RNA-seq of human gut bacterial isolates grown on seaweed polysaccharides
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ABSTRACT:
PROVIDER: PRJNA628169 | ENA |
REPOSITORIES: ENA
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Project description:Purpose: Examining the transcriptome of human gut bacteria that grow on seaweed polysaccharides as a sole carbon source Methods: Strains were grown on 5 mg/ml seaweed polysaccharides (carrageenan, agarose and/or poprhyran respective to strain) or galactose as a sole carbon source in vitro. Fold change was calculated as seaweed polysaccharide over galactose with n=2 biological replicates. Once cells reached an optical density corresponding to mid-log phase growth, RNA was isolated and rRNA depleted. Samples were multiplexed for sequencing on the Illumina HiSeq platform at the University of Michigan Sequencing Core. Data was analyzed using Arraystar software (DNASTAR, Inc.) Genes with significant up- or down-regulation were determined by the following criteria: genes with an average fold-change >10-fold and with both biological replicates with a normalized expression level >1% of the overall average RPKM expression level. READS WERE ANALYZED .......GABRIEL FILL IN Results: We identified novel polysaccharide utiilization loci in 5 strains of human gut bacteria
2020-09-01 | GSE149357 | GEO
Project description:Humans harbor numerous species of colonic bacteria that digest the fiber polysaccharides in commonly consumed terrestrial plants. More recently in history, regional populations have consumed edible seaweeds (macroalgae) containing unique polysaccharides. However, it remains unclear how extensively gut bacteria have adapted to digest these novel nutrients. Here, we show that the ability of gut bacteria to digest seaweed polysaccharides is considerably more pervasive than previously appreciated. Using culture-based approaches, we show that known Bacteroides genes involved in seaweed degradation have mobilized into many members of this genus. We also identify new marine bacteria-derived genes, and their corresponding mobile DNA elements, that are involved in degrading several seaweed polysaccharides. Some of these new genes reside in gut-resident, Gram-positive Firmicutes, for which phylogenetic analysis suggests an origin in the Epulopiscium gut symbionts of marine fishes. Our results are important for understanding the metabolic plasticity of the human gut microbiome, the global exchange of genes in the context of dietary selective pressures and identifying new functions that can be introduced or engineered to design and fill orthogonal niches for a future generation of engineered probiotics.
2021-11-04 | PXD019149 | Pride
Project description:Columbia Arabidopsis ecotype were grown hydroponically on 1 mM NH4NO3 as sole nitrogen source during 35 days under short days. Plants leaves were then sprayed with a seaweed extract or with water (control). Root and shoot samples were harvested separately 1 hour and 7 days after this spraying.
2007-01-26 | E-MEXP-573 | biostudies-arrayexpress
Project description:Hyperthermophilic bacteria of the genus Thermotoga are known to utilize a wide range of simple and complex polysaccharides. T. maritima's transcriptional response to a variety of mono- and poly-saccharides was previously studied to assign functions to genes involved in carbohydrate uptake and utilization. To compare and contrast closely-related members of the Thermotoga genus, a four-species microarray was developed by expanding a whole genome T. maritima array to include unique genes from three other species (T. neapolitana, T. petrophila, and T. sp. RQ2). This multi-species array was used to investigate the diversity of the genus, specifically the response of each of the four species to a mixture of polysaccharides (galactomannan, glucomannan, xylan, pectin, lichenan, and carboxymethyl cellulose). RNA derived from glucose-grown cultures (glu) was compared to RNA derived from polysaccharide-grown cultures (poly) using a dye swap setup.
2012-01-05 | E-GEOD-29557 | biostudies-arrayexpress
Project description:Investigation of whole genome gene expression level changes in Xylella fastidiosa grown in minimal media XFM and XFM supplied with pectin or glucan (Host polysaccharides) , compared to cell grown in the complex media PWG. The cells grown in the minimal medium XFM supplied with host polysaccharides specially pectin are transmissible by the insect vector when delivered to the vector through artificial diet system. This does not happen with cells grown in the complex media.
2009-10-03 | GSE18369 | GEO
Project description:Greenlandic seaweed (Fucus) Raw sequence reads
| PRJNA699133 | ENA
Project description:This study aimed at identification of genetic regulations for desiccation tolerance in intertidal seaweed species Ulva lactuca most commonly experienced phenomenon of intertidal communities.
2018-04-17 | GSE97868 | GEO
Project description:Pseudomonas aeruginosa (P. aeruginosa) lung infection is a significant cause of mortality in patients with cystic fibrosis (CF). Existing experimental data in our lab showed significantly different levels of virulence of "early" and "late" P. aeruginosa infection isolates in a C. elegans slow killing model. We wished to examine the expression profile of these isolates in order to explore genes that may be responsible for the observed differences. The expression profiles of two pairs of isolates (four isolates in total) were compared to each other using the Affymetrix P. aeruginosa PAO1 genome array, to gain insight into properties mediating virulence in these isolates. Data analysis was carried out using BIOCONDUCTOR software. Keywords: Comparative strain hybridization Two pairs of isolates (four isolates in total) were compared to each other when grown on Nematode Growth Medium (NGM).
2011-12-31 | E-GEOD-33275 | biostudies-arrayexpress