Cecal microbiome divergence of broiler chickens by sex and body weight

Effects of purple corn anthocyanin on slaughter performance, immune function, the caecal microbiota and the transcriptome in chickens

Poultry are susceptible to oxidative stress, which decreases immune function and negatively affects production performance under highly intensive feeding conditions. Moreover, anthocyanins can alleviate oxidative stress and improve immune functions in chickens. This study aimed to elucidate the effects of purple corn anthocyanin extract (PCE) on slaughter performance, immune function, the caecal microbiota and the transcriptome in chickens. A total of 180 female chickens were randomly divided into two groups, with one receiving a basal diet (CON) and one receiving a treatment (PCE) supplemented with 360 mg/kg PCE according to a completely randomized design. The results indicated that the levels of plasma immunoglobulin A, immunoglobulin G, immunoglobulin M, complement 3, and complement 4 in the PCE treatment group were greater (P < 0.05) than those in the CON group. The slaughter performance and caecal short-chain fatty acid parameters did not differ (P > 0.05) between the PCE and CON groups. The inclusion of PCE significantly increased (P < 0.05) the bursa of Fabricius/live weight value compared with those of the CON. Chickens receiving PCE had significantly (P < 0.05) increased relative abundances of norank_f_Muribaculaceae, Anaerofilum, Shuttleworthia, Brachyspira, and Tuzzerella but significantly decreased (P < 0.05) relative abundances of unclassified_f__Rikenellaceae, Oscillospira, norank_f__Barnesiellaceae, norank_f__Christensenellaceae, and Candidatus_Soleaferrea. A total of 2,846 differentially expressed genes (DEGs; P < 0.05), which consisted of 1,140 upregulated genes and 1,706 downregulated genes, were identified. Among them, 201 genes were annotated to the Gene Ontology and Kyoto Encyclopedia of Genes and Genomes database for immune-related genes. Protein-protein interaction network analysis revealed that DEGs associated with the joining chain of multimeric IgA and IgM were significantly upregulated immune-related genes, and those associated with forkhead box P1, cathelicidin 1, cathelicidin 2, and cathelicidin 3 were significantly downregulated immune-related genes in chickens. The findings demonstrated that dietary supplementation with PCE has the potential to improve plasma immunoglobulin, immune organ, caecal potentially beneficial bacteria levels and immune-related gene expressions, which can increase the immune function of chickens.

Impact of Chlorella vulgaris and probiotic supplementation on performance, immunity and intestinal microbiota of broiler chickens

Chlorella vulgaris has antioxidant, antimicrobial, and anti-inflammatory properties, as well as the probiotic that is important for keeping the intestinal microbiota balanced. The objective was to test the impact of supplementation with microalgae and/or probiotics on broiler chickens' performance, immunity, and intestinal microbiota. The experimental design was in randomized blocks in a 4x2 factorial scheme, with four levels of inclusion of C. vulgaris (0; 0.25; 0.50 and 1%) associated or not with a commercial probiotic with five replications of 26 chickens per experimental unit. The results showed that probiotics improved feed conversion. Probiotics increased the productivity index only at 0.25% C. vulgaris supplementation. There was a reduction in spleen weight at 42 days of age in chickens fed with probiotics, but the different treatments did not alter serum antibodies. Sampling age had a significant impact on richness addressed by the number of observed genera and diversity addressed by the Shannon index. The most abundant phylum in the chicken intestinal tract was Firmicutes followed by Bacteroidetes and Proteobacteria. Bifidobacterium spp. was found in animals receiving 1% microalgae and probiotics on day 42, suggesting that this genus has benefited from microalgae supplementation. It is concluded that the probiotic and C. vulgaris have the potential to improve performance without causing major changes in the immunity and cecal microbiota.

Microbial community profiling in intestinal tract of indigenous chickens from different villages

Village chickens (Gallus gallus domesticus) are commonly reared in rural households of South Africa and other developing countries. They play a vital role as a primary source of protein through the provision of meat and eggs. The chicken gut microbiota plays an important role in chicken's immune system, its health, physiological development of the gut, digestion of food, nutrient absorption and productivity. Thus, it is imperative to critically investigate the chicken microbial composition in order to develop effective disease control measures and increase production. In this present study, microbial DNA was isolated from 34 non-descript mixed gender matured village chickens' intestinal contents followed by high throughput Illumina sequencing targeting 16S rRNA gene. Senwamokgope village had the largest microbiota composition as compared to Itieleni and Thakgalang villages. Overall, Firmicutes (74%) was the most abundant phylum observed, followed by Proteobacteria (8%), Actinobateria (5%), and Bacteroidota (3%). At the genus level, Lactobacillus was the dominant bacteria. Other genera found included Sphingomonas (7%), Cutibacterium (4%), and Clostridium_sensu_stricto_1 (2%). The richness of female intestinal microbiota was higher compared to the male microbiota. The findings of this study provide baseline information that can assist to better understand the chicken gut microbiota and its interaction with diseases and parasites.

Assessing the impact of hatching system and body weight on the growth performance, caecal short-chain fatty acids, and microbiota composition and functionality in broilers

BACKGROUND

Variations in body weight (BW) remain a significant challenge within broiler flocks, despite uniform management practices. Chicken growth traits are influenced by gut microbiota, which are in turn shaped by early-life events like different hatching environments and timing of first feeding. Chicks hatched in hatcheries (HH) experience prolonged feed deprivation, which could adversely impact early microbiota colonization. Conversely, hatching on-farm (HOF) allows early feeding, potentially fostering a more favorable gut environment for beneficial microbial establishment. This study investigates whether BW differences among broilers are linked to the disparities in gut microbiota characteristics and whether hatching systems (HS) impact the initial microbial colonization of broilers differing in BW, which in turn affects their growth patterns. Male Ross-308 chicks, either hatched in a hatchery or on-farm, were categorized into low (LBW) and high (HBW) BW groups on day 7, making a two-factorial design (HS × BW). Production parameters were recorded periodically. On days 7, 14, and 38, cecal volatile fatty acid (VFA) and microbiota composition and function (using 16 S rRNA gene sequencing and PICRUSt2) were examined.

RESULTS

HOF chicks had higher day 1 BW, but HH chicks caught up within first week, with no further HS-related performance differences. The HBW chicks remained heavier attributed to higher feed intake rather than improved feed efficiency. HBW group had higher acetate concentration on day 14, while LBW group exhibited higher isocaproate on day 7 and isobutyrate on days 14 and 38. Microbiota analyses revealed diversity and composition were primarily influenced by BW than by HS, with HS having minimal impact on BW-related microbiota. The HBW group on various growth stages was enriched in VFA-producing bacteria like unclassified Lachnospiraceae, Alistipes and Faecalibacterium, while the LBW group had higher abundances of Lactobacillus, Akkermansia and Escherichia-Shigella. HBW microbiota presented higher predicted functional potential compared to the LBW group, with early colonizers exhibiting greater metabolic activity than late colonizers.

CONCLUSIONS

Despite differences in hatching conditions, the effects of HS on broiler performance were transient, and barely impacting BW-related microbiota. BW variations among broilers are likely linked to differences in feed intake, VFA profiles, and distinct microbiota compositions and functions.

Integrating microbial 16S rRNA sequencing and non-targeted metabolomics to reveal sexual dimorphism of the chicken cecal microbiome and serum metabolome

Background

The gut microbiome plays a key role in the formation of livestock and poultry traits via serum metabolites, and empirical evidence has indicated these traits are sex-linked.

Methods

We examined 106 chickens (54 male chickens and 52 female chickens) and analyzed cecal content samples and serum samples by 16S rRNA gene sequencing and non-targeted metabolomics, respectively.

Results

The cecal microbiome of female chickens was more stable and more complex than that of the male chickens. Lactobacillus and Family XIII UCG-001 were enriched in male chickens, while Eubacterium_nodatum_group, Blautia, unclassified_Anaerovoraceae, Romboutsia, Lachnoclostridium, and norank_Muribaculaceae were enriched in female chickens. Thirty-seven differential metabolites were identified in positive mode and 13 in negative mode, showing sex differences. Sphingomyelin metabolites possessed the strongest association with cecal microbes, while 11β-hydroxytestosterone showed a negative correlation with Blautia.

Conclusion

These results support the role of sexual dimorphism of the cecal microbiome and metabolome and implicate specific gender factors associated with production performance in chickens.

Sex-specific genetic parameter estimates of body weight in Mazandaran indigenous chickens

Body weight is an economically important trait in poultry that shows sexual dimorphism (SD). In the present study, variation in SD in Mazandaran native chickens was investigated in terms of the (Co) variance components and genetic parameters of body weight between males and females. Studied traits were body weights at hatch (BW1), 8 weeks (BW8) and 12 weeks of age (BW12). Also, for weight at sexual maturity (WSM) covariance components were only estimated in females. Cross-sex direct and maternal correlations were also estimated for studied traits except for WSM. For this purpose, a deep 21-generation pedigree and body weight data (57,576 BW1, 72,925 BW8, 62,727 BW12 and, 42,496 WSM) were used. Evaluation of SD of body weight was performed using six bivariate animal models with and without considering the genetic and permanent maternal environmental effects under the restricted maximum likelihood method in WOMBAT software. Model with direct additive genetic effects and maternal genetic effects without covariance between them was identified as the best model for BW1 and BW8. The Model including direct additive genetic effects and permanent maternal environmental effects was the best model for BW12 and WSM. Direct heritability (h2) estimates for BW1, BW8 and, BW12 were, respectively, 0.05 ± 0.013, 0.17 ± 0.02 and, 0.25 ± 0.03 in males and, 0.05 ± 0.012, 0.15 ± 0.01 and 0.21 ± 0.01 in females. Also, the direct heritability of WSM based on univariate analysis in females was estimated to be 0.40 ± 0.01. Maternal heritability (h m 2 ) varied from 0.39 ± 0.01 (BW1) to 0.04 ± 0.009 (BW8) in males, and 0.36 ± 0.10 (BW1) to 0.04 ± 0.006 (BW8) in females. The correlation between direct genetic effects between males and females for BW1 was not significantly different from one. The direct genetic correlation between the two sexes for BW8 and BW12 was significantly different from 1 concluding that these traits are dimorphic in terms of direct genetic effects and therefore independent selection in both sexes is possible.

Are there consistent effects of gut microbiota composition on performance, productivity and condition in poultry?

Microbiome of the gastrointestinal tract (GIT) has been identified as one of the crucial factors influencing the health and condition of domestic animals. The global poultry industry faces the challenge of understanding the complex relationship between gut microbiota composition and performance-related traits in birds. Considerable variation exists in the results of correlational studies using either 16S rRNA profiling or metagenomics to identify bacterial taxa associated with performance, productivity, or condition in poultry (e.g., body weight, growth rate, feeding efficiency, or egg yield). In this review, we survey the existing reports, discuss variation in research approaches, and identify bacterial taxa consistently linked to improved or deteriorated performance across individual poultry-focused studies. Our survey revealed high methodological heterogeneity, which was in contrast with vastly uniform focus of the research mainly on the domestic chicken (Gallus gallus) as a model. We also show that the bacterial taxa most frequently used in manipulative experiments and commercial probiotics intended for use in poultry (e.g., species of Lactobacillus, Bacillus, Enterococcus, or Bifidobacterium) do not overlap with the bacteria consistently correlated with their improved performance (Candidatus Arthromitus, Methanobrevibacter). Our conclusions urge for increased methodological standardization of the veterinary research in this field. We highlight the need to bridge the gap between correlational results and experimental applications in animal science. To better understand causality in the observed relationships, future research should involve a broader range of host species that includes both agricultural and wild models, as well as a broader range of age groups.

Dietary ethylenediamine dihydroiodide mitigated Escherichia coli O78-induced immune and intestinal damage of ducks via suppression of NF-κB signal

This study investigated the effect of Ethylenediamine dihydroiodide (EDDI) on growth performance, immune function and intestinal health of meat ducks challenged with Avian pathogenic Escherichia coli (APEC). A total of 360 one-day-old Cherry Valley ducks with similar body weight were randomly allocated to 6 treatments (6 floor cages, 10 birds/cage). A 3 × 2 factor design was used with 3 dietary iodine levels (0, 8, 16 mg/kg in the form EDDI and whether APEC was challenged or not at 7-day-old ducks. The feeding period lasted for 20 d. The results showed that the addition of EDDI reduced APEC-induced decrease of the 20-d weight loss of meat ducks (P < 0.05), and alleviated the inflammatory response of liver tissue induced by APEC challenge in meat ducks. In terms of immune function, EDDI supplementation reduced the immune organ index and increased the immune cell count of meat ducks, reduced the level of endotoxins in the serum of meat ducks (P < 0.05), as well as inhibited the expression levels of liver and spleen inflammatory factors and TLR signaling pathway related genes induced by APEC (P < 0.05). In terms of intestinal health, EDDI inhibited APEC-induced decreases in ZO-3 genes expression and increases in IL-1β and TNF-α expression, increased relative abundance of beneficial bacteria in the cecum and content of metabolites. Pearson correlation analysis showed that there was a significant correlation between liver inflammatory factors and TLR4 signaling pathway genes, and there might be a significant correlation between intestinal microbial flora and other physiological indexes of meat ducks, which indicated that EDDI could reduce the damage to immune function and intestinal health caused by APEC challenge through regulating the structure of intestinal flora. Collectively, our findings suggest that the EDDI can promote growth performance, improve immune function and the intestinal barrier in APEC-challenged meat ducks, which may be related to the suppression of NF-κB signal.

Dynamic effects of black soldier fly larvae meal on the cecal bacterial microbiota and prevalence of selected antimicrobial resistant determinants in broiler chickens

BACKGROUND

We had earlier described the growth-promoting and -depressive effects of replacing soybean meal (SBM) with low (12.5% and 25%) and high (50% and 100%) inclusion levels of black soldier fly larvae meal (BSFLM), respectively, in Ross x Ross 708 broiler chicken diets. Herein, using 16S rRNA gene amplicon sequencing, we investigated the effects of replacing SBM with increasing inclusion levels (0-100%) of BSFLM in broiler diets on the cecal bacterial community composition at each growth phase compared to broilers fed a basal corn-SBM diet with or without the in-feed antibiotic, bacitracin methylene disalicylate (BMD). We also evaluated the impact of low (12.5% and 25%) inclusion levels of BSFLM (LIL-BSFLM) on the prevalence of selected antimicrobial resistance genes (ARGs) in litter and cecal samples from 35-day-old birds.

RESULTS

Compared to a conventional SBM-based broiler chicken diet, high (50 to100%) inclusion levels of BSFLM (HIL-BSFLM) significantly altered the cecal bacterial composition and structure, whereas LIL-BSFLM had a minimal effect. Differential abundance analysis further revealed that the ceca of birds fed 100% BSFLM consistently harbored a ~ 3 log-fold higher abundance of Romboutsia and a ~ 2 log-fold lower abundance of Shuttleworthia relative to those fed a BMD-supplemented control diet at all growth phases. Transient changes in the abundance of several potentially significant bacterial genera, primarily belonging to the class Clostridia, were also observed for birds fed HIL-BSFLM. At the finisher phase, Enterococci bacteria were enriched in the ceca of chickens raised without antibiotic, regardless of the level of dietary BSFLM. Additionally, bacitracin (bcrR) and macrolide (ermB) resistance genes were found to be less abundant in the ceca of chickens fed antibiotic-free diets, including either a corn-SBM or LIL-BSFLM diet.

CONCLUSIONS

Chickens fed a HIL-BSFLM presented with an imbalanced gut bacterial microbiota profile, which may be linked to the previously reported growth-depressing effects of a BSFLM diet. In contrast, LIL-BSFLM had a minimal effect on the composition of the cecal bacterial microbiota and did not enrich for selected ARGs. Thus, substitution of SBM with low levels of BSFLM in broiler diets could be a promising alternative to the antibiotic growth promoter, BMD, with the added-value of not enriching for bacitracin- and macrolide-associated ARGs.

The effect of sex and dietary crude protein level on nutrient transporter gene expression and cecal microbiota populations in broiler chickens

It is well known that male and female broilers differ in their growth performance and that many physiological factors contribute to this difference. The aim of this experiment is to investigate if there are differences between male and female broilers in cecal microbiota and nutrient transporter gene expression and if these differences play a role in the growth performance of broilers. The possible effect of protein level and its interaction with sex on microbiota and expression of the nutrient transporters were also investigated. Samples were collected from male and female birds fed either standard crude protein (SCP) or reduced crude protein diets (RCP) at the age of d 35. The experiment was designed as a 2 × 2 factorial arrangement of treatments consisting of 448 Cobb 500 broilers assigned to 32-floor pens with 4 treatments, 8 replicates, and 14 birds per pen for performance measurements. The factors were sex (male or female) and dietary crude protein (CP) level (standard or reduced). Body weight gain (BWG), feed intake and feed conversion ratio were recorded for each pen. Sex had a significant effect on BWG and FCR (P < 0.001) where males had a significantly higher BWG and better FCR compared to females. There was a significant interaction between sex and protein level on feed intake (FI) (P < 0.05), where male birds had a higher FI compared to female birds only when the birds were fed SCP but not RCP diets. There was a significant interaction between CP level and sex on the expression of CAT2 (P = 0.02) and PEPT2 (P = 0.026) where the genes were significantly upregulated in females but only when the RCP diet was fed. The RCP diet upregulated the expression of BoAT (P = 0.03) as a main effect. Female birds had significantly higher expression of the PepT-2 gene compared to the males. The alpha diversity of the cecal microbiota showed differences among the treatments. The Shannon diversity index was statistically higher (P = 0.036) for males fed the SCP diet and the Chao1 index for evenness was statistically higher (P = 0.027) in females fed the SCP diet. There was also a difference in the relative abundance of the 15 most common genera found in the cecal content of the broilers in this experiment and lastly, the differential composition of microbiota between the different treatments was also significantly different. This study suggests that chickens are able to compensate for a reduction in AA substrates when fed a low CP diet through the upregulation of certain AA transporters, females may adapt to low CP diets better by such upregulation compared to males, and lastly, sex has an effect on the cecal microbial population and these differences contribute towards the performance differences between male and female broilers.

The Effect of including a Mixed-Enzyme Product in Broiler Diets on Performance, Metabolizable Energy, Phosphorus and Calcium Retention

The importance of enzymes in the poultry industry is ever increasing because they help to extract as many nutrients as possible from the raw material available and reduce environmental impacts. Therefore, an experiment was conducted to examine the effect of a natural enzyme complex (ASC) on diets low in AME, Ca and P. Male Ross 308 broilers (n = 900) were fed one of four diets: (1) positive control (PC) with no enzyme added (AME 12.55 MJ/kg, AVPhos 4.8 g/kg and AVCal 9.6 g/kg); (2) negative control (NC) with no enzyme added and reduced AME, Ca and P (AME 12.18 MJ/kg, AVPhos 3.3 g/kg, AVCal 8.1 g/kg); (3) negative control plus ASC at 200 g/t; and (4) negative control plus ASC at 400 g/t. Broiler performance, digesta viscosity, tibia mineralization and mineral content were analyzed at d 21. Between d 18 and 20, excreted DM, GE, total nitrogen, Ca, and P were analyzed. ASC at 200 g/t and 400 g/t improved the FCR (p = 0.0014) significantly when compared with that of the NC. There were no significant differences in BW or FI between the treatments. Birds fed ASC at 200 g/t and 400 g/t had significantly improved digesta viscosity (p < 0.0001) compared with that of the PC and NC birds and had significantly higher excreted DM digestibility (p < 0.01) than the NC and the PC birds with 400 g/t ASC. ASC inclusion significantly improved P retention (p < 0.0001) compared to that in the PC. Ca retention was significantly increased by 400 g/t ASC compared to that in the PC and NC (p < 0.001). AME was significantly higher (p < 0.0001) for all treatments compared to that in the NC. There were no significant differences between treatments for any of the bone measurements. This study showed that feeding with ASC can support the performance of broilers when fed a diet formulated to have reduced Ca, P and AME, with the greatest results being seen with a higher level of ASC inclusion.

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.

Sex-based responses of heat stress and subsequent recovery on the growth performance, metabolic changes, and redox status of broilers at market age

This experiment investigated the sex responses of heat stress (HS) and subsequent recovery on growth performance, serum metabolic parameters, and redox status. Two hundred 38-day-old broilers were arranged in a completely randomized design with a 2 × 2 (temperatures and sexes) factorial arrangement in five replicates. Broilers were raised at 24 ± 1 °C or 32 ± 1 °C for 3 days and returned to 24 °C for 2 days. The study showed that HS decreased both average daily feed intake (ADFI), average daily gain (ADG), serum total glutathione peroxidase (GPx), and superoxide dismutase (T-SOD). However, it increased feed conversion ratio (FCR), rectal temperature (RT), respiratory rate (RR), serum glucose, blood urea nitrogen (BUN), low-density lipoprotein cholesterol, and the protein carbonyl group (PCG). Male broilers had higher ADFI, ADG, lactic acid (LA), high-density lipoprotein cholesterol (HDL-C), and PCG, but lower FCR, albumin, total antioxidant capacity, T-SOD, and GPx. Temperature and sex significantly interacted with ADFI, ADG, LA, and HDL-C. The effects of HS on RR, RT, glucose, albumin, BUN, PCG, T-SOD, and GPx recovered after 2 days. These results indicate that HS and subsequent recovery affect growth performance, which is accompanied by disturbances in serum nutrient metabolism and abnormalities in redox function and manifested by temporal and gender differences.

A catalog of microbial genes and metagenome-assembled genomes from the quail gut microbiome

The gut microbiome plays an important role in quail feed efficiency, immunity, production, and even behavior. Gut microbial gene catalogs and reference genomes are important for understanding the quail gut microbiome. However, quail gut microbes are lacked sequenced genomes and functional information to date. In this study, we report the first catalog of the microbial genes and metagenome-assembled genomes (MAGs) in fecal and cecum luminal content samples from 3 quail breeds using deep metagenomic sequencing. We identified a total of 2,419,425 nonredundant genes in the quail genome catalog, and a total of 473 MAGs were reconstructed through binning analysis. At 95% average nucleotide identity, the 473 MAGs were clustered into 283 species-level genome bins (SGBs), of which 225 SGBs belonged to species without any available genomes in the current database. Based on the quail gene catalog and MAGs, we identified 142 discriminative bacterial species and 244 discriminative MAGs between Chinese yellow quails and Japanese quails. The discriminative MAGs suggested a strain-level difference in the gut microbial composition. Additionally, a total of 25 Kyoto Encyclopedia of Genes and Genomes functional terms and 88 carbohydrate-active enzymes were distinctly enriched between Chinese yellow quails and Japanese quails. Most of the different species and MAGs were significantly interrelated with the shifts in the functional capacities of the quail gut microbiome. Taken together, we constructed a quail gut microbial gene catalog and enlarged the reference of quail gut microbial genomes. The results of this study provide a powerful and invaluable resource for quail gut microbiome-related research.

Inonotus obliquus polysaccharide are linear molecules that alter the abundance and composition of intestinal microbiota in Sprague Dawley rats

Introduction

The macromolecular polysaccharide Inonotus obliquus polysaccharide (IOP) is composed of various monosaccharides, and it could modulate the composition and diversity of intestinal flora. However, its impact on the intestinal flora in rats of different genders remains unclear. Therefore, this study aims to investigate the structural changes of IOP and its effects on the intestinal flora after administration in male and female rats.

Methods

In this study, the molecular weight and purity of IOP were analyzed by high-performance gel permeation chromatography (HPGPC) and phenol sulfuric acid method, and NMR was used to confirm the chemical structure of IOP. Sex hormone [testosterone (T) and estradiol (E2)] levels and intestinal microbial changes were detected by enzyme-linked immunosorbent assay (ELISA) and 16S rRNA, respectively, after gavage of IOP (100 mg/kg) in male and female Sprague Dawley (SD) rats.

Results

HPGPC analysis showed that the average molecular weight (Mw) of IOP was 4,828  Da, and the total sugar content of the purified IOP was 96.2%, indicating that the polysaccharide is of high purity. NMR revealed that IOP is a linear macromolecule with an α-D-type glucose backbone. The results of ELISA and 16S rRNA showed that the IOP increased the abundance of beneficial bacteria, such as Clostridia_UCG-014 and Prevotellaceae_NK3B31, and reduced that of harmful bacteria, such as Colidextribacter and Desulfobacterota in the intestine of both male and female rats, and IOP changed the levels of sex hormones in male and female rats. Further analyses revealed that the increase in alpha diversity was higher in male than female rats. α diversity and β diversity revealed a significant difference in the composition of cecal microbiota between male and female rats in the control group, but IOP intake reduced this difference. Meanwhile, α analysis revealed a change in the composition of bacterial flora was more stable in male than female rats.

Conclusions

This study enhances our comprehension of the IOP structure and elucidates the alterations in intestinal flora following IOP administration in rats of varying genders. Nonetheless, further investigation is warranted to explore the specific underlying reasons for these discrepancies.

Phenotype Alterations in the Cecal Ecosystem Involved in the Asymptomatic Intestinal Persistence of Paratyphoid Salmonella in Chickens

The gastrointestinal ecosystem involves interactions between the host, gut microbiota, and external environment. To colonize the gut of poultry, Salmonella must surmount barriers levied by the intestine including mucosal innate immune responses and microbiota-mediated niche restrictions. Accordingly, comprehending Salmonella intestinal colonization in poultry requires an understanding of how the pathogen interacts with the intestinal ecosystem. In chickens, the paratyphoid Salmonella have evolved the capacity to survive the initial immune response and persist in the avian ceca for months without triggering clinical signs. The persistence of a Salmonella infection in the avian host involves both host defenses and tolerogenic defense strategies. The initial phase of the Salmonella-gut ecosystem interaction is characteristically an innate pro-inflammatory response that controls bacterial invasion. The second phase is initiated by an expansion of the T regulatory cell population in the cecum of Salmonella-infected chickens accompanied by well-defined shifts in the enteric neuro-immunometabolic pathways that changes the local phenotype from pro-inflammatory to an anti-inflammatory environment. Thus, paratyphoid Salmonella in chickens have evolved a unique survival strategy that minimizes the inflammatory response (disease resistance) during the initial infection and then induces an immunometabolic reprogramming in the cecum that alters the host defense to disease tolerance that provides an environment conducive to drive asymptomatic carriage of the bacterial pathogen.

Long-Term Dietary Fish Meal Substitution with the Black Soldier Fly Larval Meal Modifies the Caecal Microbiota and Microbial Pathway in Laying Hens

Feeding laying hens with black soldier fly larval (BSFL) meal improves their performance. However, the beneficial mechanism of BSFL meals in improving the performance of laying hens remains unclear. This study investigated the effects of the BSFL diet on liver metabolism, gut physiology, and gut microbiota in laying hens. Eighty-seven Julia hens were randomly assigned to three groups based on their diets and fed maize grain-and soybean meal-based diets mixed with either 3% fish meal (control diet), 1.5% fish and 1.5% BSFL meals, or 3% BSFL meal for 52 weeks. No significant differences were observed in biochemical parameters, hepatic amino acid and saturated fatty acid contents, intestinal mucosal disaccharidase activity, and intestinal morphology between BSFL diet-fed and control diet-fed laying hens. However, the BSFL diet significantly increased the abundance of acetic and propionic acid-producing bacteria, caecal short-chain fatty acids, and modified the caecal microbial pathways that are associated with bile acid metabolism. These findings indicate that consuming a diet containing BSFL meal has minimal effects on plasma and liver nutritional metabolism in laying hens; however, it can alter the gut microbiota associated with short-chain fatty acid production as well as the microbial pathways involved in intestinal fat metabolism. In conclusion, this study provides evidence that BSFL can enhance enterocyte metabolism and gut homeostasis in laying hens.

Plant essential oils improve growth performance by increasing antioxidative capacity, enhancing intestinal barrier function, and modulating gut microbiota in Muscovy ducks

Essential oils (EO) are known for their antioxidant, anti-inflammatory, antimicrobial, and growth-promoting properties. However, data rgarding their impact on the intestinal health and gut microbiota of ducks remain limited. Thus, this study aimed to investigate the effects of plant EO on the growth performance, intestinal health, and gut microbiota of Muscovy ducks. A total of 360 healthy male Muscovy ducks aged 1 d were randomly divided into 4 groups with 6 replicates and 15 ducks per replicate. Ducks were fed basal diets supplemented with 0, 100, 200, or 300 mg/kg EO. The results showed that 200 mg/kg EO supplementation significantly (P < 0.05) increased the final body weight and average daily gain, while significantly (P < 0.05) decreased the feed conversion ratio during the 56-d experimental period. Furthermore, dietary 200 mg/kg EO significantly (P < 0.05) enhanced antioxidant capacity and immune function and improved the barrier function of the intestine. Additionally, 16S rDNA sequencing analysis results showed that 200 mg/kg EO favorably modulated the cecal microbial diversities and composition evidenced by the increased (P < 0.05) the abundances of short-chain fatty acid-producing bacteria (e.g., Subdoligranulum and Shuttleworthia) and decreased (P < 0.05) abundances of potential enteric pathogenic bacteria (e.g., Alistipes, Eisenbergiella, and Olsenella). The relative abundance of beneficial bacteria was positively correlated with antioxidant, immune, and barrier function biomarkers. Overall, these findings revealed that dietary supplementation with 200 mg/kg EO had several potentially beneficial effects on the growth performance of Muscovy ducks by improving antioxidant capacity, enhancing the intestinal barrier function and favorably modulating gut microbiota.

Host genotype affects endotoxin release in excreta of broilers at slaughter age

Host genotype, early post-hatch feeding, and pre- and probiotics are factors known to modulate the gut microbiome. However, there is a knowledge gap on the effect of both chicken genotype and these dietary strategies and their interplay on fecal microbiome composition and diversity, which, in turn, can affect the release of endotoxins in the excreta of broilers. Endotoxins are a major concern as they can be harmful to both animal and human health. The main goal of the current study was to investigate whether it was possible to modulate the fecal microbiome, thereby reducing endotoxin concentrations in the excreta of broiler chickens. An experiment was carried out with a 2 × 2 × 2 factorial arrangement including the following three factors: 1) genetic strain (fast-growing Ross 308 vs. slower growing Hubbard JA757); 2) no vs. combined use of probiotics and prebiotics in the diet and drinking water; and 3) early feeding at the hatchery vs. non-early feeding. A total of 624 Ross 308 and 624 Hubbard JA757 day-old male broiler chickens were included until d 37 and d 51 of age, respectively. Broilers (N = 26 chicks/pen) were housed in a total of 48 pens, and there were six replicate pens/treatment groups. Pooled cloacal swabs (N = 10 chickens/pen) for microbiome and endotoxin analyses were collected at a target body weight (BW) of 200 g, 1 kg, and 2.5 kg. Endotoxin concentration significantly increased with age (p = 0.01). At a target BW of 2.5 kg, Ross 308 chickens produced a considerably higher amount of endotoxins (Δ = 552.5 EU/mL) than the Hubbard JA757 chickens (p < 0.01). A significant difference in the Shannon index was observed for the interaction between the use of prebiotics and probiotics, and host genotype (p = 0.02), where Ross 308 chickens with pre-/probiotics had lower diversity than Hubbard JA757 chickens with pre-/probiotics. Early feeding did not affect both the fecal microbiome and endotoxin release. Overall, the results suggest that the chicken genetic strain may be an important factor to take into account regarding fecal endotoxin release, although this needs to be further investigated under commercial conditions.

Anaerobutyricum and Subdoligranulum Are Differentially Enriched in Broilers with Disparate Weight Gains

The intestinal microbiota is critically important for animal health and productivity. However, the influence of the intestinal microbiota on animal growth efficiency remains elusive. This current study was aimed at identifying the intestinal bacteria that are associated with the growth rate of broilers in a commercial production setting. Ross 708 broilers with extremely high, medium, and extremely low body weight (BW) were separately selected for each sex from a house of approximately 18,000 chickens on day 42. The cecal content of each animal was subjected to 16S rRNA gene sequencing for microbiota profiling. Our results indicate that a number of bacteria were differentially enriched among different groups of broilers, with several showing a significant correlation (p < 0.05) with BW in both sexes or in a sex-specific manner. Subdoligranulum was drastically diminished in high-BW birds with a strong negative correlation with BW in both males and females. While one Anaerobutyricum strain showed a positive correlation with BW in both sexes, another strain of Anaerobutyricum was positively correlated with BW only in females. These sex-dependent and -independent bacteria could be targeted for improving the growth efficiency and may also be explored as potential biomarkers for the growth rate of broiler chickens.

Effect of water supplementation of Magic oil at different growing periods on growth performance, carcass traits, blood biochemistry, and ileal histomorphology of broiler chickens

Natural antibiotic substitutes have recently been used as growth promoters and to combat pathogens. Therefore, this study aimed to assess the effects of adding Magic oil (nano-emulsified plant oil) at different growing periods on growth performance, histomorphology of the ileum, carcass traits, and blood biochemistry of broiler chickens. A total of 432-day-old Ross 308 chicks were randomly assigned to 1 of 6 water supplementation treatment groups based on growing periods, with 4 groups of Magic oil programs compared to probiotic (Albovit) as a positive control and nonsupplemented group as a negative control, with 9 replicates each with 8 birds (4♂ and 4♀). The periods of adding Magic oil Magic oil were 35, 20, 23, and 19 d for T1, T2, T3, and T4, respectively. Birds' performance was evaluated during 0 to 4, 4 to 14, 21 to 30, 30 to 35, and overall days old. Carcass parameters, blood chemistry, and ileal histomorphology were examined on d 35. The findings showed that birds in the T4 group of the Magic oil supplementation program (from 1 to 4 and 21 to 35 d of age) consumed 1.82% and 4.20% more food, gained 3.08% and 6.21% more, and converted feed to meat 1.39% and 2.07% more than Albovit and negative control, respectively, during the experiment (1-35). Magic oil particularly T1 (Magic oil is supplemented throughout the growing period) and T4 programs improved intestinal histology compared to the negative control. There were no changes (P > 0.05) between treatments in carcass parameters and blood biochemistry. In conclusion, water supplementation with Magic oil for broilers improves intestinal morphometrics and growth performance similar to or better than probiotic, especially during brooding and overall periods. Further studies are needed to evaluate the effect of adding both nano-emulsified plant oil and probiotics on different parameters.

The Development of Gut Microbiota and Its Changes Following C. jejuni Infection in Broilers

The gut is home to more than millions of bacterial species. The gut bacteria coexist with the host in a symbiotic relationship that can influence the host's metabolism, nutrition, and physiology and even module various immune functions. The commensal gut microbiota plays a crucial role in shaping the immune response and provides a continuous stimulus to maintain an activated immune system. The recent advancements in high throughput omics technologies have improved our understanding of the role of commensal bacteria in developing the immune system in chickens. Chicken meat continues to be one of the most consumed sources of protein worldwide, with the demand expected to increase significantly by the year 2050. Yet, chickens are a significant reservoir for human foodborne pathogens such as Campylobacter jejuni. Understanding the interaction between the commensal bacteria and C. jejuni is essential in developing novel technologies to decrease C. jejuni load in broilers. This review aims to provide current knowledge of gut microbiota development and its interaction with the immune system in broilers. Additionally, the effect of C. jejuni infection on the gut microbiota is addressed.

Influence of sex and rearing method on performance and flock uniformity in broilers-implications for research settings

Male and female broiler chickens differ in their growth performance, carcass part weights and nutrient requirements. The potential reasons for these differences have been explored by looking at differences in nutrient digestibility, nutrient transporter gene expression as well as gut microbiota populations between male and female birds. Studies have shown that male broilers have higher crude protein requirements compared to female broilers. The expression of monosaccharide and amino acid transporters show conflicting results as expression depends on the interactions between sex and bird age and breed as well as which tissue is sampled. Differences in microbiota populations between the genders were reported which may contribute towards performance differences, however research in this area is limited. The differences observed between the sexes contribute to increased variation in nutrition trials, and the potential to rear birds as equally mixed-sex becomes an option to reduce the variation introduced by the sex effect. Difference in rearing options obviously would only be feasible provided a quick, practical and cost-effective method of sexing birds is available, a topic that is also discussed in this review.

Large intestinal dynamics differ between fowl and swine: Anatomical modifications, microbial collaboration, and digestive advantages from fibrolytic enzymes

The large intestinal systems of fowl and swine recover nutrients from ileal indigesta by a strategically different manner. Indigesta with fowl enter a short colon where retro-peristalsis using urine from the urodeum carries small particulates and solutes into both ceca while coarse materials collect in the cloaca. Fowl repetitively add fine and soluble materials into both ceca to continue fermentation until complexity of the remainder exceeds microbial action, then contents apart from faeces are entirely evacuated. Indigesta with swine initially enter a short cecum followed by a lengthy progression through to the rectal ampulla. Wall out-pocketings of circular muscle or haustrae occur throughout the length of the pig's cecum and helicoidal colon. Each pocket carries contents acquired earlier in the cecum. Motility collects fines and solutes into haustrae during their progression through the colon whereas coarse particulates assemble in the core. Haustrae contents continually ferment during movement to the distal colon with resulting volatile fatty acids (VFA) and electrolytes being absorbed. Mucin loosely covers the lumen surface in caeca as well as helicoidal colon that may capture microbes from active intestinal contents as well as release others to sustain fermentation. The microbial community continually modifies to accommodate fibre complexity as encountered. Resistant starches (RS) and simple oligosaccharides rapidly ferment to yield VFA while encouraging butyric acid in the cecum and anterior colon, whereas non-starch polysaccharides (NSP) complexity requires extended durations through the remaining colon that enhance acetic acid. Residual fibre eventually results in undue complexity for fermentation and consolidates at termination of the colon. These compact pellets are placed on core contents to form faeces having a nodular surface. Acetic, propionic, and butyric acids represent the bulk of VFA and are derived from non-digestible carbohydrates. Fibrolytic enzymes, when supplemented to feed, may increase the proportion of oligosaccharides and simpler NSP to further the rate as well as extent of fermentation. Active absorption of VFA by mucosal enterocytes employs its ionized form together with Na⁺, whereas direct membrane passage occurs when non-dissociated. Most absorbed VFA favour use by the host with a portion of butyric acid together with by-products from protein digestion being retained to reform mucin and sustain mucosal integrity.

Taxonomic and predicted functional signatures reveal linkages between the rumen microbiota and feed efficiency in dairy cattle raised in tropical areas

Ruminants digest plant biomass more efficiently than monogastric animals due to their symbiotic relationship with a complex microbiota residing in the rumen environment. What remains unclear is the relationship between the rumen microbial taxonomic and functional composition and feed efficiency (FE), especially in crossbred dairy cattle (Holstein x Gyr) raised under tropical conditions. In this study, we selected twenty-two F1 Holstein x Gyr heifers and grouped them according to their residual feed intake (RFI) ranking, high efficiency (HE) (n = 11) and low efficiency (LE) (n = 11), to investigate the effect of FE on the rumen microbial taxa and their functions. Rumen fluids were collected using a stomach tube apparatus and analyzed using amplicon sequencing targeting the 16S (bacteria and archaea) and 18S (protozoa) rRNA genes. Alpha-diversity and beta-diversity analysis revealed no significant difference in the rumen microbiota between the HE and LE animals. Multivariate analysis (sPLS-DA) showed a clear separation of two clusters in bacterial taxonomic profiles related to each FE group, but in archaeal and protozoal profiles, the clusters overlapped. The sPLS-DA also revealed a clear separation in functional profiles for bacteria, archaea, and protozoa between the HE and LE animals. Microbial taxa were differently related to HE (e.g., Howardella and Shuttleworthia) and LE animals (e.g., Eremoplastron and Methanobrevibacter), and predicted functions were significatively different for each FE group (e.g., K03395-signaling and cellular process was strongly related to HE animals, and K13643-genetic information processing was related to LE animals). This study demonstrates that differences in the rumen microbiome relative to FE ranking are not directly observed from diversity indices (Faith's Phylogenetic Diversity, Pielou's Evenness, Shannon's diversity, weighted UniFrac distance, Jaccard index, and Bray-Curtis dissimilarity), but from targeted identification of specific taxa and microbial functions characterizing each FE group. These results shed light on the role of rumen microbial taxonomic and functional profiles in crossbred Holstein × Gyr dairy cattle raised in tropical conditions, creating the possibility of using the microbial signature of the HE group as a biological tool for the development of biomarkers that improve FE in ruminants.

The replacement of bacitracin methylene disalicylate with Bacillus subtilis PB6 in the diet of male Cherry Valley Ducks reduces the feed conversion ratio by improving intestinal health and modulating gut microbiota

In this study, we compared the impacts of Bacillus subtilis PB6 (BS) and bacitracin methylene disalicylate (BMD) on the growth performance, intestinal morphology, expression of tight connection protein, and cecal microbiota community of male ducks through a 42-d trial. Three-hundred and sixty male Cherry Valley meat-type ducklings (1-day-old) were distributed into 3 groups of 6 replicates: CON group (control, basal diet), BMD group (basal diet + 45 mg/kg BMD, active ingredient dose in the feed), and BS group (basal diet + 2 × 107 CFU/kg BS in the feed). Results showed that supplementing the diet with BS reduced the average daily feed intake (ADFI) during d 15 to 42 and d 1 to 42 compared with the CON group (P = 0.032). It also reduced feed conversion ratio (FCR) during d 15 to 42 and d 1 to 42 (P < 0.05) relative to the other groups. The ileal villus height (VH) and villus height /crypt depth ratio (V/C) were increased (P < 0.05) in both the BS and BMD groups, and the jejunal VH and V/C ratio were increased in the BS group (P < 0.05). Relative to the CON, BS supplementation was associated with numerical augmentation of goblet cells in the jejunal mucosa and upregulation of jejunal zonula occludens (ZO-1) and ileal mucin2 (P < 0.05) mRNA levels. Analysis showed a negative correlation between FCR (d 0-42) and VH, V/C, and the number of goblet cells in the jejunum (P < 0.05). Additionally, BMD or BS supplementation altered the alpha diversity of colonic microbiota (P < 0.05). Correlation analysis revealed that Butyricimonas, Enterobacteriaceae, Clostridiaceae, and Tannerellaceae were positively associated with the acetic acid and butyrate concentrations (P < 0.05). Taken together, the supplementation of BS in the diet of male ducks was conducive to reducing FCR by meliorating intestinal morphology, upregulating ZO-1 and mucin2 mRNA levels, regulating the abundance of microbiota, and metabolites, and having a greater effect than BMD supplementation.

Feed Safety and the Development of Poultry Intestinal Microbiota

Simple Summary

Intensive gut colonisation of animals starts immediately after birth or hatch. Oral route of colonisation, and consequently the first feed, plays a significant role in the continual defining of the intestinal microbial community. The feed can influence colonisation in two ways: providing the microbial inoculum and providing the nutritional requirements that suit a specific type of microbes. In combination with environmental factors, feed shapes animal’s future health and performance from the first day of life. The objective of this review was to investigate feed safety aspects of animal nutrition from the gut colonisation aspect.

Abstract

The first feed offered to young chicks is likely the most important meal in their life. The complex gut colonisation process is determined with early exposure and during the first days of life before the microbial community is formed. Therefore, providing access to high-quality feed and an environment enriched in the beneficial and deprived of pathogenic microorganisms during this period is critical. Feed often carries a complex microbial community that can contain major poultry pathogens and a range of chemical contaminants such as heavy metals, mycotoxins, pesticides and herbicides, which, although present in minute amounts, can have a profound effect on the development of the microbial community and have a permanent effect on bird’s overall health and performance. The magnitude of their interference with gut colonisation in livestock is yet to be determined. Here, we present the animal feed quality issues that can significantly influence the microbial community development, thus severely affecting the bird’s health and performance.

Caecal microbial communities, functional diversity, and metabolic pathways in Ross 308 broiler chickens fed with diets containing different levels of Marama (Tylosema esculentum) bean meal

The caecum of a chicken harbors complex microbial communities that play vital roles in feed digestion, nutrient absorption, and bird health. Understanding the caecal microbial communities could help improve feed utilization efficiency and chicken product quality and, ultimately, deliver sustainable poultry production systems. Thus, this study assessed the caecal microbial communities and their functional diversity and metabolic pathways in broilers reared on diets containing different levels of marama (Tylosema esculentum) bean meal (MBM). A total of 350, day-old male Ross 308 broiler chicks were randomly allocated to five dietary treatments formulated as follows: a soybean-based standard broiler diet (Con_BC); Con_BC in which soybean products were substituted with 7 (M7_BC), 14 (M14_BC), 21 (M21_BC), and 28% (M28_BC) MBM. The dietary treatments were distributed to 35 replicate pens (10 birds each). After 42 days of feeding, the birds were slaughtered and thereafter caecal samples were collected from each replicate pen. Subsequently, the samples were pooled per treatment group for metagenomics sequence analysis. The results revealed that the bacteria domain (99.11%), with Bacteroides, Firmicutes and Proteobacteria being the most prominent phyla (48.28, 47.52, and 4.86%, respectively). Out of 846 genera obtained, the most abundant genera were Bacteroides, Clostridium, Alistipes, Faecalibacterium, Ruminococcus, Eubacterium, and Parabacterioides. At the genus level, the alpha-diversity showed significant (p < 0.05) difference across all treatment groups. Based on the SEED subsystem, 28 functional categories that include carbohydrates (14.65%), clustering-based subsystems (13.01%), protein metabolism (10.12%) were obtained. The KO analysis revealed 183 endogenous pathways, with 100 functional pathways associated with the metabolism category. Moreover, 15 pathways associated with carbohydrates were observed. The glycolysis/gluconeogenesis, galactose metabolism, pyruvate metabolism (15.32, 12.63, and 11.93%) were the most abundant pathways. Moreover, glycoside hydrolases (GH1, GH5, and GH13) were the most prominent carbohydrates-active enzymes. Therefore, results presented in this study suggest that dietary MB meal can improve microbial communities and their functional and metabolic pathways, which may help increase poultry production.

Potential Probiotics Role in Excluding Antibiotic Resistance

Background. Antibiotic supplementation in feed has been continued for the previous 60 years as therapeutic use. They can improve the growth performance and feed efficiency in the chicken flock. A favorable production scenario could favor intestinal microbiota interacting with antibiotic growth promoters and alter the gut bacterial composition. Antibiotic growth promoters did not show any beneficial effect on intestinal microbes. Scope and Approach. Suitable and direct influence of growth promoters are owed to antimicrobial activities that reduce the conflict between host and intestinal microbes. Unnecessary use of antibiotics leads to resistance in microbes, and moreover, the genes can relocate to microbes including Campylobacter and Salmonella, resulting in a great risk of food poisoning. Key Findings and Conclusions. This is a reason to find alternative dietary supplements that can facilitate production, growth performance, favorable pH, and modulate gut microbial function. Therefore, this review focus on different nutritional components and immune genes used in the poultry industry to replace antibiotics, their influence on the intestinal microbiota, and how to facilitate intestinal immunity to overcome antibiotic resistance in chicken.

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

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

Delayed access to feed early post-hatch affects the development and maturation of gastrointestinal tract microbiota in broiler chickens

Background

The first two weeks of post-hatch (PH) growth in broilers (meat-type birds) are critical for gut development and microbiota colonization. In the current broiler production system, chicks may not receive feed and water for 24 to 72 h due to variations in hatching time and hatchery management. Post-hatch feed delay affects body weight, feed efficiency, mortality, and gut development. The goal of this study was to investigate changes in the microbiome in broiler chickens early PH and the effect of delayed access to feed on the microbiota.

Results

Chicks either received feed and water immediately after hatch or access to feed was delayed for 48 h to mimic commercial hatchery settings (treatment, TRT). Both groups were sampled (n = 6) at -48, 0, 4 h, and 1 (24 h), 2 (48 h), 3 (72 h), 4 (96 h), 6 (144 h), 8 (192 h), 10 (240 h), 12 (288 h) and 14 (336 h) days PH. Ileal (IL) and cecal (CE) epithelial scrapings (mucosal bacteria, M) and digesta (luminal bacteria, L) were collected for microbiota analysis. Microbiota was determined by sequencing the V3-V4 region of bacterial 16S rRNA and analyzed using QIIME2. The microbiota of early ileal and cecal samples were characterized by high abundance of unclassified bacteria. Among four bacterial populations (IL-L, IL-M, CE-L, CE-M), IL-M was the least affected by delayed access to feed early PH. Both alpha and beta diversities were affected by delayed access to feed PH in IL-L, CE-M and CE-L. However, the development effect was more pronounced. In all four bacterial populations, significant changes due to developmental effect (time relative to hatch) was observed in taxonomic composition, with transient changes of bacterial taxa during the first two weeks PH. Delayed access to feed has limited influence on bacterial composition with only a few genera and species affected in all four bacterial populations. Predicted function based on 16S rRNA was also affected by delayed access to feed PH with most changes in metabolic pathway richness observed in IL-L, CE-L and CE-M.

Conclusions

These results show transient changes in chicken microbiota biodiversity during the first two weeks PH and indicate that delayed access to feed affects microbiota development. Proper microbiota development could be an important factor in disease prevention and antibiotic use in broiler chickens. Moreover, significant differences in response to delayed access to feed PH between luminal and mucosal bacterial populations strongly suggests the need for separate analysis of these two populations.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12866-022-02619-6.

The avian gut microbiota: Diversity, influencing factors, and future directions

The gut microbiota is viewed as the “second genome” of animals, sharing intricate relationships with their respective hosts. Because the gut microbial community and its diversity are affected by many intrinsic and extrinsic factors, studying intestinal microbes has become an important research topic. However, publications are dominated by studies on domestic or captive birds, while research on the composition and response mechanism of environmental changes in the gut microbiota of wild birds remains scarce. Therefore, it is important to understand the co-evolution of host and intestinal bacteria under natural conditions to elucidate the diversity, maintenance mechanisms, and functions of gut microbes in wild birds. Here, the existing knowledge of gut microbiota in captive and wild birds is summarized, along with previous studies on the composition and function, research methods employed, and factors influencing the avian gut microbial communities. Furthermore, research hotspots and directions were also discussed to identify the dynamics of the avian gut microbiota, aiming to contribute to studies of avian microbiology in the future.

Factors Affecting Breast Myopathies in Broiler Chickens and Quality of Defective Meat: A Meta-Analysis

Fast-growing broiler chickens are subjected to breast myopathies such as white striping (WS), wooden breast (WB), and spaghetti meat (SM). Available studies about risk factors for myopathy occurrence often used flock data whereas a few reports evaluated chicken individual data. Thus, the present study aimed to elucidate the effect of growth and slaughter traits, besides sex and genotype on myopathy occurrence. Data were obtained from eight experimental trials, which used a total of 6,036 broiler chickens. Sex, genotype, daily weight gain, slaughter weight, and breast yield were evaluated as potential risk factors by logistic regression analyses. Then, the effects of myopathy and sex were evaluated on meat rheological traits (pH, colour, cooking losses and shear force). Based on a logistic regression, WS occurrence was associated with genotype, breast weight, and breast yield. Compared with chickens with intermediate breast weight and breast yield, higher odds of having WS were found in chickens with high breast weight (OR: 1.49) and yield (OR: 1.27), whereas lower odds were found in those with low breast weight (OR: 0.57) and yield (OR: 0.82). As for WB and SM, females had lower odds of having WB (OR: 0.55) and higher odds of showing SM (OR: 15.4) compared to males. In males, higher odds of having WB were found in chickens with a high daily weight gain (OR: 1.75) compared to those with an intermediate daily weight gain. In females, higher odds of having SM were associated to a high slaughter weight (OR: 2.10) while lower odds to a low slaughter weight (OR: 0.87). As for meat quality, only WB meat was clearly different for some technological and sensorial properties, which can play a major role also in meat processing. In conclusion, our analysis identified breast development as a potential risk factor for WS, while a high growth was the risk factor for WB and SM. A different probability of having WB or SM in females and male was found.

Effect of Two Soybean Varieties Treated with Different Heat Intensities on Ileal and Caecal Microbiota in Broiler Chickens

Simple Summary

Soybeans are an essential part of today’s poultry nutrition diets because of their high protein content and quality. To ensure optimum digestibility in monogastric animals, soybeans need to be thermally processed. As required heat intensities depend on individual soybean properties, the emergence of highly heterogenic soybean batches is a challenge for adequate processing conditions. Molecular changes occurring during heat treatment can alter the microbial communities colonizing the animals’ guts. Gut microbiota is of great importance for both its host animal’s performance and health. To investigate the effect of heat treatment and soybean variety on the chickens’ microbiota, two soybean varieties were selected, treated at two different heat intensities and subjected to a feeding trial. DNA was then extracted and sequenced to identify different bacterial populations in the digesta of certain gut sections. Results showed that both the soybean variety and the applied heat treatment affected the abundance of certain bacterial species in the gut of chickens, but no effect on the taxonomy level of family or genus appeared. This underlines the sensitivity and reactivity of the highly complex microbial community to apparently small dietary differences.

Abstract

Soybean products are of high importance for the protein supply of poultry. Heat treatment of soybeans is essential to ensure optimal digestibility because of intrinsic antinutritive factors typical for this feed category. However, excessive treatment promotes the Maillard reaction and reduces protein digestibility. Furthermore, Europe’s efforts are to decrease dependence on imports of soybean products and enlarge local production. This process will include an increase in the variability of soybean batches, posing great challenges to adequate processing conditions. Intrinsic soybean properties plus heat treatment intensity might be able to modulate the gut microbiota, which is of crucial importance for an animal’s health and performance. To assess the influence of heat treatment and soybean variety on gut microbiota, 2 soybean cakes from 2 varieties were processed at 110 °C or 120 °C and subsequently fed to 336 one-day-old broiler chickens. After 36 days, the animals were slaughtered, and the digesta of the ileum and caecum was collected. Next, 16S rRNA amplicon sequencing of the extracted DNA revealed a high discrepancy between gut sections, but there were no differences between male and female birds. Significant differences attributed to the different soybean varieties and heat intensity were detected for certain bacterial taxa. However, no effect on specific families or genera appeared. In conclusion, the results indicated the potential of processing conditions and soybean variety as microbiota-modulating factors.

Microbiota and Transcriptomic Effects of an Essential Oil Blend and Its Delivery Route Compared to an Antibiotic Growth Promoter in Broiler Chickens

This study evaluated the effect of the delivery of a commercial essential oil blend containing the phytonutrients star anise, cinnamon, rosemary, and thyme oil (via different routes) on broiler chickens’ ileal and ceca microbiota and liver transcriptome compared to an antibiotic growth promoter. Eggs were incubated and allocated into three groups: non-injected, in ovo saline, and in ovo essential oil. On day 18 of incubation, 0.2 mL of essential oil in saline (dilution ratio of 2:1) or saline alone was injected into the amnion. At hatch, chicks were assigned to post-hatch treatment combinations: (A) a negative control (corn-wheat-soybean diet), (B) in-feed antibiotics, (C) in-water essential oil (250 mL/1000 L of drinking water), (D) in ovo saline, (E) in ovo essential oil, and (F) in ovo essential oil plus in-water essential oil in eight replicate cages (six birds/cage) and raised for 28 days. On days 21 and 28, one and two birds per cage were slaughtered, respectively, to collect gut content and liver tissues for further analysis. Alpha and beta diversity differed significantly between ileal and ceca samples but not between treatment groups. In-feed antibiotic treatment significantly increased the proportion of specific bacteria in the family Lachnospiraceae while reducing the proportion of bacteria in the genus Christensenellaceae in the ceca, compared to other treatments. Sex-controlled differential expression of genes related to cell signaling and tight junctions were recorded. This study provides data that could guide the use of these feed additives and a foundation for further research.

Obesity influences composition of salivary and fecal microbiota and impacts the interactions between bacterial taxa

Obesity is an increasing global health concern and is associated with a broad range of morbidities. The gut microbiota are increasingly recognized as important contributors to obesity and cardiometabolic health. This study aimed to characterize oral and gut microbial communities, and evaluate host: microbiota interactions between clinical obesity classifications. We performed 16S rRNA sequencing on fecal and salivary samples, global metabolomics profiling on plasma and stool samples, and dietary profiling in 135 healthy individuals. We grouped individuals by obesity status, based on body mass index (BMI), including lean (BMI 18-124.9), overweight (BMI 25-29.9), or obese (BMI ≥30). We analyzed differences in microbiome composition, community inter-relationships, and predicted microbial function by obesity status. We found that salivary bacterial communities of lean and obese individuals were compositionally and phylogenetically distinct. An increase in obesity status was positively associated with strong correlations between bacterial taxa, particularly with bacterial groups implicated in metabolic disorders including Fretibacterium, and Tannerella. Consumption of sweeteners, especially xylitol, significantly influenced compositional and phylogenetic diversities of salivary and fecal bacterial communities. In addition, obesity groups exhibited differences in predicted bacterial metabolic activity, which was correlated with host's metabolite concentrations. Overall, obesity was associated with distinct changes in bacterial community dynamics, particularly in saliva. Consideration of microbiome community structure and inclusion of salivary samples may improve our ability to understand pathways linking microbiota to obesity and cardiometabolic disease.

Dietary fiber modulates abdominal fat deposition associated with cecal microbiota and metabolites in yellow chickens

Excessive deposition of abdominal fat is a public concern in the yellow chicken industry related to human nutrition. The common practice of nutritionists is to increase the fiber content in feed to control abdominal fat deposition of chickens. Corncob meal (CCM) is the cheapest ingredient widely used in animal diets. The possible effects of CCM on chicken abdominal fat deposition and the possible mechanism involving cecal microbiota remain unknown. The objectives of this study were to investigate the effects of CCM in modulating abdominal fat deposition and the role of the cecal microbiota and their metabolites. A total of 200 ninety-day-old Huxu female chickens were divided into 2 dietary treatments, each with 10 replicates of 10 birds, and were fed two finisher diets, from 90 to 135 d. The diets were a typical corn-soybean control diet (CON) and that diet with CCM partially replacing corn and corn gluten meal. Results showed that the CCM diet markedly decreased live weight and abdominal fat percentage (P < 0.05); chickens fed the CCM diet exhibited lower (P < 0.01) expression in abdominal fat of fatty acid binding protein 4 (FABP4), stearoyl-CoA desaturase (SCD), fatty acid synthase (FAS), and peroxisome proliferator-activated receptor γ (PPARγ) but higher (P < 0.05) expression of estrogen receptor alpha (ESR1). The CCM increased the abundance of Akkermansia (P < 0.05) and markedly reduced the relative cecal abundance of Phascolarctobacterium (P < 0.01), Rikenellaceae (P < 0.05), and Faecalibacterium (P < 0.01). The metabolomic and biochemical analyses demonstrated that the CCM diet increased (P < 0.05) the concentrations of butyrate in cecal contents. The majority of the metabolites in cecal digesta with differences in abundance were organic acids. The CCM diet increased (P < 0.05) contents of (R)-5-diphosphomevalote, pantothenic acid, 2-epi-5-epi-valiolone 7-phosphate, D-ribose 5-diphosphate, arbutin 6-phosphate, D-ribitol 5-phosphate, undecanoic acid, nicotinic acid, 4-methyl-2-oxovaleric acid, while decreasing (P < 0.05) those of oleic acid, glutaric acid, adipic acid, suberic acid, and L-fuculose 1-phosphate. In conclusion, these findings demonstrated that the dietary CCM treatment significantly decreased abdominal fat and altered the cecal microbiota and metabolite profiles of the yellow chickens.

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

Aim

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

Methods and Results

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

Conclusions

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

Significance and Impact of the Study

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

Effects of therapeutic levels of dietary antibiotics on the cecal microbiome composition of broiler chickens

Dietary antibiotics, including antibiotic growth promoters (AGPs), have been commonly used to improve health and growth of poultry. The present study investigated the effects of therapeutic doses of dietary antibiotics, including bacitracin methylene disalicylate (BMD), penicillin G potassium (PP) and an ionophore (salinomycin, SA), on the cecal microbiome of chickens. BMD and SA treatments were given as dietary supplements from d 1 to 35 of age. The SAPP (salinomycin+ penicillin G potassium) group was given SA as a dietary supplement from d 1 to 35 of age and PP was added to drinking water from d 19 to 24 of age to simulate common practices for control of necrotic enteritis in broilers. The cecal contents were collected from all treatment groups on d 10, 24, and 35 of age and DNA was extracted for metagenomic analysis of the cecal microbiome. The results revealed that dietary or water supplementation of therapeutic levels of antibiotics and ionophores to chickens significantly altered the cecal microbial homeostasis during different stages of the chicken life. The alpha diversity analysis showed that BMD, SA, and SAPP treatments decreased diversity and evenness of the cecal microbiome of treated chickens on d 10 of age. Species richness was also reduced on d 35 following treatment with BMD. Beta diversity analyses revealed that SAPP and BMD induced significant changes in the relative abundance of Gram-positive and -negative bacteria on d 10, while no significant differences were observed on d 24. On d 35, the non-treated control group had higher relative abundance of unclassified Gram-positive and -negative bacteria compared to SA, SAPP, and BMD treatment groups. Overall, despite their beneficial role in controlling necrotic enteritis outbreaks, the findings of this study highlight the potential negative effects of dietary supplementation of therapeutic levels of antibiotics on the gut microbiome and suggest that adjusting gut bacteria may be required to restore microbial richness and diversity of the gut microbiome following treatment with these antibiotics.

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

Simple Summary

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

Abstract

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

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.

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

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

Effects of Xylanase in Corn- or Wheat-Based Diets on Cecal Microbiota of Broilers

Xylanase has been demonstrated to improve growth performance of broilers fed wheat- or corn-based diets due to its ability to degrade arabinoxylans (AX). However, content and structure of AX in corn and wheat are different, comparing effects of xylanase on cecal microbiota of broilers fed corn- or wheat-based diets could further elaborate the mechanism of the specificity of xylanase for different cereal grains. Thus, a total of 192 one-day-old broilers were randomly allotted into four dietary treatments, including wheat-soybean basal diet, wheat-soybean basal diet with 4,000U/kg xylanase, corn-soybean basal diet, and corn-soybean basal diet with 4,000U/kg xylanase to evaluate interactive effects of xylanase in corn- or wheat-based diets on broilers cecal microbiota during a 6-week production period. The results indicated that bacterial community clustering was mainly due to cereal grains rather than xylanase supplementation. Compared with broilers fed wheat-based diets, corn-based diets increased alpha-diversity and separated from wheat-based diets (p<0.05). Xylanase modulated the abundance of specific bacteria without changing overall microbial structure. In broilers fed wheat-based diets, xylanase increased the abundance of Lactobacillus, Bifidobacterium, and some butyrate-producing bacteria, and decreased the abundance of non-starch polysaccharides-degrading (NSP) bacteria, such as Ruminococcaceae and Bacteroidetes (p<0.05). In broilers fed corn-based diets, xylanase decreased the abundance of harmful bacteria (such as genus Faecalitalea and Escherichia-Shigella) and promoted the abundance of beneficial bacteria (such as Anaerofustis and Lachnospiraceae_UCG_010) in the cecum (p<0.05). Overall, xylanase supplementation to wheat- or corn-based diets improved broilers performance and cecal microbiota composition. Xylanase supplementation to wheat-based diets increased the abundance of butyrate-producing bacteria and decreased the abundance of NSP-degrading bacteria. Moreover, positive effects of xylanase on cecal microbiota of broilers fed corn-based diets were mostly related to the inhibition of potentially pathogenic bacteria, and xylanase supplementation to corn-based diets slightly affected the abundance of butyrate-producing bacteria and NSP-degrading bacterium, the difference might be related to lower content of AX in corn compared to wheat.

Metagenomic Analysis Identifies Sex-Related Cecal Microbial Gene Functions and Bacterial Taxa in the Quail

Background: Japanese quail (Coturnix japonica) are important and widely distributed poultry in China. Researchers continue to pursue genetic selection for heavier quail. The intestinal microbiota plays a substantial role in growth promotion; however, the mechanisms involved in growth promotion remain unclear.

Results: We generated 107.3 Gb of cecal microbiome data from ten Japanese quail, providing a series of quail gut microbial gene catalogs (1.25 million genes). We identified a total of 606 main microbial species from 1,033,311 annotated genes distributed among the ten quail. Seventeen microbial species from the genera Anaerobiospirillum, Alistipes, Barnesiella, and Butyricimonas differed significantly in their abundances between the female and male gut microbiotas. Most of the functional gut microbial genes were involved in metabolism, primarily in carbohydrate transport and metabolism, as well as some active carbohydrate-degrading enzymes. We also identified 308 antibiotic-resistance genes (ARGs) from the phyla Bacteroidetes, Firmicutes and Euryarchaeota. Studies of the differential gene functions between sexes indicated that abundances of the gut microbes that produce carbohydrate-active enzymes varied between female and male quail. Bacteroidetes was the predominant ARG-containing phylum in female quail; Euryarchaeota was the predominant ARG-containing phylum in male quail.

Conclusion: This article provides the first description of the gene catalog of the cecal bacteria in Japanese quail as well as insights into the bacterial taxa and predictive metagenomic functions between male and female quail to provide a better understanding of the microbial genes in the quail ceca.

Effects of Clostridium butyricum, Sodium Butyrate, and Butyric Acid Glycerides on the Reproductive Performance, Egg Quality, Intestinal Health, and Offspring Performance of Yellow-Feathered Breeder Hens

Butyrate has been reported to promote the performance and growth of chickens. The specific roles and efficacy of different sources of butyrate remained unclear. Thus, the present study aimed to investigate and compare the effects of Clostridium butyricum (CB), sodium butyrate (SB), and butyric acid glycerides (tributyrin, BAG) on the reproductive performance, egg quality, intestinal health, and offspring performance of yellow-feathered breeder hens. A total of 300 Lingnan yellow-feathered breeder hens were assigned to five treatment groups: control (CL), 1×10⁸CFU/kg CB (CBL), 1×10⁹CFU/kg CB (CBH), 500mg/kg SB, and 300mg/kg BAG. Results showed that the laying performance and egg quality were increased by CBL, CBH, and BAG. Both CB treatments increased the hatchability of fertilized eggs. Maternal supplementation with both levels of CB significantly elevated the growth performance of offspring. Treatment with CBL, CBH, SB, and BAG all improved the oviduct-related variables and reduced the plasmal antioxidant variables. The CBH, CBL, and BAG treatments also improved the intestinal morphology to different degrees. Jejunal contents of IL-6 were decreased by CBH and BAG, while those of IL-4, IL-6, IL-1β, and IgY were decreased by SB. Transcripts of nutrient transporters in jejunal mucosa were also upregulated by CBH, CBL, and SB treatments and expression of Bcl-2-associated X protein was decreased by CBL, CBH, and BAG. In cecal contents, CBL increased the abundance of Firmicutes and Bacillus, while CBH decreased the abundance of Proteobacteria. Also, the co-occurrence networks of intestinal microbes were regulated by CBH and BAG. In conclusion, dietary inclusion of CB and BAG improved the reproductive parameters, egg quality, and intestinal morphology of breeders. CB also influenced the hatching performance of breeders and growth performance of the offspring, while SB improved the oviduct-related variables. These beneficial effects may result from the regulation of cytokines, nutrient transporters, apoptosis, and gut microbiota; high-level CB had more obvious impact. Further study is needed to explore and understand the correlation between the altered gut microbiota induced by butyrate and the performance, egg quality, intestinal health, and also offspring performance.

The digestive and reproductive tract microbiotas and their association with body weight in laying hens

Body weight at the onset of egg production is a major factor influencing hen productivity, as suitable body weight is crucial to laying performance in laying hens. To better understand the association between body weight and microbial community membership and structure in different sites of the digestive and reproductive tracts in chickens, we performed 16S rRNA sequencing surveys and focused on how the microbiota may interact to influence body weight. Our results demonstrated that the microbial community and structure of the digestive and reproductive tracts differed between low and high body weight groups. In particular, we found that the species Pseudomonas viridiflava was negatively associated with body weight in the 3 digestive tract sites, while Bacteroides salanitronis was negatively associated with body weight in the 3 reproductive tract sites; and further in-depth studies are needed to explore their function. These findings will help extend our understanding of the influence of the bird digestive and reproductive tract microbiotas on body weight trait and provide future directions regarding the control of body weight in the production of laying hens.

The link between broiler flock heterogeneity and cecal microbiome composition

BACKGROUND

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

RESULTS

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

CONCLUSION

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

Effect of stocking density on performance, meat quality and cecal bacterial communities of yellow feather broilers

Totally, 315 42-day-old male Xueshan chickens were allocated into 3 caging densities, 14, 21 and 28 birds/m². Each treatment was represented by 5 replicates. The body weight (BW), slaughter performance, meat quality, behavioral assessment, and the cecal microorganisms were detected at the market age. The results showed that the BW of broilers in the low- and medium-density groups was significantly higher (p < 0.05) than that of the high-density group from the age of 10 weeks. Only the feather quality of the broilers in the low-density group improved significantly (p < 0.05) compared with those of the other two groups. And, the abdominal fat percentage and the fat content of thigh muscle of broilers in the low- and medium-density groups were higher (p < 0.05) than those in the high-density group. No significant difference (p > 0.05) was noted in the other traits. The abundance of some microbial like Akkermansiaceae, Lactobacillaceae and Faecalibacterium may be correlated with the BW and fat content of broilers. The findings of this study suggest that increasing the stocking density decreased the final BW, fat content and the feather quality, whereas no evidence was found that stocking density caused changes in other parameters.

Highly Fermentable Fiber Alters Fecal Microbiota and Mitigates Swine Dysentery Induced by Brachyspira hyodysenteriae

Simple Summary

Dietary manipulation to prevent disease is essential to reduce antimicrobial usage in the swine industry. This study aimed to evaluate whether replacing lowly fermentable fibers with highly fermentable fibers would mitigate disease during a 42 day Brachyspira hyodysenteriae challenge. Pigs fed the highly fermentable diet had improved growth performance compared with those fed diets of lower fermentability and had near absence of clinical swine dysentery. Further, several microbial genera were altered by dietary manipulation, bacteria that may be synergistic or antagonistic to Brachyspira hyodysenteriae. Taken together, this study demonstrates that replacing lowly fermentable fiber with highly fermentable fibers mitigates disease during Brachyspira hyodysenteriae challenge and may help reduce antimicrobial usage in treatment and control of this pathogen.

Abstract

Brachyspira hyodysenteriae is an etiological agent of swine dysentery (SD). Diet fermentability plays a role in development of SD, but the mechanism(s) of action are largely unknown. Thus, this study aimed to determine whether replacing lowly fermentable fiber with highly fermentable fiber would mitigate a 42 d B. hyodysenteriae challenge. Thirty-nine barrows were allocated to dietary treatment groups: (1) 20% corn distillers dried grain with solubles (DDGS), 0% beet pulp (BP) or resistant starch (RS; lowly fermentable fiber (LFF)); (2) 10% DDGS, 5% BP, 5% RS (medium fermentable fiber (MFF)); and (3) 0% DDGS, 10% BP, 10% RS (highly fermentable fiber (HFF)). On day post inoculation 0, pigs were inoculated with B. hyodysenteriae. Overall, 85% LFF pigs developed clinical SD, 46% of MFF pigs developed SD, and 15% of HFF pigs developed SD (p < 0.05). Overall average daily gain (ADG) differed among all treatments (p < 0.001), with LFF pigs having the lowest ADG. For HFF pigs, ADG was 37% greater than LFF pigs (p < 0.001) and 19% greater than MFF pigs (p = 0.037). The LFF diet had greater relative abundance of Shuttleworthia and Ruminococcus torques. Further, microbiota of pigs that developed SD had enriched Prevotellaceae. Collectively, replacing DDGS with highly fermentable fiber reduced clinical SD, improved performance, and modulated fecal microbiota during B. hyodysenteriae challenge.