Metaproteome analysis of the gastrointestinal microbiome during respiratory infections

Media type: E-Book; Thesis

Title: Metaproteome analysis of the gastrointestinal microbiome during respiratory infections

Contributor: Gierse, Laurin Christopher [Author]; Riedel, Katharina [Degree supervisor]; Seifert, Jana [Degree supervisor]

Corporation: Universität Greifswald

Published: Greifswald, September 2023

Extent: 1 Online-Ressource (PDF-Datei: 121 Seiten, 28187 Kilobyte); Illustrationen (farbig), Diagramme (farbig)

Language: English

Identifier:

RVK notation: XD 1630 : Atmungsorgane insgesamt
XD 1633 : Lungen
YB 6604 : Dissertation, Habilitationsarbeit

Keywords: Atemwegsinfektion > Lungenentzündung > Influenza-A-Virus > Proteomanalyse > Darmflora > Mikroflora > Gastrointestinaltrakt

Origination:

University thesis: Dissertation, Mathematisch-Naturwissenschaftliche Fakultät der Universität Greifswald, 2024

Footnote: Literaturverzeichnis: Seite 89-109. - Literaturangaben

Description: Influenza A Virus, Metaproteomics, Microbiome, Multi Omics, Pneumonia, Respiratory Disease

Respiratory infections are associated with high morbidity and mortality rates worldwide and represent a large burden for healthcare systems. Every year, millions of people die from diseases that are associated with bacterial or viral infections, such as pneumonia. The prevention and treatment of these respiratory infectious diseases is thus a major challenge for our time. Recent research has revealed strong links between the gastrointestinal microbiome and a variety of diseases. While this body of work suggests that a host’s microbiome plays an important role in protection against pathogenic agents, maintenance of immune homeostasis, and acquiring nutrients, our understanding of how infections affect the taxonomic and especially functional composition of the microbiome, remains in its infancy. The aim of this dissertation was to characterize the influence of monocausal respiratory infections on the structure and function of the gastrointestinal microbiome using Metaproteomics. This was done in two different biomedical models. First, infection experiments were performed in swine, a relevant natural pathogen-host system, and second, in an experimental murine infection model. Each animal model has specific advantages that allow to address different concerns. The porcine model allowed individual longitudinal characterization of the gastrointestinal tract microbiome during Influenza A virus (IAV) infection over a 30-day period (paper II), while the identification of pathogen-specific signatures during pneumonia could be performed in the murine model (paper III). As a starting point, a robust multi-omics pipeline for fecal samples that allowed standardized and reproducible analysis of porcine and murine samples was established (Paper I). Of major importance was the contact-free homogenization step for pulverization of permanently frozen fecal samples. This process helped to reduce local effects and increase the comparability of the samples, as the exact same homogenizedmaterial could now be used for each omics technique. The omics analyses were subsequently optimized with protocols designed for the extraction of specific target molecules. This significantly reduced the amount of sample required per analysis, without compromising the quality of the results. Taxonomic characterization of the microbiome from healthy and infected animals revealed commonalities as well as differences across model organisms’ intestinal microbiome compositions. One of the most prominent similarities was the dysbiosis of the gastrointestinal microbiome induced by respiratory infection. This dysbiosis was evident in an alteration of the Firmicutes/Bacteroidetes ratio in both the porcine and murine model. Longitudinal characterization of the porcine intestinal microbiome demonstrated that animals exhibited low interindividual variance and that the gastrointestinal microbiome was subject to natural dynamics. The low interindividual variance enabled the identification of consistent infection-related changes in the longitudinal development of the microbiome (paper II). Thus, IAV-induced dysbiosis of the microbial community was reflected at the taxonomic level in decreased abundance of Lachnospiraceae, Clostridiaceae, Veillonellaceae, and Selenomonadaceae, with concomitant increases in Prevotellaceae and Bacteroidaceae. In addition, the Lactobacillaceae family showed an opposite trend over time when comparing healthy and IAV-infected swine. Complementing the longitudinal data from the porcine model, we used the mouse model to characterize the effects of bacterial and viral induced pneumonia on the intestinal microbiome (paper III). Independent of the pathogen, we detected increased abundance of Desulfovibrionaceae and Odoribacteraceae during pneumonia. In contrast, the abundance of Prevotellaceae, Tannerellaceae, and Eubacteriaceae declined during bacterial and viral infection. Furthermore, the identification of pathogen specific signatures was possible, which was evident in pathogen-dependent differentiation of the intestinal microbiomes. Thus, during pneumococcal pneumonia, increased abundance of Akkermansiaceae and Spirocheataceae was detected with simultaneously reduced Clostridiaceae, whereas IAV infection resulted in an increased abundance of Staphylococcaceae. In addition to taxonomic profiling, the impact of respiratory infections on the functional composition of the intestinal microbiome of swine and mice was investigated. Despite variation in their influence on the taxonomic composition at family level, similar effects of respiratory infections on functional composition were found in both models. In mouse and swine, IAV infection resulted in increased expression of protein groups involved in the synthesis of short-chain fatty acids. This commonality across models suggests that short-chain fatty acids play an important role during respiratory infection and recovery. Analysis of the data obtained from the porcine experiments revealed that the functional composition of the healthy intestinal microbiome exhibited a largely steady state despite some temporal taxonomic dynamics. This result indicated functional redundancy within the microbiome of healthy pigs. Nevertheless, IAV infection resulted in dysbiosis of this stable state. This was reflected by a significant increase in the expression of proteins involved in the transport and metabolism of amino acids and carbohydrates, as well as proteins involved in the production of short-chain fatty acids. Finally, the influence of bacterial and viral infections on the functional composition of the murine intestinal microbiome was also investigated (paper III). Based on the pathogen-specific profiles observed with metaproteomics, it was possible to distinguish between viral and bacterial infections. For example, bacterial colonization and infection resulted in similar functional profiles, with comparable infection driven effects on the intestinal microbiome. However, the alterations in the expression profile in the microbiome of mice colonized with pneumococci were less pronounced than during acute bacterial pneumonia. In contrast, viral infection caused a significantly different functional profile. An exclusive feature of bacterial pneumonia was the decreased expression of proteins associated with energy metabolism (e.g., ATPases) with concomitant increased abundance of transporters or secretory channels (e.g., OmpA, TonB, TolA). In contrast, increased expression of proteins assigned to the ATPase complex were characteristic of viral infections. The data generated in this work provided new insights into the impact of monocausal infections on the taxonomic and functional composition of the microbial community of the gastrointestinal tract. These results may serve as a basis for future research on co-infections. Furthermore, the identification of pathogen specific signatures represents a promising observation for clinical setup.

Access State: Open Access

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