Rearing system causes changes of behavior, microbiome, and gene expression of chickens

Residue of Erycibe obtusifolia Benth as bedding materials improves welfare and microorganisms of chickens

1. This study investigated the effect of Erycibe obtusifolia Benth (EOB) plant residue on welfare, stress-related gene expression as well as microorganisms of both the gut and bedding materials of chickens.2. In this study, a total of 160, bearded chickens aged 80 d old were raised on four bedding types: EOB, rice husk (RH), EOB and RH bedding (EOB E) and EOB plus Enterococcus faecalis fermented bedding (RHEOB). Twelve behaviours, foot pad dermatitis and feather condition of each group were observed, caecal contents and bedding material were collected for microorganisms detection and brain tissues were collected for gene expression related to fear, stress and aggressive behaviour.3. Bedding had no effect on foot pad dermatitis (FPD), feather condition or abnormal behaviour. Sand bathing (p <0.05) and affinity behaviour (p <0.05) increased in birds on the EOB with rice husk bedding material. The expressions of 5-HT, HTR1A and CRH genes in brain tissue were affected by different bedding types. The mixture of EOB and rice husk reduced the relative abundance of Brevibacterium, Enterococcus and Streptococcus spp. increased the relative abundance of probiotics of Rombutz, Lactobacillus spp. and L. mucosus and improved the microflora of the bedding and caecal contents.4. EOB bedding showed good application, as EOB and rice husk mixed bedding had the best effect.

Microbiome-metabolomics analysis insight into the effects of dietary chromium picolinate on abdominal fat deposition and lipid metabolism of ducks

This research endeavored to explore the impact of Cr-Pic on the abdominal fat deposition and lipid metabolism of ducks, as well as to uncover the mechanisms at play and identify the optimal dietary supplementation level of Cr-Pic. The results showed that adding 0.6 mg/kg Cr-Pic observably increased the body weight and serum levels of adiponectin and leptin, and decreased serum levels of total cholesterol, triglyceride, and low-density lipoprotein cholesterol in ducks at 14 days (P < 0.05). The addition of 0.6 % Cr-Pic was discovered to regulate lipid metabolism and meat quality through its effects on reducing abdominal fat and drip loss, downregulating the mRNA expression of genes involved in lipid synthesis in the abdominal fat and liver, and upregulating the mRNA expression of genes associated with degradation and transport in these tissues (P < 0.05). Untargeted metabolic profiling indicated that the distinct metabolites between the Cr-Pic and Control groups were predominantly associated with pathways involving amino acids. Microbiome analysis showed that Cr-Pic administration altered the microbial genera related to the adjustment of lipid metabolism in the cecum of ducks, such as increasing the proportion of Bacteroides and Lactobacillus, and decreasing the proportions of Alistipes, Methanobrevibacter, Romboutsia, and Peptostreptococcus (P < 0.05). In summary, Cr-Pic shows promise in reducing the abdominal fat accumulation in ducks by regulating the intestinal microbial composition and the metabolic pathways of amino acids that are linked to lipid metabolism.

Influence of the rearing system on the ileum microbiome, metabolome, and transcriptome in meat rabbits

The rearing system of livestock plays a vital role in animal production, meat quality, and overall welfare. This study aimed to assess the influence of cage-rearing system and forest-rearing system on the ileum microbiota, metabolome, and ileal mucosa transcriptome in meat rabbits. Moreover, 16S rDNA sequencing revealed significant differences in the ileal microbiome composition: caged rabbits exhibited a higher abundance of the genera uncultured Erysipelotrichaceae and Delftia, whereas the levels of Muribaculaceae, unclassified Burkholderiales, and uncultured Eubacteriaceae were lower compared to rabbits reared in the forest. Metabolome analysis identified 372 differentially accumulated metabolites in the ileum content, which were predominantly mapped to amino acid metabolism, nucleotide metabolism, and energy metabolism pathways. The cage-rearing system was found to positively correlate with the efficient utilization of nutrient sources. Additionally, transcriptome analysis of the ileal mucosa revealed 984 differentially expressed genes, predominantly involved in metabolic pathways, signal transduction pathways, and immune response processes. Through Pearson correlation analysis, we were able to elucidate the metabolic pathway, immune responses, and disease resistance mechanisms were affected by the rearing system. Overall, the findings suggested that metabolic adaptation, nutrient utilization, and immune response play crucial roles in how rabbits adjust to different rearing systems. While the cage system may enhance nutrient efficiency, it appears to suppress immune function and disease resistance.

Exploring the relationship between rearing system and carcass traits of Danzhou chicken: a microbial perspective

This study investigated the effects of free-range (FR) and cage-rearing (CR) systems on intestinal health, carcass traits, and microbial diversity in the Danzhou chicken breed. Two groups of 125 hens in each group, aged 42 wk, were reared under FR and CR systems. At 50 wk, 50 hens from each group were randomly selected for carcass analysis and 10 hens for intestinal morphology and microbiota profiling. Results indicated a significant increase in villus height (VH) in the duodenum (P < 0.05), jejunum (P < 0.01), and ileum (P < 0.001) of the CR group. Additionally, the ratio of VH to crypt depth (VR) significantly (P < 0.001) increased in the jejunum, while crypt depth (CD) decreased significantly (P < 0.001) in the same section in the CR group. Carcass traits, including dress weight (DW), eviscerated with giblet weight (EGW), eviscerated weight (EW), and leg muscle weight (LW) significantly improved (P < 0.05) in the CR group. Microbial diversity showed significant β-diversity differences, with Lactobacillus, Enterococcus, and Oxalobacteraceae as dominant biomarkers in the CR group. Conversely, Actinomycetaceae, Erysipelotrichaceae, Coriobacteriaceae, Eubacterium, Actinomyces, Scardovia, and Lachnospiraceae were dominant in the FG group. Correlation analysis showed duodenum Lactobacillus was positively correlated with VH (P < 0.05), EW (P < 0.05), and LW (P < 0.001). Jejunum Lactobacillus was positively correlated considerably with VH (P < 0.01), VR (P < 0.05), DW (P < 0.05), EGW (P < 0.01), and LW (P < 0.001). Ileum Lactobacillus was positively correlated with EGW (P < 0.01), EW (P < 0.05), and LW (P < 0.01). Aeriscardovia in duodenum was positively (P < 0.01) associated with EGW. Enterococcus in the duodenum was positively (P < 0.05) associated with EGW and in Jejunum positively correlated with VH (P < 0.05) and VR (P < 0.01). The study concludes that cage rearing improves intestinal health, carcass traits, and microbial diversity in Danzhou chickens, with Lactobacillus and Enterococcus playing key roles.

Impacts of access to legume- or grass-based pasture on behaviour, physiological responses and bacterial load of laying hens

Despite the plethora of studies on the impacts of access to runs on chickens, there is a paucity of information on the welfare and behavioural repertoire of hens raised in the deep litter houses with or without access to legume- or grass-based pasture. Therefore, this study aimed to evaluate the impact of access to grass or legume pastures by laying hens on behaviour, physiological responses and bacterial load. The study was conducted to evaluate the influence of exposure of egg-type chickens to runs on grass or legume pastures on their welfare and behaviours. The study involved the use of 240 ISA brown pullets from 12 weeks of age and and lasted for 48 weeks. The treatments were deep litter housing with grass-based pasture run (PG), deep litter housing with legume-based pasture run (PL) and deep litter housing without runs (LD) having 80 pullets with four replicates of twenty birds each. Behavioural observations of the hens in each pen were made at 52 weeks of age and tonic immobility was assessed by making the birds lie on their back with their head resting in a U-shaped wooden cradle. The measurements of the respiratory rate and rectal temperature of the hens were assessed at 1:00 p.m. at different laying phases. The gastrointestinal and egg bacterial counts were conducted at 60 weeks of age. Results revealed that the proportion of time spent eating was highest (p < 0.05) in the deep litter housing system, while the legume and grass pasture were similar. The hens spent most of their time standing and eating in the three treatments. However, the time spent standing in PL and PG was similar but significantly higher (p < 0.05) than in LD. Results on tonic immobility duration showed that the time spent by the hens in LD during the reaction was significantly longer than those of the PL and PG in the first, second and third phases of the experiments. However, the time spent by the hens in PL and PG was similar. The rectal temperatures of PL and PG birds were comparable and higher than those of LD during the second phase. On the other hand, there was no difference in the respiratory rate. Plasma triiodothyronine (T3) of the hens did not follow a consistent pattern. The bacterial count in the large intestine in LD and PL was similar but significantly (P < 0.05) higher than that of the PG. It was concluded that access to pasture influenced the behaviours of hens and that tonic immobility duration was shorter in the hens on the pasture, suggesting that access to pasture favoured hens' welfare.

Comparing Gut Microbial Composition and Functional Adaptations between SPF and Non-SPF Pigs

The gut microbiota is a key factor significantly impacting host health by influencing metabolism and immune function. Its composition can be altered by genetic factors, as well as environmental factors such as the host's surroundings, diet, and antibiotic usage. This study aims to examine how the characteristics of the gut microbiota in pigs, used as source animals for xenotransplantation, vary depending on their rearing environment. We compared the diversity and composition of gut microbiota in fecal samples from pigs raised in specific pathogen-free (SPF) and conventional (non-SPF) facilities. The 16S RNA metagenome sequencing results revealed that pigs raised in non-SPF facilities exhibited greater gut microbiota diversity compared to those in SPF facilities. Genera such as Streptococcus and Ruminococcus were more abundant in SPF pigs compared to non-SPF pigs, while Blautia, Bacteroides, and Roseburia were only observed in SPF pigs. Conversely, Prevotella was exclusively present in non-SPF pigs. It was predicted that SPF pigs would show higher levels of processes related to carbohydrate and nucleotide metabolism, and environmental information processing. On the other hand, energy and lipid metabolism, as well as processes associated with genetic information, cell communication, and diseases, were predicted to be more active in the gut microbiota of non-SPF pigs. This study provides insights into how the presence or absence of microorganisms, including pathogens, in pig-rearing facilities affects the composition and function of the pigs' gut microbiota. Furthermore, this serves as a reference for tracing whether xenotransplantation source pigs were maintained in a pathogen-controlled environment.

Identification of Metabolites in Muscles of Lueyang Black-Bone Chickens: A Comparative Analysis of Caged and Cage-Free Rearing Modes Using Untargeted Metabolomic Techniques

The Lueyang black-bone chicken is a specific native chicken strain in China. This study aimed to investigate the effects of different rearing systems on the meat quality of Lueyang black-bone chickens. Six hundred Lueyang black-bone hens were randomly divided into two groups at 7 weeks of age and raised in cage and cage-free systems for 20 weeks. The carcass yield, meat quality, and total metabolites were measured in both the leg and breast muscles. By comparison, the carcass yield of hens in the cage-free (CF) group (1.26 ± 0.09 kg) was significantly lower than that in the caged rearing (CR) group (1.52 ± 0.15 kg). However, the shear force of leg muscles in the CF group (27.98 ± 2.43 N) was significantly greater than that in the CR group (24.15 ± 1.93 N). In addition, six samples from each group were randomly selected and their metabolites were detected by the non-targeted metabolomics technique. Among these metabolites, 408 and 354 significantly differentially abundant metabolites were identified in breast and leg muscles, which were mainly involved in glycerophospholipid metabolism, unsaturated fatty acid biosynthesis, arginine and proline metabolism, and nucleotide metabolism. We found that the levels of 19 phospholipids, mainly phosphatidylcholines and lysophosphatidylcholines, were significantly greater in the CF group than in the CR group. Additionally, the contents of eight unsaturated fatty acids, linoleic acid, and linolenic acid were dramatically greater in the CF group than in the caged group. The accumulation of 4-hydroxy-proline, glutamate, and adenosine 3'-monophosphate (AMP) was enhanced in the CF group. Moreover, many more volatile organic compounds were identified in the muscles of the cage-free group, enhancing the flavor of the chicken meat. In conclusion, the cage-free rearing mode facilitates the accumulation of nutrients and flavor substances in the chicken meat and is a better rearing system for Lueyang black-bone chickens.

Impact of housing system on intestinal microbiota of laying hens - A systematic review

Studies on the housing system's impact on laying hens' intestinal microbiota were retrieved from the Web of Science, PubMed, and Scopus (between 2017 and 2022). Inclusion criteria were studies that discussed measurable effects related to the topic written in English, Portuguese, and Spanish. Of 3281 articles in the identification stage, 12 studies were used in the systematic review. Asia developed most research relating to the subject. Most studies compared the intestinal microbiota of laying hens from conventional cages versus Cage-Free or Free-Range. However, no study has evaluated the intestinal microbiota of laying hens maintained in an organic system. Greengene and Silva were the most used reference in the studies. According to the results observed in the studies included in the systematic review, there is greater alpha diversity in the alternative system and a high dissimilarity between the conventional and alternative systems. Exposure to environmental factors such as soil, vegetation, natural lighting, access to pastures, and ingesting fibrous foods can lead to changes in the intestinal microbiota. A brief outline of published scientific evidence demonstrates that the housing system can change the gut microbiome of hens. This study summarises the relationship between the housing system and the intestinal microbiome of laying hens and provides a roadmap for future research regarding the gut microbiome of hens.

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.

Early fecal microbiota transplantation from high abdominal fat chickens affects recipient cecal microbiome and metabolism

Abdominal fat deposition (AFD) in chickens is closely related to the gut microecological balance. In this study, the gut microbiota from high-AFD chickens was transplanted into the same strain of 0-day-old chicks via fecal microbiota transplantation (FMT). The FTM from chickens with high AFD had no obvious effects on growth traits, adult body weight, carcass weight, abdominal fat weight, and abdominal fat percentage, but did reduce the coefficient of variation of AFD traits. FMT significantly decreased cecal microbiome richness, changed the microbiota structure, and regulated the biological functions associated with energy metabolism and fat synthesis. Additionally, the cecal metabolite composition and metabolic function of FMT recipient chickens were also significantly altered from those of the controls. Transplantation of high-AFD chicken gut microbiota promoted fatty acid elongation and biosynthesis and reduced the metabolism of vitamins, steroids, and carbohydrates in the cecum. These findings provide insights into the mechanisms by which chicken gut microbiota affect host metabolic profiles and fat deposition.

Versatile, vigilance, and gut microbiome support the priority of high-ranking hens

Dominance hierarchy exists in social animals and shows profound impacts on animals' survival, physical and mental health, and reproductive success. Aggressive interaction, as the main indicator used to calculate social hierarchy, however, is not found in some female animals. In this study, we aimed to figure out the establishment of social hierarchy in hens that almost perform aggressive behaviors and investigated the interactions of social hierarchy with production performance and gut microbiome. Forty 49-day-old Qingyuan hens were randomly divided into four groups. The social hierarchy of hens was calculated by the relative position around the feeder. The rank 1 (R1), R2, R3, R4, R5, R6, R7, R8, R9, and R10 birds were determined in ascending order. Then, R1 and R2 birds (four duplicates, n = 8) were named as the high-ranking hens (HR) group, while R9 and R10 individuals were named as the low-ranking hens (LR) group (four duplicates, n = 8). The heart index (p = 0.01), number of visits per day, daily feed intake, and occupation time per day were higher in the HR group than LR group, but the LR group had a higher feed intake per visit than the HR group. The alpha diversity was significantly lower in the HR group than the LR group (p = 0.05). The relative abundance of phylum Firmicutes was higher while that of phylum Deferribacterota was lower in the HR group than LR group (p < 0.05). At the genus level, the relative abundance of Succinatimonas, Eubacterium hallii group, and Anaerostipes were higher in HR group than in LR group. The relative abundance of Bacteroides, Mucispirillum, Subdoligranulum, and Barnesiellaceae unclassified was higher in the LR group than HR group (p < 0.05). In conclusion, the rank of hens could be calculated by the relative position around the feeder when they compete for food. The dominant hens have a versatile. Moreover, they are more vigilant and have priority when foraging. Low-ranking hens adopt strategies to get enough food to sustain themselves. Hens of high-rank possess beneficial bacteria that use favorable substances to maintain the balance of the gut environment.

A comprehensive longitudinal study of gut microbiota dynamic changes in laying hens at four growth stages prior to egg production

OBJECTIVE

The poultry industry is a primary source of animal protein worldwide. The gut microbiota of poultry birds, such as chickens and ducks, is critical in maintaining their health, growth, and productivity. This study aimed to identify longitudinal changes in the gut microbiota of laying hens from birth to the pre-laying stage.

METHODS

From a total of 80 Hy-Line Brown laying hens, birds were selected based on weight at equal intervals to collect feces (n = 20 per growth) and ileal contents (n = 10 per growth) for each growth stage (days 10, 21, 58, and 101). The V4 regions of the 16S rRNA gene were amplified after extracting DNA from feces and ileal contents. Amplicon sequencing was performed using Illumina, followed by analysis.

RESULTS

Microbial diversity increased with growth stages, regardless of sampling sites. Microbial community analysis indicated that Firmicutes, Proteobacteria, and Bacteroidetes were the dominant phyla in the feces and ileal. The abundance of Lactobacillus was highest on day 10, and that of Escherichia-shigella was higher on day 21 than those at the other stages at the genus level (for the feces and ileal contents; p<0.05). Furthermore, Turicibacter was the most abundant genus after changing feed (for the feces and ileal contents; p<0.05). The fecal Ruminococcus torques and ileal Lysinibacillus were negatively correlated with the body weights of chickens (p<0.05).

CONCLUSION

The gut microbiota of laying hens changes during the four growth stages, and interactions between microbiota and feed may be present. Our findings provide valuable data for understanding the gut microbiota of laying hens at various growth stages and future applied studies.

Uncovering changes in microbiome profiles across commercial and backyard poultry farming systems

The microbiome profiles of poultry production systems significantly impact bird health, welfare, and the environment. This study investigated the influence of broiler-rearing systems on the microbiome composition of commercial and backyard chicken farms and their environment over time. Understanding these effects is vital for optimizing animal growth, enhancing welfare, and addressing human and environmental health implications. We collected and analyzed various samples from commercial and backyard farms, revealing significant differences in microbial diversity measurements between the two systems. Backyard farms exhibited higher alpha diversity measurements in soil and water samples, while commercial farms showed higher values for litter and feeder samples. The differences in microbial diversity were also reflected in the relative abundance of various microbial taxa. In backyard farms, Proteobacteria levels increased over time, while Firmicutes levels decreased. Campilobacterota, including the major poultry foodborne pathogen Campylobacter, increased over time in commercial farm environments. Furthermore, Bacteroides, associated with improved growth performance in chickens, were more abundant in backyard farms. Conversely, pathogenic Acinetobacter was significantly higher in backyard chicken fecal and feeder swab samples. The presence of Brevibacterium and Brachybacterium, associated with low-performing broiler flocks, was significantly higher in commercial farm samples. The observed differences in microbial composition and diversity suggest that farm management practices and environmental conditions significantly affect poultry health and welfare and have potential implications for human and environmental health. Understanding these relationships can inform targeted interventions to optimize poultry production, improve animal welfare, and mitigate foodborne pathogens and antimicrobial resistance risks. IMPORTANCE The microbiome of poultry production systems has garnered significant attention due to its implications on bird health, welfare, and overall performance. The present study investigates the impact of different broiler-rearing systems, namely, commercial (conventional) and backyard (non-conventional), on the microbiome profiles of chickens and their environment over time. Understanding the influence of these systems on microbiome composition is a critical aspect of the One-Health concept, which emphasizes the interconnectedness of animal, human, and environmental health. Our findings demonstrate that the type of broiler production system significantly affects both the birds and their environment, with distinct microbial communities associated with each system. This study reveals the presence of specific microbial taxa that differ in abundance between commercial and backyard poultry farms, providing valuable insights into the management practices that may alter the microbiome in these settings. Furthermore, the dynamic changes in microbial composition over time observed in our study highlight the complex interplay between the poultry gut microbiome, environmental factors, and production systems. By identifying the key microbial players and their fluctuations in commercial and backyard broiler production systems, this research offers a foundation for developing targeted strategies to optimize bird health and welfare while minimizing the potential risks to human and environmental health. The results contribute to a growing body of knowledge in the field of poultry microbiome research and have the potential to guide future improvements in poultry production practices that promote a sustainable and healthy balance between the birds, their environment, and the microbial communities they host.

Collagen adhesin protein and necrotic enteritis B-like toxin as biomarkers for early diagnosis of necrotic enteritis in commercial broiler chickens

Mouse monoclonal antibodies (mAbs) reactive with Clostridium perfringens collagen adhesin protein (CNA) and necrotic enteritis B-like toxin (NetB) were developed. The best capture/detection mAb pairs for CNA and NetB were selected based on their affinity and specificity to develop sandwich enzyme-linked immunosorbent assays (ELISAs) to detect CNA and NetB proteins, respectively, in jejunal digesta samples from commercial broiler farms in the United States. Prior to the analysis of samples from commercial broiler flocks, the specificity and sensitivity of the CNA and NetB ELISAs were validated using sera, jejunal digesta, and fecal samples from chickens coinfected with Eimeria maxima and CNA+/NetB+C. perfringens in an animal model of necrotic enteritis (NE). Subsequently, a total of 251 field samples were collected from 74 commercial poultry farms. Among these, 18 samples were from 6 broiler farms that used certified organics (CO), and 155 samples were from 42 farms with nonantibiotics (NA). In jejunal digesta samples, CNA levels ranged from 0.02 to 0.59 ng/mL and NetB levels ranged from 0.09 to 1.91 ng/mL. CNA and NetB levels showed a positive correlation with each other (Pearson correlation coefficient r = 0.772, P < 0.001). CNA and NetB levels in jejunal digesta were significantly decreased in CO farms compared with those from NA farms (P < 0.001). In conclusion, these new C. perfringens antigen-specific sandwich ELISAs offer a sensitive and specific means to detect C. perfringens CNA and NetB proteins as biomarkers of early NE occurrence in field samples from commercial broiler chickens.

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 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.

Gut Microbiome Studies in Livestock: Achievements, Challenges, and Perspectives

The variety and makeup of the gut microbiome are frequently regarded as the primary determinants of health and production performances in domestic animals. High-throughput DNA/RNA sequencing techniques (NGS) have recently gained popularity and permitted previously unheard-of advancements in the study of gut microbiota, particularly for determining the taxonomic composition of such complex communities. Here, we summarize the existing body of knowledge on livestock gut microbiome, discuss the state-of-the-art in sequencing techniques, and offer predictions for next research. We found that the enormous volumes of available data are biased toward a small number of globally distributed and carefully chosen varieties, while local breeds (or populations) are frequently overlooked despite their demonstrated resistance to harsh environmental circumstances. Furthermore, the bulk of this research has mostly focused on bacteria, whereas other microbial components such as protists, fungi, and viruses have received far less attention. The majority of these data were gathered utilizing traditional metabarcoding techniques that taxonomically identify the gut microbiota by analyzing small portions of their genome (less than 1000 base pairs). However, to extend the coverage of microbial genomes for a more precise and thorough characterization of microbial communities, a variety of increasingly practical and economical shotgun techniques are currently available.

Connecting gut microbiomes and short chain fatty acids with the serotonergic system and behavior in Gallus gallus and other avian species

The chicken gastrointestinal tract has a diverse microbial community. There is increasing evidence for how this gut microbiome affects specific molecular pathways and the overall physiology, nervous system and behavior of the chicken host organism due to a growing number of studies investigating conditions such as host diet, antibiotics, probiotics, and germ-free and germ-reduced models. Systems-level investigations have revealed a network of microbiome-related interactions between the gut and state of health and behavior in chickens and other animals. While some microbial symbionts are crucial for maintaining stability and normal host physiology, there can also be dysbiosis, disruptions to nutrient flow, and other outcomes of dysregulation and disease. Likewise, alteration of the gut microbiome is found for chickens exhibiting differences in feather pecking (FP) behavior and this alteration is suspected to be responsible for behavioral change. In chickens and other organisms, serotonin is a chief neuromodulator that links gut microbes to the host brain as microbes modulate the serotonin secreted by the host's own intestinal enterochromaffin cells which can stimulate the central nervous system via the vagus nerve. A substantial part of the serotonergic network is conserved across birds and mammals. Broader investigations of multiple species and subsequent cross-comparisons may help to explore general functionality of this ancient system and its increasingly apparent central role in the gut-brain axis of vertebrates. Dysfunctional behavioral phenotypes from the serotonergic system moreover occur in both birds and mammals with, for example, FP in chickens and depression in humans. Recent studies of the intestine as a major site of serotonin synthesis have been identifying routes by which gut microbial metabolites regulate the chicken serotonergic system. This review in particular highlights the influence of gut microbial metabolite short chain fatty acids (SCFAs) on the serotonergic system. The role of SCFAs in physiological and brain disorders may be considerable because of their ability to cross intestinal as well as the blood-brain barriers, leading to influences on the serotonergic system via binding to receptors and epigenetic modulations. Examinations of these mechanisms may translate into a more general understanding of serotonergic system development within chickens and other avians.

Early life environment affects behavior, welfare, gut microbiome composition, and diversity in broiler chickens

This study aimed to identify whether early-life conditions in broiler chickens could affect their behavior and welfare, and whether or not this was associated with an altered gut microbiome composition or diversity. Broilers were tested in a 2 x 2 factorial design with hatching conditions [home pen (OH) or at the hatchery (HH)] and enrichment (dark brooder (EE) or no brooder (NE) until 14 days of age) as factors (N = 6 per treatment combination). Microbiota composition was measured in the jejunum on days (d) 7, 14, and 35 and in pooled fecal samples on day 14. A novel environment test (NET) was performed on days 1 and 11, and the behavior was observed on days 6, 13, and 33. On day 35, composite asymmetry was determined and footpad dermatitis and hock burn were scored. In their home pen, HH showed more locomotion than OH (P = 0.05), and NE were sitting more and showed more comfort behavior than EE at all ages (P <0.001 and P = 0.001, respectively). On days 6 and 13 NE showed more eating and litter pecking while sitting, but on day 33 the opposite was found (age^*enrichment: P = 0.05 and P <0.01, respectively). On days 1 and 11, HH showed more social reinstatement in the NET than OH, and EE showed more social reinstatement than NE (P <0.05). Composite asymmetry scores were lower for EE than NE (P <0.05). EE also had less footpad dermatitis and hock burn than NE (P <0.001). Within OH, NE had a more diverse fecal and jejunal microbiome compared to EE on day 14 (feces: observed richness: P = 0.052; jejunum: observed richness and Shannon: P <0.05); the principal component analysis (PCA) showed differences between NE and EE within both HH and OH in fecal samples on day 14, as well as significant differences in bacterial genera such as Lactobacillus and Lachnospiraceae (P <0.05). On day 35, PCA in jejunal samples only showed a trend (P = 0.068) for differences between NE vs. EE within the OH. In conclusion, these results suggest that especially the dark brooder affected the behavior and had a positive effect on welfare as well as affected the composition and diversity of the microbiome. Whether or not the behavior was modulated by the microbiome or vice versa remains to be investigated.

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.

Gut microbiota activity in chickens from two genetic lines and with outdoor-preferring, moderate-preferring, and indoor-preferring ranging profiles

Despite the existing research into the gut microbiome of meat chickens, the associations between gut microbiome composition, its activity and chicken outdoor ranging frequency remain unexplored. The aim of this study was to determine the gut microbiota composition, activity and metabolic products in chickens of 2 different lines and 3 ranging profiles. Sixty non-beak trimmed birds, either Sasso or Green-legged Partridge were housed with access to outdoor ranges from wk. 5 to 10 of age. Outdoor ranges were video recorded to obtain frequencies of the birds’ range use. The information about relative abundance of selected bacterial groups in the ceca including Lactobacillus spp., E. coli, Bifidobacterium spp., and Clostridium spp. was obtained with the PCR method. Gut microbiota activity was assessed based on the glycolytic activity of bacterial enzymes including, α-glucosidase, β-glucosidase, α-galactosidase, β-galactosidase, and β-glucuronidase as well as based on the concentration of short-chain fatty acids (SCFA) in the caecal digesta. Statistical analysis was conducted by generalized linear mixed models, applying the breed and ranging profile as fixed effects and pen as a random factor. The lowest relative abundance of Bifidobacterium spp. was found in the cecal content of indoor-preferring Sasso birds (0.01 ± 0.001), as compared to all other birds in the experiment (ranging from 0.03 ± 0.01 to 0.11 ± 0.07; P = 0.0002). The lowest relative abundance of E. coli was identified for all outdoor-preferring birds and indoor- preferring Sasso birds (0.01 ± 0.001; P = 0.0087). Cecal activity of: α-glucosidase, β-glucuronidase and β-galactosidase was higher in Green-legged Partridges, as compared to Sasso (P = 0.013; P = 0.008; P = 0.004). Valeric acid concentrations were higher in moderate Green-legged Partridges than in Sasso of the same ranging profile (2.03 ± 0.16 vs. 1.5 ± 0.17; 0.016). The majority of the current results confirmed an effect of genotype and ranging profile on the various analyzed parameters. In outdoor-preferring birds, the consumption of pasture originating feed sources as a supplement to the indoor accessible cereal-based diet likely caused the positive effects on the birds’ microbial profile.

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.

Role of Physiology, Immunity, Microbiota, and Infectious Diseases in the Gut Health of Poultry

“Gut health” refers to the physical state and physiological function of the gastrointestinal tract and in the livestock system; this topic is often focused on the complex interacting components of the intestinal system that influence animal growth performance and host-microbial homeostasis. Regardless, there is an increasing need to better understand the complexity of the intestinal system and the various factors that influence gut health, since the intestine is the largest immune and neuroendocrine organ that interacts with the most complex microbiome population. As we face the post-antibiotic growth promoters (AGP) era in many countries of the world, livestock need more options to deal with food security, food safety, and antibiotic resilience to maintain agricultural sustainability to feed the increasing human population. Furthermore, developing novel antibiotic alternative strategies needs a comprehensive understanding of how this complex system maintains homeostasis as we face unpredictable changes in external factors like antibiotic-resistant microbes, farming practices, climate changes, and consumers’ preferences for food. In this review, we attempt to assemble and summarize all the relevant information on chicken gut health to provide deeper insights into various aspects of gut health. Due to the broad and complex nature of the concept of “gut health”, we have highlighted the most pertinent factors related to the field performance of broiler chickens.

Myeloperoxidase expression in diencephalon is potentially associated with fear‐related behavior in chicks of laying hen

Preventing feather pecking (FP) in adult laying hens is important for the welfare of intensively poultry farming. Fear-related behavior in growing female layer chicks may predict FP in adult hens. In this study, in two representative laying breeds (White Leghorn [WL] and Rhode Island Red [RIR]) that have different FP frequencies, we identified a candidate gene associated with fear-related behavior in chicks and FP in adult hens. In the tonic immobility test and open-field test, the behavioral activity was lower in WL chicks than in RIR chicks (P < 0.01), suggesting that WL chicks were more fearful than RIR chicks. Based on previous studies, 51 genes that have been found to be differentially expressed in the brain between high- and low-FP populations were chosen, and their expression levels were screened in the chick diencephalon. This analysis revealed that myeloperoxidase (MPO) gene expression level was higher in WL chicks than that in RIR chicks (P < 0.05). Furthermore, STRING analysis predicted the gene network including MPO and MPO-related genes and revealed the association of these genes with fear-related behavior. These results suggest that MPO is potentially associated with fear-related behavior in growing female layer chicks and FP in adult hens.

Gut Microbiota Implications for Health and Welfare in Farm Animals: A Review

Simple Summary

Farm animal health and welfare have been paid increasing concern in the world, which is generally assessed by the measurements of physical health, immune response, behavior, and physiological indicators, such as stress-related hormone, cortisone, and norepinephrine. Gut microbiota as a “forgotten organ” has been reported for its great influence on the host phenotypes through the immune, neural, and endocrine pathways to affect the host health and behavior. In addition, fecal microbiota transplantation as a novel approach is applied to regulating the composition and function of the recipient farm animals. In this review, we summarized recent studies that gut microbiota influenced health, immunity, behavior, and stress response, as well as the progress of fecal microbiota transplantation in farm animals. The review will provide new insights into the measurement of farm animal health and welfare concerning gut microbiota, and the implication of fecal microbiota transplantation to improve productivity, health, and welfare. Above all, this review suggests that gut microbiota is a promising field to evaluate and improve animal welfare.

Abstract

In the past few decades, farm animal health and welfare have been paid increasing concern worldwide. Farm animal health and welfare are generally assessed by the measurements of physical health, immune response, behavior, and physiological indicators. The gut microbiota has been reported to have a great influence on host phenotypes, possibly via the immune processes, neural functions, and endocrine pathways, thereby influencing host phenotypes. However, there are few reviews regarding farm animals’ health and welfare status concerning the gut microbiota. In this point of view, (1) we reviewed recent studies showing that gut microbiota (higher alpha diversity, beneficial composition, and positive functions) effectively influenced health characteristics, immunity, behaviors, and stress response in farm animals (such as pigs, chickens, and cows), which would provide a novel approach to measure and evaluate the health status and welfare of farm animals. In addition, fecal microbiota transplantation (FMT) as one of the methods can modulate the recipient individual’s gut microbiota to realize the expected phenotype. Further, (2) we highlighted the application of FMT on the improvement of the production performance, the reduction in disease and abnormal behavior, as well as the attenuation of stress in farm animals. It is concluded that the gut microbiota can be scientifically used to assess and improve the welfare of farm animals. Moreover, FMT may be a helpful strategy to reduce abnormal behavior and improve stress adaption, as well as the treatment of disease for farm animals. This review suggests that gut microbiota is a promising field to evaluate and improve animal welfare.

Research Note: Integrated gut microbiome and short-chain fatty acids responds to dominance hierarchy in roosters

The dominant chickens have priority over the use of resources, such as resting places and the announcement of dawn. While cooperation from the subdominant animal is of great help to reduce conflict and maintain the sustainability of a group. However, whether the dominance hierarchy is associated with individuals' health is not yet known. In this study, we first determined the dominance hierarchy within a group of roosters, to figure out its effects on individuals' health status by the determination of microbial composition and short-chain fatty acids (SCFAs). Sixteen Weining roosters were kept in a group in order to fix and determine the ranking of dominance hierarchy, as R1 (the highest-ranking rooster), R2, R3, and R4. Results show that the R1 roosters had the highest aggression behavior followed by R2, R3 and R4 (P < 0.05). The alpha diversity of R1, R2, and R4 was higher than R3 roosters (P < 0.05). There were several top 10 phylum and genus microbes among the different ranking roosters (P < 0.05). The acetic acid, propionic acid, butyric acid, and valerate acid concentrations were higher, while isobutyric acid concentration was lower in the higher rank roosters (R1 and R2) than the lower rank roosters, respectively (R3 and R4) (P < 0.05). Our results show that the variation of dominance hierarchy contributes to changes of microbial composition, diversity and metabolites. Dominant roosters seem to benefit from SCFAs activities while subdominant roosters profit from microbial functions.

Exogenous Fecal Microbial Transplantation Alters Fearfulness, Intestinal Morphology, and Gut Microbiota in Broilers

Fecal microbiota transplantation (FMT) documented transplanting a donor fecal sample to a receipt individual for a desired physiologic effect. However, whether the gut microbiota construction, intestinal maturation, and behavioral plasticity are modulated by FMT during the early life of broilers is waiting for verification. To evaluate the role of transfer of fecal microbiota from aged broilers donor (BD) to another individual, 96 birds were equally divided into a check (CK, control) group and a broiler recipient (BR) group. FMT was conducted daily from 5 to 12 days of age to determine the future impact on body weight, behavior, intestinal development, and gut microbiota. Results indicated that fearfulness in the CK group was higher than the BR group in both the behavioral tests (p < 0.05). The muscularis mucosa, thickness of muscle layer, and thickness of serous membrane layer in the BR group were higher compared with those of the CK group in the jejunum (p < 0.05). In the gut microbiota, Shannon diversity showed no difference, while beta diversity presented a difference in principal coordination analysis (PCoA) between the CK and BR groups. At the phylum level, the relative abundance of Lentisphaerae in the CK group was lower than the BR (p = 0.052) and BD (p = 0.054) groups. The relative abundance of Tenericutes in the BD group was higher than that in the CK and BR groups (p < 0.05). At the genus level, Megamonas in the CK group was higher than the BR (p = 0.06) and BD (p < 0.05) groups. In the BR group, the functional capabilities of microbial communities analyzed by the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway were increased in the glutamatergic synapse and N-glycan biosynthesis pathways in comparison with the CK and BD groups (p < 0.05). Some characteristics of gut microbiota in the donor chickens could be transferred to recipient chickens by FMT. In conclusion, exogenous FMT as a probiotic-like administration might be an efficient way to improve the physiology and behavior of chickens. Notably, the role of microbiota for various individuals and periods remains undefined, and the mechanism of microbiota on behaviors still needs further investigation.

Functional enrichment of gut microbiome by early supplementation of Bacillus based probiotic in cage free hens: a field study

BACKGROUND

The chicken gut microbiota passes through different stages of maturation; therefore, strengthening it with well characterised probiotics increases its resilience required for optimum gut health and wellbeing. However, there is limited information on the interaction of Bacillus based probiotics with gut microbial community members in cage free laying chickens both in rearing and production phases of life. In the current study, we investigated the changes in the gut microbiome of free range hens in the field after Bacillus based probiotic supplementation.

RESULTS

Overall, at phylum level, probiotic supplementation increased the populations of Bacteroidetes and Proteobacteria mainly at the expense of Firmicutes. The population of Bacteroidetes significantly increased during the production as compared to the rearing phase, and its higher population in the probiotic-supplemented chickens reflects the positive role of Bacillus based probiotic in gut health. Core differences in the beta diversity suggest that probiotic supplementation decreased microbial compositionality. The non-significant difference in alpha diversity between the probiotic and control chickens showed that the composition of community structure did not change. No Salmonella spp. were isolated from the probiotic supplemented birds. Egg internal quality was significantly higher, while egg production and body weight did not differ. Functional prediction data showed that probiotic supplementation enriched metabolic pathways, such as vitamin B6 metabolism, phenylpropanoid biosynthesis, monobactam biosynthesis, RNA degradation, retinol metabolism, pantothenate and CoA biosynthesis, phosphonate and phosphinate metabolism, AMPK signaling pathway, cationic antimicrobial peptide (CAMP) resistance and tyrosine metabolism.

CONCLUSIONS

Overall, age was the main factor affecting the composition and diversity of gut microbiota, where probiotic supplementation improved the abundance of many useful candidates in the gut microbial communities. The generated baseline data in the current study highlights the importance of the continuous use of Bacillus based probiotic for optimum gut health and production.

Cecal Microbiota Modulates Fat Deposition in Muscovy Ducks

Ducks with the same genetic background vary greatly in their adiposity phenotypes. The gut microbiota plays an essential role in host physiological development and metabolism including fat deposition. However, the association of the gut microbiota with the lipogenic phenotype of ducks remains unknown. In this study, we investigated the cecal microbiota of adult Muscovy ducks and the correlation of the cecal microbiota with fat phenotypes. A total of 200 Muscovy ducks were selected from a population of 5,000 Muscovy ducks to record their abdominal fat weight and collect their cecal contents after being slaughtered and defeathered. The cecal contents were subjective to DNA isolation and 16S rRNA gene sequencing. The results were sorted according to the percentage of abdominal fat and the top 20% (n = 40) and the bottom 20% (n = 40) were set as the high and low groups, respectively. Our results indicated that in the cecum of Muscovy ducks, Bacteroidetes, Firmicutes, and Fusobacteria were the predominant phyla while Bacteroides, Oscillospiraceae_uncultured, Parabacteroides, and Bacteroidales_norank were the top 4 dominant genera. Abdominal fat weight (18.57~138.10 g) and percentage of abdominal fat (1.02~27.12%) were significantly correlated (R² = 0.92, P < 0.001). Although the lipogenic phenotypes of ducks had a significant difference (P < 0.05), the α-diversities of the high and low groups were not significantly different (P > 0.05). Nevertheless, after random forest analysis, we identified two genera, Treponema and Ruminococcus_torques_group, that were significantly associated with fat deposition in Muscovy ducks. In addition, the abundances of Treponema and Ruminococcus_torques_group gave a significantly negative and positive association with abdominal fat weight, respectively (P < 0.05). Ducks with a low level of Treponema exhibited a tendency toward a high percentage of abdominal fat (P < 0.01), while the percentage of abdominal fat in ducks with high Ruminococcus_torques_group abundance tended to be higher than that in ducks with low Ruminococcus_torques_group abundance (P < 0.01). These findings could provide the basic data on the cecal microbiota in Muscovy ducks as well as a theoretical foundation to limit the fat deposition by modulating the gut microbiota in the duck industry.

Specific Microbial Taxa and Functional Capacity Contribute to Chicken Abdominal Fat Deposition

Genetically selected chickens with better growth and early maturation show an incidental increase in abdominal fat deposition (AFD). Accumulating evidence reveals a strong association between gut microbiota and adiposity. However, studies focusing on the role of gut microbiota in chicken obesity in conventional breeds are limited. Therefore, 400 random broilers with different levels of AFD were used to investigate the gut microbial taxa related to AFD by 16S rRNA gene sequencing of 76 representative samples, and to identify the specific microbial taxa contributing to fat-related metabolism using shotgun metagenomic analyses of eight high and low AFD chickens. The results demonstrated that the richness and diversity of the gut microbiota decrease as the accumulation of chicken abdominal fat increases. The decrease of Bacteroidetes and the increase of Firmicutes were correlated with the accumulation of chicken AFD. The Bacteroidetes phylum, including the genera Bacteroides, Parabacteroides, and the species, B. salanitronis, B. fragilis, and P. distasonis, were correlated to alleviate obesity by producing secondary metabolites. Several genera of Firmicutes phylum with circulating lipoprotein lipase activity were linked to the accumulation of chicken body fat. Moreover, the genera, Olsenella and Slackia, might positively contribute to fat and energy metabolism, whereas the genus, Methanobrevibacter, was possible to enhance energy capture, and associated to accumulate chicken AFD. These findings provide insights into the roles of the gut microbiota in complex traits and contribute to the development of effective therapies for the reduction of chicken fat accumulation.

Integrated Microbiome and Metabolome Analysis Reveals a Positive Change in the Intestinal Environment of Myostatin Edited Large White Pigs

Myostatin (MSTN) functional inactivation can change the proportion of lean meat and fat content in pigs. While both genotype and microbial composition are known to affect the host phenotype, so far there has been no systematic study to detect the changes in the intestinal microbial composition and metabolome of MSTN single copy mutant pigs. Here, we used 16S rDNA sequencing and metabolome analysis to investigate how MSTN gene editing affects changes in the microbial and metabolome composition in the jejunum and the cecum of Large White pigs. Our results showed that Clostridium_sensu_stricto_1, Bifidobacterium, Lachnospiraceae_UCG-007, Clostridium_sensu_stricto_6, Ruminococcaceae_UCG-002, and Ruminococcaceae_UCG-004 were significantly upregulated; while Treponema_2 and T34_unclassified were significantly downregulated in the jejunum of MSTN pigs. Similarly, Phascolarctobacterium, Ruminiclostridium_9, Succinivibrio, Longibaculum, and Candidatus_Stoquefichus were significantly upregulated, while Barnesiella was significantly downregulated in the cecum of MSTN pigs. Moreover, metabolomics analysis showed significant changes in metabolites involved in purine, sphingolipid and tryptophan metabolism in the jejunum, while those associated with glycerophospholipid and pyrimidine metabolism were changed in the cecum. Spearman correlation analysis further demonstrated that there was a significant correlation between microflora composition and metabolites. Our analyses indicated the MSTN editing affects the composition of metabolites and microbial strains in the jejunum and the cecum, which might provide more useable nutrients for the host of MSTN± Large White pigs.

Removal of roosters alters the domestic phenotype and microbial and genetic profile of hens

Hens are raised apart from roosters in modern poultry production, a substantial change from their natural social structure. We compared productivity, injuries, behavior, physiology, microbiome and transcriptome of hens housed with (R+) or without (R-) roosters to quantify the effects of this change in social structure. Hens were raised free-range from 70 to 280 days when 30 birds per treatment were assigned to battery cages until Day 315 (R+C vs. R-C), while 30 birds per treatment remained in free-range pens (R+F vs. R-F). Response to a novel environment and object, behavioral time budgets, cecum microbiome, blood composition and transcriptomic sequencing of thigh muscle and spleen were analyzed. Hens housed without roosters showed better survival, consumed less food, produced more eggs and had better feed conversion. R+F hens clustered around the rooster and were less mobile in the novel environment and object tests. R+F hens displayed the richest microbiome, and the presence of roosters resulted in differentially expressed genes related to muscle development, cellular processes, environmental information processing and immune function. Removing roosters from housed hens intensified desirable characteristics favored by domestication probably operating by deprivation of mating behavior and reduced fear, along with altered microbial and genetic function.

Effects of housing systems and glucose oxidase on growth performance and intestinal health of Beijing You Chickens

We investigated the effects of housing systems and dietary glucose oxidase (GOD) on the growth performance and intestinal health of Beijing You chickens (BYC). The experiment was designed as a factorial arrangement of 2 housing systems × 2 dietary treatments. Chickens were fed a basal diet or a diet with 200 U/kg GOD and were reared on the floor with deep litter or in the cages. Compared with the litter floor groups, the decreased average daily feed intake of 1 to 42 d, decreased feed conversion ratio (FCR), improved average daily gain of 42 to 77 d, and the whole period were identified in the cage rearing groups (P < 0.05). The FCR of 42 to 77 d and the whole period, the 42-d ileal pH, and 77-d jejunal and ileal pH decreased with the supplement of GOD (P < 0.05). Additionally, 16S rRNA gene of ileum contents was sequenced by high-throughput sequencing. Sequencing data indicated that the Firmicutes phylum of 42 d and the Bacteroidetes phylum were significantly higher in the litter group with GOD supplement (P < 0.05). The jejunal Occludin, Mucin-2 mRNA expression levels were higher in the litter floor groups than those in the cage rearing groups on 42 d (P < 0.05). The Mucin-2 and TNF-α mRNA expression levels increased with cage rearing on 77 d (P < 0.05). The Occludin and TLR-4 mRNA expression levels increased with the supplementation of GOD on 77 d (P < 0.05). Moreover, the upregulation effects of Occludin and ZO-1 mRNA expression levels were more obvious in the litter floor group fed with GOD diet on 77 d (P < 0.05). The serum endotoxin content of 42-day-old cage rearing groups were higher than that of the litter floor groups, and the serum endotoxin content significantly decreased with the supplement of GOD on 77 d. The results indicated that the litter floor systems were beneficial to the development of intestinal barrier junction in the early stage, but the cage systems were more conducive to the growth performance of BYC. The dietary GOD could inhibit the harmful bacteria and promote the beneficial bacteria, which might be related to the improvement of the growth performance and intestinal barrier function.

Adaptive response to a future life challenge: consequences of early-life environmental complexity in dual-purpose chicks

Conditions in early life play profound and long-lasting effects on the welfare and adaptability to stress of chickens. This study aimed to explore the hypothesis that the provision of environmental complexity in early life improves birds' adaptive plasticity and ability to cope with a challenge later in life. It also tried to investigate the effect of the gut-brain axis by measuring behavior, stress hormone, gene expression, and gut microbiota. One-day-old chicks were split into 3 groups: (1) a barren environment (without enrichment items) group (BG, n = 40), (2) a litter materials group (LG, n = 40), and (3) a perches with litter materials group (PLG, n = 40). Then, enrichment items were removed and simulated as an environmental challenge at 31 to 53 d of age. Birds were subjected to a predator test at 42 d of age. In the environmental challenge, when compared with LG, PLG birds were characterized by decreased fearfulness, lower plasma corticosterone, improved gut microbial functions, lower relative mRNA expression of GR, and elevated mRNA expressions of stress-related genes CRH, BDNF, and NR2A in the hypothalamus (all P < 0.05). Unexpectedly, the opposite was true for the LG birds when compared with the BG (P < 0.05). Decreased plasma corticosterone and fearfulness were accompanied by altered hypothalamic gene mRNA expressions of BDNF, NR2A, GR, and CRH through the HPA axis in response to altered gut microbial compositions and functions. The findings suggest that gut microbiota may integrate fearfulness, plasma corticosterone, and gene expression in the hypothalamus to provide an insight into the gut-brain axis in chicks. In conclusion, having access to both perches and litter materials in early life allowed birds to cope better with a future challenge. Birds in perches and litter materials environment may have optimal development and adaptive plasticity through the gut-brain axis.

Effects of Housing Types on Cecal Microbiota of Two Different Strains of Laying Hens During the Late Production Phase

Due to animal welfare issues, European Union has banned the use of conventional cages (CC) and non-EU countries including the US are also under constant public pressure to restrict their use in egg production. Very limited information is available on the composition of the microbial community of hens raised in different housing environments. This study was conducted to determine the effects of CC and enriched colony cages (EC) on cecal microbiota of two commercial laying hen strains, Hy-Line W36 (W36) and Hy-Line Brown (HB) during the late production stage (53, 58, 67, and 72 weeks of age). Cecal microbiota was studied by analyzing 16S rRNA gene sequences with Quantitative Insights Into Microbial Ecology (QIIME) 2 ver. 2018.8. Differentially abundant taxa were identified by Linear discriminant analysis Effect Size (LEfSe) analysis (P < 0.05, LDA score > 2.0). At phylum level, Actinobacteria was significantly enriched in W36 at all time points while Synergistetes (53 weeks), Spirochaetes (58 weeks), and Synergistetes and Spirochaetes (67 weeks) were significantly higher in HB. At genus level, Bifidobacterium (at all time points) and butyric acid producing genera such as Butyricicoccus and Subdoligranulum (58 and 72 weeks) were significantly higher in W36 as compared to HB. Moreover, Proteobacteria (72 weeks) and its associated genus Campylobacter (67 and 72 weeks) were significantly enriched in EC as compared to CC. Alpha diversity was significantly higher in HB (at all time points) and in EC (67 weeks) as compared to W36 and CC, respectively. Similarly, there was a significant difference in community structure (beta diversity) between W36 and HB (all time points) as well as between EC and CC (67 weeks). The effect of housing and strains was not only seen at the bacterial composition and structure but also reflected at their functional level. Notably, KEGG metabolic pathways predicted to be involved in carbohydrates degradation and amino acids biosynthesis by PICRUSt analysis were significantly different between W36 and HB housed at CC and EC. In sum, cecal microbiota composition, diversities, and their functional pathways were affected by housing type which further varied between two commercial laying hen strains, HB and W36. This suggests that both housing and genetic strains of laying hens should be considered for selection of the alternative housing systems such as enriched colony cage.