A Multi-Omics Study of Chicken Infected by Nephropathogenic Infectious Bronchitis Virus

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Abstract

Chicken gout resulting from nephropathogenic infectious bronchitis virus (NIBV) has become a serious kidney disease problem in chicken worldwide with alterations of the metabolic phenotypes in multiple metabolic pathways. To investigate the mechanisms in chicken responding to NIBV infection, we examined the global transcriptomic and metabolomic profiles of the chicken’s kidney using RNA-seq and GC–TOF/MS, respectively. Furthermore, we analyzed the alterations in cecal microorganism composition in chickens using 16S rRNA-seq. Integrated analysis of these three phenotypic datasets further managed to create correlations between the altered kidney transcriptomes and metabolome, and between kidney metabolome and gut microbiome. We found that 2868 genes and 160 metabolites were deferentially expressed or accumulated in the kidney during NIBV infection processes. These genes and metabolites were linked to NIBV-infection related processes, including immune response, signal transduction, peroxisome, purine, and amino acid metabolism. In addition, the comprehensive correlations between the kidney metabolome and cecal microbial community showed contributions of gut microbiota in the progression of NIBV-infection. Taken together, our research comprehensively describes the host responses during NIBV infection and provides new clues for further dissection of specific gene functions, metabolite affections, and the role of gut microbiota during chicken gout.

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Most cited references 55

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Innate antiviral responses by means of TLR7-mediated recognition of single-stranded RNA.

Sandra S. Diebold, Tsuneyasu Kaisho, Hiroaki Hemmi … (2004)

Interferons (IFNs) are critical for protection from viral infection, but the pathways linking virus recognition to IFN induction remain poorly understood. Plasmacytoid dendritic cells produce vast amounts of IFN-alpha in response to the wild-type influenza virus. Here, we show that this requires endosomal recognition of influenza genomic RNA and signaling by means of Toll-like receptor 7 (TLR7) and MyD88. Single-stranded RNA (ssRNA) molecules of nonviral origin also induce TLR7-dependent production of inflammatory cytokines. These results identify ssRNA as a ligand for TLR7 and suggest that cells of the innate immune system sense endosomal ssRNA to detect infection by RNA viruses.

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Recognition of single-stranded RNA viruses by Toll-like receptor 7.

Jennifer Lund, Lena Alexopoulou, Ayuko Sato … (2004)

Viral infection of mammalian host results in the activation of innate immune responses. Toll-like receptors (TLRs) have been shown to mediate the recognition of many types of pathogens, including viruses. The genomes of viruses possess unique characteristics that are not found in mammalian genomes, such as high CpG content and double-stranded RNA. These genomic nucleic acids serve as molecular signatures associated with viral infections. Here we show that TLR7 recognizes the single-stranded RNA viruses, vesicular stomatitis virus and influenza virus. The recognition of these viruses by plasmacytoid dendritic cells and B cells through TLR7 results in their activation of costimulatory molecules and production of cytokines. Moreover, this recognition required intact endocytic pathways. Mice deficient in either the TLR7 or the TLR adaptor protein MyD88 demonstrated reduced responses to in vivo infection with vesicular stomatitis virus. These results demonstrate microbial ligand recognition by TLR7 and provide insights into the pathways used by the innate immune cells in the recognition of viral pathogens.

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Amino acids and immune function.

Peng Li, Yu-Long Yin, Defa Li … (2007)

A deficiency of dietary protein or amino acids has long been known to impair immune function and increase the susceptibility of animals and humans to infectious disease. However, only in the past 15 years have the underlying cellular and molecular mechanisms begun to unfold. Protein malnutrition reduces concentrations of most amino acids in plasma. Findings from recent studies indicate an important role for amino acids in immune responses by regulating: (1) the activation of T lymphocytes, B lymphocytes, natural killer cells and macrophages; (2) cellular redox state, gene expression and lymphocyte proliferation; and (3) the production of antibodies, cytokines and other cytotoxic substances. Increasing evidence shows that dietary supplementation of specific amino acids to animals and humans with malnutrition and infectious disease enhances the immune status, thereby reducing morbidity and mortality. Arginine, glutamine and cysteine precursors are the best prototypes. Because of a negative impact of imbalance and antagonism among amino acids on nutrient intake and utilisation, care should be exercised in developing effective strategies of enteral or parenteral provision for maximum health benefits. Such measures should be based on knowledge about the biochemistry and physiology of amino acids, their roles in immune responses, nutritional and pathological states of individuals and expected treatment outcomes. New knowledge about the metabolism of amino acids in leucocytes is critical for the development of effective means to prevent and treat immunodeficient diseases. These nutrients hold great promise in improving health and preventing infectious diseases in animals and humans.

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Author and article information

Journal

Journal ID (nlm-ta): Viruses

Journal ID (iso-abbrev): Viruses

Journal ID (publisher-id): viruses

Title: Viruses

Publisher: MDPI

ISSN (Electronic): 1999-4915

Publication date (Electronic): 16 November 2019

Publication date Collection: November 2019

Volume: 11

Issue: 11

Electronic Location Identifier: 1070

Affiliations

[1 ]Jiangxi Provincial Key Laboratory for Animal Health, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang 330045, China; 18979191421@ 123456jxau.edu.cn (P.X.); Pingliujx@ 123456163.com (P.L.); zcm@ 123456jxau.edu.cn (C.Z.); taildog@ 123456163.com (Q.W.); yangyitian0810@ 123456163.com (Y.Y.); liguyue66@ 123456126.com (G.L.)

[2 ]School of Computer and Information Engineering, Jiangxi Agricultural University, Nanchang 330045, China; shiyan0015@ 123456126.com

Author notes

[* ]Correspondence: hgljx3818@ 123456163.com (G.H.); xqguo20720@ 123456aliyun.com (X.G.)

[†]

These authors contributed equally to this work.

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Xiaoquan Guo https://orcid.org/0000-0001-6041-8765

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Publisher ID: viruses-11-01070

DOI: 10.3390/v11111070

PMC ID: 6893681

PubMed ID: 31744152

SO-VID: af3890ef-a89f-4dac-b85b-4e2ffaac7063

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Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license ( http://creativecommons.org/licenses/by/4.0/).

A Multi-Omics Study of Chicken Infected by Nephropathogenic Infectious Bronchitis Virus

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Abstract

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MDPI: Coronavirus

Most cited references 55

Innate antiviral responses by means of TLR7-mediated recognition of single-stranded RNA.

Recognition of single-stranded RNA viruses by Toll-like receptor 7.

Amino acids and immune function.

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