The FibroChip, a functional DNA microarray to monitor cellulolysis and hemicellulolysis activities of rumen microbiota
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ABSTRACT: Ruminants are the most efficient herbivorous animals to transform plant biomass into edible products, principally thanks to the rumen microbiota that produces a large array of enzymes responsible for the hydrolysis of plant cell wall polysaccharides. Several biotic and abiotic factors influence the efficiency of fiber degradation, which can ultimately impact the animal productivity and health. To provide more insight on mechanisms involved in the modulation of fibrolytic activity, a functional DNA microarray targeting genes coding for key enzymes involved in cellulose and hemicellulose degradation by rumen microbiota was designed. The DNA microarray, designated FibroChip, was validated using targets of increasing complexity. This new tool demonstrated sensitivity and specificity as well as explorative and semi-quantitative potential. The FibroChip was designed with the objective to propose a high throughput tool that enables to get a rapid picture of the capacity of rumen microorganisms to degrade cellulose and hemicellulose based on a targeted metatranscriptomics approach. We chose to focus on a few number of genes by targeting main ruminal fibrolytic microorganisms and selected CAZyme families that may have a pivotal role in cellulose and hemicellulose degradation. The microarray targets the coding sequence of catalytic domains from 8 CAZyme families involved in cellulose and hemicellulose degradation (i.e. glycoside hydrolases GH5, GH9, GH10, GH11, GH43 and GH48, and carbohydrate esterases CE1 and CE6). Taken together, these families present complementary activities needed for the complete degradation of cellulose and hemicellulose. In total, 392 nucleic sequences encoding 363 GH and 29 CE were kept for the microarray design. These sequences originated from 41 bacterial species, 4 protozoal species and 10 fungal species. The microarray is composed of 1631 25-mer probes. GoArrays strategy consisting by associating 2 25-mer probes targeting the same gene (Rimour et al., 2005) was also emplyed to determine 2618 composite probes of 54-mers. Triplicate of probes of 25 and 54-mers were synthetized in situ on an Agilent 8x15K DNA microarray. The microarray contained also 382 Agilent internal control probes including positive controls, negative controls and quality control probes. Probes were randomly placed on the array to avoid position bias.
ORGANISM(S): Bacteroides ovatus uncultured Neocallimastigales Bacteroides fragilis Fibrobacter succinogenes subsp. succinogenes S85 Ruminococcus albus Fibrobacter intestinalis Bifidobacterium animalis Selenomonas ruminantium Piromyces sp. Lactococcus lactis Bacteroides thetaiotaomicron Piromyces sp. 'equi' Xylanibacter ruminicola Polyplastron multivesiculatum Orpinomyces joyonii Roseburia hominis Neocallimastix patriciarum Orpinomyces sp. Acetivibrio clariflavus Bacteroides sp. Ruminococcus champanellensis Cellulosilyticum ruminicola Piromyces rhizinflatus Bifidobacterium adolescentis Neocallimastix frontalis Ruminococcus sp. Epidinium ecaudatum Enterococcus faecium Roseburia intestinalis Escherichia coli K-12 Eudiplodinium maggii Pseudobacteroides cellulosolvens Bacteroides xylanisolvens [Eubacterium] cellulosolvens Segatella bryantii Acetivibrio thermocellus Butyrivibrio hungatei Butyrivibrio fibrisolvens Bifidobacterium longum Agathobacter rectalis Cellulomonas flavigena Clostridium acetobutylicum Limosilactobacillus fermentum Enterobacter sp. Ruminococcus flavefaciens Cellulomonas fimi Bacteroides xylanisolvens XB1A Clostridioides difficile bovine gut metagenome Ruminiclostridium cellulolyticum Lachnospira eligens Clostridium beijerinckii Epidinium caudatum Fibrobacter succinogenes Clostridium cellulovorans Levilactobacillus brevis Piromyces communis Pseudobutyrivibrio xylanivorans
PROVIDER: GSE107550 | GEO | 2017/12/01
SECONDARY ACCESSION(S): PRJNA420557
REPOSITORIES: GEO
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