Microbiome Applications for Laying Hen Performance and Egg Production

Deep culturing the fecal microbiota of healthy laying hens

BACKGROUND

The microbiota is implicated in several aspects of livestock health and disease. Understanding the structure and function of the poultry microbiota would be a valuable tool for improving their health and productivity since the microbiota can likely be optimized for metrics that are important to the industry such as improved feed conversion ratio, lower greenhouse gas emissions, and higher levels of competitive exclusion against pathogens. Most research into understanding the poultry microbiota has relied on culture-independent methods; however, the pure culture of bacteria is essential to elucidating the roles of individual bacteria in the microbiota and developing novel probiotic products for poultry production.

RESULTS

In this study, we have used a deep culturing approach consisting of 76 culture conditions to generate a culture collection of 1,240 bacterial isolates from healthy chickens. We then compared the taxonomy of cultured isolates to the taxonomic results of metagenomic sequencing to estimate what proportion of the microbiota was cultured. Metagenomic sequencing detected DNA from 545 bacterial species while deep culturing was able to produce isolates for 128 bacterial species. Some bacterial families, such as Comamonadaceae and Neisseriaceae were only detected via culturing - indicating that metagenomic analysis may not provide a complete taxonomic census of the microbiota. To further examine sub-species diversity in the poultry bacteriome, we whole genome sequenced 114 Escherichia coli isolates from 6 fecal samples and observed a great deal of diversity.

CONCLUSIONS

Deep culturing and metagenomic sequencing approaches to examine the diversity of the microbiota within an individual will yield different results. In this project we generated a culture collection of enteric bacteria from healthy laying hens that can be used to further understand the role of specific commensals within the broader microbiota context and have made this collection available to the community. Isolates from this collection can be requested by contacting the corresponding author and will be provided at cost.

LAYING RATE WAS CORRELATED WITH MICROBIAL Fecal microbiota transplantation improves the laying performance by changing the gut microbiota composition in late laying period

This research investigated the differences and succession patterns of microbes in different ages, the performance of laying hens, and the effect of Fecal Microbiota Transplantation (FMT) on aged laying hens. First, based on the different laying rates and age, we divided the laying hens into four groups: 75-week-old high-yield (OH, laying rate (LR) > 90%), 75-week-old low-yield (OL, LR < 60%), 75-week-old non-laying hens (OZ, LR = 0%) and 35-week-old high-yield (YH, LR > 90%) with 5 replicates in each group and 6 chickens in each replicate. The microbial metabolic patterns between different ages and laying rates were determined using 16S rDNA technology. Then, to verify the results of microbiome research, we utilized FMT technology to transplant the gut microbiota from OH to OZ (OZFMT-OH), thereby revealing the connection between gut microbes and production performance. The results showed that high-yielding hens (YH and OH groups) had higher levels of Superoxide dismutase (SOD) and Immunoglobulin A (IgA) compared to OL and OZ groups. The Villus height to Crypt depth ratio(V/C) was significantly higher in the YH group than in 75-week-old hens (P < 0.05). Alpha diversity indicated higher microbial diversity in the YH group compared to older hens (P < 0.05), with YH hens harboring more Megamonas, OH hens more Bacteroides, and OL and OZ groups showing higher levels of harmful bacteria. The villus height, V/C, mucosal layer thickness, cup cell number acetic acid level, and LR in the OZFMT-OH group were significantly higher than those in the OZ group (P < 0.05), while the IL-2 level, crypt depth and cecal intestinal wall thickness were significantly lower than those in OZ group (P < 0.05). FMT also changed the morphological structure of grade follicles and small yellow follicles, improved the microbe composition of cecum and increased Bacteroides abundance. In the late laying period, if the intestinal flora cannot maintain the dynamic balance and carry out timely replacement, the production performance may be decreased, and the increase of Bacteroides abundance in the intestinal tract can improve the intestinal health and production performance of laying hens in the late laying period.

Impact of gut microbial diversity on egg production performance in chickens

Chickens are one of the most economically important poultry species, and their egg-laying performance is a crucial economic trait. The intestinal microbiome plays a significant role in the egg-laying performance. To clarify the diversity of chicken intestinal microbiota and its connection to egg-laying performance, this study utilized 16S rRNA sequencing technology to characterize the intestinal microbiomes of 101 chickens from 13 breeds with varying levels of egg production. The results reveal significant differences in gut microbiota structure among chicken groups with varying egg production levels. High egg-producing chickens showed significantly higher abundances of Firmicutes, Proteobacteria, and Lactobacillus, while low egg-producing chickens displayed greater microbial α-diversity and more complex community structures. These differences in gut microbiota influence key physiological functions, including nutrient absorption and hormone regulation through metabolic pathways, and directly affect egg production performance. The low and medium production groups partially overlapped on the principal coordinates analysis plot, whereas the high-production group was distinctly separate. This study provides a scientific basis and intestinal microbiome data for selecting probiotics related to high egg production in chickens.

IMPORTANCE

This study elucidates the critical role of gut microbiota in the egg-laying performance of chickens, a key economic indicator in the poultry industry. By employing 16S rRNA sequencing, we uncovered distinct microbial profiles associated with varying levels of egg production. High egg-producing chickens exhibit a higher abundance of specific bacterial taxa, such as Firmicutes and Proteobacteria, which are linked to enhanced nutrient absorption and metabolic efficiency. Conversely, lower and medium egg-producing chickens display greater microbial diversity, suggesting a more complex but less efficient gut ecosystem. Our findings provide valuable insights into the relationship between gut microbiota and egg production, offering a scientific foundation for the selection of probiotics that could potentially improve the egg-laying performance of chickens. This research not only advances our understanding of avian gut microbiology but also has practical implications for optimizing poultry farming practices and enhancing economic outcomes.

Manure odor profiling for flock-level monitoring on commercial layer pullet farms: Vaccination events as a model stressor

Continuous, non-invasive, and objective methods to detect flock-level responses to stressors, including intestinal health deviations, are currently lacking in poultry. This proof of principle study investigated the potential of manure odor profiling in monitoring stress responses in Lohmann Brown Classic, Lohmann LSL Classic and Lohmann LSL Lite layer pullets. Stressors were represented by a Salmonella vaccination given to the pullets at wk 3 of age (Dataset 1 and Dataset 2) and wk 16 of age (Dataset 4) and a viral/bacterial vaccine cocktail given at wk 12 of age (Dataset 3). Fresh manure was sampled daily, from 2 days before vaccination to 4 days after vaccination, with 4 pooled manure samples per day per dataset. Manure volatiles were concentrated into stainless steel sorbent tubes and analyzed by a thermal desorption system coupled with gas chromatography-mass spectrometry. Dataset, breed and sample location did not affect the manure volatile profiles before vaccination. Age did affect the manure volatile profiles, with beta-camphor, (Z)-6-Tridecene and serinol peak intensities elevated in young pullets and carbonyl sulfide and trimethylamine elevated in older pullets. Salmonella vaccination at wk 3 of age led to the most consistent changes in volatile peak intensities. (Z)-6-Tridecene was decreased in Dataset 1, Dataset 3, and Dataset 4 after either the Salmonella vaccination or the viral/bacterial vaccine cocktail, despite differences in hen age and house. The injected viral/bacterial vaccine cocktail created a more clear time-dependent shift in the manure volatile profile than the orally-provided Salmonella vaccination in older pullets at resp. wk 12 and 16 of age. No overlapping trends in upregulated or downregulated volatiles were found between all datasets. To conclude, volatile profiles of rearing hen manure are affected by vaccinations as a proxy for stressors, and the magnitude and direction of the response depends on the age of the pullets at vaccination, the vaccination method, and the pathogenic properties of the vaccine. The reduced peak intensities of volatiles after vaccination in 3 out of 4 flocks suggests the potential of manure odor profiling in monitoring stress responses in layer pullets.

Variations in gut microbiota composition and reproductive hormone levels between laying and broody Muscovy ducks

High broodiness in Muscovy ducks impedes animal husbandry growth. The interaction between endocrine hormones and gut microbiota has been proven to play a crucial role in reproductive performance, and whether it can regulate the broody behavior of Muscovy ducks requires further research. Nine laying ducks (Laying group) and nine broody ducks (Broodiness group) were selected. Corresponding serum, ileum, and cecum chyme were collected for further research. The results showed that, compared to the laying group, the serum concentration of prolactin decreased, while the levels of Mullerian inhibiting substance, follicle-stimulating hormone, and follistatin increased in the broodiness group (P < 0.05). 16S rDNA sequencing showed that, the broodiness group exhibited lower abundance levels of Rothia, Streptococcus, and Lactobacillus, whereas the abundance of Turicibacter, Aliicoccus, and Facklamia was higher in the ileum compared to the laying group (P < 0.05). In the cecum, the broodiness group exhibits a significant reduction in the abundance of Butyricicoccus and unclassified_f_Rikenellaceae, while the abundance of Christensenellaceae_R-7_group, Ruminococcus_torques_group, Parabacteroides, norank_f_Oscillospiraceae, Cloacibacillus, Sellimonas, Shuttleworthia, norank_f_UCG-010, unclassified_f_Lachnospiraceae, Oscillospira, Synergistes, Family_XIII_AD3011_group and Eubacterium_nodatum_group is higher compared to the laying group. A Spearman correlation analysis reveals that both in the ileum and cecum, serum hormones exhibit significant correlations with the top 20 abundant intestinal microbial genera. Among these, serum follistatin has most entries of significant correlations with the detected microbial genera (P < 0.05). In conclusion, the broody behavior of Muscovy ducks can be modulated by the interaction between hormones and gut microbiota. Notably, the relationship between Follistatin and the composition of gut microbiota, specifically Firmicutes, is the most prominent.

Precision glycan supplementation: A strategy to improve performance and intestinal health of laying hens in high-stress commercial environments

In the dynamic world of animal production, many challenges arise in disease control, animal welfare and the need to meet antibiotic-free demands. Emerging diseases have a significant impact on the poultry industry. Managing gut microbiota is an important determinant of poultry health and performance. Introducing precision glycans as feed additives adds another dimension to this complex environment. The glycans play pivotal roles in supporting gut health and immunological processes and are likely to limit antibiotic usage while enhancing intestinal well-being and overall poultry performance. This study explores precision glycan product as a feed additive supplemented at a continuous dose of 900 g per tonne of feed, in a free-range production system on a large commercial farm. Forty thousand 17-week-old pullets were randomly allocated to one of two separated sections of the production shed, with individual silos and egg-collecting belts. The flock performance, gut microbiota and its functionality were analysed throughout the laying cycle until 72 weeks of age. The results demonstrated that introducing precision glycans improved a range of performance indicators, including reduced cumulative mortality, especially during a major smothering event, where the birds pile up until they suffocate. There was also significantly increased hen-housed egg production, reduced gut dysbiosis score and undigested feed, increased number of goblet cells and improved feed conversion ratio. Additionally, microbiota analysis revealed significant changes in the composition of the gizzard, ileum content, ileum mucosa, and caecal and cloacal regions. Overall, the findings suggest that precision glycans have the potential to enhance poultry egg production in challenging farming environments.

Fermented Aronia melanocarpa pomace improves the nutritive value of eggs, enhances ovarian function, and reshapes microbiota abundance in aged laying hens

Introduction

There is a decline in the quality and nutritive value of eggs in aged laying hens. Fruit pomaces with high nutritional and functional values have gained interest in poultry production to improve the performance.

Methods

The performance, egg nutritive value, lipid metabolism, ovarian health, and cecal microbiota abundance were evaluated in aged laying hens (320 laying hens, 345-day-old) fed on a basal diet (control), and a basal diet inclusion of 0.25%, 0.5%, or 1.0% fermented Aronia melanocarpa pomace (FAMP) for eight weeks.

Results

The results show that 0.5% FAMP reduced the saturated fatty acids (such as C16:0) and improved the healthy lipid indices in egg yolks by decreasing the atherogenicity index, thrombogenic index, and hypocholesterolemia/hypercholesterolemia ratio and increasing health promotion index and desirable fatty acids (P < 0.05). Additionally, FAMP supplementation (0.25%-1.0%) increased (P < 0.05) the ovarian follicle-stimulating hormone, luteinizing hormone, and estrogen 2 levels, while 1.0% FAMP upregulated the HSD3B1 expression. The expression of VTG II and ApoVLDL II in the 0.25% and 0.5% FAMP groups, APOB in the 0.5% FAMP group, and ESR2 in the 1% FAMP group were upregulated (P < 0.05) in the liver. The ovarian total antioxidant capacity was increased (P < 0.05) by supplementation with 0.25%-1.0% FAMP. Dietary 0.5% and 1.0% FAMP downregulated (P < 0.05) the Keap1 expression, while 1.0% FAMP upregulated (P < 0.05) the Nrf2 expression in the ovary. Furthermore, 1.0% FAMP increased cecal acetate, butyrate, and valerate concentrations and Firmicutes while decreasing Proteobacteria (P < 0.05).

Conclusion

Overall, FAMP improved the nutritive value of eggs in aged laying hens by improving the liver-blood-ovary function and cecal microbial and metabolite composition, which might help to enhance economic benefits.

Integrated omics analysis reveals a correlation between gut microbiota and egg production in captive African penguins (Spheniscus demersus)

The egg production of captive African penguins differs considerably between individuals. An understanding of the physiological differences in African penguins with relatively greater and lesser egg production is meaningful for the captive breeding program of this endangered species. The objective of this study was to investigate differential microbial composition and metabolites in captive African penguins with different egg production. Fecal samples were collected from captive female African penguins during the breeding season. The results of 16 S rRNA gene sequencing showed that African penguins with different egg production had similar microbial diversities, whereas a significant difference was observed between their microbial community structure. African penguins with relatively greater egg production exhibited a higher relative abundance of Alphaproteobacteria, Rhizobiales, Bradyrhizobiaceae, Bradyrhizobium and Bosea. Meanwhile, penguins with relatively lesser egg production had an increased proportion of Klebsiella and Plesiomonas. We further identified a total of 1858 metabolites in female African penguins by liquid chromatography-mass spectrometry analysis. Among these metabolites, 13 kinds of metabolites were found to be significantly differential between African penguins with different egg production. In addition, the correlation analysis revealed that the egg production had significant correlations with most of the differential microbial bacteria and metabolites. Our findings might aid in understanding the potential mechanism underlying the phenomenon of abnormal egg production in captive African penguins, and provide novel insights into the relationship between gut microbiota and reproduction in penguins.

The buzz within: the role of the gut microbiome in honeybee social behavior

Gut symbionts influence the physiology and behavior of their host, but the extent to which these effects scale to social behaviors is an emerging area of research. The use of the western honeybee (Apis mellifera) as a model enables researchers to investigate the gut microbiome and behavior at several levels of social organization. Insight into gut microbial effects at the societal level is critical for our understanding of how involved microbial symbionts are in host biology. In this Commentary, we discuss recent findings in honeybee gut microbiome research and synthesize these with knowledge of the physiology and behavior of other model organisms to hypothesize how host-microbe interactions at the individual level could shape societal dynamics and evolution.

Salmonella in eggs and egg-laying chickens: pathways to effective control

Eggs contaminated with Salmonella have been internationally significant sources of human illness for several decades. Most egg-associated illness has been attributed to Salmonella serovar Enteritidis, but a few other serovars (notably S. Heidelberg and S. Typhimurium) are also sometimes implicated. The edible interior contents of eggs typically become contaminated with S. Enteritidis because the pathogen's unique virulence attributes enable it to colonize reproductive tissues in systemically infected laying hens. Other serovars are more commonly associated with surface contamination of eggshells. Both research and field experience have demonstrated that the most effective overall Salmonella control strategy in commercial laying flocks is the application of multiple interventions throughout the egg production cycle. At the preharvest (egg production) level, intervention options of demonstrated efficacy include vaccination and gastrointestinal colonization control via treatments such as prebiotics, probiotics, and bacteriophages, Effective environmental management of housing systems used for commercial laying flocks is also essential for minimizing opportunities for the introduction, transmission, and persistence of Salmonella in laying flocks. At the postharvest (egg processing and handling) level, careful regulation of egg storage temperatures is critical for limiting Salmonella multiplication inside the interior contents.

Improvement in ovarian function following fecal microbiota transplantation from high-laying rate breeders

The underlying mechanism between the gut microbiota and reproductive function is not yet well-known. This study was conducted to investigate the effect of the administration of fecal microbiota transplantation (FMT) from highly laying rate donors on the cecal microbiota, intestinal health and ovarian function in broiler breeders. A total of 60 broiler breeders (53 wk of age) were selected by their laying rate [high (HP, 90.67 ± 0.69%; n = 10) and low (LP, 70.23 ± 0.87%; n = 20)]. The LP breeders were then be transplanted with fecal microbiota from HP hens (FMTHP; n = 10) or the same dosage of PBS (FMTCON; n = 10) for 28 d. The results revealed that FMT from HP donors increased egg-laying rate and serum hormone levels [17β-estradiol (E2), anti-Müller hormone], also decreased proinflammatory cytokine levels (interleukin-6, interleukin-8, tumor necrosis factor-α) of LP breeders (P < 0.05). The FMTHP group breeders had higher villus height, villus height/crypt depth ratio, and upregulated mRNA expression of jejunum barrier-related gene (ZO-2 and mucin-2) and estrogen, follicle-stimulating hormone (FSH) and anti-Müller hormone (AMH) receptor genes (ESR1, ESR2, FSHR, AMHR) (P < 0.05) than FMTCON group. FMT from HP donors led to higher mRNA expression of Bcl2 and sirtuin1 (SIRT1), while it downregulated the proapoptotic genes (Bax, caspase-3, caspase-8, and caspase-9) mRNA expressions in ovary compared with the FMTCON breeders (P < 0.05), and this pattern was also observed in HP donors. Also, HP breeder had higher observed_species and alpha-diversity indexes (Chao1 and ACE) than FMTCON group, while FMTHP can increase observed_species and alpha-diversity indexes (Chao1 and ACE) than FMTCON group (P < 0.05). The bacteria enrichment of Firmicutes (phylum), Bacteroidetes (phylum), Lactobacillus (genus), Enterococcus (genus), and Bacteroides (genus) were increased by FMTHP treatment. The genera Butyricicoccus, Enterococcus, and Lactobacillus were positively correlated with egg-laying rate. Therefore, cecal microbiomes of breeders with high egg-laying performance have more diverse activities, which may be related to the metabolism and health of the host; and FMT from high-yield donors can increase the hormone secretion, intestinal health, and ovarian function to improve egg-laying performance and the SIRT1-related apoptosis and cytokine signaling pathway were involved in this process.

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.