Protective role of dryland rearing on netting floors against mortality through gut microbiota-associated immune performance in Shaoxing ducks

Integrated 16S rRNA and metagenomic sequencing reveals the distribution of key antibiotic resistance genes in duck gut microbiota

The duck gut microbiota is essential for host health and is considered a potential reservoir for antibiotic resistance genes (ARGs). However, research on ARGs in the duck gut microbiota is limited. This study collected 120 intestinal content samples from five segments (duodenum, jejunum, ileum, cecum, and colorectum) of ducks raised under two rearing conditions (with or without an open-air swimming pool). We compiled a comprehensive inventory of microbial genes in the duck gut and conducted an analysis of microbial composition and function across all intestinal segments using 16S rRNA gene sequencing combined with metagenomics. The findings revealed that Firmicutes were the most prevalent microbes in all intestinal segments. In the foregut (duodenum, jejunum, and ileum), microbial functions were mainly related to genetic information processing such as transcription, translation, replication, and glycosynthesis/gluconeogenesis. Conversely, in the hindgut (cecum and colorectum), microbial functions were primarily associated with the biosynthesis of secondary metabolites and various metabolic pathways. The analysis of ARGs indicated a higher relative abundance of ARGs in the cecum and colorectum (P < 0.05) of ducks in the presence of an open-air swimming pool compared to the absence of one. Furthermore, through co-occurrence network analysis, we identified Bacteroides, Roseburia, Ruminococcus, and Blautia as potential hosts of ARGs such as tetQ, tet32, tet37, vanR, vanG, and acrB in the hindgut. This study provides new insights into the complex relationship between ARGs and the microbial community in duck intestines, laying a theoretical groundwork for understanding the transmission dynamics of ARGs in these ecosystems.

Dietary Bacillus toyonensis BCT-7112T Supplementation Influences Performance, Egg Quality, Ammonia Emission, and Cecal Microbiome in Laying Ducks

This study evaluated the effects of Bacillus toyonensis BCT-7112T on laying duck performance, egg quality, ammonia emission, and cecal microbiota. Two hundred twenty 32-week-old Khaki Campbell ducks were assigned to four dietary treatments (0, 200, 500, or 1000 ppm Toyocerin® 109 premixture, containing 1 × 10⁹ B. toyonensis BCT-7112T CFU/g) with five replicate pens of eleven birds each. Data on productivity, egg quality, and ammonia emissions were collected weekly, and cecal microbiota were analyzed at 44 weeks of age. Supplementation with 1000 ppm B. toyonensis BCT-7112T significantly increased average egg weight (p < 0.001) and eggshell thickness (p = 0.007). Egg mass also improved at higher supplementation levels (p < 0.05), though feed intake, feed conversion, daily egg production, and most egg quality parameters were unaffected (p > 0.05). Ammonia emissions in litter decreased significantly (p < 0.05) with probiotic inclusion. Cecal microbiota analysis revealed higher diversity in ducks fed 1000 ppm, with a notable shift in predominant phyla from Bacteroidetes (35.12%) and Firmicutes (34.93%) in the controls to Bacteroidetes (40.52%), Firmicutes (34.08%), and Deferribacteres (9.54%) in the treated ducks. The findings suggest that 1000 ppm B. toyonensis BCT-7112T enhances egg production, eggshell quality, and microbial diversity while reducing ammonia emissions in laying duck systems.

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.

Effect of Bacillus toyonensis BCT-7112T supplementation on growth performance, intestinal morphology, immune-related gene expression, and gut microbiome in Barbary ducks

This study aimed to investigate the effect of Bacillus toyonensis BCT-7112T supplementation on growth performance, intestinal morphology, immune-related gene expression, and the cecal microbiota of meat ducks. A total of 150 one-day-old male Barbary ducks were divided into 3 groups with 5 replicates (n = 10 ducks per replicate) by completely randomized design and offered diets supplemented with the commercial product Toyocerin (containing 1 × 109B. toyonensis BCT-7112T viable spores/g product) at the levels of 0, 500, or 1,000 mg/kg (0, 500, or 1,000 ppm), respectively, for 8 wk. The results showed that although ducks in the 500 ppm B. toyonensis BCT-7112T group displayed numerically better values (e.g., weight gain and feed conversion ratio) than those in the control group, the growth performance of ducks fed diets supplemented with B. toyonensis BCT-7112T did not differ significantly from that of the control group (P > 0.05). There were no significant differences in the intestinal mucosal morphology of ducks across the experimental groups (P > 0.05). However, ducks in the 500 ppm B. toyonensis BCT-7112T group showed a trend of greater values, for example, villus height per crypt depth of duodenum (P = 0.16) and ileum (P = 0.12) compared with those in the control group. The relative expression of immune-related genes, for example, interferon (IFN) and interleukin-6 (IL-6) in the meat duck spleen was significantly lower in both B. toyonensis BCT-7112T groups at 14 d and 35 d than in the control group (P < 0.05). Beta diversity analysis of the cecal microbiota of ducks in either the 500 ppm or the 1,000 ppm B. toyonensis BCT-7112T group showed to have higher diversity than that in the control group, where at the phylum level, Bacteroidetes was the most abundant, followed by Firmicutes, and at the genus level, Bacteroides, Fusobacterium, and Ruminococcaceae were the top 3 most abundant genera. In conclusion, our study demonstrates that 500 ppm supplementation with B. toyonensis BCT-7112T in duck diets can reduce proinflammatory cytokine gene expression, improve immunological function, and increase the variety of microbial communities in the ceca of meat-type ducks.

Effects and Mechanisms of Cage versus Floor Rearing System on Goose Growth Performance and Immune Status

Currently, FRS and CRS are the two predominant dryland rearing systems in the goose industry. However, the effects of these two systems on goose growth performance and health, as well as the underlying mechanisms, have not been fully clarified. Thus, this study aimed to compare growth performance and immune status, as well as investigate the genome-wide transcriptomic profiles of spleen in geese, between CRS and FRS at 270 d of age. Phenotypically, the body weight and body size traits were higher in geese under FRS, while the weight and organ index of spleen were higher in geese under CRS (p < 0.05). Noticeably, the bursa of Fabricius of geese under FRS was degenerated, while that under CRS was retained. At the serum level, the immune globulin-G (IgG) and interleukin-6 (IL-6) levels were higher in geese under CRS (p < 0.05). At the transcriptomic level, we identified 251 differentially expressed genes (DEGs) in the spleen between CRS and FRS, which were mainly enriched in scavenger receptor activity, inflammatory response, immune response, neuroactive ligand-receptor interaction, phenylalanine metabolism, ECM receptor interaction, calcium signaling pathway, phenylalanine, tyrosine, and tryptophan biosynthesis, regulation of actin cytoskeleton, and MAPK signaling pathways. Furthermore, through protein-protein interaction (PPI) network analysis, ten candidate genes were identified, namely, VEGFA, FGF2, NGF, GPC1, NKX2-5, FGFR1, FGF1, MEIS1, CD36, and PAH. Further analysis demonstrated that geese in CRS could improve their immune ability through the "phenylalanine metabolism" pathway. Our results revealed that the FRS improved growth performance, whereas the CRS improved goose immune function by increasing levels of IL-6 and IgG in serum. Moreover, the phenylalanine metabolism pathway could exert positive effects on immune function of geese under CRS. These results can provide reliable references for understanding how floor and cage rearing systems affect goose growth performance and immune capacity.

Biosecurity and water, sanitation, and hygiene (WASH) interventions in animal agricultural settings for reducing infection burden, antibiotic use, and antibiotic resistance: a One Health systematic review

Prevention and control of infections across the One Health spectrum is essential for improving antibiotic use and addressing the emergence and spread of antibiotic resistance. Evidence for how best to manage these risks in agricultural communities-45% of households globally-has not been systematically assembled. This systematic review identifies and summarises evidence from on-farm biosecurity and water, sanitation, and hygiene (WASH) interventions with the potential to directly or indirectly reduce infections and antibiotic resistance in animal agricultural settings. We searched 17 scientific databases (including Web of Science, PubMed, and regional databases) and grey literature from database inception to Dec 31, 2019 for articles that assessed biosecurity or WASH interventions measuring our outcomes of interest; namely, infection burden, microbial loads, antibiotic use, and antibiotic resistance in animals, humans, or the environment. Risk of bias was assessed with the Systematic Review Centre for Laboratory Animal Experimentation tool, Risk of Bias in Non-Randomized Studies of Interventions, and the Appraisal tool for Cross-Sectional Studies, although no studies were excluded as a result. Due to the heterogeneity of interventions found, we conducted a narrative synthesis. The protocol was pre-registered with PROSPERO (CRD42020162345). Of the 20 672 publications screened, 104 were included in this systematic review. 64 studies were conducted in high-income countries, 24 studies in upper-middle-income countries, 13 studies in lower-middle-income countries, two in low-income countries, and one included both upper-middle-income countries and lower-middle-income countries. 48 interventions focused on livestock (mainly pigs), 43 poultry (mainly chickens), one on livestock and poultry, and 12 on aquaculture farms. 68 of 104 interventions took place on intensive farms, 22 in experimental settings, and ten in smallholder or subsistence farms. Positive outcomes were reported for ten of 23 water studies, 17 of 35 hygiene studies, 15 of 24 sanitation studies, all three air-quality studies, and 11 of 17 other biosecurity-related interventions. In total, 18 of 26 studies reported reduced infection or diseases, 37 of 71 studies reported reduced microbial loads, four of five studies reported reduced antibiotic use, and seven of 20 studies reported reduced antibiotic resistance. Overall, risk of bias was high in 28 of 57 studies with positive interventions and 17 of 30 studies with negative or neutral interventions. Farm-management interventions successfully reduced antibiotic use by up to 57%. Manure-oriented interventions reduced antibiotic resistance genes or antibiotic-resistant bacteria in animal waste by up to 99%. This systematic review highlights the challenges of preventing and controlling infections and antimicrobial resistance, even in well resourced agricultural settings. Most of the evidence emerges from studies that focus on the farm itself, rather than targeting agricultural communities or the broader social, economic, and policy environment that could affect their outcomes. WASH and biosecurity interventions could complement each other when addressing antimicrobial resistance in the human, animal, and environmental interface.

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.

Effects of Swimming Pool Conditions and Floor Types on White Roman Geese's Physical Condition Scores and Behaviors in an Indoor Rearing System

Biosecurity problems, including the continual risk of avian influenza spread by wild birds, have severely affected traditional free-range waterfowl production systems. Regulations and techniques for indoor goose production require more considerations for animal welfare. This study investigated the effects of swimming pool conditions and different floor types on the physical condition scores and behaviors of indoor-reared White Roman geese. A total of 48 male and 48 female White Roman geese reared from the age of 15 to 84 days were randomly allocated to pens with or without a swimming pool and with either mud or perforated plastic floors. Providing a swimming pool improved geese's eye and feather cleanliness and breast blister scores at the age of 84 days. Compared with geese reared on a mud floor, those reared on a perforated plastic floor had better feather cleanliness and higher breast blister scores at the age of 56 and 84 days. Providing a swimming pool to indoor-reared geese may reduce the proportion of abnormal behaviors, such as injurious feather pecking, by increasing water-related behaviors. This study suggests a more appropriate environment design for better balancing commercial goose production with animal welfare in an indoor rearing system.

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.

The Application of Copper Waterline on Laying Performance and Gut Health of Aged Laying Hens

The effect of the application of copper waterline on the performance and gut health of aged laying hens was evaluated in this study. Forty-eight 70-week-old laying hens were divided into two groups (three replicates of eight hens each): control and copper (Cu) groups provided with normal polyvinyl chloride (PVC) waterline or Cu waterline. The laying performance was measured during the four-week period of the experiment. The intestinal antioxidant status and the microbiota diversity of the cecal content were determined. Moreover, a bacteriostasis test on Escherichia coli and Salmonella enteritidis was conducted after inoculation in waterline and hens, respectively. The water Cu²⁺ content was increased by Cu waterline compared to the control (P<0.05). Cu waterline had no detectable effect on most production performances, however, it increased the egg weight (P<0.05). Cu waterline increased the Cu level in the eggshell. Cu level in excreta increased with time, especially in the final two weeks, however, there was no significant change in fecal Cu excretion. The lipid peroxidation product malondialdehyde content in ileum decreased (P<0.01), while the activities of CuZn-superoxide dismutase (SOD) of ileum and glutathione peroxidase (GSH-PX) activity of jejunum and ileum increased after Cu treatment. The relative abundance and richness of cecal microbiota increased after Cu treatment (P<0.05). Cu waterline changed the microbial composition, including the increased proportion of Methanocorpusculum, Paludibacter, and decreased proportion of Fucobacterium, Anaerobiospirillum, and Campylobacter. The colonization of E. coli and S. enteritidis in Cu waterline was suppressed by Cu treatment, indicating that Cu waterline had potential antibacterial properties. The result suggests that Cu waterline could inhibit the colonization of pathogenic microorganisms such as E. coli and Salmonella and facilitate the enrichment of cecal microbiota diversity.

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.

Effects of rearing systems on production performance, antioxidant capacity and immune status of meat ducks at different ages

As potential substitutes for traditional free-range rearing system, floor-rearing system (FRS) and net-rearing system (NRS) are the current predominant dryland duck rearing systems. However, the influence of these two systems on production performance and duck health is poorly understood. In this study, a 2 × 3 factorial arrangement with two rearing systems (FRS and NRS) and three ages (4w, 8w and 13w) was conducted to study the effects of FRS and NRS on production, antioxidant capacity and immune status of Nonghua ducks. The production performance was mainly affected by the effect of rearing systems at 8w. Body weight, average daily gain, eviscerated weight and semi-eviscerated weight were higher in NRS ducks at 8w, but carcass yield at 8w and 13w was decreased (P < 0.05). Lipid deposition was enhanced in NRS and higher sebum and abdominal fat yields were seen at 8w and 13w (P < 0.05). NRS resulted in developmental retardation of the liver at 4w and decreased gizzard index at all ages (P < 0.05). Antioxidant capacity indicators were unaffected by rearing systems (P > 0.05), however, in NRS, slightly better antioxidant capacity was seen at 4w, while glutathione peroxidase (GSH-Px) activity was higher at 13w (P < 0.05). NRS ducks had higher thymus weight at 8w and higher spleen weight at 13w (P < 0.05). Immune cytokines were extensively affected by rearing system (P < 0.05) and higher levels of interferon-γ, interleukin-1β, interleukin-4 and immunoglobulins were seen in NRS ducks. Serum biochemical parameters (aspartate aminotransferase (AST), alanine aminotransferase (ALT) and alkaline phosphatase (ALP)) showed that NRS was better for liver health, and in the liver of FRS ducks, ALP was higher at 13w, and both ALP and interferon-γ were higher at 13w than at 4w and 8w (P < 0.05). In conclusion, this study showed that NRS was, to an extent, conducive to production performance and duck liver health, but compared to FRS, defects were seen in visceral organ development and lipid deposition. Although antioxidant capacity was not significantly affected, NRS ducks may have better antioxidant capacity at the early breeding stage, and GSH-Px activity was increased for scavenging excess free radicals at the later one. NRS increased serum levels of interferon-γ, interleukin-1β, interleukin-4 and immunoglobulins and promoted thymus and spleen development, thus improving duck immune function. These findings will provide a reliable reference for selecting a rearing system.

Effects of different rearing systems on intramuscular fat content, fatty acid composition, and lipid metabolism-related genes expression in breast and thigh muscles of Nonghua ducks

Rearing system is a critical nongenetic factor influencing meat quality of ducks. In this study, a total of 360 birds were randomly allocated into floor rearing system (FRS) and net rearing system (NRS) to compare their effects on intramuscular fat (IMF) deposition, fatty acid composition, and related gene expression in muscles of Nonghua ducks. Sawdust bedding and stainless mesh bed were equipped in FRS and NRS, respectively. At the eighth week (8w) and 13th week (13w), the breast and thigh muscles of ducks were collected to determine the profiles of lipids composition and the expressions of lipid metabolism-related genes. The IMF content was higher in 13w-FRS than 8w-FRS and 8w-NRS in breast muscle, whereas it was higher in 13w-NRS than other groups in thigh muscle (P < 0.05). C16:1, C20:5(n-3) of muscles were higher in 8w-NRS than 8w-FRS, whereas C18:1(n-9)c, C18:2(n-6)c, Ʃ monounsaturated fatty acid (MUFA), and ƩMUFA/Ʃsaturated fatty acid (SFA) ratio of muscles were higher in 13w-NRS than 8w-FRS and 8w-NRS (P < 0.05). C22:6(n-3), C20:4(n-6) of breast muscle and C20:3(n-6) of thigh muscle were higher in 13w-NRS than 13w-FRS (P < 0.05). Fatty acids variation was studied by principal component analysis, exhibiting extensive positive loadings on principal components. SREBP1, ACADL, and FABP3 were downregulated in breast muscle, whereas PPARα and ELOVL5 were upregulated in thigh muscle of NRS ducks at 13w. Principal components were extensively correlated with lipids composition parameters, and principal components of breast muscle 1 and principal components of thigh muscle 1 were correlated with SREBP1 and PPARα, respectively (P < 0.05). In conclusion, with increasing age, FRS enhanced IMF deposition in breast muscle, and the same promotion in thigh muscle was because of NRS. The variation of fatty acids in muscles was uniform, and the change of single fatty acid was unable to distinguish NRS and FRS. However, as NRS downregulated SREBP1, ACADL and FABP3 in breast muscle and upregulated PPARα and ELOVL5 in thigh muscle, NRS could improve nutrient value and meat quality by increasing ƩMUFA, ƩMUFA/ƩSFA ratio, and important PUFA levels. Therefore, NRS was more recommended than FRS for Nonghua ducks during week 8 to 13 posthatching.