus of the midgut epithelial cells of different treatments were observed by transmission electron microscope, and the expression of inflammation-related genes was detected by real-time quantitative PCR (qRT-PCR). Finally, 16S rDNA analysis was conducted on the differences in the composition of the intestinal microbes of Drosophila.

RESULTS

In the current study, we showed that pPMTLs significantly prolonged the life span of SDS-inflamed flies from 5 days to 6 days. And pPMTLs reduced the rupture of microvilli in the midgut and restored the nuclear structure. In addition, pPMTLs significantly improved expression level of immune-related genes in Inflammation Drosophila especially the defensin (4.32 ± 0.75 vs 9.97 ± 0.52 SDS-polysaccharide group: SDS group, p < 0.001). The analysis of intestinal microbiota showed that pPMTLs decreased the relative abundance of Raoultella while Wolbachia increased (p < 0.05).

CONCLUSIONS

Collectively, our results revealed the potential application of pPMTLs in enhancing inflammation defense, which would be enormous significance for the inflammation-related disorders treatment.

The link between broiler flock heterogeneity and cecal microbiome composition

BACKGROUND

Despite low genetic variation of broilers and deployment of considerate management practices, there still exists considerable body weight (BW) heterogeneity within broiler flocks which adversely affects the commercial value. The purpose of this study was to investigate the role of the cecal microbiome in weight differences between animals. Understanding how the gut microbiome may contribute to flock heterogeneity helps to pave the road for identifying methods to improve flock uniformity and performance.

RESULTS

Two hundred eighteen male broiler chicks were housed in the same pen, reared for 37 days, and at study end the 25 birds with highest BW (Big) and the 25 birds with lowest BW (Small) were selected for microbiome analysis. Cecal contents were analyzed by a hybrid metagenomic sequencing approach combining long and short read sequencing. We found that Big birds displayed higher microbial alpha diversity, higher microbiome uniformity (i.e. lower beta diversity within the group of Big birds), higher levels of SCFA-producing and health-associated bacterial taxa such as Lachnospiraceae, Faecalibacterium, Butyricicoccus and Christensenellales, and lower levels of Akkermansia muciniphila and Escherichia coli as compared to Small birds.

CONCLUSION

Cecal microbiome characteristics could be linked to the size of broiler chickens. Differences in alpha diversity, beta diversity and taxa abundances all seem to be directly associated with growth differences observed in an otherwise similar broiler flock.