Metagenomic bacterial community profiles of chicken embryo gastrointestinal tract by using T-RFLP analysis

Ilina, Larisa; Yildirim, E. A.; Никонов, И Н; Филиппова, В. А.; Laptev, G. Yu.; Novikova, N. I.; Grozina, A.A.; Lenkova, T.N.; Manukyan, V.A.; Егоров, И. А.; Фисинин, В.И.

doi:10.1134/s1607672916010130

Cited by 13 publications

(11 citation statements)

References 11 publications

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“…Lower UniFrac distance from ceca to extraintestinal sites (blood, femur and tibia) and spatiotemporal distribution of microbiota at day 1 may suggest the gut as the source of extraintestinal microbiota ( Figures 5 , 6 ). Ilina et al ( 26 ) discovered 38 phylotypes of microbiota were able to colonize the gastrointestinal tract of the chicken embryo using terminal restriction fragment length polymorphism (T-RFLP). However, higher alpha diversity index (OTUs, Chao 1 and PD_whole_tree) in the extraintestinal site of chicks than ceca at day 1 portrays a different story.…”

Section: Discussionmentioning

confidence: 99%

Microbiota Analysis of Chickens Raised Under Stressed Conditions

et al. 2020

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A substantial progress has been made toward understanding stress-associated gut and extraintestinal microbiota. However, a comprehensive understanding of the extraintestinal microbiota of chickens raised under stressed conditions is lacking. In this study, chickens were raised on a wire-floor model to induce stress, and the microbiota in the gut (ceca) and extraintestinal sites (blood, femur, and tibia) were characterized at different ages (1, 17, and 56 days) using 16S rRNA gene microbiota profiling. Open reference OTU picking showed extraintestinal sites had a significantly higher number of unassigned OTUs compared to ceca across all ages of chickens. Extraintestinal sites of all ages, irrespective of body sites, as well as ceca of 1 day-old chickens had significantly lower alpha diversity than ceca of older chickens. Intriguingly, bacterial diversity (alpha and beta) and OTU interaction network analysis showed relatively stable bacterial composition within the extraintestinal sites of chickens regardless of age and sites compared to ceca. Furthermore, assessment using UniFrac distance suggested the gut as a possible source of extraintestinal bacteria. Lastly, LEfSe analysis showed that both commensal and pathogenic bacteria were translocated into the extraintestinal tissues and organs under the stress. Extraintestinal sites have highly abundant novel taxa that need to be further explored. In ovo microbiota colonization and/or translocation of circulating maternal blood microbiota into ovarian follicles might be the source of intestinal and extraintestinal microbiota in 1 day-old chickens. Our comprehensive microbiota data including extraintestinal sites in reference to gut provide unique insights into microbiota of chickens raised under stressed conditions, which may be relevant in other animal species as well.

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Section: Discussionmentioning

confidence: 99%

Microbiota Analysis of Chickens Raised Under Stressed Conditions

et al. 2020

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“…The composition of the bacterial community in the caecum of birds was examined by the terminal restriction fragment length polymorphism (T-RFLP) method [90,91,92,93]. T-RFLP based on the analysis of the nucleotide sequences of the 16S rRNA gene is a fairly reliable and up-to-date technique for analysing the microflora of complex communities including those in the gut lumen of chickens [94], and its results are comparable to those obtained using high-throughput sequencing [95].…”

Section: Methodsmentioning

confidence: 99%

Examination of the Expression of Immunity Genes and Bacterial Profiles in the Caecum of Growing Chickens Infected with Salmonella Enteritidis and Fed a Phytobiotic

Laptev¹,

Филиппова²,

Kochish

et al. 2019

Animals

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Simple SummarySalmonellosis is among the most common infectious poultry diseases that also represent a high risk to human health. The pathological process caused by Salmonella enterica serovar Enteritidis (SE) triggers in the caecum the expression of certain genes, e.g., avian β-defensins (gallinacins), cytokines (interleukins), etc. On the other hand, gut microbiota influences the infection potential of pathogens. The present study aimed at revealing the differential expression of genes associated with the immune system and changes in the bacterial communities in the intestine of growing chickens in response to SE infection. We also tested a feed additive, essential oils-based phytobiotic Intebio, as a potential alternative to antibiotics and showed effects of its administration on the caecal microbiome composition and the expression of some genes related to immunity. The phytobiotic showed its efficiency for application in poultry rearing and production.AbstractThis study was performed to investigate the differential expression of eight immunity genes and the bacterial profiles in the caecum of growing chickens challenged with Salmonella enterica serovar Enteritidis (SE) at 1 and 23 days post inoculation (dpi) in response to SE infection at 19 days of age and administration of the phytobiotic Intebio. Following infection, the genes CASP6 and IRF7 were upregulated by greater than twofold. Chicks fed Intebio showed at 1 dpi upregulation of AvBD10, IL6, IL8L2, CASP6 and IRF7. At 23 dpi, expression of AvBD11, IL6, IL8L2, CASP6 and IRF7 lowered in the experiment subgroups as compared with the control. Examination of the caecal contents at 1 dpi demonstrated a significant decrease in the microbial biodiversity in the infected subgroup fed normal diet. Bacterial content of Lactobacillus and Bacillus declined, while that of Enterobacteriaceae rose. In the infected subgroup fed Intebio, a pronounced change in composition of the microflora was not observed. In the early infection stages, the phytobiotic seemed to promote response to infection. Subsequently, an earlier suppression of the inflammatory reaction took place in chickens fed Intebio. Thus, use of Intebio as a drug with phytobiotic activity in chickens, including those infected with Salmonella, proved to be promising.

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“…Binek et al ( 94 ) reported results revealing the identification of similar microbial populations: Entercoccus sp., Micrococcus sp., and Bacillus sp. Additionally, Ilina et al ( 96 ) used terminal restriction fragment length polymorphism (T-RFLP) to determine the structure and composition of the microbial populations present in the GITs of chick embryos on the 16th day of incubation in two different breeds of Hajseks chickens (Brown and White breeds). This study indicated that by 16 days of incubation, the chick embryo contains microbiota with relatively rich taxonomic diversity, reporting that the Hajseks Brown breed samples to contained 38 different phylotypes, while 30 were observed in the Hajseks White breed samples ( 96 ).…”

Section: Git Microbiome Developmentmentioning

confidence: 99%

Applications of In Ovo Technique for the Optimal Development of the Gastrointestinal Tract and the Potential Influence on the Establishment of Its Microbiome in Poultry

2016

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As the current poultry production system stands, there is a period of time when newly hatched chicks are prevented from access to feed for approximately 48–72 h. Research has indicated that this delay in feeding may result in decreased growth performance when compared to chicks that are fed immediately post-hatch. To remedy this issue, in ovo methodology may be applied in order to supply the embryo with additional nutrients prior to hatching and those nutrients will continue to be utilized by the chick post-hatch during the fasting period. Furthermore, in ovo injection of various biologics have been researched based on the ability of not only supplying the chick embryo with additional nutrients that would promote improved growth but also compounds that may benefit the future health of the chicken host. Such compounds include various immunostimulants, live beneficial bacteria, prebiotics, and synbiotics. However, it is important to determine the site and age of the in ovo injection for the most productive effects. The primary focus of the current review is to address these two issues [the most effective site(s) and age(s) of in ovo injection] as well as provide the framework for the development of the gastrointestinal tract (GIT) of the chick embryo. Additionally, recent research suggests the colonization of the microbiota in the developing chick may occur during the late stages of embryogenesis. Therefore, we will also discuss the potentials of the in ovo injection method in establishing a healthy and diverse community of microorganisms to colonize the developing GIT that will provide both protection from pathogen invasion and improvement in growth performance to developing chicks.

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Metagenomic bacterial community profiles of chicken embryo gastrointestinal tract by using T-RFLP analysis

Cited by 13 publications

References 11 publications

Microbiota Analysis of Chickens Raised Under Stressed Conditions

Microbiota Analysis of Chickens Raised Under Stressed Conditions

Examination of the Expression of Immunity Genes and Bacterial Profiles in the Caecum of Growing Chickens Infected with Salmonella Enteritidis and Fed a Phytobiotic

Applications of In Ovo Technique for the Optimal Development of the Gastrointestinal Tract and the Potential Influence on the Establishment of Its Microbiome in Poultry

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