Lactobacillus
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA788690 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR17226955_1.fastq.gz | Fastqsanger.gz | |||
| SRR17226955_2.fastq.gz | Fastqsanger.gz | |||
| SRR17226956_1.fastq.gz | Fastqsanger.gz | |||
| SRR17226956_2.fastq.gz | Fastqsanger.gz | |||
| SRR17226957_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 36 |
Similar Datasets
Project description:The genus Lactobacillus contains over 100 different species that were traditionally considered to be uniformly non-motile. However, at least twelve motile species are known to exist in the L. salivarius clade of this genus. Of these, Lactobacillus rumnis is the only motile species that is also autochthonous to the mammalian gastrointestinal tract. The genomes of two L. ruminis strains, ATCC25644 (human isolate, non-motile) and ATCC27782 (bovine isolate, motile) were sequenced and annotated to identify the genes responsible for flagellum biogenesis and chemotaxis in this species. Transcriptome analysis revealed that motility genes were transcribed at a significantly higher level in motile L. ruminis ATCC27782 than in non-motile ATCC25644 during the motile growth phase.
2012-07-10 | GSE31556 | GEO
Project description:Bacterial membrane vesicles have been implicated in a broad range of functions in microbial communities from pathogenesis to gene transfer. Though first thought to be a phenomenon associated with Gram-negative bacteria, vesicle production in Staphylococcus aureus, Lactobacillus plantarum, and other Gram-positives has recently been described. Here we characterize MVs from three different Lactobacillus species (L. acidophilus, L. casei, and L. reuteri), determining that the size and protein composition of Lactobacillus-derived MVs have both similarities and differences with those produced by Gram-negative bacteria. Using proteomics, we identified more than 80 protein components from Lactobacillus-derived MVs, including some that were enriched in the vesicles themselves. For each species, vesicular proteins were categorized based on biological pathway and examined for subcellular localization signals in an effort to identify possible sorting mechanisms for MV proteins. Additionally, differences between MVs of other Lactobacillus species and Gram positive bacteria were highlighted. Information in this study will assist in elucidation of the formation and functions of MVs, as well as the development of therapeutic tools for vaccines, diagnosis, and therapeutic delivery.
2019-11-12 | PXD011278 | Pride
Project description:The genus Flaveria has been extensively used as a model to study the evolution of C4 photosynthesis as it contains both C3 and C4 species as well as a number of species that exhibit intermediate types of photosynthesis. The current phylogenetic tree of the Flaveria genus contains 21 of the 23 known Flaveria species and has been constructed using a combination of morphologicial data and three non-coding DNA sequences (nuclear encoded ETS, ITS and chloroplast encoded trnl-F). However, recent studies have suggested that phylogenetic trees inferred using a small number of molecular sequences may often be incorrect. Moreover, studies in other genera have often shown substantial differences between trees inferred using morphological data and those using molecular sequence. To provide new insight into the phylogeny of the genus Flaveria we utilize RNA-Seq data to construct a multi-gene concatenated phylogenetic tree of 17 Flaveria species. Furthermore, we use this new data to identify 14 C4 specific non-synonymous mutation sites, 12 of which (86%) can be independently verified by public sequence data. We propose that the data collection method provided in this study can be used as a generic method for facilitating phylogenetic tree reconstruction in the absence of reference genomes for the target species. 18 Flaveria sample including 11 species are sequenced, other three samples were also sequenced as out-group. In all, 21 samples.
2015-01-08 | E-GEOD-54339 | biostudies-arrayexpress
Project description:Lactobacillus draft genomes_Jiangnan University
| PRJNA658852 | ENA
Project description:Background: Lactobacillus plantarum is found in a variety of fermented foods and as such, consumed for centuries. Some strains are natural inhabitants of the human gastro-intestinal tract and like other Lactobacillus species, L. plantarum has been extensively studied for its immunomodulatory properties and its putative health-promoting effects (probiotic). Being the first line of host defense intestinal epithelial cells (IEC) are key players in the recognition and initiation of responses to gut microorganisms. Results: Using high-density oligonucleotide microarrays we examined the gene expression profiles of differentiated Caco-2 cells exposed to various doses of L. plantarum. In addition, the effects were correlated to monolayer permeability studies and measurement of lactic acid production. A transcriptional dose-dependent IEC response to L. plantarum was found. Incubation of Caco-2 with a low bacterial dose induced a specific response, not due to cytotoxicity or production of lactic acid, including modulation of cell cycle and cell signaling functions. Exposure of Caco-2 cells to larger amounts of bacteria, accompanied by the production of lactic acid and glucose depletion, provoked increased permeability and supposed non-specific defense responses. Conclusions: These results suggest that IEC are able to sense and react to the presence of gut bacteria. This study provides the first description of global transcriptional response of human IEC to a commensal lactic acid bacterium, and it shows the importance of choosing physiological bacterial doses to prevent the observation of non-specific host reactions. Caco-2 cells were exposed for 10h to Lactobacillus. Fourteen samples are analyzed: 4 control Caco-2, 4 Caco-2 exposed to a low dose (10) of Lactobacillus, 4 Caco-2 exposed to a medium dose (100) of Lactobacillus, 2 Caco-2 exposed to a high dose (1000) of Lactobacillus. All 14 RNA samples are labeled with Cy5 and hybridized to a common reference (undifferentiated Caco-2, untreated) RNA labeled with Cy3
2010-06-11 | E-GEOD-4325 | biostudies-arrayexpress
Project description:The Xenopus genus is well known for the high degree of polyploidy observed in its constituent species, but there is minimal information about transcriptional changes observed in these highly polyploid vertebrates. Xenopus andrei, an octoploid species within the Xenopus genus, presents a novel system for assessing a polyploid transcriptome during vertebrate development. RNA-Seq data was generated at nine different developmental stages ranging from unfertilized eggs through late tailbud stages. Additionally, using Trinity, RNA-seq data from all nine stages was pooled to create a draft de novo assembly of the transcriptome. This represents the first published assembly of an octoploid vertebrate transcriptome. This RNA-Seq and transcriptome data will be useful in comparing polyploid transcriptomes across Xenopus species, as well as understanding evolutionary implications of whole-genome duplication in vertebrates.
2018-03-10 | GSE111639 | GEO
Project description:Lactobacillus casei is remarkably adaptive to diverse habitats. To understand the evolution and adaptation of Lb. casei strains isolated from different environments, the gene content of 22 Lb. casei strains isolated from various habitats (cheeses, n=8; plant materials, n=8; and human sources, n=6) were examined by comparative genome hybridization with an Lb. casei ATCC 334-based microarray. Comparative genome hybridization was performed against an Affymetrix custom microarray designed to include 2,661 (97%) chromosomal and 17 (85%) plasmid CDSs predicted to occur in Lb. casei ATCC 334, as well as all predicted CDSs in the draft Lb. helveticus CNRZ 32 genome. CDSs that were not included in the microarray design were all transposase-encoding genes.
2010-06-21 | E-GEOD-15030 | biostudies-arrayexpress
Project description:The Lactobacillus genus, a use case for Bactopia.
| PRJNA608517 | ENA
Project description:In the present study we characterized the sRNA profile of Lactobacillus casei BL23 using conventional and mDOT-seq approaches. In total 307 potential sRNAs were identified, 28 of which were validated by Northern hybridization. As a major portion of predicted sRNAs were shown to be conserved among the related species of Lactobacillus casei group (LCG), the results obtained in this study could serve as a valuable resource for achieving a better understanding of LCG physiology or even improving their applications in industry and medicine.
2021-05-20 | GSE166930 | GEO