Microbiota of Chickens and Their Environment in Commercial Production

Lack of consistency in poultry dust microbial taxa associated with high and low-performing commercial broiler flocks

The microbial communities of the gastrointestinal tract play an essential role in poultry health and productivity. Poultry dust has been used to investigate bacterial taxa associated with performance in commercial broiler farms. This study investigated the commonalities of poultry dust microbial taxa associated with performance in samples collected from three broiler integrator companies and their stability in a successive flock of the same companies using deep sequencing of the 16S rRNA gene. Poultry dust samples (n = 248) were collected on days 14 and 35 of the production cycle from 38 commercial broiler flocks (2 flocks from each of 19 farms). The farms were ranked as low or high performers based on the feed conversion ratio corrected for body weight. Permutational analysis of variance based on Bray-Curtis index using abundance data for bacterial community structure results showed that company explained the most variation in the bacterial community structure (7.5 %), followed by bird age (2 %) and the least variation was explained by performance (1.9 %), with significant interactions among these factors (P < 0.001). No bacterial taxa in high or low-performing farms overlapped in all three companies or successive flocks from the same company. Some taxa associated with high performance in a company were associated with low performance in another company (e.g., Bifidobacterium), corroborating other studies highlighting the lack of universal microbial markers of productivity. In conclusion, there were no consistent microbial taxa across companies and flocks within a company under the conditions of this study.

Single-cell transcriptomic atlas of the chicken cecum reveals cellular responses and state shifts during Eimeria tenella infection

Eimeria tenella (E. tenella) infection is a major cause of coccidiosis in chickens, leading to significant economic losses in the poultry industry due to its impact on the cecum. This study presents a comprehensive single-cell atlas of the chicken cecal epithelium by generating 7,394 cells using 10X Genomics single-cell RNA sequencing (scRNA-seq). We identified 13 distinct cell types, including key immune and epithelial populations, and characterized their gene expression profiles and cell-cell communication networks. Integration of this single-cell data with bulk RNA-seq data from E. tenella-infected chickens revealed significant alterations in cell type composition and state, particularly a marked decrease in APOB+ enterocytes and an increase in cycling T cells during infection. Trajectory analysis of APOB+ enterocytes uncovered shifts toward cellular states associated with cell death and a reduction in those linked to mitochondrial and cytoplasmic protection when infected with E. tenella. These findings highlight the substantial impact of E. tenella on epithelial integrity and immune responses, emphasizing the parasite's role in disrupting nutrient absorption and energy metabolism. Our single-cell atlas serves as a critical resource for understanding the cellular architecture of the chicken cecum and provides a valuable framework for future investigations into cecal diseases and metabolic functions, with potential applications in enhancing poultry health and productivity.

Decoding the chicken gastrointestinal microbiome

Metataxonomic studies have underpinned a vast understanding of microbial communities residing within livestock gastrointestinal tracts, albeit studies have often not been combined to provide a global census. Consequently, in this study we characterised the overall and common 'core' chicken microbiota associated with the gastrointestinal tract (GIT), whilst assessing the effects of GIT site, bird breed, age and geographical location on the GIT resident microbes using metataxonomic data compiled from studies completed across the world. Specifically, bacterial 16S ribosomal DNA sequences from GIT samples associated with various breeds, differing in age, GIT sites (caecum, faeces, ileum and jejunum) and geographical location were obtained from the Sequence Read Archive and analysed using the MGnify pipeline. Metataxonomic profiles produced across the 602 datasets illustrated the presence of 3 phyla, 25 families and 30 genera, of which core genera (defined by presence in over 90% of datasets) belonged to Lactobacillus, Faecalibacterium, Butyricicoccus, Eisenbergiella, Subdoligranulum, Oscillibacter, Clostridium & Blautia. PERMANOVA analysis also showed that GIT site, bird breed, age and geographical location all had a significant effect on GIT microbial diversity, regardless of dietary factors, which were not considered in this study. On a genus level, Faecalibacterium was most abundant in the caeca, Lactobacillus was most abundant in the faeces, ileum and jejunum, with the data showing that the caeca and faeces were most diverse. AIL F8 progeny, Ross 308 and Cobb 500 breeds GIT bacteria were dominated by Lactobacillus, and Eisenbergiella, Megamonas and Bacteroides were most abundant amongst Sasso-T451A and Tibetan chicken breeds. Microbial communities within each GIT site develop with age, from a Lactobacillus and Streptococcus dominated community during the earlier stages of growth, towards a Faecalibacterium, Eisenbergiella, Bacteroides, Megamonas, and Lactobacillus dominated community during the later stages of life. Geographical locations, and thus environmental effectors, also impacted upon gastrointestinal tract microbiota, with Canadian and European datasets being dominated by Lactobacillus, whilst UK and Chinese datasets were dominated by Eisenbergiella and Bacteroides respectively. This study aids in defining what 'normal' is within poultry gastrointestinal tract microbiota globally, which is imperative to enhancing the microbiome for productive and environmental improvements.

16S rRNA gene sequencing for bacterial identification and infectious disease diagnosis

16S rRNA gene sequence is the most common housekeeping genetic marker to study bacterial phylogeny and taxonomy. Therefore, 16S rRNA gene sequencing has the potential to identify novel bacteria and diagnose bacteria. This study compared 16S rRNA gene sequencing with conventional PCR for bacterial identification and disease diagnosis. The bacterial community in healthy and diseased hosts was analyzed by 16S rRNA gene sequencing. 16S rRNA gene sequencing is more sensitive than conventional PCR in detecting bacteria. Moreover, 16S rRNA gene sequencing is adequate to identify novel bacteria. 16S rRNA gene sequencing demonstrated that most pathogenic bacteria persist in diseased or healthy hosts in different abundance. Pathogenic bacteria, such as well-known chicken pathogen Avibacterium paragallinarum, Ornithobacterium rhinotracheale, and Gallibacterium anatis, were identified as indicator species of diseased samples. Alpha diversity analysis showed that the healthy group species is significantly higher than in the diseased groups. Beta diversity analysis also demonstrated differences between healthy and infected groups. The study concluded that 16S rRNA gene sequencing is a more sensitive method for detecting pathogens, and microbiota analysis can distinguish between healthy and diseased samples. Eventually, 16S rRNA gene sequencing has represented the potential in human and animal clinical diagnosis and novel bacterial identification.

The pharmaceutical effect of Korean wild ginseng residue extract on the performance, microbiota quality, cytokine expression, and the ginseng saponin content of laying hen

In this study, a total of 312 Hyline brown laying hen of 1.92 ± 0.12 kg acquired at 24-wk old were employed to evaluate the pharmaceutical effect of Korean wild ginseng residue extract administered via drinking water on the performance, microbiota quality, cytokine expression, and the ginsenoside saponin (GS) content of laying hen for 12 wk. In the experiments, basic feed (CON) was compared with basic feed + 0.05% wild ginseng in drinking water (WGD1), basic feed + 0.1% wild ginseng in drinking water (WGD2), and basic feed + 0.5% wild ginseng in drinking water (WGD3). At the end of study, hen-day egg production (HDEP), average egg weight (AEW), and egg mass (EM) were linearly higher (p < 0.05) in WGD3 at wk 30 to 33, 34 to 37 wk, and the cumulative wk compared with CON. Feed conversion ratio (FCR) was linearly lower in WGD3 at 34 to 37 wk, and the cumulative wk compared with CON. Relative expression of tumor necrosis factor alpha (TNF-α) was linearly lower (p < 0.05) in the WGD3 at wk 30 to 33, and 34 to 37 wk compared with CON. The GS in egg yolk was linearly higher (p < 0.05) in laying hens supplemented the WGD3 treatment at wk 34 to 37, while the fecal microflora quantity of Lactobacillus was linearly higher (p < 0.05) in WGD3 at wk 30 to 33, till 34 to 37 wk, and Escherichia coli (E. coli) was linearly lower (p < 0.05) in the WGD2 and WGD3 from 2637 wk compared with CON. We concluded the result in HDEP, AEW, EM, and FCR were due to the increase in GS content, tentatively leading to an improvement in the TNF-α, and fecal microflora quality such as Lactobacillus and E. coli in the WGD3. We therefore recommend the use of WGD3 at application level 0.5% in drinking water for optimum laying performance from 30 to 37 wk.

Contact with adult hens affects the composition of skin and respiratory tract microbiota in newly hatched chicks

Chickens in commercial production are hatched in hatcheries without any contact with their parents and colonization of their skin and respiratory tract is therefore dependent on environmental sources only. However, since chickens evolved to be hatched in nests, in this study we evaluated the importance of contact between hens and chicks for the development of chicken skin and tracheal microbiota. Sequencing of PCR amplified V3/V4 variable regions of the 16S rRNA gene showed that contact with adult hens decreased the abundance of E. coli, Proteus mirabilis and Clostridium perfringens both in skin and the trachea, and Acinetobacter johnsonii and Cutibacterium acnes in skin microbiota only. These species were replaced by Lactobacillus gallinarum, Lactobacillus aviarius, Limosilactobacillus reuteri, and Streptococcus pasterianus in the skin and tracheal microbiota of contact chicks. Lactobacilli can be therefore investigated for their probiotic effect in respiratory tract in the future. Skin and respiratory microbiota of contact chickens was also enriched for Phascolarctobacterium, Succinatimonas, Flavonifractor, Blautia, and [Ruminococcus] torque though, since these are strict anaerobes from the intestinal tract, it is likely that only DNA from nonviable cells was detected for these taxa.