Project description:We investigated daily oscillations in salivary miRNA and microbial RNA to explore relationships between these components of the gut-brain-axis and their implications in human health. Nine subjects provided 120 saliva samples at designated times, on repeated days. Samples were divided into three sets for exploration and cross-validation. Identification and quantification of host miRNA and microbial RNA was performed using next generation sequencing. Eleven miRNAs and 11 microbial RNAs demonstrated consistent diurnal oscillation across the first 2 sample sets and accurately predicted collection time in the hold-out set based on multivariate logistic regression modeling. Associations among five circadian miRNAs and four circadian microbial RNAs were observed.
Project description:We recruited 24 Mongolian volunteers,6 of which were T2D cases(sample T1-T6), 6 were prediabetes cases(sample P1-P6), and 12 were health cases(sample C1-C12). The metagenomic analysis of gut microbiota from the volunteers’ fecal samples was performed. We compared the microbial differences in the three groups, and analyzed the differences of the stool microbial function.
Project description:To determine whether and how warming affects the functional capacities of the active microbial communities, GeoChip 5.0 microarray was used. Briefly, four fractions of each 13C-straw sample were selected and regarded as representative for the active bacterial community if 16S rRNA genes of the corresponding 12C-straw samples at the same density fraction were close to zero.
Project description:Morphine causes microbial dysbiosis. In this study we focused on restoration of native microbiota in morphine treated mice and looked at the extent of restoration and immunological consequences of this restoration. Fecal transplant has been successfully used clinically, especially for treating C. difficile infection2528. With our expanding knowledge of the central role of microbiome in maintenance of host immune homeostasis17, fecal transplant is gaining importance as a therapy for indications resulting from microbial dysbiosis. There is a major difference between fecal transplant being used for the treatment of C. difficile infection and the conditions described in our studies. The former strategy is based on the argument that microbial dysbiosis caused by disproportionate overgrowth of a pathobiont can be out-competed by re-introducing the missing flora by way of a normal microbiome transplant. This strategy is independent of host factors and systemic effects on the microbial composition. Here, we show that microbial dysbiosis caused due to morphine can be reversed by transplantation of microbiota from the placebo-treated animals.
Project description:To study the microbial functions, metaproteomes were extracted from 36 samples of fermented tea leaves and subjected to LC-MS/MS analyses. The MS/MS data were searched against the UniProt-protein database of the dominant microorganisms in the sample as identified by previous meta-barcoding analysis. In total, 5442479 microbial proteins, including amine oxidase, aminopeptidase, carboxypeptidase and catalase, were identified in each sample.
Project description:To identify the mechanism of Microbial Influenced Corrosion (MIC) and the bacterial response toward corrosion, we conducted whole genome microarray expression profile. At log phase, the cell of Clostridium carboxidivorans using iron granule as an electron donor (corroding iron) was collected as a sample, and that of using syngas as an electron donor was collected as a control.
Project description:Up to date, most metaproteomic studies of the gut microbiota describe the use of stool sample pretreatment methods to enrich for microbial components. However, a specific investigation aimed at assessing if, how and to what extent this may impact on the final taxonomic and functional results is still lacking. Here, stool replicates were either pretreated by differential centrifugation (DC) or not centrifuged (NC). Protein extracts were then processed by filter-aided sample preparation, single-run LC and high-resolution MS, and the metaproteomic data were compared by spectral counting. DC led to a higher number of identifications, a significantly richer microbial diversity, as well as to reduced information on the non-microbial components (host and food) when compared to NC. Nevertheless, dramatic differences in the relative abundance of many gut microbial taxa were also observed, including a significant change in the Firmicutes/Bacteroidetes ratio. Furthermore, several microbial functional categories, including cell surface enzymes, membrane-associate proteins, and flagella, were significant reduced after DC. In conclusion, this work underlines that a critical evaluation is needed when selecting the appropriate stool sample processing protocol in the context of a metaproteomic study, depending on the specific target to which the research is aimed.