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ABSTRACT:
PROVIDER: PRJNA879196 | ENA |
REPOSITORIES: ENA
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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:Our aim was to use next-generation sequencing to identify the miRNAs associated with caste determination in queen-destined and worker-destined larvae of the bumble bee, Bombus terrestris. We found that two miRNAs (miR-6001-5p and miR-6001-3p) were upregulated in queen-destined larvae that had passed the critical developmental period when caste becomes irreversible in this species. The two miRNAs form a duplex that is expressed from the gene VHDL, a homologue of Vitellogenin. This finding suggests a new connection between miRNAs and a key protein known to play multiple roles in regulating reproductive division of labour in eusocial Hymenoptera .
2017-03-31 | GSE77870 | GEO
Project description:A challenging task to reveal health and disease-associated microbiome signatures is to disentangle regulatory networks of microbes among themselves and with their host. Using the integrated Drosophila-commensal-pathogen model system, we here reported that Drosophila and commensal bacterium L. plantarum cooperated to compete with the opportunistic pathogen S. marcescens. At first, we found that Drosophila larvae and L. plantarum efficiently antagonized S. marcescens in the coexisting niche by suppressing population size and altering metabolism. Drosophila and L. plantarum synergistically enforced the transcriptional reprogramming of S. marcescens, including lipopolysaccharide synthesis, peptidoglycan synthesis, and cationic antimicrobial peptide (CAMP) resistance. More importantly, bacterial single-cell RNA sequencing reveals that larvae and L. plantarum modulated carbon utilization and resistance heterogeneity of S. marcescens. On the other hand, L. plantarum adjusted the transcriptional reprogramming in adaption to the alliance with larvae for colonization resistance to S. marcescen. Altogether, our findings provide amenable insight into the host–microbe–microbe interplays at both bulk and single-cell resolutions, advancing fundamental concepts of interactome and precise manipulation of bacterial communities.
2024-10-01 | GSE251782 | GEO
Project description:A challenging task to reveal health and disease-associated microbiome signatures is to disentangle regulatory networks of microbes among themselves and with their host. Using the integrated Drosophila-commensal-pathogen model system, we here reported that Drosophila and commensal bacterium L. plantarum cooperated to compete with the opportunistic pathogen S. marcescens. At first, we found that Drosophila larvae and L. plantarum efficiently antagonized S. marcescens in the coexisting niche by suppressing population size and altering metabolism. Drosophila and L. plantarum synergistically enforced the transcriptional reprogramming of S. marcescens, including lipopolysaccharide synthesis, peptidoglycan synthesis, and cationic antimicrobial peptide (CAMP) resistance. More importantly, bacterial single-cell RNA sequencing reveals that larvae and L. plantarum modulated carbon utilization and resistance heterogeneity of S. marcescens. On the other hand, L. plantarum adjusted the transcriptional reprogramming in adaption to the alliance with larvae for colonization resistance to S. marcescen. Altogether, our findings provide amenable insight into the host–microbe–microbe interplays at both bulk and single-cell resolutions, advancing fundamental concepts of interactome and precise manipulation of bacterial communities.
2024-10-01 | GSE251781 | GEO
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. Agilent one-color CGH experiment and one-color Gene Expresssion expereiment,Organism: Genotypic designed Agilent-17159 Genotypic designed Agilent Multibacterial 8x15k Array , Labeling kits: Agilent Genomic DNA labeling Kit (Part Number: 5190-0453) and Agilent Quick Amp Kit PLUS (Part number: 5190-0442).
2012-12-01 | E-GEOD-38004 | biostudies-arrayexpress
Project description:Bacterial communities in Megastigmus spermotrophus (Hymenoptera: Torymidae) adult, pupae and larvae characterized by 16S-amplicon 454 pyrosequencing
| PRJNA239784 | 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