16S rRNA gene sequencing reveals an altered composition of the gut microbiota in chickens infected with a nephropathogenic infectious bronchitis virus

Xu, Puzhi; Shi, Yan; Liu, Ping; Yang, Yulin; Zhou, Changming; Li, Guyue; Luo, Junrong; Zhang, Caiying; Hu, Guoliang; Guo, Xiaomin

doi:10.1038/s41598-020-60564-8

Cited by 18 publications

(21 citation statements)

References 69 publications

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“…The microbial dysbiosis in broilers can be linked to antibiotic resistance. Moreover, the association of microbial dysbiosis with antibiotic resistance in poultry could be supported by a previous study linking the predominance of Proteobacteria with microbial dysbiosis in ilea of nephropathogenic infectious bronchitis virus-infected chickens [48]. The over dominance of various pathobionts (E. coli, Klebsiella pneumonia, Salmonella enterica, Shigella flexneri) in this study is supported by the fact that an increased abundance of Proteobacteria has been linked with the emergence of pathogenic microbes [49,50].…”

Section: Discussionsupporting

confidence: 81%

Next-Generation Sequencing Based Gut Resistome Profiling of Broiler Chickens Infected with Multidrug-Resistant Escherichia coli

Afridi

Ali

Chang

2020

Animals

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The study was designed to investigate the fecal microbiome and resistome of broiler chickens infected with multidrug-resistant (MDR) Escherichia coli (E. coli). Fecal samples (n = 410) from broiler chickens were collected from thirteen randomly selected sites of Khyber Pakhtunkhwa and screened for the presence of MDR E. coli. Upon initial screening, thirteen (13) MDR E. coli isolates were then subjected to shotgun metagenome next-generation sequencing (NGS). NGS based resistome analysis identified the multidrug efflux pump system-related genes at the highest prevalence (36%) followed by aminoglycoside (26.1%), tetracycline (15.9%), macrolide-lincosamide-streptogramin (9.6%), beta-lactam (6.6%), rifampin (2%), sulphonamide (1.3%), phenicol (0.91%), vancomycin (0.62%), trimethoprim (0.34%), colistin (0.30%), and quinolone (0.33%). The most abundant virulence-associated genes (VAGs) identified were iroN, iutA, iss, and iucA. NGS based taxonomic profiling at the phylum level revealed the predominance of Proteobacteria (38.9%) followed by Firmicutes (36.4%), Bacteroidetes (15.8%), and Tenericutes (8.9%). Furthermore, pathobionts such as E. coli, Salmonella enterica, Klebsiella pneumoniae, and Shigella flexneri belonging to the family Enterobacteriaceae were predominantly found. This study revealed the widespread presence of MDR genes, diverse VAGs, and a dysbiotic gut in the broiler chickens infected with MDR E. coli of Khyber Pakhtunkhwa for the first time using NGS.

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Section: Discussionsupporting

confidence: 81%

Next-Generation Sequencing Based Gut Resistome Profiling of Broiler Chickens Infected with Multidrug-Resistant Escherichia coli

Afridi

Ali

Chang

2020

Animals

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“…We then investigated the associations between the caecal microbiota composition and immune phenotypes of the challenged animals in the total population and in the V-Ch and NV-Ch groups separately. A recent study reported the effect of nephropathogenic IBV (NIBV) infection on the ileal microbiota of Hy-Line brown chickens 33 . It was observed that NIBV disturbed the intestinal epithelium, with an hyperplasia of goblet cells, and a lowered ratio of the villus height to crypt depth.…”

Section: Discussionmentioning

confidence: 99%

Caecal microbiota composition of experimental inbred MHC-B lines infected with IBV differs according to genetics and vaccination

Borey

Bed’Hom

Bruneau

et al. 2022

Sci Rep

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Interactions between the gut microbiota and the immune system may be involved in vaccine and infection responses. In the present study, we studied the interactions between caecal microbiota composition and parameters describing the immune response in six experimental inbred chicken lines harboring different MHC haplotypes. Animals were challenge-infected with the infectious bronchitis virus (IBV), and half of them were previously vaccinated against this pathogen. We explored to what extent the gut microbiota composition and the genetic line could be related to the immune response, evaluated through flow cytometry. To do so, we characterized the caecal bacterial communities with a 16S rRNA gene amplicon sequencing approach performed one week after the IBV infectious challenge. We observed significant effects of both the vaccination and the genetic line on the microbiota after the challenge infection with IBV, with a lower bacterial richness in vaccinated chickens. We also observed dissimilar caecal community profiles among the different lines, and between the vaccinated and non-vaccinated animals. The effect of vaccination was similar in all the lines, with a reduced abundance of OTU from the Ruminococcacea UCG-014 and Faecalibacterium genera, and an increased abundance of OTU from the Eisenbergiella genus. The main association between the caecal microbiota and the immune phenotypes involved TCRϒδ expression on TCRϒδ+ T cells. This phenotype was negatively associated with OTU from the Escherichia-Shigella genus that were also less abundant in the lines with the highest responses to the vaccine. We proved that the caecal microbiota composition is associated with the IBV vaccine response level in inbred chicken lines, and that the TCRϒδ+ T cells (judged by TCRϒδ expression) may be an important component involved in this interaction, especially with bacteria from the Escherichia-Shigella genus. We hypothesized that bacteria from the Escherichia-Shigella genus increased the systemic level of bacterial lipid antigens, which subsequently mitigated poultry γδ T cells.

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“…In addition, the GreenGene database and MUSCLE software (version 3.8.31) were used to annotate the taxonomic information and conduct the multiple sequence alignment, respectively [44]. The alpha diversity index (Chao1, ACE, Shannon, Simpson indices), the beta diversity index, PCoA, NMDS and ANOSIM were conducted as previously described [45].…”

Section: Analysis Of Microbial Diversitymentioning

confidence: 99%

Clinical Breakpoint of Apramycin to Swine Salmonella and Its Effect on Ileum Flora

Dai

Guo

et al. 2022

IJMS

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The purpose of this study was to establish the clinical breakpoint (CBP) of apramycin (APR) against Salmonella in swine and evaluate its effect on intestinal microbiota. The CBP was established based on three cutoff values of wild-type cutoff value (COWT), pharmacokinetic-pharmadynamic (PK/PD) cutoff value (COPD) and clinical cutoff value (COCL). The effect of the optimized dose regimen based on ex vivo PK/PD study. The evolution of the ileum flora was determined by the 16rRNA gene sequencing and bioinformatics. This study firstly established the COWT, COPD in ileum, and COCL of APR against swine Salmonella, the value of these cutoffs were 32 µg/mL, 32 µg/mL and 8 µg/mL, respectively. According to the guiding principle of the Clinical Laboratory Standards Institute (CLSI), the final CBP in ileum was 32 µg/mL. Our results revealed the main evolution route in the composition of ileum microbiota of diarrheic piglets treated by APR. The change of the abundances of Bacteroidetes and Euryarchaeota was the most obvious during the evolution process. Methanobrevibacter, Prevotella, S24-7 and Ruminococcaceae were obtained as the highest abundance genus. The abundance of Methanobrevibacter increased significantly when APR treatment carried and decreased in cure and withdrawal period groups. The abundance of Prevotella in the tested groups was significantly lower than that in the healthy group. A decreased of abundance in S24-7 was observed after Salmonella infection and increased slightly after cure. Ruminococcaceae increased significantly after Salmonella infection and decreased significantly after APR treatment. In addition, the genera of Methanobrevibacter and Prevotella were defined as the key node. Valine, leucine and isoleucine biosynthesis, D-Glutamine and D-glutamate metabolism, D-Alanine metabolism, Peptidoglycan and amino acids biosynthesis were the top five Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways in the ileum microbiota of piglets during the Salmonella infection and APR treatment process. Our study extended the understanding of dynamic shift of gut microbes during diarrheic piglets treated by APR.

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16S rRNA gene sequencing reveals an altered composition of the gut microbiota in chickens infected with a nephropathogenic infectious bronchitis virus

Cited by 18 publications

References 69 publications

Next-Generation Sequencing Based Gut Resistome Profiling of Broiler Chickens Infected with Multidrug-Resistant Escherichia coli

Next-Generation Sequencing Based Gut Resistome Profiling of Broiler Chickens Infected with Multidrug-Resistant Escherichia coli

Caecal microbiota composition of experimental inbred MHC-B lines infected with IBV differs according to genetics and vaccination

Clinical Breakpoint of Apramycin to Swine Salmonella and Its Effect on Ileum Flora

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