Ontology highlight
ABSTRACT:
PROVIDER: PRJNA886445 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR21814847.fastq.gz | Fastqsanger.gz | |||
| SRR21814848.fastq.gz | Fastqsanger.gz |
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Project description:Microbial fermentation is involved in the processing of a dark tea popular for centuries in Northwest China which has shown many health benefits. This study will examine anti-obesity, hyperlipidemic and hyperglycemic effects of CGMCC No.8730 Eurotium cristatum (EC) fermented dark tea (8730DT).
2019-07-14 | GSE84496 | GEO
Project description:The effects of increasing addition of green tea in dietary changes the bacterial populations in broiler ileum were evaluated. Four hundreds of AA broilers were randomly assigned to four groups with green tea addition of 0, 0.5, 1 and 2 percent in the diet. The body weight showed no difference but a digital increase positively correlated with addition of green tea. The content of green tea had a linear effect of lengthening the ileum villi. The barcoded DNA pyrosequencing method was used to reveal 15 phyla, 1157phylotypes and 3098 16S operational taxonomic units (OTUs). The most predominant bacterial phyla were Firmicutes (56.89%), Actinobacteria (30.58%), Proteobacteria (8.61%) and Bacteroidetes (2.72%). As the proportion of additional green tea increased, the abundance of phylum Actinobacteria (p=0.003) and Proteobacteria (p=0.049) almost linearly increased, while the proportion of Firmicutes (p=0.027) linearly decreased. Only 2 OTUs were significantly affected by the increased additive, Corynebacteriaceae (p=0.011) and Staphylococcaceae (p= 0.006). Triplot analysis suggested that the dominant phyla of Verrucomicrobia, TM7 and Actinobacteria were clearly related to the addition of green tea. Moreover, green tea addition influenced the construction of microbiota, and lengthened the villus in ileum by Monte Carlo permutation test. These findings provide a new understanding of the ileal microbial ecology, which may be useful in modulating the gut microbiome, and also the proper usage of powdered green tea.
2015-09-29 | GSE73516 | GEO
Project description:Purpose: Microarray technologies provide a unique opportunity to deeply investigate bacterial molecular responses to treatments. Pseudomonas syringae pv. actinidiae (Psa) is the causal agent of the bacterial canker of kiwifruit causing severe economic losses worldwide. At present, integrated control strategies include chemical treatments with copper-based products and preventive measures but the high virulence and fast spreading of the bacterium are hardly controlled by such measures, and especially copper use is questioned because of the possible appearance of copper resistant bacterial strains. The present project aims at the identification of Psa responses to green tea treatment (Gunpowder variety) at sub-lethal concentration (0.4 mg/ml). Methods: Psa cells were cultured in liquid KB (controls) or in KB supplemented with Gunpowder tea (Gunpowder-trateted) at 0.4 mg/ml EGCG for 24 h at 28°C. The microarray experiments on Gunpowder treated or untreated samples in biological triplicate resulted in 6 samples to be analyzed. Conclusions: This work identified important molecular mechanisms involved in Psa responses upon Gunpowder green tea treatment.
2019-09-23 | GSE137806 | GEO
Project description:Bacterial and Fungal Communities in Puer Tea
| PRJNA683684 | ENA
Project description:Understanding the bacterial community structure, and their functional analysis for active bioremediation process is essential to design better and cost effective strategies. Microarray analysis enables us to simultaneously study the functional and phylogenetic markers of hundreds of microorganisms which are involved in active bioremediation process in an environment. We have previously described development of a hybrid 60-mer multibacterial microarray platform (BiodegPhyloChip) for profiling the bacterial communities and functional genes simultaneously in environments undergoing active bioremediation process (Pathak et al; Appl Microbiol Biotechnol,Vol. 90, 1739-1754). The present study involved profiling the status of bacterial communities and functional (biodegradation) genes using the developed 60-mer oligonucleotide microarray BiodegPhyloChip at five contaminated hotspots in the state of Gujarat, in western India. The expression pattern of functional genes (coding for key enzymes in active bioremediation process) at these sites was studied to understand the dynamics of biodegradation in the presence of diverse group of chemicals. The results indicated that the nature of pollutants and their abundance greatly influence the structure of bacterial communities and the extent of expression of genes involved in various biodegradation pathways. In addition, site specific factors also play a pivotal role to affect the microbial community structure as was evident from results of 16S rRNA gene profiling of the five contaminated sites, where the community structure varied from one site to another drastically.
2012-12-01 | GSE38004 | GEO
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.
2023-12-30 | E-MTAB-13326 | biostudies-arrayexpress
Project description:Background: While the luminal microbiome composition in the human cervicovaginal tract has been defined, the presence and impact of tissue-adherent ectocervical microbiota remain incompletely understood. Studies of luminal and tissue-associated bacteria in the gastrointestinal tract suggest that they may have distinct roles in health and disease. Here, we performed a multi-omics characterization of paired luminal and tissue samples collected from a clinically well-characterized cohort of Kenyan women. Results: We identified a tissue-adherent bacterial microbiome, with a higher alpha diversity than the luminal microbiome, in which dominant genera overall included Gardnerella and Lactobacillus, followed by Prevotella, Atopobium, and Sneathia. About half of the L. iners dominated luminal samples had a corresponding Gardnerella dominated tissue microbiome. Broadly, the tissue-adherent microbiome was associated with fewer differentially expressed host genes than the luminal microbiome. Gene set enrichment analysis revealed that L. crispatus-dominated tissue-adherent communities were associated with protein translation and antimicrobial activity, whereas a highly diverse microbiome was associated with epithelial remodeling and pro-inflammatory pathways. Communities dominated by L. iners and Gardnerella were associated with low host transcriptional activity. Tissue-adherent microbiomes dominated by Lactobacillus and Gardnerella correlated with host protein profiles associated with epithelial barrier stability, and with a more pro-inflammatory profile for the Gardnerella-dominated microbiome group. Tissue samples with a highly diverse composition had a protein profile representing cell proliferation and pro-inflammatory activity. Conclusion: We identified ectocervical tissue-adherent bacterial communities in all study participants. These communities were distinct from cervicovaginal luminal microbiota in a significant proportion of individuals. This difference could possibly explain that L. iners dominant luminal communities have a high probability of transitioning to high diverse bacterial communities including high abundance of Gardnerella. By performing integrative multi-omics analyses we further revealed that bacterial communities at both sites correlated with distinct host gene expression and protein levels. The tissue-adherent bacterial community is similar to vaginal biofilms that significantly impact women’s reproductive and sexual health.
2023-02-10 | GSE194276 | GEO
Project description:The rate, timing, and mode of species dispersal is recognized as a key driver of the structure and function of communities of macroorganisms, and may be one ecological process that determines the diversity of microbiomes. Many previous studies have quantified the modes and mechanisms of bacterial motility using monocultures of a few model bacterial species. But most microbes live in multispecies microbial communities, where direct interactions between microbes may inhibit or facilitate dispersal through a number of physical (e.g., hydrodynamic) and biological (e.g., chemotaxis) mechanisms, which remain largely unexplored. Using cheese rinds as a model microbiome, we demonstrate that physical networks created by filamentous fungi can impact the extent of small-scale bacterial dispersal and can shape the composition of microbiomes. From the cheese rind of Saint Nectaire, we serendipitously observed the bacterium Serratia proteamaculans actively spreads on networks formed by the fungus Mucor. By experimentally recreating these pairwise interactions in the lab, we show that Serratia spreads on actively growing and previously established fungal networks. The extent of symbiotic dispersal is dependent on the fungal network: diffuse and fast-growing Mucor networks provide the greatest dispersal facilitation of the Serratia species, while dense and slow-growing Penicillium networks provide limited dispersal facilitation. Fungal-mediated dispersal occurs in closely related Serratia species isolated from other environments, suggesting that this bacterial-fungal interaction is widespread in nature. Both RNA-seq and transposon mutagenesis point to specific molecular mechanisms that play key roles in this bacterial-fungal interaction, including chitin utilization and flagellin biosynthesis. By manipulating the presence and type of fungal networks in multispecies communities, we provide the first evidence that fungal networks shape the composition of bacterial communities, with Mucor networks shifting experimental bacterial communities to complete dominance by motile Proteobacteria. Collectively, our work demonstrates that these strong biophysical interactions between bacterial and fungi can have community-level consequences and may be operating in many other microbiomes.
2017-08-02 | GSE85095 | GEO