Effects of rearing system and narasin on growth performance, gastrointestinal development, and gut microbiota of broilers

Genetic analysis of feed efficiency and novel feeding behavior traits measured in group-housed broilers using electronic feeders

This study aimed to estimate genetic parameters for feeding behavior (FB) traits and to assess their genetic relationship with performance traits in group-housed broilers. In total, 99,472,151 visits were recorded for 95,711 birds between 2017 and 2022 using electronic feeders. The visits were first clustered into 2,667,617 daily observations for ten FB traits: daily feed intake (DFI), daily number of visits (NVIS), time spent at the feeders (TSF), number of visited feeders (NVF), visiting activity interval (VAI), feeding rate (FR), daily number of meals (NMEAL), average intake per meal (INTMEAL), number of visits per meal (VISMEAL) and interval between meals (MEALIVL). All FB traits were then considered as the average per bird across the feeding test period. Three growth traits (body weight at the start - SBW and at the end of the feeding test - FBW, and weight gain over the test period - BWG), and 2 feed efficiency (FE) traits (Feed Conversion Rate - FCR and Residual Feed Intake - RFI) were also recorded. The (co)variance components were estimated using multitrait animal mixed models. For growth and FE, the heritability (h2) estimates were moderate, ranging from 0.20 ± 0.01 (BWG) to 0.32 ± 0.02 (RFI). Overall, the h2 estimates for FB traits were higher than for productive traits, ranging from 0.31 ± 0.01 (DFI) to 0.56 ± 0.02 (TSF). DFI presented high genetic correlations (0.53-0.86) with all performance traits. Conversely, the remaining FB traits presented null to moderate genetic correlations with these traits, ranging from -0.38 to 0.42 for growth traits and between -0.14 and 0.25 for FE traits. Genetic selection for favorable feeding behavior is expected to exhibit a fast genetic response. The results suggest that it is possible to consider different feeding strategies without compromising the genetic progress of FE. Conversely, breeding strategies prioritizing a higher bird activity might result in lighter broiler lines in the long term, given the negative genetic correlations between visit-related traits (NV, NVF, and NMEAL) and growth traits (SBW and FBW).

Effects of rearing systems (cage versus floor) on the microbial composition and transcriptome of goose ileum

There is a gradual transition from water to dryland rearing of geese. In this study, we performed 16S rRNA sequencing (16S rRNA-seq) and transcriptome sequencing (RNA-seq) to reveal the effects of cage rearing (CR) and floor rearing (FR) systems on the microbial composition and transcriptome of the goose ileum. Through 16S rRNA-seq, Linear Discriminant Analysis Effect Size (LEfSe) analysis identified 2 (hgcI_clade and Faecalibacterium) and 14 (Bacteroides, Proteiniphilum, Proteiniclasticum, etc.) differential microbiota in CR and FR, respectively. The rearing system influenced 4 pathways including biosynthesis of amino acids in ileal microbiota. Moreover, we identified 1,198 differentially expressed genes (DEGs) in the ileum mucosa, with 957 genes up-regulated in CR and 241 genes up-regulated in FR. In CR, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed the significant enrichment (p < 0.05) of 28 KEGG pathways, most of which were associated with amino acid metabolism. In FR, up-regulated DEGs were mainly enriched in KEGG pathways associated with cellular processes, including apoptosis, necroptosis, and cellular senescence. Spearman correlation analysis of differential microbiota and amino acid metabolism-related DEGs in CR showed a significant positive correlation. Additionally, differential microbiota of FR, Phascolarctobacterium and Sutterella, were positively correlated with FGF10 (p < 0.05) and PIK3R1 (p < 0.01), respectively. In conclusion, there might be differences in ileal amino acid metabolism levels between CR and FR geese, and the observed increase in harmful bacterial species in FR might impact the activity of ileal cells.

Effects of cage vs. net-floor mixed rearing system on goose spleen histomorphology and gene expression profiles

Due to the demands for both environmental protection and modernization of the goose industry in China, the traditional goose waterside rearing systems have been gradually transitioning to the modern intensive dryland rearing ones, such as the net-floor mixed rearing system (MRS) and cage rearing system (CRS). However, the goose immune responses to different dryland rearing systems remain poorly understood. This study aimed to investigate and compare the age-dependent effects of MRS and CRS on the splenic histomorphological characteristics and immune-related genes expression profiles among three economically important goose breeds, including Sichuan White goose (SW), Gang goose (GE), and Landes goose (LD). Morphological analysis revealed that the splenic weight and organ index of SW were higher under CRS than under MRS (p < 0.05). Histological observations showed that for SW and LD, the splenic corpuscle diameter and area as well as trabecular artery diameter were larger under MRS than under CRS at 30 or 43 weeks of age (p < 0.05), while the splenic red pulp area of GE was larger under CRS than under MRS at 43 weeks of age (p < 0.05). Besides, at 43 weeks of age, higher mRNA expression levels of NGF, SPI1, and VEGFA in spleens of SW were observed under MRS than under CRS (p < 0.05), while higher levels of HSPA2 and NGF in spleens of LD were observed under MRS than under CRS (p < 0.05). For GE, there were higher mRNA expression levels of MYD88 in spleens under CRS at 30 weeks of age (p < 0.05). Moreover, our correlation analysis showed that there appeared to be more pronounced positive associations between the splenic histological parameters and expression levels of several key immune-related genes under MRS than under CRS. Therefore, it is speculated that the geese reared under MRS might exhibit enhanced immune functions than those under CRS, particularly for SW and LD. Although these phenotypic differences are assumed to be associated with the age-dependent differential expression profiles of HSPA2, MYD88, NGF, SPI1, and VEGFA in the goose spleen, the underlying regulatory mechanisms await further investigations.

Isolation and in vitro assessment of chicken gut microbes for probiotic potential

Poultry production occupies an important place in the economy of any country. High broiler production in recent years has badly affected its profitability due to bad feed quality, excessive use of chemotherapeutic agents, emergence of diverse pathogens, and the deficiencies in management practices during rearing cycle. Microbiological improvement of the meat quality using potential probiotics can be beneficial for broiler farming. Present study was initiated to isolate chicken gastrointestinal tract (GIT) bacteria with probiotic potential. To isolate probiotics from chicken gut, alimentary canal of chickens of known sizes and ages was suspended in ringers soln. Under shaking conditions for overnight followed by serial dilutions of ringers soln. Bacterial isolates were analyzed via growth curve analysis, biochemical testing using RapID™ NF Plus Panel kit, molecular characterization, antimicrobial activity assay, antibiotic sensitivity assay, GIT adherence assay, bile salt and gastric acid resistant assay, and cholesterol assimilation assay. Four bacteria isolated in present study were identified as Limosilactobacillus antri strain PUPro1, Lactobacillus delbrueckii strain PUPro2, Lacticaseibacillus casei strain PUPro3, and Ligilactobacillus salivarius strain PUPro4. L. delbrueckii strain PUPro2 grew extremely fast. All isolates exhibited exceptional resistance to increasing concentrations of NaCl and bile salts with value of p >0.5. L. delbrueckii strain PUPro2 adhered to chicken ileum epithelial cells and demonstrated the highest viable counts of 320 colony forming units (CFUs). Antagonistic action was found in all isolates against P. aeruginosa, B. subtilis, B. proteus, and S. aureus, with value of p >0.5. Antibiotic susceptibility testing showed sensitivity to all the antibiotics used. Cholesterol assimilation was detected in all bacteria, with values ranging from 216.12 to 192.2 mg/dL. All isolates exhibited γ-hemolysis. In future, these bacteria might be tested for their impact on broilers meat quality and growth and can be recommended for their use as supplements for broilers diet with positive impact on poultry production.

Profiles of biliary microbiota in biliary obstruction patients with Clonorchis sinensis infection

Background

Clonorchis sinensis (C. sinensis) is a epidemiologically significant food-borne parasite, causing several hepatobiliary diseases. Biliary microbiota community structure might be influenced by infection with pathogens. However, the biliary microbiome of biliary obstruction patients infected with C. sinensis is still an unexplored aspect.

Methods

A total of 50 biliary obstruction patients were enrolled, including 24 infected with C. sinensis and 26 non-infected subjects. The bile samples were collected by Endoscopic Retrograde Cholangiopancretography. Biliary microbiota alteration was analyzed through high-throughput 16S ribosomal RNA (rRNA) gene sequencing.

Results

Our findings revealed that there was significant increase in both richness and diversity, as well as changes in the taxonomic composition of the biliary microbiota of C. sinensis infected patients. At the phylum level, C. sinensis infection induced Proteobacteria increased and Firmicutes reduced. At the genus level, the relative abundance of Pseudomonas and Staphylococcus increased significantly, while Enterococcus decreased prominently in infected groups (P < 0.05). The PICRUSt analysis further showed remarkably different metabolic pathways between the two groups.

Conclusion

C. sinensis infection could modify the biliary microbiota, increasing the abundance and changing the phylogenetic composition of bacterial in biliary obstruction patients. This study may help deepen the understanding of the host-biliary microbiota interplay with C. sinensis infection on the background of biliary obstruction and provide new insights into understanding the pathogenesis of clonorchiasis.

Effects of housing systems and feed additive on growth, carcass traits, liver function, oxidative status, thyroid function, and immune parameters of broilers

The effects of rearing Cobb500 broiler chickens under 3 different housing systems (floor litter, floor plastic, and batteries) without or with feed additive (Butinov) on broiler performance, blood parameters and carcass traits were evaluated. Three hundred 1-day-old chicks were distributed in a 3 × 2 factorial arrangement (6 treatments each of 5 replicates). The results showed that reared broilers on litter or plastic floors had high values (P ≤ 0.01) of bird's weight (BW), weight gain (WG), and feed intake (FI) throughout the entire study period (1-42 d of age) compared with rearing on batteries. Rearing broilers in the different housing systems and with or without feed additives did not affect (P ≥ 0.05) total feed conversion (FCR). Different rearing systems or feed additives did not influence broiler chicks' carcass traits and some serum blood parameters. The plastic floor system significantly increased (P ≤ 0.05) blood serum corticosterone compared with litter and batteries. Feed additive (Butinov) decreased the level of T4 (P ≤ 0.05) in blood serum. Plastic floors or batteries significantly increased (P ≤ 0.01) the level of antibody titer against avian influenza virus (HIAV) compared to chicken reared on a litter floor. The results suggested that using housing systems of litter or plastic floors could improve broiler growth performance without adversely affecting carcass traits and blood characteristics compared with rearing in batteries. Also, broiler diets' feed additive (Butinov) and their interaction with rearing systems did not improve broiler growth performance.

Effect of rearing systems on immune status, stress parameters, intestinal morphology, and mortality in conventional and local chicken breeds

The majority of poultry meat used to be sourced from intensively housed birds. However, consumer preference has since demanded poultry producers develop more sustainable farming systems. Although free-range farming is considered beneficial for animal welfare, it is not as easy to standardize as an intensive system, which makes the choice of bird genotype appear crucial for alternative systems. In this study, we aimed to evaluate the effect of conventional and free-range rearing systems on the immune status, stress parameters, intestinal morphology and mortality in commercial hybrids (Ross 308) and local poultry strains, Bionda Piemontese (BP), Robusta Maculata (RM), BP x Sasso (BPxS), and RM x Sasso (RMxS). RNA was extracted from the jejunum and spleen to assess the mRNA expression of IL-2, IL-6, IL-10, IL-18, IL-1β, inducible nitric oxide synthase (iNOS), toll-like receptor (TLR)-4, and interferon gamma (IFN-γ). The heterophil:lymphocyte (H/L) ratio and intestinal histomorphometric evaluation were also calculated. We found that compared to the conventional system, the rearing system significantly affected the jejunum expression of IL-10, iNOS, IL-2, and IL-6, where these genes were upregulated in free-range system. A significant interaction between the rearing system and the genotype was also shown. More specifically, local breeds showed a significantly higher expression (P < 0.001) of IL-6 in the free-range system compared to the same genotypes in the conventional system. Moreover, IL-6 is constantly upregulated in local breeds within the free-range system compared to Ross hybrids. We also found significantly increased H/L and mortality rates in the latter, compared to the local breeds in the free-range reared system. The jejunum morphology also demonstrated a significantly higher villus height in BP and BPxS compared to the Ross hybrids. Overall, the results of our study confirm that the intense selection for growth in broiler chickens may have reduced their ability to react to the environmental stimuli related to free-range systems, resulting in a lower adaptability to a free-range environment, thus making them inappropriate for any farming system other than the conventional one. On the contrary, local chicken breeds are able to adapt and survive in the free-range system of rearing, and represent a genetic resource especially when adaptability to free-range conditions is required.

Enzymatically prepared alginate oligosaccharides improve broiler chicken growth performance by modulating the gut microbiota and growth hormone signals

BACKGROUND

Alginate oligosaccharide (AOS) holds great potential as a novel feed supplement in farm animals. However, the effects of AOS on chicken health and the underlying mechanisms are not fully understood. This study aimed to optimize the enzymatic preparation of AOS by using bacterial alginate lyases expressed in yeast, investigate the effects of the prepared AOS on the growth performance and gut health of broiler chickens, and reveal the underlying mechanisms.

RESULTS

Five alginate lyases from bacteria were cloned into Pichia pastoris GS115 and the alginate lyase PDE9 was expressed at relatively high yield, activity and stability in P. pastoris. Animal trials were carried out using 320 1-day-old male Arbor Acres broilers (four groups; 8 replicates/group × 10 chicks/replicate) receiving either a basal diet or the same diet supplemented with 100, 200 and 400 mg/kg PDE9-prepared AOS for 42 d. The results showed that dietary supplementation of 200 mg/kg AOS displayed the highest activity in promoting the birds' ADG and ADFI (P < 0.05). AOS ameliorated the intestinal morphology, absorption function and barrier function, as indicated by the enhanced (P < 0.05) intestinal villus height, maltase activity, and the expression of PEPT, SGLT1, ZNT1, and occludin. AOS also increased serum insulin-like growth factor-1, ghrelin (P < 0.05), and growth hormone (P < 0.1). Moreover, the concentrations of acetate, isobutyrate, isovalerate, valerate, and total SCFAs in cecum of birds fed AOS were significantly higher than the control birds (P < 0.05). Metagenomic analysis indicated that AOS modulated the chicken gut microbiota structure, function, and microbial interactions and promoted the growth of SCFAs-producing bacteria, for example, Dorea sp. 002160985; SCFAs, especially acetate, were found positively correlated with the chicken growth performance and growth-related hormone signals (P < 0.05). We further verified that AOS can be utilized by Dorea sp. to grow and to produce acetate in vitro.

CONCLUSIONS

We demonstrated that the enzymatically produced AOS effectively promoted broiler chicken growth performance by modulating the chicken gut microbiota structure and function. For the first time, we established the connections among AOS, chicken gut microbiota/SCFAs, growth hormone signals and chicken growth performance.

Effect of housing system and housing density on performance, viability, and gastrointestinal tract growth of broiler chicks during the first 2 wk of age

This experiment was conducted to study the effect of housing systems and housing densities on the performance and digestive tract growth of broiler chicks during the first 2 wk of age. A total of 3,600 Cobb500 day-old chicks were stocked at 4 densities (30, 60, 90, and 120 chicks/m2), and reared under 2 housing systems (conventional housing system and newly developed housing system), yielding a 2 × 4 factorial arrangement. The studied traits were performance, viability, and gastrointestinal tract development. The results indicated that housing systems and housing densities significantly (P < 0.001) affected the performance and GIT development of chicks. There were no significant interactions between housing system and housing density for body weight, body weight gain, feed intake, and feed conversion. The results also showed that the effects of housing density were age-dependent. That is, the higher the density, the lower the performance and digestive tract growth with advancing age. In conclusion, birds in the conventional system outperformed birds in the newly developed housing system, and further work is needed to improve the new housing system. To achieve the highest performance, digestive tract growth, and digesta content, a density of 30 chicks/m2 is recommended for chicks up to 14-days old.

Effects of indoor and outdoor rearing system on geese biochemical parameters and cecal microbial composition

The present study aimed to investigate the impact of indoor and outdoor rearing systems on the biochemistry and microbial composition of White Roman geese, with a particular focus on the gut microbiome. Our results showed that geese reared in an outdoor system had significantly lower serum aspartate aminotransferase (AST) compared to those reared indoors, but lower levels of high-density lipoprotein (HDL) and higher levels of low-density lipoprotein (LDL). Moreover, the cecal microbiota of geese reared outdoors exhibited higher species evenness and increased alpha diversity, with a significant alteration in the F/B ratios. The bacterial taxonomy composition also differed between the 2 rearing systems, with higher relative abundances of the Firmicutes and Actinobacteria and lower relative abundances of the Bacteroidetes and Proteobacteria in the outdoor system. These findings suggest that rearing systems may play a critical role in shaping the gut microbiome and overall health of geese. Notably, our data demonstrated that indoor rearing was associated with a higher abundance of pathogenic genera and a lower abundance of commensal genera compared to outdoor rearing. Our study supports the hypothesis that rearing systems may alter the physiological functions and microbial composition of geese, and highlights the need for further research to confirm and expand upon these findings. In summary, our study underscores the importance of considering the impact of rearing systems on the gut microbiome and health of geese.

The Effect of Encapsulated Propyl Propane Thiosulfonate (PTSO) on Apparent Ileal Digestibility and Productive Performance in Broiler Chickens

This study analyzed the effects of different dietary doses of encapsulated propyl propane thiosulfonate (Pe-PTSO) on the apparent ileal digestibility (AID) of nutrients and productive performance in broilers. A total of 100 one-day-old Cobb 500 were housed in battery cages for 20 days. At 10 days of age, the birds were assigned to one of five diets: negative control (P0), 250 mg/kg of Pe-PTSO (P250), 500 mg/kg of Pe-PTSO (P500), 750 mg/kg of Pe-PTSO (P750), and positive control, nicarbazin-narasin (ION). Titanium dioxide was the external marker, which was added to the diets from day 17 to 20. In the birds fed the P250 diet, there was a significant difference (p ≤ 0.05) in the AID values for amino acids and energy compared to those that consumed the P0 diet. Furthermore, the P250 diet significantly increased (p ≤ 0.05) the average daily weight gain compared to the P0 diet. No significant differences were observed between treatments in average daily feed intake and feed conversion ratio. In summary, the inclusion of 250 mg of encapsulated PTSO per kg in broiler chickens diet improved the digestibility of amino acids and energy, as well as weight gain.

Persistence and molecular epidemiology of blaNDM-positive Gram-negative bacteria in three broiler farms: A longitudinal study (2015-2021)

Although carbapenems have not been approved for animal use, bla_NDM-positive bacteria (NPB) are increasingly being detected in farm animals. It is important to investigate the routes and underlying mechanisms of evolution and transmission of animal-borne NPB. In this study, NPB recovered from chicken feces and environmental samples in three adjacent broiler farms were investigated. We found that 13.0% of Escherichia coli strains recovered from chicken feces during the period 2015-2016 carried the bla_NDM gene. In 2017-2021, however, as many as 55.8% chicken and environmental samples collected during the breeding period were found to harbor NPB. Importantly, such strains were detectable in samples from farmland (10.3%, 8/78), vegetable fields (7.3%, 3/41), and environment of chicken farms (25.6%, 41/160) which had been left vacant for a long period of time. Intriguingly, different sequence types of NPB became dominant in different years. Both clonal dissemination of NPB and horizontal transmission of bla_NDM-bearing plasmids were observed among different farms and among the environment niches inside and outside the farm houses. Worryingly, transmission of NPB and bla_NDM-bearing plasmids between these farms and other places was also observed. All in all, our results suggested the persistence of NPB in chickens and farm environments, presumably due to extensive contamination by exogenous materials and transmission of NPB within the farm system. These events were aggravated by the increase in antibiotic usage and poor sanitary conditions in the farm houses. Stringent control measures should be implemented to arrest transmission of animal-borne NPB to the environment and the community.

Effects of Dietary Ferulic Acid on Intestinal Health and Ileal Microbiota of Tianfu Broilers Challenged with Lipopolysaccharide

Lipopolysaccharide (LPS) has been considered the primary agent to establish animal models of inflammation, immunological stress, and organ injury. Previous studies have demonstrated that LPS impaired gastrointestinal development and disrupted intestinal microbial composition and metabolism. Ferulic acid (FA) isolated from multiple plants exhibits multiple biological activities. This study investigated whether FA ameliorated intestinal function and microflora in LPS-challenged Tianfu broilers. The results showed that LPS challenge impaired intestinal function, as evidenced by decreased antioxidant functions (p < 0.05), disrupted morphological structure (p < 0.05), and increased intestinal permeability (p < 0.05); however, these adverse effects were improved by FA supplementation. Additionally, FA supplementation preserved sIgA levels (p < 0.05), increased mRNA expression levels of CLDN and ZO-1 (p < 0.05), and enhanced epithelial proliferation (p < 0.05) in the ileal mucosa in LPS-challenged chickens. Moreover, FA supplementation rectified the ileal microflora disturbances in the LPS-challenged broilers. The results demonstrate that dietary FA supplementation decreased LPS-induced intestinal damage by enhancing antioxidant capacity and maintaining intestinal integrity. Furthermore, FA supplementation protects intestinal tight junctions (TJs), elevates secretory immunoglobulin A (sIgA) levels, and modulates ileal microflora composition in LPS-challenged broilers.

Selenium deficiency increased duodenal permeability and decreased expression of antimicrobial peptides by activating ROS/NF-κB signal pathway in chickens

Selenium (Se) is an essential trace element for the body. Various organs of the body, including the intestine, are affected by its deficiency. Se deficiency can induce oxidative stress and inflammatory responses in the intestine. It can also increase intestinal permeability and decrease intestinal immune function in mammals. However, the detailed studies, conducted on the intestinal molecular mechanisms of Se deficiency-induced injury in poultry, are limited. This study explored the adverse effects of Se deficiency on intestinal permeability and its mechanism. A Se-deficient chicken model was established, and the morphological changes in the chicken duodenum tissues were observed using a light microscope and transmission electron microscope (TEM). Western blotting, qRT-PCR, and other methods were used to detect the expression levels of selenoproteins, oxidative stress indicators, inflammatory factors, tight junction (TJ) proteins, antimicrobial peptides, and other related indicators in intestinal tissues. The results showed that Se deficiency could decrease the expression levels of selenoproteins and antioxidant capacity, activate the nuclear factor kappa-B (NF-κB) pathway, cause inflammation, and decrease the expression levels of TJ proteins and antimicrobial peptides in the duodenum tissues. The study also demonstrated that Se deficiency could increase intestinal permeability and decrease antimicrobial peptides via reactive oxygen species (ROS)/NF-κB. This study provided a theoretical basis for the scientific prevention and control of Se deficiency in poultry. Se deficiency decreased the expression levels of selenoproteins and increased ROS levels to activate the NF-κB pathway, resulting in the production of pro-inflammatory cytokines, reducing the expression levels of TJ protein, and weakening the expression of antimicrobial peptides, which contributed to the higher intestinal permeability. Oxidative stress weakened the expression of antimicrobial peptides.

Effects of rearing system and antibiotic treatment on immune function, gut microbiota and metabolites of broiler chickens

BACKGROUND

In China, cage systems with a high space utilization have gradually replaced ground litter systems, but the disease incidence of chickens in cages is higher. Broilers in the ground litter pens may be stimulated by more environmental microbes during the growth process and show strong immune function and status, but knowledge of which microbes and their metabolites play an immunomodulatory role is still limited. This study aimed to explore the differences and correlations in the immune function, gut microbiota and metabolites and the importance of gut microbiota of broilers raised in cages and ground litter pens.

METHODS

The experiment involved a 2 × 2 factorial arrangement, with rearing systems (cages or ground litter pens) and antibiotic treatment (with or without broad-spectrum antibiotics in drinking water) as factors.

RESULTS

The results showed that, compared with the cage group, the ground litter broilers had stronger nonspecific immune function (Macrophages% and NO in blood), humoral immune function (IgG in blood, LPS stimulation index in ileum) and cellular immune function (T%, Tc%, ConA stimulation index and cytokines in blood). Antibiotic (ABX) treatment significantly reduced nonspecific immune function (Macrophages% and NO in blood, iNOS and Mucin2 mRNA expression in ileum), humoral immune function (IgG in blood and sIgA in ileum) and cellular immune function (T% and cytokines in blood, Th and Tc ratio, TLRs and cytokines mRNA expression in ileum). Furthermore, the ground litter broilers had higher α diversity of microbiota in ileum. The relative abundance of Staphylococcus, Jeotgalicoccus, Jeotgalibaca and Pediococcus in the ileum of ground litter broilers were higher. ABX treatment significantly reduced the α diversity of ileal microbiota, with less Chloroplast and Mitochondria. In addition, the levels of acetic acid, isobutyric acid, kynurenic acid and allolithocholic acid in the ileum of ground litter broilers were higher. Spearman correlation analysis showed that Jeotgalibaca, Pediococcus, acetic acid, kynurenic acid and allolithocholic acid were related to the immune function.

CONCLUSIONS

There were more potential pathogens, litter breeding bacteria, short-chain fatty acids, kynurenine, allolithocholic acid and tryptophan metabolites in the ileum of broilers in ground litter pens, which may be the reason for its stronger immune function and status.

Comparison and Correlation Analysis of Immune Function and Gut Microbiota of Broiler Chickens Raised in Double-Layer Cages and Litter Floor Pens

This study aimed to compare the immune function and gut microbiota between double-layer caged and litter floor pen-raised broiler chickens. Eighty meaty male chicks were selected and divided into cage group and litter floor group, with 20 replicates in each group. The broilers were raised in the same chicken house. The rearing density of the two rearing systems was same. The broilers were sampled on days 13 and 34. The results showed that compared with the cage group, the litter floor broilers had worse growth performance (23.24% increase in feed conversion ratio) in the early stage; better slaughter performance at day 42; stronger peripheral immune function (including higher lysozyme activity, T-cell ratio, Th-cell ratio, Tc-cell ratio, CD4/CD8, IL-10, B-cell ratio, IgG and IgA levels; and spleen immune-related gene expression); and stronger intestinal immune function (including higher ileum CD80, AvBD2, Mucin2, NF-κB, IL-8, IFN-γ/IL-4, and IgA mRNA expression levels and ileal mucosa sIgA levels). Compared with the cage group, the alpha diversity of ileum microbiota of the litter floor broilers was higher, and the relative abundance levels of litter breeding bacteria (Facklamia, Globicatella, and Jeotgalicoccus) and potential pathogenic bacteria (Streptococcus and Staphylococcus) were higher (P < 0.05). Through Spearman correlation analysis, it was found that enriched microbes in the ileum of litter floor broilers were positively correlated with immune function. In summary, compared with cage broilers, litter floor broilers had more potential pathogenic bacteria and litter breeding bacteria in the ileum, which may be one of the important reasons for the stronger immune function status. IMPORTANCE In China, the three-dimensional rearing system (cage) for broilers has gradually become a trend. In production, it was found that the incidence of disease in broiler chickens raised in cage systems was significantly higher than that of ground litter. Given that broilers raised on ground litter systems may be exposed to more environmental microbes, it is important to understand whether the rearing environment affects the function and status of the host immune system by altering the gut microbiota. In this study, rearing environment-derived gut microbes associated with stronger immune function in ground litter broilers were provided, which will provide new insights into strategies to target gut microbes to promote immune function and status in broilers raised in cages.

Gut microbiota and meat quality

Sustainable meat production is important to providing safe and quality protein sources for humans worldwide. Intensive artificial selection and high energy input into the diet of many commercial animals for the last decade has significantly increased the daily gain of body weight and shortened the raising period, but unexpectedly decreased the meat quality. The gastrointestinal tract of animals harbors a diverse and complex microbial community that plays a vital role in the digestion and absorption of nutrients, immune system development, pathogen exclusion, and meat quality. Fatty acid composition and oxidative stress in adipose and muscle tissue influences meat quality in livestock and poultry. Recent studies showed that nutraceuticals are receiving increased attention, which could alter the intestinal microbiota and regulate the fat deposition and immunity of hosts to improve their meat quality. Understanding the microbiota composition, the functions of key bacteria, and the host-microbiota interaction is crucial for the development of knowledge-based strategies to improve both animal meat quality and host health. This paper reviews the microorganisms that affect the meat quality of livestock and poultry. A greater understanding of microbial changes that accompany beneficial dietary changes will lead to novel strategies to improve livestock and poultry meat product quality.

A balanced gut microbiota is essential to maintain health in captive sika deer

Certain animals harbor a high proportion of pathogens, particular the zoonotic pathogens, in their gut microbiome but are usually asymptomic; however, their carried pathogens may seriously threaten the public health. By understanding how the microbiome overcomes the negative effects of pathogens to maintain host health, we can develop novel solutions to control animal-mediated pathogen transmission including identification and application of beneficial microbes. Here, we analyzed the gut microbiota of 10 asymptomic captive sika deer individuals by full-length 16S rDNA sequencing. Twenty-nine known pathogens capable of infecting humans were identified, and the accumulated proportions of the identified pathogens were highly variable among individuals (2.33 to 39.94%). The relative abundances of several beneficial bacteria, including Lactobacillus and Bifidobacterium, were found to be positively correlated with the relative abundances of accumulated pathogens. Whole-genome metagenomic analysis revealed that the beneficial- and pathogenic-associated functions, such as genes involved in the synthesis of short chain fatty acids and virulence factors, were also positively correlated in the microbiome, indicating that the beneficial and pathogenic functions were maintained at a relatively balanced ratio. Furthermore, the bacteriophages that target the identified pathogens were found to be positively correlated with the pathogenic content in the microbiome. Several high-quality genomes of beneficial bacteria affiliated with Lactobacillus and Bifidobacterium and bacteriophages were recovered from the metagenomic data. Overall, this study provides novel insights into the interplay between beneficial and pathogenic content to ensure maintenance of a healthy gut microbiome, and also contributes to discovery of novel beneficial microbes and functions that control pathogens. KEY POINTS: • Certain asymptomic captive sika deer individuals harbor relatively high amounts of zoonotic pathogens. • The beneficial microbes and the beneficial functions are balanced with the pathogenic contents in the gut microbiome. • Several high-quality genomes of beneficial bacteria and bacteriophages are recovered by metagenomics.

Research Note:Effects of different anticoccidial regimens on the growth performance, hematological parameters, immune response, and intestinal coccidial lesion scores of yellow-feathered broilers

Yellow-feathered broiler chickens generally have a longer growth cycle than white broilers and therefore face different coccidiosis challenges. General single vaccine and drug regimens struggle to prevent coccidiosis for yellow broilers. In this study, a single vaccine, and a combination of coccidiostat regimens was employed to explore the preventative and control effects of different pilot regimens on coccidiosis in yellow-feathered broilers. A total of 2,000 one day old Chinese Huang Youma female broilers were allocated into 4 experimental groups, each with 5 replicates. All birds were fed the same starter feed from Days 1 to 25, and all groups were inoculated with a vaccine on Day 4. After Day 26, the groups were then fed as follows: (1) Negative control group: basal diet + vaccine (NC); (2) NC + maduramycin (NCMD); (3) NC + narasin (NCNR); and (4) NC + salinomycin (NCSL). From Days 26 to 75, the NCNR group had a lower FCR than the other groups. The 75-d BW was higher in the NCNR group than in the NCSL group but was not significantly higher than that in the NC and NCMD groups. The growth performance followed the same trend during the whole experiment (Days 1–75). Compared to the NC group, the NCNR and NCSL groups had higher intestinal mucosa SIgA concentrations at Day 40 and Day 60 (P < 0.001); however the NCMD group had lower IgG levels at Day 40 and Day 60 (P = 0.036, P = 0.006 respectively). The combination groups had significantly reduced AKP levels and urine acid concentrations at Day 60 in comparison to those of the NC group (P = 0.004). The NCNR and NCMD groups had less severe intestinal coccidiosis lesion scores than the NC and NCSL groups in older birds. Thus, a single vaccine and/or combinations with different coccidiostats had different effects on broilers. The NCNR group showed comparatively better growth performance, blood biochemical indices, immune response, and coccidiosis lesion scores.

Effects of cage versus floor rearing system on goose intestinal histomorphology and cecal microbial composition

Due to the demand for modern goose production and the pressure of environmental protection, the rearing systems of geese are changing from traditional waterside rearing to intensive rearing systems such as floor rearing (FR) and cage rearing (CR) systems. However, little is known about the effects of different rearing systems on goose intestinal functions and cecal microbial composition. Therefore, this study aimed to compare intestinal histomorphology and cecal microbial composition differences in geese reared under CR and FR at 270 d of age. Histomorphological analysis showed that the ileal villus height (VH) to crypt depth (CD) ratio was significantly greater in CR than in FR (P < 0.001). Taxonomic analysis showed that the dominant bacteria of cecal microorganisms in both rearing systems were roughly similar, with Bacteroidota, Firmicutes, Fusobacteriota, and Proteobacteria being the dominant phyla while Bacteroides, Fusobacterium, and uncultured_bacterium_o_Bacteroidales being the dominant genera. Differentially abundant taxa between CR and FR were also identified using Linear Discriminant Analysis Effect Size (LEfSe) analysis (P < 0.05, LDA score > 3.5). Megamonas and Anaerobiospirillum were significantly enriched in the CR group at the genus level, while uncultured_bacterium_f_Rikenellaceae and Sutterella were significantly enriched in the FR group. Notably, we found that the relative abundance of uncultured_bacterium_f_Rikenellaceae was significantly negatively correlated with the ileal VH and VH/CD (P < 0.05). The relative abundance of Megamonas and Anaerobiospirillum were significantly negatively correlated with abdominal fat weight and relative abdominal fat weight (P < 0.01), whereas that of Sutterella was significantly positively correlated with abdominal fat weight and relative abdominal fat weight (P < 0.01). Furthermore, PICRUSt2 analysis indicated that the lipid metabolism pathways of cecal microorganisms were lower enriched in CR than in FR. In conclusion, compared with FR, the CR significantly changed goose ileal histomorphological characteristics and cecal microbial composition, thereby affecting goose physiological functions and production performance.

Comparison of Bacterial Community Structure in PM2.5 within Broiler Houses under Different Rearing Systems in China

Background: In intensive poultry farming, high concentrations of indoor particulate matter (PM) impact production performance and welfare. In this study, PM2.5 level and bacterial community diversity were investigated in a multilayer cage house rearing system (CH) and a net flooring house rearing system (FH) during different growth stages to clarify the effects of the rearing systems on the diversity of airborne bacteria and help improve health management. Methods: The IC and high-throughput sequencing were used for ion composition and bacterial diversity analysis of PM2.5 collected from CH and FH. Results: The concentrations of NH3, CO2 and PM2.5 in CH were significantly lower than FH (p < 0.001) in both middle and late rearing stages. PM concentrations gradually increased with broiler growth only in FH. The water-soluble ions of PM2.5 samples had no significant difference between the two systems (p > 0.05). Firmicutes, Actinobacteria and Proteobacteria were the most abundant phyla in both the atmosphere and the broiler houses, but the composition was significantly different. The bacterial community in the broiler houses had strong correlations with temperature, humidity and PM of extremely high concentrations. Ions had stronger correlations with microbial community structure. Conclusions: The superiority of CH in environmental control over FH indicates that improved techniques in environmental control and breeding management can greatly reduce farming air pollution and improve the health management of broiler houses.

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.