Global ETD Search
Search theses and dissertations gathered from participating repositories worldwide. Every result links back to the library that holds it. No account is needed.
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Showing 1 to 19 of 19 for “"shotgun metagenomics"”.
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Shotgun metagenomics exploration of fermented food microbiomes
… foods from various parts of the world using shotgun metagenomics. These 58 foods consist of a wide range of products, many of which have seen a recent resurgence in popularity, due to the emerging importance of the human microbiome and health. Many of these foods have not been investigated …
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Shotgun metagenomics-based exploration of kefir microbiomes
… can provide. Chapter 2 is focused on the shotgun metagenomics-based analysis of 256 kefir milk samples produced from milk kefir grains sourced from various parts of the world. This chapter provides considerable insight into the heterogeneity of these populations, while also uncovering …
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From genomes to metagenomes: Big data analysis of microbes related to public health
… growing on hospital showerheads using shotgun metagenomics, (2) evaluate the response of the gut microbiome to acute diarrhea episodes along a rural-to-urban gradient in Northern Ecuador, and (3) detect and quantify recent gene transfer events among closely related genomes as the …
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Recovery and quality estimation of metagenomic assembled genomes of eukaryotes
… microbial communities (e.g on the human skin). Shotgun metagenomics can provide access to the combined genetic information of a community in a culture independent manner. Using de novo assembly and post processing methods, it can lead to the generation of so called metagenomic assembled genomes …
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Molecular characterization of microbial communities in small-scale biodigesters using whole genome shotgun metagenomic approach
… in rural areas. This study employs whole-genome shotgun metagenomics integrating data from metagenomic reads, contigs, and metagenome-assembled genomes (MAGs) can achieve a more comprehensive understanding of microbial taxonomy and functional capabilities in biodigesters. This study investigates …
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The mucosal microbiome of inflammatory bowel diseases
… the viability of using mucosal samples for shotgun metagenomics or metatranscriptomics. Taxonomic classification is a corner stone for the characterisation of microbial communities, but currently many studies are limited to genus level classification. Thus, we developed SPINGO, a flexible …
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Using Culturomics to Characterize the Gastrointestinal Microbiota of Donors for Patients with Bipolar Disorder Experiencing Depression
… from fecal samples were characterized using shotgun metagenomics. From the donor stool, 78 different species of bacteria were isolated across 43 genera including Bacteroides, Bifidobacterium, Collinsella, Streptococcus, Dorea, and Coprococcus. Patients diagnosed with BD, experiencing severe …
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Enabling the discovery of novel bioactives and enzymes from billions of protein sequences
… of these microorganisms have yet to be cultured. Metagenomics- based methods allow the culture-independent analysis of any biome through sequencing the whole DNA content of an environment sample and analysing it with computational methods. MGnify is one of the most widely used platforms for the …
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Tracking Antibiotic Resistance throughout Agroecosystems
… through 16S rRNA amplicon sequencing and shotgun metagenomics. Although antibiotic concentrations dissipated in the soil after 28 days after amendment application, antibiotic resistance presence was recoverable throughout the entire 120d growing season in the compost and manure amendments, …
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An integrated multi-omics approach to improve our understanding of ageing and neurodegeneration
… analyse single-nucleus transcriptomics and shotgun metagenomics data types along with their integration at the pathway level. From our transcriptomics analysis on 84 healthy individuals across the human life span, we identified that the astrocytes in prefrontal cortex assist in brain …
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LARGE-SCALE METAGENOMIC ANALYSIS TO IDENTIFY HUMAN GUT MICROBIOME BIOMARKERS OF CARDIOMETABOLIC HEALTH
… and host lipid metabolism. We integrated shotgun metagenomics and metabolomics from stool samples to assess the effects of two RS types, RS2 and RS4. Each RS promoted distinct shifts in both the microbiome’s taxonomic composition and metabolic potential, including the upregulation of genes …
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Multi-omics approaches for diagnosis, prognosis and response to treatment of colorectal cancer.
… approach (coding and non-coding transcriptome, metagenomics, and mutational status) investigated in different types of biospecimens from the same subjects (stool, plasma, primary tissue) for the diagnosis and prognosis of patients with CRC, identifying specific signatures. Samples collected from …
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Impact assessment of different agricultural practices in grapevine soil and must microbiota
… (16S rRNA and ITS2) for taxonomic profiling, and shotgun metagenomics for functional analysis. The results showed that vintage and location were the primary factors influencing both bacterial and fungal microbiota in soil and must. The evaluated agricultural practices had a smaller, though …
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GENOMIC AND MICROBIOME ANALYSIS TO IMPROVE FILLET YIELD AND QUALITY TRAITS IN RAINBOW TROUT
… we employed both 16S rRNA gene sequencing and shotgun metagenomics to identify taxa and pathways predictive of fillet color. Fish with red fillets were enriched (LDA score > 1.5) for Leuconostoc lactis, Corynebacterium variabile, Jeotgalicoccus halotolerans, and Leucobacter …
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Leveraging community-based sequencing approaches to characterise the dairy microbiome
… in food or food-related samples. In this thesis, shotgun metagenomic sequencing was employed to investigate microbial communities in bulk tank milk. First, shotgun sequencing was used to determine the impact of farm cleaning methods on the microbiome. The results revealed that seasonality and …
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Development and application of genomic tools for characterising genetic variation in soil-transmitted helminths
… to: (i) evaluate the feasibility of low-depth shotgun metagenomic analysis, also known as ‘genome skimming,’ using faecal samples to diagnose helminth infections and recover genetic information from helminths; (ii) examine the genetic variation of nuclear and mitochondrial DNA targets …
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A comprehensive study of Salmonella infections and microbial analysis of probiotics on beef cattle
… were subjected to 16S rRNA and targeted enriched shotgun metagenomics to evaluate microbial communities and resistance genes of bacteria present. A portion of the liver abscess and mesenteric lymph nodes were tested for presence of Salmonella using PCR with further analysis of enumeration and …
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Mapping the Gut Microbiota and its Protective Functions Against Bacterial Enterocolitis
… studies. Nearly 2,500 mouse gut-derived shotgun metagenomes were used to characterise the taxonomic structure of the global mouse gut microbiota and identify factors associated with variation between studies. These analyses found that virtually every species of the mouse gut microbiota …
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MICROBIAL GUARDIANS OF THE SAVANNAH: UNRAVELING THE GUT MICROBIOME FOR AFRICAN CARNIVORE CONSERVATION
<p>Non-invasive fecal sampling is essential for wildlife gut microbiome (GMB) research, yet field conditions often limit preservation options. I compared gut bacterial communities in paired fecal samples preserved in stabilization tubes and air-dried in paper bags collected from anesthetized …