Amplicon-based metagenomic association analysis of gut microbiota in relation to egg-laying period and breeds of hens

Characterization of airborne bacterial diversity in conventional hen houses, enriched colonies and aviaries, and link between possible bioaerosol sources

BACKGROUND

Canada's transition toward alternative housing systems for laying hens may have an impact on bioaerosol content and concentrations in those environments. This project aimed to characterize the airborne bacterial diversity in six conventional hen houses, six enriched colonies and six aviaries. The bacterial diversity found in bioaerosols was also compared to the diversity found in feces or litter samples from each corresponding housing type to investigate similarities between possible bioaerosol sources and bioaerosols.

RESULTS

Specific richness (Sobs) and CHAO1 indexes were higher in air samples from conventional hen houses and enriched colonies, compared to their corresponding fecal or litter samples, which was not the case for aviaries samples. No significant differences were found between the Shannon and inverse Simpson (InvSimpson) indexes of air samples, compared to their corresponding fecal or litter samples. Firmicutes were the dominant phyla in all samples, followed by Actinobacteria. Dominant genera were Lactobacillus, unclassified Lanchnospiraceae, unclassified Actinomycetales, unclassified Clostridales and unclassified Ruminococcaceae. OTUs (Operational Taxonomic Units) were associated with hen microbiota and gut microbiota, and soil. Homogeneity of molecular variance analyses (HOMOVA) revealed significant differences between air samples from aviaries, compared to air samples from conventional and enriched cage houses. Significant differences were found between air and fecal or litter samples from conventional hen houses and enriched colonies, but not among aviary samples.

CONCLUSIONS

Findings highlight the effects of housing types on airborne bacterial diversity, and similarities in bacterial diversity between air and fecal or litter samples from three types of husbandry. Most dominant OTUs were shared across all samples, but were different in proportions, which may account for the differences in alpha and beta diversities. The overlap in bacterial diversities between air and litter samples collected in aviaries brings out the contribution of litter to ambient bioaerosols.

Characteristics of fecal mycobiota and bacteriota in laying hens during different laying periods

Mycobiota represents an important component of the gut microbiome in poultry and plays important roles in host nutrition and metabolism. However, the understanding of gut mycobiota in laying hens during the production cycle is limited. The present study aimed to characterize the structure and diversity of fecal mycobiota and bacteriota and examine the interplays between both microbial communities in laying hens during different laying periods. Sequencing of the internal transcribed spacer 1 (ITS1) and 16S rRNA gene amplicon was performed on 50 fecal samples of laying hens at 5 different time points during the laying cycle. The analysis yielded 1314 and 3840 amplicon sequence variants (ASVs), respectively. The results showed that Ascomycota and Basidiomycota were the most predominant. The statistical analysis of fecal flora composition succession in laying hens showed that different laying periods were one of the main factors affecting the fecal flora of laying hens. Mycobiota displayed greater variability across different laying periods compared to the bacterial community, in terms of taxonomic structure and community diversity. Co-occurrence analysis revealed varying degrees of interaction between the mycobiota and bacteriota during different laying periods. The present study aimed to improve the understanding of the fecal mycobiota and bacterial community of laying hens across different laying periods and has provided basic data support for further research into the complex fecal microbiota of laying hens.

Lactiplantibacillus plantarum ameliorated the negative effects of a low-protein diet on growth performance, antioxidant capacity, immune status, and gut microbiota of laying chicks

This experiment was conducted to investigate the effects of adding Lactiplantibacillus plantarum to a low-protein diet on the growth performance, ability immune status, and intestinal microbiota of 0-21-day-old layer chickens. A total of 180 one-day-old healthy Hy-line brown laying chicks were randomly divided into three groups with three replicates each of 20 chicks. The control group was fed a basal diet containing 19% protein, the low-protein (LP) group was fed a diet containing 17% protein, and the probiotic (LPL) group was fed with the 17% protein diet supplemented with L. plantarum (1.0 × 109 CFU/kg). The growth performance, antioxidant capacity, immune status, and gut microbiota of laying chickens were detected. We found that L. plantarum supplementation increased the activities of superoxide dismutase (SOD) and glutathione peroxidase (GSH-Px), total antioxidant capacity (T-AOC), and levels of immunoglobulin (Ig) A, IgG, and interleukin-10 (IL-10) in serum of 17% protein +1.0 × 109 CFU/kg L. plantarum (LPL) compared to the 19% protein group (control). Furthermore, L. plantarum supplementation increased the liver index, GSH-Px and T-AOC activity in serum, and changed the microflora structure, diversity, and polyketose unit bioanabolic metabolism of 17% protein +1.0 × 109 CFU/kg L. plantarum (LPL) compared to the 17% protein group (LP). In conclusion, L. plantarum supplementation could compensate for the adverse effects of low-protein diets in chicks, and the combination of a low-protein diet and L. plantarum is a feasible way to reduce protein in the diet.

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.

Effects of dietary rosemary ultrafine powder supplementation on aged hen health and productivity: a randomized controlled trial

Recently, poultry industry has been seeking antibiotic residue-free poultry products and safe nutritious feed additives. Whether rosemary ultrafine powder (RUP) affects productive performance by regulating the intestinal microbiome of aged layers remains unclear. Here, we investigated the effects of dietary RUP supplementation on the production performance, egg quality, antioxidant capacity, intestinal microbial structure, and metabolome of aged hens. The results indicate that RUP had no significant effect on production performance but significantly enhanced Thick albumen height, Haugh unit, yolk color (P < 0.05), daily feed intake, and qualified egg rate. Serum content of non-esterified fatty acids, catalase, and glutathione peroxidase increased significantly (P < 0.05). Furthermore, the liver total protein content was significantly increased (P < 0.05). 16S rRNA sequence analysis revealed that RUP significantly impacted both α- and β-diversity of the caecum microbiota. Linear discriminant analysis of effect size and random forest identified Bacteroides, Muribaculum, Butyricimonas, Odoribacter, and Prevotella as biomarkers in groups A and B. In comparing groups A and C, Barnesiella, Turicibacter, and Acholeplasma were critical bacteria, while comparing groups A and D highlighted Barnesiella and Candidatus Saccharimonas as differential bacteria. FAPROTAX analysis of the caecum microbiota revealed that the functional genes associated with harmful substance biodegradation were significantly increased in the RUP-fed group. Based on Spearman correlation analysis, alterations in microbial genera were associated with divergent metabolites. In summary, dietary RUP can improve egg quality and antioxidant capacity and regulate the intestinal microbiome and metabolome in aged breeders. Therefore, RUP can potentially be used as a feed additive to extend breeder service life at an appropriate level of 1.0 g/kg.

Longitudinal survey of total airborne bacterial and archaeal concentrations and bacterial diversity in enriched colony housing and aviaries for laying hens

Conventional cages for laying hens will be banned in Canada as of 2036, and the egg industry is transitioning toward enriched colony housing and aviaries. While higher concentrations of particulate matter have been previously reported in aviaries and other cage-free housing systems, concentrations of total bacteria and archaea suspended in the air are still uncharacterized in Canadian enriched colonies and aviaries. The aim of the present study was to conduct a longitudinal survey of airborne total bacteria and of airborne total archaea in twelve enriched colonies and twelve aviaries in Eastern Canada during a whole laying period. High-throughput sequencing of 16S rRNA gene amplicons was used to reveal and compare bacterial diversity at the start and the end of the production cycle, and during the cold and the warm seasons. Total bacterial and archaeal concentrations were significantly higher in aviaries (p < 0.05) versus enriched colonies, and in the cold season for both housing types (p < 0.05). While flock age did not have a significant effect on total bacterial and archaeal concentrations, it did on bacterial diversity in both enriched colony houses and aviaries (p < 0.05). The 2 housing systems were significantly different in their diversity of bacteria.

Modulation of Poultry Cecal Microbiota by a Phytogenic Blend and High Concentrations of Casein in a Validated In Vitro Cecal Chicken Alimentary Tract Model

Phytogenic blends (PBs) consist of various bioactive plant-derived compounds that are used as growth promoters for farm animals. Feed additives based on PBs have beneficial effects on farm animals' production performance, health, and overall well-being, as well as positive modulating effects on gut microbiota. In this study, we used a validated in vitro cecal chicken alimentary tract model (CALIMERO-2) to evaluate the effects of a PB (a mix of components found in rosemary, cinnamon, curcuma, oregano oil, and red pepper), alone or in combination with casein (control), on poultry cecal microbiota. Supplementation with the PB significantly increased the abundance of bacteria associated with energy metabolism (Monoglobus) and growth performance in poultry (Lachnospiraceae UCG-010). The PB also decreased the abundance of opportunistic pathogens (Escherichia-Shigella) and, most importantly, did not promote other opportunistic pathogens, which indicates the safety of this blend for poultry. In conclusion, the results of this study show promising perspectives on using PBs as feed additives for poultry, although further in vivo studies need to prove these data.

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

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