FibroChip, a Functional DNA Microarray to Monitor Cellulolytic and Hemicellulolytic Activities of Rumen Microbiota
| Autor: | Sophie Comtet-Marre, Frédérique Chaucheyras-Durand, Ourdia Bouzid, Pascale Mosoni, Ali R. Bayat, Pierre Peyret, Evelyne Forano |
|---|---|
| Přispěvatelé: | Microbiologie Environnement Digestif Santé (MEDIS), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Lallemand S.A.S., Centre de Développement des Energies Renouvelables, Natural Resources Institute Finland (LUKE), Association Nationale de la Recherche et de la Technologie (ANRT) 783/2010, Region Auvergne (Bourse Innovation et Transfert de Technologie) 1145, Lallemand SAS, Blagnac, France 23000695, INRA Clermont-Ferrand-Theix-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]) |
| Jazyk: | angličtina |
| Rok vydání: | 2018 |
| Předmět: |
0301 basic medicine
Microbiology (medical) hemicellulolysis carbohydrate esterases animal structures activité cellulolytique enzyme hémicellulolytique 030106 microbiology lcsh:QR1-502 microbiote digestif Cellobiose Microbiology lcsh:Microbiology 03 medical and health sciences Rumen chemistry.chemical_compound Methods Glycoside hydrolase glycoside hydrolase cellulolysis Gene metatranscriptomic 2. Zero hunger rumen Fibrobacter succinogenes metatranscriptomics carbohydrate esterase functional DNA microarray biology Microbiology and Parasitology adn food and beverages biology.organism_classification Microbiologie et Parasitologie 030104 developmental biology [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology Biochemistry chemistry Protozoa glycoside hydrolases DNA microarray Bacteria |
| Zdroj: | Frontiers in Microbiology Frontiers in Microbiology, 2018, 9, ⟨10.3389/fmicb.2018.00215⟩ Frontiers in Microbiology, Vol 9 (2018) Frontiers in Microbiology, Frontiers Media, 2018, 9, ⟨10.3389/fmicb.2018.00215⟩ Frontiers in Microbiology (9), . (2018) |
| ISSN: | 1664-302X |
| DOI: | 10.3389/fmicb.2018.00215⟩ |
| Popis: | International audience; Ruminants fulfill their energy needs for growth primarily through microbial breakdown of plant biomass in the rumen. Several biotic and abiotic factors influence the efficiency of fiber degradation, which can ultimately impact animal productivity and health. To provide more insight into mechanisms involved in the modulation of fibrolytic activity, a functional DNA microarray targeting genes encoding key enzymes involved in cellulose and hemicellulose degradation by rumen microbiota was designed. Eight carbohydrate-active enzyme (CAZyme) families (GH5, GH9, GH10, GH11, GH43, GH48, CE1, and CE6) were selected which represented 392 genes from bacteria, protozoa, and fungi. The DNA microarray, designated as FibroChip, was validated using targets of increasing complexity and demonstrated sensitivity and specificity. In addition, FibroChip was evaluated for its explorative and semi-quantitative potential. Differential expression of CAZyme genes was evidenced in the rumen bacterium Fibrobacter succinogenes S85 grown on wheat straw or cellobiose. FibroChip was used to identify the expressed CAZyme genes from the targeted families in the rumen of a cow fed a mixed diet based on grass silage. Among expressed genes, those encoding GH43, GH5, and GH10 families were the most represented. Most of the F. succinogenes genes detected by the FibroChip were also detected following RNA-seq analysis of RNA transcripts obtained from the rumen fluid sample. Use of the FibroChip also indicated that transcripts of fiber degrading enzymes derived from eukaryotes (protozoa and anaerobic fungi) represented a significant proportion of the total microbial mRNA pool. FibroChip represents a reliable and high-throughput tool that enables researchers to monitor active members of fiber degradation in the rumen. |
| Databáze: | OpenAIRE |
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