Ontology highlight
ABSTRACT:
PROVIDER: PRJNA612021 | ENA |
REPOSITORIES: ENA
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Project description:Platanthera praeclara soil orchid mycorrhizal fungi
| PRJNA421973 | ENA
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 parasitic amoeba, Neoparamoeba perurans is the causative agent of Amoebic Gill Disease in salmonids. The parasite has previously been reported to lose virulence during prolonged in vitro maintenance. In this study, the impact of prolonged culture on N. perurans virulence and its proteome was investigated. Three isolates of N. perurans maintained in culture for varying durations were compared. Two isolates, attenuated and virulent, had their virulence assessed in an experimental trial using Atlantic salmon smolts and their bacterial community composition was evaluated by 16S rRNA Illumina MiSeq sequencing. Soluble proteins were isolated from a newly acquired, virulent and attenuated N. perurans culture and were analysed using two-dimensional electrophoresis (2D PAGE) coupled with liquid chromatography tandem mass spectrometry (LC-MS/MS). An experimental challenge trial using Atlantic salmon smolts confirmed a loss in virulence in an N. perurans culture that was maintained in vitro for 3 years. A greater diversity of bacterial communities was found in the microbiome of the virulent isolate harbouring predominant genera belonging to Pseudoaltermonas spp, Vibrio spp and Fluviicola spp. Microbial community richness was reduced in the attenuated microbiome, with a singular species, Thalassopira xiamenensis, representing a large proportion of its microbiome. A collated proteome database of N. perurans, Amoebozoa and four bacterial genera resulted in 24 proteins differentially expressed between the three cultures. The present LC-MS/MS results indicate protein synthesis, oxidative stress and the plausible occurrence of immunomodulation are ultimately upregulated in a newly acquired N. perurans culture and future studies may exploit these protein identifications for therapeutic purposes in infected farmed fish.
2021-09-09 | PXD022328 | Pride
Project description:Disrupted interactions between host and intestinal bacteria are implicated in the development of colorectal cancer (CRC). However, the functional impacts of these inter-kingdom interactions remain poorly defined. To examine this interplay, we performed mouse and microbiota RNA-sequencing on colon tissue from germ-free (GF) and gnotobiotic ApcMin/+;Il10-/- mice associated with microbes from biofilm-positive human CRC tumor (BT) and biofilm-negative healthy (BX) tissues. The bacteria in BT mice differentially expressed >2,900 genes related to bacterial secretion, virulence and biofilms, but only affected 62 host genes. Importantly, the bacterial communities from BT mice were transmissible and carcinogenic when administered to a new GF ApcMin/+;Il10-/- cohort, maintaining a set of 13 bacterial genera. Our findings suggest complex interactions within bacterial communities affecting bacterial composition and CRC development.
2019-12-30 | GSE108156 | GEO
Project description:Orchid associated bacteria Metagenome
| PRJNA483367 | ENA
Project description:Anthropogenic activities have dramatically increased the inputs of reactive nitrogen (N) into terrestrial ecosystems, with potentially important effects on the soil microbial community and consequently soil C and N dynamics. Our analysis of microbial communities in soils subjected to 14 years of 7 g N m-2 year-1 Ca(NO3)2 amendment in a Californian grassland showed that the taxonomic composition of bacterial communities, examined by 16S rRNA gene amplicon sequencing, was significantly altered by nitrate amendment, supporting the hypothesis that N amendment- induced increased nutrient availability, yielded more fast-growing bacterial taxa while reduced slow-growing bacterial taxa. Nitrate amendment significantly increased genes associated with labile C degradation (e.g. amyA and xylA) but had no effect or decreased the relative abundances of genes associated with degradation of more recalcitrant C (e.g. mannanase and chitinase), as shown by data from GeoChip targeting a wide variety of functional genes. The abundances of most N cycling genes remained unchanged or decreased except for increases in both the nifH gene (associated with N fixation), and the amoA gene (associated with nitrification) concurrent with increases of ammonia-oxidizing bacteria. Based on those observations, we propose a conceptual model to illustrate how changes of functional microbial communities may correspond to soil C and N accumulation.
2017-11-21 | GSE107168 | GEO
Project description:Bacterial communities associated with three terrestrial orchid species as revealed by 16S rRNA gene metabarcoding
| PRJEB40289 | ENA
Project description:Disrupted interactions between host and intestinal bacteria are implicated in the development of colorectal cancer (CRC). However, the functional impacts of these inter-kingdom interactions remain poorly defined. To examine this interplay, we performed small RNA sequencing on the stool of from germ-free (GF) and gnotobiotic ApcMin/+;Il10-/- mice associated with microbes from biofilm-positive human CRC tumor (BT) and biofilm-negative healthy (BX) tissues. revealed a group of significant differentially expressed miRNAs specific to BT compared to BX associated ApcMin/+;Il10-/- mice and several miRNAs that correlated with bacterial genera abundances. Our findings suggest complex interactions within bacterial communities affecting host-derived miRNA and CRC development.
2019-12-30 | GSE108164 | GEO