Project description:Here we have compared adult wildtype (N2) C. elegans gene expression when grown on different bacterial environments/fod sources in an effort to model naturally occuring nematode-bacteria interactions at the Konza Prairie. We hypothesize that human-induced changes to natural environments, such as the addition of nitrogen fertalizer, have effects on the bacterial community in soils and this drives downstream changes in the structure on soil bacterial-feeding nematode community structure. Here we have used transcriptional profiling to identify candidate genes involved in the interaction of nematodes and bacteria in nature.
2009-05-02 | GSE15923 | GEO
Project description:Genome sequencing and assembly of bacteria isolated from different environments
Project description:Many studies have shown that space environments can affect bacteria to varying degrees and cause a range of mutations. However, so far, there have been no relevant studies on the effects of long-term space flight (>1 month) on bacteria and the effects of different space residence time on bacteria. Therefore, we utilized the Staphylococcus warneri isolated from the Shenzhou-10 spacecraft that had experienced a space flight to carry into space again, in order to study the influence of the long flight formed by two space flights on the proteomic level.
Project description:Bacterial transcription factors (TFs) regulate gene expression to adapt to changing environments; when combined, the TF’s regulatory actions comprise transcriptional regulatory networks (TRNs). The chromatin immunoprecipitation (ChIP) assay is the major contemporary method for mapping in vivo protein-DNA interactions in the genome. It enables the genome-wide study of transcription factor binding sites (TFBSs) and gene regulation. Although rapidly accumulating publicly-available ChIP data are a valuable resource for the study of gene regulation, there are no full datasets of ferric uptake regulator (Fur) across gram-negative bacteria. Here, we present the genome-wide binding for Fur in multi-species.
Project description:Bacteria belonging to phylum Gemmatimonadetes are found in a wide variety of environments and are particularly abundant in soils. To date, only two Gemmatimonadetes strains have been characterized. Here we report the complete genome sequence and methylation pattern of Gemmatirosa kalamazoonensis KBS708 (ATCC BAA-2150; NCCB 100411), the first characterized Gemmatimondetes strain isolated from soil. Examination of the methylome of Gemmatirosa kalamazoonenis KBS708 using kinetic data from single-molecule, real-time (SMRT) sequencing on the PacBio RS
Project description:Intracellular bacterial pathogens can exhibit large heterogeneity in growth rate inside host cells with major consequences for the infection outcome. If and how the host responds to this heterogeneity remains poorly understood. Here, we combined a fluorescent reporter of bacterial cell division with single-cell RNA-seq analysis to study the macrophage response to different intracellular states of the model pathogen Salmonella enterica serovar Typhimurium. The transcriptomes of individual infected macrophages revealed a spectrum of functional host response states to dividing and non-dividing bacteria. Intriguingly, macrophages harboring non-dividing Salmonella display hallmarks of the pro-inflammatory M1 polarization state and differ little from bystander cells, suggesting that non-dividing bacteria evade recognition by intracellular immune receptors. By contrast, macrophages containing dividing bacteria have turned into an anti-inflammatory, M2-like state, as if fast-growing intracellular Salmonella overcome host defense by reprogramming macrophage polarization. Additionally, our clustering approach reveals intermediate host functional states between these extremes. Altogether our data suggest that gene expression variability in infected host cells shapes different cellular environments, some of which may favor a growth arrest of Salmonella facilitating immune evasion and the establishment of a long-term niche; while others allow Salmonella to escape intracellular antimicrobial activity and proliferate.
Project description:Microorganisms exist and survive in complex and variable environments. Bacteria communities response and adapt to the changing conditions. The Mechanisms underlying bacterial survival can be elucidated through the use of multi-omics techniques. Here, we test an approach for measuring how different temperatures affected bacterial physiological functions. Proteomic and metabolomic analyses were conducted on Vibrio parahaemolyticus LF1113 under different temperatures
Project description:Dictyostelium discoideum amoebae feed by ingesting bacteria, then killing them in phagosomes. Ingestion and killing of different bacteria have been shown to rely on largely different molecular mechanisms. One would thus expect that D. discoideum adapts its ingestion and killing machinery when encountering different bacteria. In this study, we investigated by RNA sequencing if and how D. discoideum amoebae respond to the presence of different bacteria by modifying their gene expression patterns. Each bacterial species analyzed induced a specific modification of the transcriptome. Bacteria such as Bacillus subtilis, Klebsiella pneumoniae, or Mycobacterium marinum induced a specific and different transcriptional response, while Micrococcus luteus did not trigger a significant gene regulation. Although folate has been proposed to be one of the key molecules secreted by bacteria and recognized by hunting amoebae, it elicited a very specific and restricted transcriptional signature, distinct from that triggered by any bacteria analyzed here. Our results indicate that D. discoideum amoebae respond in a highly specific, almost non-overlapping manner to different species of bacteria. We additionally identify specific sets of genes that can be used as reporters of the response of D. discoideum to different bacteria.