Project description:Metagenome data from soil samples were collected at 0 to 10cm deep from 2 avocado orchards in Channybearup, Western Australia, in 2024. Amplicon sequence variant (ASV) tables were constructed based on the DADA2 pipeline with default parameters.
Project description:This clinical trial studies universal screening for deoxyribonucleic acid (DNA) mismatch repair deficiency in patients with endometrial cancer, mutations in the genes responsible for Lynch syndrome (inherited forms of endometrial cancers) and other DNA changes that could help guide treatment strategies. Universal tumor DNA sequencing may help doctors better understand how to personalize care, increase length of life, and increase quality of life in patients with endometrial cancer and their relatives.
Project description:Thiabendazole (TBZ), a benzimidazole used against postharvest fungal growth and as anthelmintic in livestock farming, is highly persistent in soil (DT50> 1-2 years) and therefore challenging concerning its environmental management. In our recent copious attempts to isolate organisms that degrade TBZ, at best, we ended up with a soil microbial enrichment capable of accelerated TBZ degradation. Here, we employed a multi-omic approach combined with DNA stable isotope probing (SIP) for elucidating the underlying system complexity. We obtained 18 high-quality metagenome-assembled genomes, with six being dominant and versatile concerning their putative xenobiotics degradation ability. SIP combined with microbiome analysis verified our previous results about the key role of a Sphingomonas strain in TBZ degradation. Next to this, metabolomics suggested minimal/no cross-feeding events, and Sphingomonas being the sole TBZ degrader. RNA sequencing and proteomics analysis of the consortium using TBZ or succinate as sole carbon sources showed the enhanced expression in Sphingomonas of a carbazole dioxygenase locus with putative role in the TBZ degradation. Gene expression networking analysis suggested the interaction of Sphingomonas with a Hydrogenophaga strain that possibly contributes to the overall cobalamin balance. Our study depicts the need for integrated omic approaches for understanding complex interactions frequently occurring in bioremediation.
Project description:The aim of this study was to identify TBBPA-degrading organisms in a complex microbial community by a metagenome-based functional metaproteomic approach, using protein-based stable isotope probing (protein-SIP). Firstly, the degradation kinetics were evaluated in order to simulate the decrease of residual mass of the labelled compound based on experimental data. In sequence, a metagenome was generated, and biomass was collected in different time-points for protein-SIP in incubations with 13C-TBBPA. This approach allowed for the identification organisms assimilating labelled carbon from the cometabolic degradation of a micropollutant.
Project description:The goal of this observational study is to screen and differentiate common cancers in participants with or without suspicious lesions. The main question the investigators aim to answer is: Can the developed model, using peripheral blood cell-free DNA sequencing, work well in screening and classifying common cancers especially in the early stages? Participants will undergo the collection of 15~20ml of blood and 1~2 telephone follow-up calls.
Project description:Dietary intake of fruits and vegetables (FV) has been inversely associated with lower risk of ulcerative colitis. A pig model was used to evaluate the impact of feeding FV on the host response to dextran sulfate sodium (DSS)-induced colitis. Methods: Six-week-old pigs were fed a grower diet alone or supplemented with lyophilized FV equivalent to the half (half-FV) or full (full-FV) daily levels recommended for humans by the Dietary Guidelines for Americans (DGA). Pigs were fed a 1) grower diet alone (negative control), 2) grower diet and orally treated with 4% DSS for 10 days to induce colitis (positive control), 3) half-FV diet treated with 4% DSS or 4) full-FV diet treated with 4% DSS. Pigs were monitored for the development of clinical signs of colitis. Proximal colon (PC) contents and mucosa (PCM) were collected for gut metagenome, tissue transcriptome and histopathological analysis. Results: Pigs fed the full-FV diet did not exhibit diarrhea, showed less fecal occult blood (FOB), PCM crypt hyperplasia but with no differential expressed genes (DEG) or changes in PC microbiome diversity (p < 0.05). Pigs within the half-FV group exhibited increased group FOB and DEG associated with tissue remodeling, crypt and goblet cell hyperplasia in the PCM and no changes in PC microbiome diversity and two pigs exhibiting diarrhea (p < 0.05). Pigs within the DSS positive control group exhibited a reduced DEG involved with intestinal immune response and PC microbiome diversity with altered metagenome, increased group PCM erosion and FOB with persistent diarrhea in one pig (p < 0.05) Conclusions: Overall, our results showed that pigs fed a three-week full-FV supplemented diet, were resistant to DSS-induced colitis with a differential dose-dependent protective effect on host intestinal tissue and gut metagenome when exposed to an inflammatory challenge.
Project description:By using metagenome resolved protein stable isotope probing (protein-SIP) through incubations of identical reactors with 13C labelled bicarbonate over a period of 48 hours, the study aims to map differences in the metabolic behaviour of the microbial community during anaerobic digestion.
Project description:<p>Integrative taxonomy is a fundamental part of biodiversity and combines traditional morphology with additional methods such as DNA sequencing or biochemistry. Here, we aim to establish untargeted metabolomics for use in chemotaxonomy. We used three thallose liverwort species <em>Riccia glauca</em>, <em>R. sorocarpa</em> and <em>R. warnstorfii</em> (order Marchantiales, Ricciaceae) with <em>Lunularia cruciata</em> (order Marchantiales, Lunulariacea) as an outgroup. Liquid chromatography high-resolution mass-spectrometry (UPLC/ESI-QTOF-MS) with data-dependent acquisition (DDA-MS) were integrated with DNA marker-based sequencing of the trnL-trnF region and high-resolution bioimaging. Our untargeted chemotaxonomy methodology enables us to distinguish taxa based on chemophenetic markers at different levels of complexity: (1) molecules, (2) compound classes, (3) compound superclasses and (4) molecular descriptors. For the investigated <em>Riccia</em> species, we identified 71 chemophenetic markers at the molecular level, a characteristic composition in 21 compound classes, and 21 molecular descriptors largely indicating electron state, presence of chemical motifs and hydrogen bonds. Our untargeted approach revealed many chemophenetic markers at different complexity levels that can provide more mechanistic insight into phylogenetic delimitation of species within a clade than genetic-based methods coupled with traditional morphology-based information. However, analytical and bioinformatics analysis methods still need to be better integrated to link the chemophenetic information at multiple scales.</p><p><br></p><p>To characterize, classify and name species, taxonomy is a fundamental part of biodiversity research. Integrative taxonomy combines traditional morphology-based methods with additional methods from different disciplines like sequencing. Bioinformatics analysis methods and research data are becoming increasingly important but greater integration is needed to link the information at multiple scales. Here, we present a reference dataset that investigates the principles of integrating metabolomics, sequencing, and phenotypic data into integrative taxonomy.</p>
Project description:Replacement of high-value fish species with cheaper varieties or mislabelling of food unfit for human consumption is a global problem violating both consumers’ rights and safety. For distinguishing fish species in pure samples, DNA approaches are available; however, authentication and quantification of fish species in mixtures remains a challenge. In the present study, a novel high-throughput shotgun DNA sequencing approach applying masked reference libraries was developed and used for authentication and abundance calculations of fish species in mixed samples. Results demonstrate that the analytical protocol presented here can discriminate and predict relative abundances of different fish species in mixed samples with high accuracy. In addition to DNA analyses, shotgun proteomics tools based on direct spectra comparisons were employed on the same mixture. Similar to the DNA approach, the identification of individual fish species and the estimation of their respective relative abundances in a mixed sample also were feasible. Furthermore, the data obtained indicated that DNA sequencing using masked libraries predicted species-composition of the fish mixture with higher specificity, while at a taxonomic family level, relative abundances of the different species in the fish mixture were predicted with slightly higher accuracy using proteomics tools. Taken together, the results demonstrate that both DNA and protein-based approaches presented here can be used to efficiently tackle current challenges in feed and food authentication analyses.