Dynamic distribution of gut microbiota during embryonic development in chicken

Variations in seminal microbiota and their functional implications in chickens adapted to high-altitude environments

Seminal fluid, once believed to be sterile, is now recognized as constituting a complex and dynamic environment inhabited by a diverse community of micro-organisms. However, research on the seminal microbiota in chickens is limited, and microbiota variations among different chicken breeds remain largely unexplored. In this study, we collected semen samples from Beijing You Chicken (BYC) and Tibetan Chicken (TC) and explored the characteristics of the microbiota using 16S rRNA gene sequencing. Additionally, we collected cloacal samples from the TC to control for environmental contamination. The results revealed that the microbial communities in the semen were significantly different from those in the cloaca. Firmicutes and Actinobacteriota were the predominant phyla in BYC and TC semen, respectively, with Lactobacillus and Phyllobacterium being the dominant genera in each group. Additionally, the seminal microbiota of BYC exhibited greater richness and evenness than that of TC. Principal coordinate analysis (PCoA) indicated significant intergroup differences between the seminal microbiotas of BYC and TC. Subsequently, by combining linear discriminant analysis effect size and random forest analyses, we identified Lactobacillus as the predominant microorganism in BYC semen, whereas Phyllobacterium dominated in TC semen. Furthermore, co-occurrence network analysis revealed a more intricate network in the BYC group than in the TC group. Additionally, unique microbial functional characteristics were observed in each breed, with TC exhibiting metabolic features potentially associated with their ability to adapt to high-altitude environments. The results of this study emphasized the unique microbiota present in chicken semen, which may be influenced by genetics and evolutionary history. Significant variations were observed between low-altitude and high-altitude breeds, highlighting the breed-specific implications of the seminal microbiota for reproduction and high-altitude adaptation.

A metagenomic investigation of the faecal RNA virome structure of asymptomatic chickens obtained from a commercial farm in Durban, KwaZulu-Natal province, South Africa

BACKGROUND

Virome studies on birds, including chickens are relatively scarce, particularly from the African continent. Despite the continuous evolution of RNA viruses and severe losses recorded in poultry from seasonal viral outbreaks, the information on RNA virome composition is even scantier as a result of their highly unstable nature, genetic diversity, and difficulties associated with characterization. Also, information on factors that may modulate the occurrence of some viruses in birds is limited, particularly for domesticated birds. Viral metagenomics through advancements in sequencing technologies, has enabled the characterization of the entire virome of diverse host species using various samples.

METHODS

The complex RNA viral constituents present in 27 faecal samples of asymptomatic chickens from a South African farm collected at 3-time points from two independent seasons were determined, and the impact of the chicken's age and collection season on viral abundance and diversity was further investigated. The study utilized the non-invasive faecal sampling method, mRNA viral targeted enrichment steps, a whole transcriptome amplification strategy, Illumina sequencing, and bioinformatics tools.

RESULTS

The results obtained revealed a total of 48 viral species spanning across 11 orders, 15 families and 21 genera. Viral RNA families such as Coronaviridae, Picornaviridae, Reoviridae, Astroviridae, Caliciviridae, Picorbirnaviridae and Retroviridae were abundant, among which picornaviruses, demonstrated a 100% prevalence across the three age groups (2, 4 and 7 weeks) and two seasons (summer and winter) of the 27 faecal samples investigated. A further probe into the extent of variation between the different chicken groups investigated indicated that viral diversity and abundance were significantly influenced by age (P = 0.01099) and season (P = 0.00099) between chicken groups, while there was no effect on viral shedding within samples in a group (alpha diversity) for age (P = 0.146) and season (P = 0.242).

CONCLUSION

The presence of an exceedingly varied chicken RNA virome, encompassing avian, mammalian, fungal, and dietary-associated viruses, underscores the complexities inherent in comprehending the causation, dynamics, and interspecies transmission of RNA viruses within the investigated chicken population. Hence, chickens, even in the absence of discernible symptoms, can harbour viruses that may exhibit opportunistic, commensal, or pathogenic characteristics.

Exploring the complexities of poultry respiratory microbiota: colonization, composition, and impact on health

An accurate understanding of the ecology and complexity of the poultry respiratory microbiota is of utmost importance for elucidating the roles of commensal or pathogenic microorganisms in the respiratory tract, as well as their associations with health or disease outcomes in poultry. This comprehensive review delves into the intricate aspects of the poultry respiratory microbiota, focusing on its colonization patterns, composition, and impact on poultry health. Firstly, an updated overview of the current knowledge concerning the composition of the microbiota in the respiratory tract of poultry is provided, as well as the factors that influence the dynamics of community structure and diversity. Additionally, the significant role that the poultry respiratory microbiota plays in economically relevant respiratory pathobiologies that affect poultry is explored. In addition, the challenges encountered when studying the poultry respiratory microbiota are addressed, including the dynamic nature of microbial communities, site-specific variations, the need for standardized protocols, the appropriate sequencing technologies, and the limitations associated with sampling methodology. Furthermore, emerging evidence that suggests bidirectional communication between the gut and respiratory microbiota in poultry is described, where disturbances in one microbiota can impact the other. Understanding this intricate cross talk holds the potential to provide valuable insights for enhancing poultry health and disease control. It becomes evident that gaining a comprehensive understanding of the multifaceted roles of the poultry respiratory microbiota, as presented in this review, is crucial for optimizing poultry health management and improving overall outcomes in poultry production.

Effect of in ovo feeding of xylobiose and xylotriose on plasma immunoglobulin, cecal metabolites production, microbial ecology, and metabolic pathways in broiler chickens

BACKGROUND

Dietary supplementation of xylooligosaccharides (XOS) has been found to influence gut health by manipulating cecal microbiota and producing microbe-origin metabolites. But no study investigated and compared the effect of in ovo feeding of xylobiose (XOS2) and xylotriose (XOS3) in chickens. This study investigated the effect of in ovo feeding of these XOS compounds on post-hatch gut health parameters in chickens. A total of 144 fertilized chicken eggs were divided into three groups: a) non-injected control (CON), b) XOS2, and c) XOS3. On the 17th embryonic day, the eggs of the XOS2 and XOS3 groups were injected with 3 mg of XOS2 and XOS3 diluted in 0.5 mL of 0.85% normal saline through the amniotic sac. After hatching, the chicks were raised for 21 d. Blood was collected on d 14 to measure plasma immunoglobulin. Cecal digesta were collected for measuring short-chain fatty acids (SCFA) on d 14 and 21, and for microbial ecology and microbial metabolic pathway analyses on d 7 and 21.

RESULTS

The results were considered significantly different at P < 0.05. ELISA quantified plasma IgA and IgG on d 14 chickens, revealing no differences among the treatments. Gas chromatography results showed no significant differences in the concentrations of cecal SCFAs on d 14 but significant differences on d 21. However, the SCFA concentrations were lower in the XOS3 than in the CON group on d 21. The cecal metagenomics data showed that the abundance of the family Clostridiaceae significantly decreased on d 7, and the abundance of the family Oscillospiraceae increased on d 21 in the XOS2 compared to the CON. There was a reduction in the relative abundance of genus Clostridium sensu stricto 1 in the XOS2 compared to the CON on d 7 and the genus Ruminococcus torques in both XOS2 and XOS3 groups compared to the CON on d 21. The XOS2 and XOS3 groups reduced the genes for chondroitin sulfate degradation I and L-histidine degradation I pathways, which contribute to improved gut health, respectively, in the microbiome on d 7. In contrast, on d 21, the XOS2 and XOS3 groups enriched the thiamin salvage II, L-isoleucine biosynthesis IV, and O-antigen building blocks biosynthesis (E. coli) pathways, which are indicative of improved gut health. Unlike the XOS3 and CON, the microbiome enriched the pathways associated with energy enhancement, including flavin biosynthesis I, sucrose degradation III, and Calvin-Benson-Bassham cycle pathways, in the XOS2 group on d 21.

CONCLUSION

In ovo XOS2 and XOS3 feeding promoted beneficial bacterial growth and reduced harmful bacteria at the family and genus levels. The metagenomic-based microbial metabolic pathway profiling predicted a favorable change in the availability of cecal metabolites in the XOS2 and XOS3 groups. The modulation of microbiota and metabolic pathways suggests that in ovo XOS2 and XOS3 feeding improved gut health during the post-hatch period of broilers.

Prophybiotics for in-ovo stimulation; validation of effects on gut health and production of broiler chickens

Probiotics and phytobiotics have demonstrated effective improvement of gut health in broiler chickens when individually administered in-ovo. However, their combined use in-ovo, has not been studied to date. We coined the term "prophybiotic" (probiotic + phytobiotic) for such a combination. The current study therefore, aimed to elucidate the effects of combined use of a selected probiotic and a phytobiotic in-ovo, on broiler gut health and production parameters, as opposed to use of probiotics alone. ROSS 308 hatching eggs were injected with either Leuconostoc mesenteroides (probiotic: PB) or L. mesenteroides with garlic aqueous extract (prophyiotic: PPB) on the 12th day of incubation. Relative abundances of bacteria in feces and cecal content (qPCR), immune related gene expression in cecal mucosa (qPCR) and histomorphology of cecal tissue (PAS staining) were analyzed along with production parameters (hatch quality, body weight, feed efficiency and slaughter and meat quality). PPB treatment increased the abundance of faecalibacteria and bifidobacteria in feces (d 7) and Akkermansia sp. in cecal content. Moreover, it decreased Escherichia coli abundance in both feces (d 34) and cecal content. PB treatment only increased the faecalibacteria in feces (d 7) and Akkermansia sp. in the cecal content. Moreover, PPB treatment resulted in up-regulation of immune related genes (Avian beta defensing 1, Free fatty acid receptor 2 and Mucin 6) and increased the crypt depth in ceca whereas PB treatment demonstrated a higher crypt depth and a tendency to increase Mucin 6 gene expression. Both treatments did not impair the production parameters studied. In conclusion, our results suggest that in-ovo PPB treatment may have enhanced potential in boosting the immune system without compromising broiler production and efficiency, as compared to the use of probiotic alone. Our study, highlights the potential of carefully selected PPB combinations for better results in improving gut health of broiler chickens.

Characteristics of gut microbiota and metabolomic of Hainan Tunchang pigs at various growth stages

Numerous gut microorganisms residing in the gut tract and their metabolites play an important role in animal growth. Diet, as the main factor, affects the changes of gut microbiota, and host genetics also have a significant impact on gut microbiota, including growth stages. However, the differences of gut microbiota and its metabolites at various growth stages in local pig breed remains unclear. We used 16S rRNA gene sequencing and untargeted metabolomics to investigate the fecal microbiota and metabolites in different developmental stages of Hainan Tunchang pigs. The relative proportions of dominant bacteria Firmicutes and Spirochaetes increased, Bacteroidetes and Proteobacteria decreased with the development. As age increased, different physiological states led to structural and functional changes in animal nutrition metabolism and immune needs, as well as changes in gut microbiota and its metabolites. We have detected several statistically different microbial and metabolic biomarkers at different growth stages. Meanwhile, through correlation analysis between differential bacteria and metabolites, it was found that the bacteria forming networks with their significant related metabolites were different at various growth stages, Holdemanella, Sharpea, Subdoligranulum, and uncultured_bacterium_o_Bacteroidales were enriched between preweaning piglets and weaning piglets, and they all positive correlated with related metabolites. We also found that the differential bacteria were significantly related to short-chain fatty acid. These findings might provide new insights into the developmental changes of gut microbiota in local pig breeds and the interaction mechanism between the body, and improve pig growth performance and efficiency by regulating the composition of gut microbiota and metabolites.

Nearly (?) sterile avian egg in a passerine bird

During early ontogeny, microbiome affects development of the gastrointestinal tract, immunity, and survival in vertebrates. Bird eggs are thought to be (1) initially sterile (sterile egg hypothesis) and (2) colonized after oviposition through horizontal trans-shell migration, or (3) initially seeded with bacteria by vertical transfer from mother oviduct. To date, however, little empirical data illuminate the contribution of these mechanisms to gut microbiota formation in avian embryos. We investigated microbiome of the egg content (day 0; E0-egg), embryonic gut at day 13 (E13) and female faeces in a free-living passerine, the great tit (Parus major), using a methodologically advanced procedure combining 16S rRNA gene sequencing and microbe-specific qPCR assays. Our metabarcoding revealed that the avian egg is (nearly) sterile, but acquires a slightly richer microbiome during the embryonic development. Of the three potentially pathogenic bacteria targeted by qPCR, only Dietzia was found in E0-egg (yet also in negative controls), E13 gut and female samples, which might indicate possible vertical transfer. Unlike in poultry, we have shown that major bacterial colonization of the gut in passerines does not occur before hatching. We emphasize that protocols that carefully check for environmental contamination are critical in studies with low-bacterial biomass samples.

Dynamic distribution of gut microbiota in posthatching chicks and its relationship with average daily gain

The colonization and development of gut microbiota are essential for the health and growth of chicks after hatching. However, the colonization and prevalence of gut microbiota have not been well characterized, and knowledge of which microbes and their relationship with average daily gain in chicks is still limited. This study characterized the dynamic succession of microbiota in the intestinal tract of chicks and investigated its relationship with daily weight gain. A total of 121 fecal samples across 7 time points from d 0 to 10 posthatching were collected from 19 chicks randomly selected from 1,950 chicks. Using 16S rRNA gene sequencing examined microbial composition of fecal samples. The observed species index of alpha diversity increased with age, gradually achieving stability at 3 d of age. The microbiota of chicks after hatching was primarily Clostridium_sensu_stricto_1 (34.49%), and its relative abundance diminishes with age. In contrast, Lactobacillus had a low relative abundance in the first 2 d after hatching and gradually increased with age. Predicted functional capacities found that the microbiota of early-stage posthatching (d 0 and 1 after hatching) was involved in metabolism, including amino acid metabolism, metabolism of cofactors and vitamins, and nitrogen metabolism. However, at the later stage posthatching (from d 3-10 after hatching), the intestinal microbial function was involved in carbohydrate metabolism, amino acid metabolism, cell growth and death, and methane metabolism. It was identified that 47 operational taxonomic units were associated with average daily gain of chicks, 12 of which were annotated with Lactobacillus and significantly positive associated with average daily gain. In addition, Clostridium_sensu_stricto_1 was significantly negatively associated with average daily gain. Taken together, we characterized the dynamic successions of intestinal microbiota in hatching chicks. The intestinal microbiota of chicks has an impact on the host average daily gain. Our findings should be instrumental in improving local chick production.

Supplementing Genistein for Breeder Hens Alters the Growth Performance and Intestinal Health of Offspring

Recent research revealed that dietary genistein supplementation for breeder hens can improve the immune function of offspring chicks. However, it remains unknown whether this maternal effect could improve the intestinal health of offspring. This study was conducted to explore the mechanism involved in the maternal effect of genistein on the intestinal mucosa and microbial homeostasis of chicken offspring. A total of 120 Qiling breeder hens were fed a basal diet, a 20 mg/kg genistein-supplemented diet, or a 40 mg/kg genistein-supplemented diet for 4 weeks before collecting their eggs. After hatching, 180 male offspring (60 chickens from each group) were randomly selected and divided into three groups: (1) the offspring of hens fed a basal diet (CON); (2) the offspring of hens fed a low-dose genistein-supplemented diet (LGE); (3) the offspring of hens fed a high-dose genistein-supplemented diet (HGE). At 17 d, 72 male offspring (48 chickens from CON and 24 chickens from LGE) were divided into three groups: (1) the offspring of hens fed a basal diet (CON); (2) the CON group challenged with LPS (LPS); (3) the LGE group challenged with LPS (LPS + LGE). The results showed that maternal genistein supplementation increased the birth weight and serum level of total protein (TP), followed by improved intestinal villus morphology. Continuously, the maternal effect on the body weight of chicks lasted until 21 d. Additionally, it was observed that maternal genistein supplementation exhibited protective effects against LPS-induced morphological damage and intestinal mucosal barrier dysfunction by upregulating the expression of tight junction proteins, specifically ZO-1, Claudin1, E-cadherin, and Occludin, at 21 d. Using 16S rRNA gene sequencing, we demonstrated that maternal supplementation of genistein has the potential to facilitate the maturation of newly hatched chicken offspring by enhancing the abundance of Escherichia coli. Additionally, maternal genistein supplementation can effectively reduce the abundance of Gammaproteobacteria, thus mitigating the risk of bacterial diversity impairment of LPS. In light of these findings, maternal genistein supplementation holds promise as a potential strategy for ameliorating intestinal mucosal damage and modulating the microbiome in chicken offspring.

A meta-analysis of the effect of Eimeria spp. and/or Clostridium perfringens infection on the microbiota of broiler chickens

Coccidiosis in chickens is caused by Eimeria spp. The infection provides a growth advantage to Clostridium perfringens (CP), frequently leading to necrotic enteritis. One approach to alleviate the negative impacts of the diseases is to improve the bacterial composition in chickens, and many experiments investigating chicken enteric health in recent years include the characterization of the bacterial microbiota. This meta-analysis synthesized the data of studies investigating the intestinal microbiota after infection with coccidia and/or CP to provide a basis for future research. Inclusion criteria were that experiments contained a group infected with one or both pathogens and an uninfected control group, the use of 16SrRNA Illumina sequencing and the availability of raw data. A total of 17 studies could be included. Meta-analyses of 3 different data sets were performed: 1 on data of 9 experiments on chickens infected with coccidia only; the second on data of 4 studies on chickens infected with CP only; the third on raw data of 8 experiments with chickens infected with coccidia and CP. The meta-analysis of relative abundance and alpha diversity of the data sets was performed in R using the SIAMCAT and metafor packages. The number of families of interest identified by the analyses of experiments with infection with coccidia only, CP only and the combined infection were 23, 2, and 29, respectively. There was an overlap of 13 families identified by analyses of experiments with infection with coccidia only and of experiments with the combined infections. Machine learning was not able to find a model to predict changes of the microbiota in either 1 of the 3 analyses. Meta-analyses of functional profiles showed a more uniform reaction to the infections with the relative abundance of many pathways significantly altered. Alpha diversity was not affected by infection with either pathogen or the combination. In conclusion, the heterogeneity of these microbiota studies makes recognizing common trends difficult, although it seems that coccidia infection affects the microbiota more than an infection with CP. Future studies should focus on the bacterial functions that are changed due to these infections using metagenome techniques.

Dietary Bacillus licheniformis shapes the foregut microbiota, improving nutrient digestibility and intestinal health in broiler chickens

Bacillus licheniformis is considered a potential alternative to antibiotic growth promoters of animal growth and health. However, the effects of Bacillus licheniformis on the foregut and hindgut microbiota, and their relationships with nutrient digestion and health, in broiler chickens remain unclear. In this study, we aimed to identify the effects of Bacillus licheniformis BCG on intestinal digestion and absorption, tight junctions, inflammation, and the fore- and hind-gut microbiota. We randomly assigned 240 1-day-old male AA broilers into three treatment groups: CT (basal diet), BCG1 (basal diet + 1.0 × 10⁸ CFU/kg B. licheniformis BCG), and BCG2 (basal diet + 1.0 × 10⁹ CFU/kg B. licheniformis BCG). On day 42, the jejunal and ileal chyme and mucosa were subjected to analysis of digestive enzyme activity, nutrient transporters, tight junctions, and signaling molecules associated with inflammation. The ileal and cecal chyme were subjected to microbiota analysis. Compared with the CT group, the B. licheniformis BCG group showed significantly greater jejunal and ileal α-amylase, maltase, and sucrase activity; moreover, the α-amylase activity in the BCG2 group was higher than that in the BCG1 group (P < 0.05). The transcript abundance of FABP-1 and FATP-1 in the BCG2 group was significantly greater than that in the CT and BCG1 groups, and the GLUT-2 and LAT-1 relative mRNA levels were greater in the BCG2 group than the CT group (P < 0.05). Dietary B. licheniformis BCG resulted in significantly higher ileal occludin, and lower IL-8 and TLR-4 mRNA levels than observed in the CT group (P < 0.05). B. licheniformis BCG supplementation significantly decreased bacterial community richness and diversity in the ileum (P < 0.05). Dietary B. licheniformis BCG shaped the ileac microbiota by increasing the prevalence of f_Sphingomonadaceae, Sphingomonas, and Limosilactobacillus, and contributed to nutrient digestion and absorption; moreover, it enhanced the intestinal barrier by increasing the prevalence of f_Lactobacillaceae, Lactobacillus, and Limosilactobacillus. Dietary B. licheniformis BCG decreased microbial community diversity by diminishing Desulfovibrio, Alistipes, Campylobacter, Vibrio, Streptococcus, and Escherichia coli-Shigella levels, and down-regulating inflammatory associated molecule expression. Therefore, dietary B. licheniformis BCG contributed to digestion and absorption of nutrients, enhanced the intestinal physical barrier, and decreased intestinal inflammation in broilers by decreasing microbial diversity and optimizing the microbiota structure.

Lactobacillus Plantarum injection at the embryonic stage alters the early growth performance and lipid metabolism of broilers by specific genera of bacteria

The main objective of this study was to explore the effects of broiler embryonic injection of Lactobacillus Plantarum on the growth performance, lipid metabolism of serum and liver, microbial diversity, and short-chain fatty acids of broiler intestines after hatching. On d 14 of incubation, 720 eggs of Arbor Acres were randomly divided into 4 experimental groups: no treatment control (C), Treatments injected with stroke-physiological saline solution (S), Supernatant of MRS medium culture of lactobacillus (Q) and Lactobacillus Plantarum spp. (J). The Hatch rate for each replicate was counted at 1 d of age. After hatching, each group were divided into six replicates of 10 broilers, and chicken from groups C, Q and J were reared until 14 d of age. The production performance of the three groups of chicks from 1 to 14 days was recorded and statistically analyzed separately. Serum and liver tissue were collected at 7 and 14 days of age for the detection of lipid metabolism index. 16S rDNA sequencing and Short-Chain Fatty Acids measurement of cecum contents were performed at 14 days of age. Overall, Lactobacillus injection significantly reduced feed conversion ratio (FCR) at 1-7 and 1-14 days of age, compared to the other 2 groups (P < 0.05). 16S rRNA sequencing results showed that the Roseburia and coprobacillus had a significantly positive correlation with body weight (P < 0.05). The Roseburia and lachnospira were significantly correlated with FCR (P < 0.05), and the absolute abundance of g_Anaerostipes as a biomarker in the J group was higher than in the C group (P < 0.05). The Q and J group increased the content of acetic, propionic, butyric, and total acid in the cecum contents (P < 0.05). In the jejunum, the J group increased the content of acetic, propionic, butyric, and total acids compared to the C and Q groups (P < 0.05). The J group increased the blood of total cholesterol (TC) content at 1 day of age and the triglyceride (TG) content of 7- and 14-day-old broilers (P < 0.05). and the J group raised the TG, TC, and high-density lipoprotein (HDL) level in the liver of 14-day-old broilers (P < 0.05). The J group reduced the liver's low-density lipoprotein (LDL) at 14 days of age (P < 0.05). In conclusion, the lactobacillus Plantarum injection at the embryonic stage alters lipid metabolism by short-chain fatty acids especially butyric produced by the specific bacteria of Roseburia and Anaerostipes.

Dynamic Changes in the Gut Microbiota and Metabolites during the Growth of Hainan Wenchang Chickens

Gut microbiota and their metabolites play important roles in animal growth by influencing the host's intake, storage, absorption, and utilization of nutrients. In addition to environmental factors, mainly diet, chicken breed and growth stage also affect changes in the gut microbiota. However, little research has been conducted on the development of gut microbiota and its metabolites in local chickens. In this study, the cecal microbiota and metabolites in different developmental stages of Hainan Wenchang chickens (a native breed of Bantam) were investigated using 16S rRNA sequencing and untargeted metabolomics. With aging, the structure of gut microbiota tended to be more stable. The relative proportions of dominant bacteria phyla Firmicutes, Bacteroidetes, and Proteobacteria showed stage changes with the development. With aging, gut microbiota and their metabolites may have structural and functional changes in response to nutrient metabolism and immune requirements in different physiological states. Several microbial and metabolic biomarkers with statistical differences were detected in different development stages. The bacteria that form networks with their significant related metabolites were different in various growth stages, including uncultured_bacterium_f_Ruminococcaceae, Ruminococcaceae_UCG-014, Faecalibacterium, uncultured_bacterium_o_Bacteroidales, and uncultured_bacterium_f_Lachnospiraceae. Partially differential bacteria were significantly correlated with short-chain fatty acids such as butyric acid. These findings may provide new insights into the physiological and molecular mechanisms of developmental changes of local chicken breeds, as well as resources for microbial and metabolic biomarker identification to improve growth efficiency.

Red osier dogwood and its use in animal nutrition: A review

As the human population increases globally, the food animal industry has not been spared from the monumental demand for edible animal products, particularly meat. This has necessitated the simultaneous expansion of the productivity of the animal sector to meet the ever-growing human needs. Although antibiotics have been used in food animal production with commendable positive impacts on their growth performance, their sole contributive factor to the increasing incidence of antimicrobial resistance has ushered the strict restrictions placed on their use in the animal sector. This has handed a setback to both animals and farmers; thus, the intense push for a more sustainable antibiotic alternative for use in animal production. The use of plants with concentrated phytogenic compounds has gained much interest due to their beneficial bioactivities, including antioxidant and selective antimicrobial. While the reported beneficial activities of phytogenic additives on animals vary due to their varying total polyphenol concentrations (TPC), red osier dogwood (ROD) plant materials boast of high TPC with excellent antioxidant prowess and growth improvement capacities compared to some plant extracts commonly used in research. However, its adoption in research and commercial scale is still low. Thus, the present review aims to provide concise information on the dietary potential of ROD plant materials in animal feeding.

Microbial composition of egg component and its association with hatchability of laying hens

The internal quality of eggs is critical for human consumption and embryonic development. However, microorganisms inside eggs have not been thoroughly investigated for their roles in determining the egg's internal quality. Here, a total of 21 hens were selected from more than 1,000 chickens based on their hatching results and were divided into high- and low-hatchability groups. Then, we collected 72 eggs from these 21 hens to obtain egg whites and yolks, including 54 fresh eggs and 18 eggs after 12 days of incubation. We characterized the microbial composition of egg yolks and whites, the microbial change along incubation, and differences in microbial abundance between the high- and low-hatchability groups. The results indicated that egg whites are not sterile. Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes were the dominant phyla in egg yolk and white. There was a large difference in the microbial composition between egg whites and yolks, and this difference increased after 12 days of incubation. Egg whites have lower microbial diversity than egg yolks owing to the presence of antibacterial substances such as lysozyme in the egg white. After a 12-day incubation, the microbial diversity decreased in egg whites but increased slightly in egg yolks. Meanwhile, the microbes in egg white can migrate to egg yolk during incubation. Additionally, Genus Muribaculaceae was identified as a biomarker in egg yolks incubated for 12 days and was more often detected in healthy groups. On the contrary, more genus Rothia were found in the fresh egg yolk of the low hatchability groups and was considered to have low virulence. These findings shed light on the composition and differences in microbiota between egg yolks and whites and may open new avenues for studying embryonic development in chickens.

Sodium humate alters the intestinal microbiome, short-chain fatty acids, eggshell ultrastructure, and egg performance of old laying hens

This study investigated the effect of sodium humate supplementation on changes in the intestinal microbiome, intestinal short-chain fatty acids production, and trace element absorption in older laying hens, with consequent effects on egg performance and shell quality. We used the same hens as their own control; a total of 720 laying hens aged 422 days were randomly divided into three replicates, with the CON group fed a commercial diet at 422–441 days of age and the HANa group fed a commercial diet supplemented with 0.05% sodium humate at 442–461 days of age. Compared with the CON group, in the HANa group, Bacteroidetes and Actinobacteria were significantly increased, whereas, Firmicutes was significantly decreased. Further, Veillonella, Enterococcus, Lactobacillus, and Turricibacter significantly decreased, and Peptoniphilus, Helcococcus, GW-34, Psychrobacter, Anaerococcus, Corynebacterium, Facklamia, Trichococcus, Gallicola, Clostridium, and Oscillospira were significantly increased. The results showed that sodium humate significantly altered the alpha and beta diversity and changed the structure of the intestinal microbiome. Acetic acid, isovaleric acid, and isobutyric acid, among short-chain fatty acids were significantly increased in the HANa group, whereas trace elements such as Mn, Zn, and Fe were significantly reduced. The eggshell strength and ultrastructure were significantly altered. In this study, sodium humate was found to alter the intestinal microbiome structure of aged hens, change the production of short-chain fatty acids, and promote the absorption of trace elements to keep aged hens from experiencing a decrease in egg production performance.

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.

Dynamic Changes in the Gut Microbial Community and Function during Broiler Growth

During the entire growth process, gut microbiota continues to change and has a certain impact on the performance of broilers. Here, we used 16S rRNA gene sequencing to explore the dynamic changes in the fecal bacterial communities and functions in 120 broilers from 4 to 16 weeks of age. We found that the main phyla (Firmicutes, Fusobacteria, Proteobacteria, and Bacteroides) accounted for more than 93.5% of the total bacteria in the feces. The alpha diversity of the fecal microbiota showed a downward trend with time, and the beta diversity showed significant differences at various time points. Then, the study on the differences of microbiota between high-weight (HW) and low-weight (LW) broilers showed that there were differences in the diversity and composition of microbiota between high- and low-weight broilers. Furthermore, we identified 22 genera that may be related to the weight change of broilers. The analysis of flora function reveals their changes in metabolism, genetic information processing, and environmental information processing. Finally, combined with microbial function and cecal transcriptome results, we speculated that microorganisms may affect the immune level and energy metabolism level of broilers through their own carbohydrate metabolism and lipid metabolism and then affect body weight (BW). Our results will help to expand our understanding of intestinal microbiota and provide guidance for the production of high-quality broilers.

IMPORTANCE The intestinal microbiota has a certain impact on the performance of broilers. However, the change of intestinal microbiota after 4 weeks of age is not clear, and the mechanism of the effect of microorganisms on the weight change of broilers needs more exploration. After 4 weeks of age, the alpha diversity of microorganisms in broiler feces decreased, and the dominant bacteria were Firmicutes, Fusobacteria, Proteobacteria, and Bacteroides. There were differences in microbiota diversity and composition between high- and low-weight broilers. Intestinal microorganisms may affect the immune level and energy metabolism level of broilers through their own carbohydrate metabolism and lipid metabolism and then affect the body weight. The results are helpful to increase the understanding of intestinal microbiota and provide reference for the production of high-quality broilers.

Dynamic description of temporal changes of gut microbiota in broilers

The diversity of bacteria and fungi in the gut microbiota of commercial broilers that raised in cages from hatch to the end of the production cycle were examined by an analysis of 3,592 and 3,899 amplicon sequence variants (ASVs), respectively. More than 90% sequences in bacterial communities were related to Firmicutes and Proteobacteria. More than 90% sequences in fungal communities were related to Ascomycota, Basidiomycota, and Glomeromycota. A statistical analysis of the microbiota composition succession showed that age was one of the main factors affecting the intestinal microbial communities of broilers. The increasingly complex community succession of transient microbiota occurred along with an increase of age. This dynamic change was observed to be similar between bacteria and fungi. The gut microbiota had a special structure in the first 3 d after birth of broiler. The microbiota structure was quite stable in the period of rapid skeletal growth (d 14–21), and then changed significantly in the period of rapid gaining weight (d 35–42), thus indicating the composition of gut microbiota in broilers had unique structures at different developmental stages. We observed that several bacteria and fungi occupied key functions in the gut microbiota of broilers, suggesting that the gut homeostasis of broilers might be affected by losses of bacteria and fungi via altering interactions between microbiota. This study aimed to provide a data basis for manipulating the microbiota at different developmental stages, in order to improve production and the intestinal health of broilers.

Intestinal Immune Development Is Accompanied by Temporal Deviation in Microbiota Composition of Newly Hatched Pigeon Squabs

Identifying the interaction between intestinal mucosal immune system development and commensal microbiota colonization in neonates is of paramount importance for understanding how early life events affect resistance to disease later in life. However, knowledge about this interaction during the early posthatch development period in altrices is limited. To fill this gap, samples of intestinal content and tissue were collected from newly hatched pigeon squabs at four time points (days 0, 7, 14, and 21) for microbial community analysis and genome-wide transcriptome profiling, respectively. We show that the first week after hatching seems to be the critical window for ileal microbiota colonization and that a potentially stable microbiota has not yet been well established at 21 days of age. Regional transcriptome differences revealed that the jejunum rather than the ileum plays a crucial role in immunity at both the innate and adaptive levels. In the ileum, temporal deviation in innate immune-related genes mainly occurs in the first week of life and is accompanied by a temporal change in microbiota composition, indicating that the ileal innate mucosal immune system development regulated by microbial colonization occurs mainly in this period. Furthermore, we provide evidence that colonization by Escherichia and Lactobacillus within the first week of life is likely one of the causative factors for the induction of proinflammatory cytokine expression in the ileum. We also demonstrate that cellular adaptive immune responses mediated by Th17 cells following commensal-induced proinflammatory cytokine production in the ileum begin as early as the first week posthatch, but this cellular immunity seems to be less effective in terms of maintaining the inflammatory response balance. Because the induction of high levels of mucosal secretory IgA (SIgA) seems to take approximately 3 weeks, we favor the idea that humoral adaptive immunity might be less active, at least, during the first 2 weeks of life. Our data may help to explain the phenomenon of the occurrence of intestinal infections mainly in the ileum of pigeon squabs during the early posthatch period. IMPORTANCE The pigeon (Columba livia), an altricial bird, is one of the most economically important farmed poultry for table purposes. Identifying the interaction between intestinal mucosal immune system development and commensal microbiota colonization in neonates is of paramount importance for understanding how early life events affect resistance to disease and potential productivity later in life. However, knowledge about this interaction during the early posthatch development period in altricial birds is limited. The study described herein is the first to try to provide insights into this interaction. Our data provide evidence on the mutual relationship between intestinal mucosal immune system development and commensal microbiota colonization in pigeon squabs and may help to explain the phenomenon of the occurrence of intestinal infections mainly in the ileum of pigeon squabs during the early posthatch period.

Intestinal microbiota of layer hens and its association with egg quality and safety

The intestinal microbiota has attracted tremendous attention in the field of the poultry industry due to its critical role in the modulation of nutrient utilization, immune system, and consequently the improvement of the host health and production performance. Accumulating evidence implies intestinal microbiota of laying hens is a potential mediator to improve the prevalent issues in terms of egg quality decline in the late phase of laying production. However, the regulatory effect of intestinal microbiota on egg quality in laying hens remains elusive, which requires consideration of microbial baseline composition and succession during their long lifespans. Notable, although Firmicutes, Bacteroidetes, and Proteobacteria form the vast majority of intestinal microbiota in layer hens, dynamic intestinal microbiota succession occurs throughout all laying periods. In addition to the direct effects on egg safety, intestinal microbiota and its metabolites such as short-chain fatty acids, bile acids, and tryptophan derivatives, are suggested to indirectly modulate egg quality through the microbiota-gut-liver/brain-reproductive tract axis. These findings can extend our understanding of the crosstalk between intestinal microbiota and the host to improve egg quality and safety. This paper reviews the compositions of intestinal microbiota in different physiological stages of laying hens and their effects on egg quality and proposes that intestinal microbiota may become a potential target for modulating egg quality and safety by nutritional strategies in the future.

Effects of in ovo feeding and dietary addition oils on growth performance and immune function of broiler chickens

This study aimed to investigate the effects of in ovo feeding (IOF) and dietary addition (DA) oils on growth, development and immune function of broiler chickens. In experiment 1, a total of 500 eggs were randomly assigned to 3 treatments: non-injected group (CON) with 100 eggs; soybean oil injected group (SO) with 200 eggs and linseed oil injected group (LO) with 200 eggs. Results showed that there were no detrimental effects of IOF of oils on embryonic development. In experiment 2, a two factor experimental design was adopted. After hatching, 120 chicks which came from each oil-injected group were divided into 2 treatments with 6 replicates, and chickens were fed soybean oil diet and linseed oil diet, respectively. The results showed that DA linseed oil increased final body weight (FBW) of broilers at d 21 post hatch, IOF of linseed oil decreased average daily feed intake (ADFI) and feed conversion ratio (FCR) of broilers from d 1 to 21 (P < 0.05), while the plasma leptin level of 21-day-old broilers was increased by IOF or DA linseed oil (P < 0.05). Main effect analysis showed that DA linseed oil increased the spleen index and mRNA expression of IFN-γ in spleen of broilers at 7 d of age (P < 0.05). IOF of linseed oil upregulated the mRNA expression of IFN-γ in the spleen of chicks at 1 d and mRNA expression of IL-2 and IL-4 in spleen of broilers at 21 d (P < 0.05), and the interaction effect showed that IOF and DA linseed oil synergically increased the expression of IL-2 and IL-4 in spleen of broilers at 21 d. Compared with SO group, LO increased the Shannon index of hatching-day cecum microflora (P < 0.05). Principal co-ordinates analysis (PcoA) showed that LO group clearly separated from CON and SO groups. Finally, Spearman correlation analysis also manifested that Alkalicoccus was significantly correlated with spleen index and mRNA expression of IL-2, and Phreatobacter was significantly correlated with the mRNA expression of IL-2 and IFN-γ in spleen, Acinetobacter had a positive correlation with thymus index (P < 0.05). In conclusion, IOF of linseed oil reduced the ADFI and FCR of broilers and increased the species diversity and changed the structure of cecal microflora of chicken embryos at the 19th day of incubation (E19). Immune function of broilers spleen was also regulated by IOF and DA linseed oil.

Non-Antibiotics Strategies to Control Salmonella Infection in Poultry

Salmonella spp. is a facultative intracellular pathogen causing localized or systemic infections, involving economic and public health significance, and remains the leading pathogen of food safety concern worldwide, with poultry being the primary transmission vector. Antibiotics have been the main strategy for Salmonella control for many years, which has allowed producers to improve the growth and health of food-producing animals. However, the utilization of antibiotics has been reconsidered since bacterial pathogens have established and shared a variety of antibiotic resistance mechanisms that can quickly increase within microbial communities. The use of alternatives to antibiotics has been recommended and successfully applied in many countries, leading to the core aim of this review, focused on (1) describing the importance of Salmonella infection in poultry and the effects associated with the use of antibiotics for disease control; (2) discussing the use of feeding-based (prebiotics, probiotics, bacterial subproducts, phytobiotics) and non-feeding-based (bacteriophages, in ovo injection, vaccines) strategies in poultry production for Salmonella control; and (3) exploring the use of complementary strategies, highlighting those based on -omics tools, to assess the effects of using the available antibiotic-free alternatives and their role in lowering dependency on the existing antimicrobial substances to manage bacterial infections in poultry effectively.

Developmental Change of Yolk Microbiota and Its Role on Early Colonization of Intestinal Microbiota in Chicken Embryo

Although the fertilized eggs were found to contain microbes in early studies, the detailed composition of yolk microbiota and its influence on embryo intestinal microbiota have not been satisfactorily examined yet. In this study, the yolk microbiota was explored by using 16s rRNA sequencing at different developmental stages of the broiler embryo. The results showed that the relative abundance of yolk microbiota was barely changed during embryogenesis. According to the KEGG analysis, the yolk microbiota were functionally related to amino acid, carbohydrate, and lipid metabolisms during chicken embryogenesis. The yolk microbiota influences the embryonic intestinal microbiota through increasing the colonization of Proteobacteria, Firmicutes, and Bacteroidetes in the intestine, particularly. The intestinal microbes of neonatal chicks showed higher proportions of Faecalibacterium, Blautia, Coprococcus, Dorea, and Roseburia compared to the embryonic intestinal microbiota. Our findings might give a better understanding of the composition and developmental change of yolk microbiota and its roles in shaping the intestinal microbiota.

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

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

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

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

Supplemental L-Arginine Improves the Embryonic Intestine Development and Microbial Succession in a Chick Embryo Model

Early colonization of intestinal microbiota plays an important role in intestinal development. However, the microbial succession at an embryonic stage and its assembly patterns induced by prenatal nutrition are unknown. In the present study, we used a chick embryo model to investigate the effects of in ovo feeding (IOF) of L-arginine (Arg) on the intestinal development and microbial succession of embryos. A total of 216 fertile eggs were randomly distributed into 2 groups including the non-injected control group and IOF of Arg group with 7 mg/egg. The results showed that IOF Arg increased the intestinal index, absolute weight of jejunum, and improved jejunal morphology in terms of villus width and surface area (p < 0.05). The relative mRNA expressions of mTOR and 4E-BP1 were up-regulated and accompanied by higher contents of Mucin-2 in the Arg group (p < 0.05). There was a significant elevation in contents of serum glucose and high-density lipoprotein cholesterol, whereas there was a decreased low-density lipoprotein cholesterol in the Arg group (p < 0.05). Additionally, Proteobacteria and Firmicutes were major intestinal bacteria species at the embryonic stage. However, Arg supplementation targeted to shape assembly patterns of microbial succession and then changed microbial composition (p = 0.05). Meanwhile, several short-chain fatty acids (SCFAs)-producing bacteria, such as Roseburia, Blautia, and Ruminococcus were identified as biomarkers in the Arg group (LDA > 3, p < 0.05). Accordingly, significant elevated concentrations of SCFAs, including lactic acid and formic acid, were observed in the Arg group (p < 0.05), accompanied by the higher concentration of butyric acid (0.05 < p < 0.10). In conclusion, prenatal Arg supplementation improved embryonic intestine development by regulating glucose and lipid homeostasis to supply more energy for chick embryos. The possible mechanism could be the roles of Arg in shaping the microbial assembly pattern and succession of the embryonic intestine, particularly the enrichment of potential probiotics. These findings may contribute to exploring nutritional strategies to establish health-promoting microbiota by manipulating prenatal host-microbe interactions for the healthy development of neonates.

Caecal microbiota could effectively increase chicken growth performance by regulating fat metabolism

It has been established that gut microbiota influences chicken growth performance and fat metabolism. However, whether gut microbiota affects chicken growth performance by regulating fat metabolism remains unclear. Therefore, seven‐week‐old chickens with high or low body weight were used in the present study. There were significant differences in body weight, breast and leg muscle indices, and cross‐sectional area of muscle cells, suggesting different growth performance. The relative abundance of gut microbiota in the caecal contents at the genus level was compared by 16S rRNA gene sequencing. The results of LEfSe indicated that high body weight chickens contained Microbacterium and Sphingomonas more abundantly (P < 0.05). In contrast, low body weight chickens contained Slackia more abundantly (P < 0.05). The results of H & E, qPCR, IHC, WB and blood analysis suggested significantly different fat metabolism level in serum, liver, abdominal adipose, breast and leg muscles between high and low body weight chickens. Spearman correlation analysis revealed that fat metabolism positively correlated with the relative abundance of Microbacterium and Sphingomonas while negatively correlated with the abundance of Slackia. Furthermore, faecal microbiota transplantation was performed, which verified that transferring faecal microbiota from adult chickens with high body weight into one‐day‐old chickens improved growth performance and fat metabolism in liver by remodelling the gut microbiota. Overall, these results suggested that gut microbiota could affect chicken growth performance by regulating fat metabolism.

Effect of chitosan coating incorporated with oregano or cinnamon essential oil on the bacterial diversity and shelf life of roast duck in modified atmosphere packaging

The present study aimed to investigate the effect of chitosan edible coating containing 0.15% oregano essential oil (OEO) or 0.60% cinnamon essential oil (CEO) on the quality characteristics and dynamic changes in the bacterial community of roast duck slices under modified atmosphere packaging (MAP, 30% CO₂/70% N₂) during 21 days of storage at 2 ± 2 °C. The results showed that the application of chitosan coating (CH) alone inhibited the growth of microorganisms and prevented lipid oxidation throughout storage. Moreover, the storage stability was further improved by including OEO or CEO, which lowered (P < 0.05) values for total viable count (TVC), Enterobacteriaceae, 2-thiobarbituric acid reactive substance (TBARS) and total volatile basic nitrogen (TVB-N). Based on the microbiological results, the shelf-life of CH-OEO and CH-CEO treated roast duck slices was prolonged by at least 7 days compared to that of the control. In addition, packaging types applied in this study played a major role in the bacterial community development. Notably, Vibrio spp. were the most predominant bacteria in all samples, when TVC values approached the shelf-life threshold, suggesting that this bacterium may be the main contributor to the spoilage of roast duck. The growth inhibition of Vibrio spp. in the CH-OEO and CH-CEO treatments during the early period of chilled storage might be the reason for the extension of the shelf life. Taken together, CH incorporated with OEO or CEO could be developed as prospective edible packaging materials to preserve roast duck meat.