Interactive functional networks in microbiota
The aim of this thesis was to elucidate how various microbial communities work, with a focus on next generation sequencing data. The introduction in chapter 1 focuses on the history of biology, how the field of systems biology arose, and how the rise of nucleic acid sequencing has shaped a completely new field (among others), the microbiome research. In chapter 2, an overview is given how the microbiota can be studied, in connection to metabolic syndrome and its sub-pathologies, including obesity, type II diabetes, elevated blood pressure, and dyslipidemia. We summarize which different methodologies (16S rRNA amplicon sequencing, metagenomics, metatranscriptomics) can be used to investigate the microbiome with different foci, and how as a next step the microbiome can be modelled, in vitro and in silico. Chapter 3 describes the genome and transcriptome of the rat gut commensal Romboutsia ilealis CRIBT. We characterized genomic properties, including those related to metabolism and sporulation abilities. The transcriptome allowed us to investigate the organism’s carbohydrate degradation abilities, including its potential regulation. Chapter 4 is an investigation of an in vitro fermentation system, inoculated with human faecal material and the potential prebiotic Isomalto/malto-polysaccharides. The metatranscriptome of this system gave an insight into which genes are involved in the carbohydrate degradation, and which different types of organisms are involved and potentially need to cooperate for a full utilization of this carbohydrate. In chapter 5, the cow rumen microbiota is investigated under different feeding regimes. The metatranscriptome of the cow rumen microbiota showed distinct patterns depending on the ratio of starch or cellulose enriched feed components, namely maize vs. grass silage. The increase in starch led to a decrease in methane emissions of the cow rumen microbiota, which was reflected in the metatranscriptomics data. Most notably, lower expression levels of genes encoding for proteins involved in methanogenic pathways of the rumen archaeon Methanobrevibacter smithii was observed. The last chapter, the general discussion, mainly discusses the research described in this thesis with a focus on the relevant issues with modelling microbial communities, as well as overall scientific integrity in relationship with microbiome research.
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| Format: | Doctoral thesis biblioteca |
| Language: | English |
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Wageningen University
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| Subjects: | Life Science, |
| Online Access: | https://research.wur.nl/en/publications/interactive-functional-networks-in-microbiota |
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| Summary: | The aim of this thesis was to elucidate how various microbial communities work, with a focus on next generation sequencing data. The introduction in chapter 1 focuses on the history of biology, how the field of systems biology arose, and how the rise of nucleic acid sequencing has shaped a completely new field (among others), the microbiome research. In chapter 2, an overview is given how the microbiota can be studied, in connection to metabolic syndrome and its sub-pathologies, including obesity, type II diabetes, elevated blood pressure, and dyslipidemia. We summarize which different methodologies (16S rRNA amplicon sequencing, metagenomics, metatranscriptomics) can be used to investigate the microbiome with different foci, and how as a next step the microbiome can be modelled, in vitro and in silico. Chapter 3 describes the genome and transcriptome of the rat gut commensal Romboutsia ilealis CRIBT. We characterized genomic properties, including those related to metabolism and sporulation abilities. The transcriptome allowed us to investigate the organism’s carbohydrate degradation abilities, including its potential regulation. Chapter 4 is an investigation of an in vitro fermentation system, inoculated with human faecal material and the potential prebiotic Isomalto/malto-polysaccharides. The metatranscriptome of this system gave an insight into which genes are involved in the carbohydrate degradation, and which different types of organisms are involved and potentially need to cooperate for a full utilization of this carbohydrate. In chapter 5, the cow rumen microbiota is investigated under different feeding regimes. The metatranscriptome of the cow rumen microbiota showed distinct patterns depending on the ratio of starch or cellulose enriched feed components, namely maize vs. grass silage. The increase in starch led to a decrease in methane emissions of the cow rumen microbiota, which was reflected in the metatranscriptomics data. Most notably, lower expression levels of genes encoding for proteins involved in methanogenic pathways of the rumen archaeon Methanobrevibacter smithii was observed. The last chapter, the general discussion, mainly discusses the research described in this thesis with a focus on the relevant issues with modelling microbial communities, as well as overall scientific integrity in relationship with microbiome research. |
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