Ontology highlight
ABSTRACT:
PROVIDER: PRJNA783776 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Background: Germ-free or axenic organisms are valuable tools for studying immunity, digestion, and development in different hosts. Although most of these studies have been conducted on mice, recently, germ-free invertebrate models (e.g. Drosophila and Apis) are used due to their easy husbandry, low cost for production, maintenance and the high number of individuals per generation they produce. However, a limitation of using these insects is the simple bacterial community present in their guts. The gut of the American cockroach Periplaneta americana displays a complex gut bacterial community composed of hundreds of species. Using P. americana, we developed a germ-free omnivorous invertebrate model to investigate how gut bacteria stimulate and shape normal gut development and metabolism. To determine if the insect host is directly affected by the presence of specific members of their bacterial community, gnotobiotic cockroaches were generated by inoculating a set of various P. americana gut-endemic Gram-negative (Bacteroidetes; n=11) and Gram-positive (Firmicutes; n=2) bacterial strains into germ-free insects. Additionally, we were able to recover the ‘normal’ bacterial-induced gut phenotype by co-housing germ-free cockroaches with wildtype P. americana to produce gut-bacteria conventionalized insects. Changes in gene expression profiles from two distinct regions (midgut and hindgut) of P. americana guts were quantified by RNA-Seq analysis of the germfree, gnotobiotic and conventionalized insects. Basic transcriptomics description: High-resolution transcriptome profiling of germ-free, gnotobiotic, and conventionalized treated P. americana midgut and hindguts. Ca. 43 million reads were obtained for each treatment. A de-novo assembly of all sequence reads was performed by Trinity assembler. Transcriptome assembly yielded 369,082 gene models and 554,155 isoforms. After running Trinotate pipeline, 65,047 (12 %) these transcripts matched an annotated product in at least one of the reference databases used (Uniprot, pfam, KEGG, COG). Additionally, 1,008 putative bacterial genes were annotated in the P. americana genome and ultimately excluded from these analyses. After bacteria decontamination, 553,147 assembled isoforms were used for transcript quantification and differential expression analysis using the DESeq2 pipeline. DESeq2 analysis detected 6,730 and 3,958 differentially expressed transcripts among the germ-free, gnotobiotic and conventionalized treatments in P. americana hindgut and midgut, respectively.
2021-07-30 | GSE159954 | GEO
Project description:actinomycetes were isolated from the intestinal tract of Periplaneta americana. Genome sequencing and assembly
| PRJNA765746 | ENA
Project description:Firs 1106 16S rDNA data for the Flemish Gut Flora Project
| EGAD00001001936 | EGA
Project description:Various organic and natural pesticides play a vital role in insect control, leading to variation in their protein profile (Abubakar et al., 2019; James & Xu, 2012). The sex, size, weight, and growth conditions could be the possible factors associated with fluctuations in the concentration of protein production in the cockroach (Bouchebtiet al., 2022) The current study of Perplanata americana under pesticide activity considered to observe the proteomics of Brain and protein expression under stressed conditions. 15 cockroaches were exposed to 5g of Laxman Rekha (11:1 ratio) to assess the impact of pesticide on protein synthesis. National and international research conducted on aqueous and alcoholic extraction of gut, exoskeleton and brain protein of Periplaneta spp. and Blatta spp have revealed 10 potential antibacterial proteins between 18 kDa to 72kDa range. These proteins were purified using chromatographic techniques like single dimension reducing PAGE, FPLC-MS, LC-MS, MALDI TOF-MS etc. The current study is aimed at isolation, identification and characterisation of proteins from cockroach brain tissue lysate using Liquid chromatography and Orbitrap Mass spectrometer technique. The data analysis was done using Thermo Proteome Discoverer software version 2.2. 0.388. The database used was Uniprot-Periplaneta americana.
2024-06-27 | PXD052356 | Pride
Project description:In this study, we performed a comparative analysis of gut microbiota composition and gut microbiome-derived bacterial extracellular vesicles (bEVs) isolated from patients with solid tumours and healthy controls. After isolating bEVs from the faeces of solid tumour patients and healthy controls, we performed spectrometry analysis of their proteomes and next-generation sequencing (NGS) of the 16S gene. We also investigated the gut microbiomes of faeces from patientsand controls using 16S rRNA sequencing. Machine learning was used to classify the samples into patients and controls based on their bEVs and faecal microbiomes.
2024-08-08 | PXD047510 | Pride
Project description:We compared the microbiota of paired mouse caecal contents and faeces by applying a multi-omic approach, including 16S rDNA sequencing, shotgun metagenomics, and shotgun metaproteomics. The aim of the study was to verify whether faecal samples are a reliable proxy for the mouse colonic luminal microbiota, as well as to identify changes in taxonomy and functional activity between caecal and faecal microbial communities, which have to be carefully considered when using stool as sample for mouse gut microbiota investigations.
2017-03-31 | PXD004911 | Pride
Project description:Periplaneta americana Genome sequencing and assembly
| PRJNA600417 | ENA