Analysis of miRNAs expression in the ileum during broiler chickens against subclinical necrotic enteritis through Bacillus licheniformis H2 supplement
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ABSTRACT:
PROVIDER: PRJNA636656 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR11906653.fastq.gz | Fastqsanger.gz | |||
| SRR11906654.fastq.gz | Fastqsanger.gz | |||
| SRR11906655.fastq.gz | Fastqsanger.gz | |||
| SRR11906656.fastq.gz | Fastqsanger.gz | |||
| SRR11906657.fastq.gz | Fastqsanger.gz |
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Project description:Subclinical necrotic enteritis (SNE) is one of the serious threats to the poultry industry. Probiotics have been proven to exert the beneficial effects in controlling SNE. However, the exact mechanisms of probiotics have not been fully elucidated, and few researchs have focused on their impact on miRNAs. Therefore, the purpose of this study was to explore the miRNA expression profles in the ileum of broiler chickens during probiotic supplement treatment for SNE. 180 newly hatched male chicks were randomly allocated in three groups, including negative control group(NC), SNE infection group(PC) and Bacillus licheniformis H2 pre-treatment group (BL). Illumina high-throughput sequencing was conducted to identify the miRNA expression of three groups. The results showed that 628 miRNAs, including 582 known miRNAs and 46 novel miRNAs, were detected in libraries. The target genes of 57 significantly differentially expressed miRNAs were predicted and annotated, which were found to partly enrich in pathways related to immunity and inflammation such as tumor necrosis factor receptor binding, immune response-regulating signaling pathway, activation of NF-kappaB-inducing kinase activity, interleukin-15 production, Toll-like receptor 2 signaling pathway and MAP kinase tyrosine/serine/threonine phosphatase activity. Our results provided comprehensive miRNA expression profles of these three different treatment groups. And these findings suggested that H2 could exert beneficial effects in controlling SNE may through immune and inflammatory response associated to altered miRNA expression.
2020-06-03 | GSE151627 | GEO
Project description:Purpose: Analyze gene expression of necrotic enteritis C. perfringens in intestinal chicken loops comparing with in vitro conditions
2016-10-07 | GSE79456 | GEO
Project description:BackgroundChicken meat is one of the most consumed meats worldwide and poultry production is increasing at an exponential rate. Reducing antibiotic usage has resulted in the recurrence of subclinical necrotic enteritis again and influenced global poultry production. Probiotics are potential antibiotic substitutes that can be used to prevent subclinical necrotic enteriti. However, the precise mechanism of action of probiotics and information on which gut microbes confer this efficacy remain elusive.Methods and resultsThe subclinical necrotic enteritis animal model was used to reveal the mechanism underlying the effect of probiotics on intestinal health through RNA sequencing and 16S rDNA amplicon sequencing. Bacillus licheniformis H2 feeding significantly reduced the relative abundance of Clostridium perfringens in the ileum and markedly ameliorated the pathological damage in the ileum and liver. In addition, oral administration of B. licheniformis H2 contributed to the enhancement of the intestinal barrier function and epithelial renewal, reducing energy consumption, and improving enteral nutrition absorption. Probiotic B. licheniformis H2 also ameliorated the inflammatory response and increased the immunity of subclinical necrotic enteritis infected broilers. Finally, B. licheniformis H2 feeding regulated liver gene expression to suppress immune response and promoted growth and metabolism depending on the gut microbiota.ConclusionsThese results indicated the mechanism of probiotic action of B. licheniformis H2 in maintaining intestinal health and thus promoting growth and B. licheniformis H2 may serve as an antibiotic substitute to prevent subclinical necrotic enteritis in poultry farming.
| S-EPMC8972058 | biostudies-literature
Project description:Increasing studies have focused on the beneficial effects of Lactobacillus johnsonii in certain diseases. Here, we studied the prevention ability of a probiotic strain, L. johnsonii BS15 on subclinical necrotic enteritis (SNE), and its underlying mechanism. 180 male Cobb 500 chicks were randomly allotted into three groups and administrated with BS15 (1 × 106 cfu/g) or Man Rogosa Sharpe liquid medium throughout a 28-day experimental period. With the exception of the normal group, SNE infection was treated for the remaining experimental period after the chicks were fed with normal diet 14 days. Results showed that BS15 notably suppressed the SNE-induced loss of average daily gain and liver functional abnormality. Additionally, BS15 facilitated lipid metabolism of SNE boilers when the contents of peroxisome proliferator activated receptor ? and adipose triglyceride lipase in adipose tissue and serum high-density lipoprotein cholesterol decreased. BS15 also attenuated the hepatic lipid accumulation of stricken chicks by suppressing the genes expression of acetyl-CoA carboxylase, fatty acid synthase and sterol regulatory element binding protein-1c as well as stimulating the genes expression of peroxisome proliferator activated receptor ? and carnitine palmitoyltransferase-1. Moreover, BS15 enhanced the development of SNE gut by improving the intestinal development and digestion as well as adjusting the gut microflora. Therefore, BS15 may provide a promising natural preventative strategy against SNE, which may be contributed to the amelioration of lipid metabolism and intestinal microflora.
| S-EPMC5484656 | biostudies-literature
Project description:Purpose: Analyze gene expression during C. perfringens colonization in the chicken Transcriptomic profile of mRNA from C. perfrinegns from in vivo and in vitro conditions were determined in biological duplicates by RNA-Seq using Illumina HiSeq 2500 Comparison of gene expression through RNA sequencing of necrotic enteritis C. perfrinegns type A of in vivo (chicken loops) and in vitro (lab culture)
2015-10-30 | E-GEOD-70701 | biostudies-arrayexpress
Project description:Along with banning of antibiotics, necrotic enteritis (NE), especially subclinical NE (SNE) whereby no clinical signs are present in chicks, has become one of the most threatening problems in poultry industry. Therefore, increasing attention has been focused on research and application of effective probiotic strains, as an alternative to antibiotics, to prevent SNE in broilers. In the present study, we evaluated the effects of Lactobacillus johnsonii BS15 on the prevention of SNE in broilers. Specifically, assessment determined the growth performance and indexes related to intestinal mucosal immunity in the ileum and cecal tonsil of broilers. A total of 300 1-day-old Cobb 500 chicks were randomly distributed into the following 5 groups: control group (fed with basal diet?+?de Man, Rogosa, and Sharpe liquid medium [normal diet]), SNE group (normal diet), BS15 group (basal diet?+?1?×?106 colony-forming units BS15/g as fed [BS15 diet]), treatment group (normal diet [days 1-28]?+?BS15 diet [days 29-42]), and prevention group (BS15 diet [days 1-28]?+?normal diet [days 29-42]) throughout a 42-day experimental period. SNE infection was treated for all chicks in the SNE, BS15, treatment, and prevention groups. The present results demonstrated that BS15 supplementation of feeds in BS15 and prevention groups exerted a positive effect on preventing negative influences on growth performance; these negative influences included low body weight gain and increased feed conversion ratio caused by SNE. Although no changes were detected in all determined indexes in cecal tonsils, BS15-treated broilers were free from SNE-caused damage in villi in the ileum. BS15 inhibited SNE-caused decrease in immunoglobulins in the ileum. In the lamina propria of ileum, T cell subsets of lymphocytes influenced by SNE were also controlled by BS15. BS15 affected antioxidant abilities of the ileum and controlled SNE-induced mitochondrion-mediated apoptosis by positively changing contents and/or mRNA expression levels of apoptosis-related proteins. These findings indicate that BS15 supplementation may prevent SNE-affected growth decline mainly through enhancing intestinal immunity in broilers.
| S-EPMC5701917 | biostudies-literature
Project description:Subclinical necrotic enteritis (NE) was induced in broiler chicks using a high dose of Eimeria spp. vaccine in the drinking water on day 9, and Clostridium perfringens (Cp) culture mixed in the feed on days 14 and 15. The aim was to evaluate the effects of probiotic Bacillus amyloliquefaciens strain H57 (H57) in preventing NE in chicks. Day-old Ross 308, male broilers were weighed and randomly assigned to 6 treatment groups (6 replicate cages/treatment and 8 birds/cage). Birds in group 1 (control) were fed the basal wheat-soybean diet without H57 or NE infection; in group 2 (Eimeria) were treated with Eimeria alone; in group 3 (Cp) were treated with Cp alone; in group 4 (NE) received both Eimeria and Cp; in group 5 (NE-H57) received NE infection and H57; and group 6 (H57) received H57. The basal diet of chicks in groups 5 and 6 was supplemented with H57 at a density of 2 × 108 spores/g feed from 1 D of age. On day 21, there were no significant treatment effects on BW and feed intake between control and H57 birds. However, on day 21, the feed conversion ratio of NE-H57 birds was significantly improved when compared with NE birds (1.28 vs. 1.36; P < 0.001). Birds challenged with NE had a higher occurrence of pasty vent than birds infected with either Eimeria, Cp, or NE-H57 (41 vs. 27 vs. 29 vs. 19%, respectively; P < 0.001). Intestinal lesion scores of NE birds were also higher than those of Eimeria, Cp, and NE-H57 birds (5.67 vs. 2.56 vs. 2.78 vs. 2.10, respectively; P < 0.001) and correlated with pasty vent (Pearson's r = 0.56; P < 0.001). Microscopic evaluation showed mucosal damage and necrosis in NE birds. In contrast, villi from NE-H57 birds were normal, with no damage or infiltration with Eimeria or Cp. H57 appears to be effective in challenged birds, as it maintained epithelial barrier integrity and improved feed efficiency.
| S-EPMC7597999 | biostudies-literature
Project description:BackgroundIntestinal microbiota is critical for maintaining animal health and homeostasis. However, involvement of the fungal community, also known as the mycobiota, in animal health and disease is poorly understood. This study was aimed to examine the association between the intestinal mycobiota and the severity of necrotic enteritis (NE), an economically significant poultry disease.MethodsA total of 90 day-of-hatch Cobb broilers were infected with Eimeria maxima on d 10, followed by an oral challenge with C. perfringens on d 14 to induce NE, while another 10 broilers were served as mock-infected controls. On d 17, the lesions in the jejunum were scored, and the ileal digesta were subjected to DNA isolation and real-time PCR quantification of total bacterial and fungi populations. Internal transcribed spacer 2 (ITS2) amplicon sequencing was also performed to profile the ileal mycobiota composition. Changes in the ileal mycobiota in response to NE were investigated. Spearman correlation analysis was further conducted to identify the correlations between relative abundances of individual ileal fungi and the severity of NE.ResultsWhile the total bacterial population in the ileum was increased by 2- to 3-fold in NE chickens, the total fungal population was progressively declined in more exacerbated NE, with the most severely infected chickens showing a nearly 50-fold reduction relative to mock-infected controls. Richness of the ileal mycobiota also tended to reduce in chickens with NE (P = 0.06). Compositionally, among 30 most abundant fungal amplicon sequence variants (ASVs), 11 were diminished and 7 were enriched (P < 0.05), while 12 remained largely unchanged in NE-afflicted chickens (P > 0.05). Multiple Wallemia and Aspergillus species were markedly diminished in NE (P < 0.05) and also showed a significant negative correlation with NE severity (P < 0.05).ConclusionsDysbiosis of the ileal mycobiota is induced evidently by NE and the extent of the dysbiosis is positively correlated with disease severity. These findings suggest a possible role of the intestinal mycobiota in NE pathogenesis and highlight the mycobiota as a new potential target for NE mitigation in poultry.
| S-EPMC8501549 | biostudies-literature
Project description:The withdrawal of antibiotic growth promoters from poultry feed has increased the risk of necrotic enteritis (NE) outbreaks. This study examined the effects of a probiotic (PROB) or probiotic/prebiotic/essential oil supplement (PPEO) during a subclinical NE challenge. On day (d) of hatch, 960 male broilers were randomized to four groups (8 pens/treatment, 30 birds/pen) including (1) negative control (NC): corn-soybean meal diet; (2) positive control (PC): NC + 20 g Virginiamycin/ton diet; (3) NC + 227 g PROB/ton diet; and (4) NC + 453 g PPEO/ton diet. One d after placement, birds were challenged by a coccidia vaccine to induce NE. Feed intake and body weights were measured on d 8 (NE onset) and end of each feeding period. On d 8, the small intestines of three birds/pen were examined for NE lesions. Jejunum samples and ileal mucosal scrapings from one bird/pen were respectively collected to measure mRNA abundance (d 8 and d 14) and profile the microbiota (d 8 and d 42). Data were analyzed in JMP or QIIME 2 and significance between treatments identified by LSD (P < 0.05). PROB and PPEO had significantly lower mortality (d 0-14) and NE lesion scores compared to NC. Feed conversion ratio was significantly lower in PC, PROB, and PPEO, while average daily gain was higher in PPEO and PC groups compared to NC from d 0-42. On d 8 and d 14, mRNA abundance of claudin-3 was higher in PPEO compared to NC. On d 14, compared to NC, mRNA abundance of sIgA and PGC-1? in PROB and PPEO were lower and higher, respectively. Compared to NC, PPEO increased mTOR abundance on d 14. On d 8, relative abundance of Clostridium sensu stricto 1, Ruminiclostridium9, Prevotellaceae, Prevotellaceae UCG-014, ASF356, and Muribaculaceae was higher in NC compared to PPEO and PROB, while Lactobacillus was lower in NC. Escherichia-Shigella had higher abundance in PC compared to PPEO and PROB. Collectively, these data indicate that during a subclinical naturally occurring NE, supplementation of PROB or PPEO supports performance and reduces intestinal lesions, potentially through modifying tight junction proteins, gut microbiota, immune responses, and cell metabolism.
| S-EPMC7725796 | biostudies-literature
Project description:BackgroundNecrotic enteritis (NE) is a severe intestinal infection that affects both humans and poultry. It is caused by the bacterium Clostridium perfringens (CP), but the precise mechanisms underlying the disease pathogenesis remain elusive. This study aims to develop an NE broiler chicken model, explore the impact of the microbiome on NE pathogenesis, and study the virulence of CP isolates with different toxin gene combinations.MethodsThis study established an animal disease model for NE in broiler chickens. The methodology encompassed inducing abrupt protein changes and immunosuppression in the first experiment, and in the second, challenging chickens with CP isolates containing various toxin genes. NE was evaluated through gross and histopathological scoring of the jejunum. Subsequently, jejunal contents were collected from these birds for microbiome analysis via 16S rRNA amplicon sequencing, followed by sequence analysis to investigate microbial diversity and abundance, employing different bioinformatic approaches.ResultsOur findings reveal that CP infection, combined with an abrupt increase in dietary protein concentration and/or infection with the immunosuppressive variant infectious bursal disease virus (vIBDV), predisposed birds to NE development. We observed a significant decrease (p < 0.0001) in the abundance of Lactobacillus and Romboutsia genera in the jejunum, accompanied by a notable increase (p < 0.0001) in Clostridium and Escherichia. Jejunal microbial dysbiosis and severe NE lesions were particularly evident in birds infected with CP isolates containing cpa, netB, tpeL, and cpb2 toxin genes, compared to CP isolates with other toxin gene combinations. Notably, birds that did not develop clinical or subclinical NE following CP infection exhibited a significantly higher (p < 0.0001) level of Romboutsia. These findings shed light on the complex interplay between CP infection, the gut microbiome, and NE pathogenesis in broiler chickens.ConclusionOur study establishes that dysbiosis within the jejunal microbiome serves as a reliable biomarker for detecting subclinical and clinical NE in broiler chicken models. Additionally, we identify the potential of the genera Romboutsia and Lactobacillus as promising candidates for probiotic development, offering effective alternatives to antibiotics in NE prevention and control.
| S-EPMC10799374 | biostudies-literature