FibroChip, a Functional DNA Microarray to Monitor Cellulolytic and Hemicellulolytic Activities of Rumen Microbiota

Frontiers in Microbiology
Sophie Comtet-MarreEvelyne Forano

Abstract

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 bacteriumFibrobacter succinogenesS85 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...Continue Reading

References

Dec 1, 1975·Journal of General Microbiology·C G Orpin
Jul 1, 1988·Journal of Bacteriology·M McGavin, C W Forsberg
Nov 10, 2000·Nucleic Acids Research·M D KaneS J Madore
Nov 9, 2004·Bioinformatics·Sébastien RimourPierre Peyret
Feb 11, 2005·Molecular Biology and Evolution·Angus Davison, Mark Blaxter
Jul 8, 2005·Applied and Environmental Microbiology·Zhili HeJizhong Zhou
Mar 15, 2006·Applied Microbiology and Biotechnology·Takamitsu AraiRoy H Doi
Mar 18, 2008·Applied and Environmental Microbiology·Zhili He, Jizhong Zhou
Jun 3, 2008·The FEBS Journal·Maria MatulovaEvelyne Forano
Nov 26, 2008·FEMS Microbiology Letters·Ayelet PeerIlya Borovok
Feb 3, 2009·Proceedings of the National Academy of Sciences of the United States of America·Jennifer M BrulcBryan A White
Dec 17, 2009·BMC Bioinformatics·Christiam CamachoThomas L Madden
Feb 23, 2010·Bioresource Technology·F M GírioR Bogel-Łukasik
Jan 11, 2011·Bioinformatics·Eric Dugat-BonyPierre Peyret
Jan 29, 2011·Science·Matthias HessEdward M Rubin
Jun 22, 2011·Genome Research·Daniel H HusonStephan C Schuster
Sep 8, 2011·Environmental Microbiology·Eric Dugat-BonyPierre Peyret
Nov 22, 2011·Current Opinion in Biotechnology·Zhili HeJizhong Zhou
May 11, 2012·Gut Microbes·Harry J FlintEvelyne Forano
May 31, 2012·Nucleic Acids Research·Yanbin YinYing Xu
Sep 21, 2012·BMC Evolutionary Biology·Henrik AspeborgBernard Henrissat
Nov 26, 2013·Nucleic Acids Research·Vincent LombardBernard Henrissat
Jul 9, 2014·Annual Review of Microbiology·Bryan A WhiteHarry J Flint
Oct 25, 2016·Animal Science Journal = Nihon Chikusan Gakkaihō·Takumi ShinkaiAkio Takenaka

❮ Previous
Next ❯

Citations

Sep 27, 2018·Animal : an International Journal of Animal Bioscience·J S ForbeyA M Felton
May 6, 2019·FEMS Microbiology Reviews·Sarah Moraïs, Itzhak Mizrahi
Sep 10, 2020·Frontiers in Bioengineering and Biotechnology·Qingwen LiQingyuan Li

❮ Previous
Next ❯

Datasets Mentioned

BETA
GSE107550
AAG18439
SRP070140
MF773967
ACX76028
ACX73672

Methods Mentioned

BETA
PCR
electrophoresis
nucleic acid extraction
Chip
Feature Extraction
RNA-seq

Software Mentioned

Delphi
GoArrays
dbCAN
Feature Extraction
MEGAN
HiSpOD
BLAST
BLASTX BLAST

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.