Genomic Analysis of Actinomyces sp. Strain CtC72, a Novel Fibrolytic Anaerobic Bacterium Isolated from Cattle Rumen
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A xylanolytic and cellulolytic anaerobic bacterium strain CtC72 was isolated from cattle rumen liquor. Phylogenetic analysis of 16S rRNA gene sequences revealed that strain CtC72 shared only 97.78% homology with its nearest phylogenetic affiliate Actinomyces ruminicola, showing its novelty. The strain could grow on medium containing xylan, carboxymethyl cellulose and avicel producing CO2, acetate, and ethanol as major fermentation products. The whole genome analysis of the strain CtC72 exhibited a broad range of carbohydrate-active enzymes required for the breakdown and utilization of lignocellulosic biomass. Genes related to the production of ethanol and stress tolerance were also detected. Further there were several unique genes in CtC72 for chitin degradation, pectin utilization, sugar utilization, and stress response in comparison with Actinomyces ruminicola. The results show that the strain CtC72, a putative novel bacterium can be used for lignocellulosic biomass based biotechnological applications.
Abstract
A xylanolytic and cellulolytic anaerobic bacterium strain CtC72 was isolated from cattle rumen liquor. Phylogenetic analysis of 16S rRNA gene sequences revealed that strain CtC72 shared only 97.78% homology with its nearest phylogenetic affiliate Actinomyces ruminicola, showing its novelty. The strain could grow on medium containing xylan, carboxymethyl cellulose and avicel producing CO2, acetate, and ethanol as major fermentation products. The whole genome analysis of the strain CtC72 exhibited a broad range of carbohydrate-active enzymes required for the breakdown and utilization of lignocellulosic biomass. Genes related to the production of ethanol and stress tolerance were also detected. Further there were several unique genes in CtC72 for chitin degradation, pectin utilization, sugar utilization, and stress response in comparison with Actinomyces ruminicola. The results show that the strain CtC72, a putative novel bacterium can be used for lignocellulosic biomass based biotechnological applications.
참고문헌 (47)
- Viikari L, "Lignocellulosic ethanol: from science to industry", Biomass Bioenergy, 46, pp.13~24 (2012)[DOI]
- Arevalo-Gallegos A, "Lignocellulose: A sustainable material to produce value-added products with a zero waste approach-A review", Int. J. Biol. Macromol., 99, pp.308~318 (2017)[DOI]
- Lynd LR, "Microbial cellulose utilization: fundamentals and biotechnology", Microbiol. Mol. Biol. Rev., 66, pp.506~577 (2002)[DOI]
- Sirohi SK, "Molecular tools for deciphering the microbial community structure and diversity in rumen ecosystem", Appl. Microbiol. Biotechnol., 95, pp.1135~1154 (2012)[DOI]
- Hess M, "Metagenomic discovery of biomass-degrading genes and genomes from cow rumen", Science, 331, pp.463~467 (2011)
- Dagar S, "Role of anaerobic fungi in wheat straw degradation and effects of plant feed additives on rumen fermentation parameters in vitro", Benef. Microbes., 6, pp.353~360 (2014)
- Miller TL, "A serum bottle modification of the Hungate technique for cultivating obligate anaerobes", Appl. Microbiol., 27, pp.985~987 (1974)
- Suzuki MT, "Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR", Appl. Environ. Microbiol., 62, pp.625~630 (1996)
- Singh KG, "Optimization for butanol production using Plackett-Burman Design coupled with Central Composite Design by Clostridium beijerenckii strain CHTa isolated from distillery waste manure", J. Biochem. Tech., 7, pp.1063~1068 (2016)
- Dighe AS, "Selenomonas lipolytica sp. nov., an obligately anaerobic bacterium possessing lipolytic activity", Int. J. Syst. Bacteriol., 48, pp.783~791 (1998)[DOI]
- Aziz RK, "The RAST Server: rapid annotations using subsystems technology", BMC Genomics, 9, pp.75~ (2008)
- Van Domselaar GH, "BASys: a web server for automated bacterial genome annotation", Nucleic Acids Res., 33, pp.W455~W459 (2005)[DOI]
- Kanehisa M, "The KEGG resource for deciphering the genome", Nucleic Acids Res., 32, pp.D277~D280 (2004)[DOI]
- Yin Y, "dbCAN: a web resource for automated carbohydrate-active enzyme annotation", Nucleic Acids Res., 40, pp.W445~W451 (2012)[DOI]
- Tamura K, "MEGA6: molecular evolutionary genetics analysis version 6.0", Mol. Biol. Evol., 30, pp.2725~2729 (2013)[DOI]
- Meier-Kolthoff JP, "Genome sequence-based species delimitation with confidence intervals and improved distance functions", BMC Bioinformatics, 14, pp.60~ (2013)[DOI]
- Yoon SH, "A large-scale evaluation of algorithms to calculate average nucleotide identity", Anton. Leeuw., 110, pp.1281~1286 (2017)[DOI]
- Alikhan NF, "BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons", BMC Genomics, 12, pp.402~ (2011)
- Weber T, "antiSMASH 3.0-a comprehensive resource for the genome mining of biosynthetic gene clusters", Nucleic Acids Res., 43, pp.W237~W243 (2015)
- van Heel AJ, "BAGEL3: automated identification of genes encoding bacteriocins and (non-) bactericidal posttranslationally modified peptides", Nucleic Acids Res., 41, pp.W448~W453 (2013)[DOI]
- Jia B, "CARD 2017: expansion and model-centric curation of the comprehensive antibiotic resistance database", Nucleic Acids Res., 45, pp.D566~D573 (2017)[DOI]
- Kim M, "Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes", Int. J. Syst. Evol. Microbiol., 64, pp.346~351 (2014)[DOI]
- Cimmino T, "Genome sequence and description of Actinomyces polynesiensis str. MS2 sp. nov. isolated from the human gut", New Microbes New Infect, 12, pp.1~5 (2016)[DOI]
- NA SP, "Actinomyces succiniciruminis sp. nov. and Actinomyces glycerinitolerans sp. nov., two novel organic acid-producing bacteria isolated from rumen", Syst. Appl. Microbiol., 39, pp.445~452 (2016)[DOI]
- Gao B, "Genome sequencing reveals the complex polysaccharide-degrading ability of novel deep-sea bacterium Flammeovirga pacifica WPAGA1", Front. Microbiol., 8, pp.600~ (2017)
- Dodd D, "Enzymatic deconstruction of xylan for biofuel production", GCB Bioenergy, 1, pp.2~17 (2009)[DOI]
- Schafers C, "Complete genome sequence of Thermus brockianus GE-1 reveals key enzymes of xylan", xylose metabolism, 2017, pp.12, 22~
- Reid MF, "Molecular characterization of microbial alcohol dehydrogenases", Crit. Rev. Microbiol., 20, pp.13~56 (1994)[DOI]
- Radianingtyas H, "Alcohol dehydrogenases from thermophilic and hyperthermophilic archaea and bacteria", FEMS Microbiol. Rev., 27, pp.593~616 (2003)[DOI]
- Littlechild J, "Hyperthermophilic dehydrogenase enzymes", Biochem. Soc. Trans., 32, pp.255~258 (2004)[DOI]
- Keller MW, "Ethanol production by the hyperthermophilic archaeon Pyrococcus furiosus by expression of bacterial bifunctional alcohol dehydrogenases", Microb. Biotechnol., 10, pp.1535~1545 (2017)[DOI]
- Andrietta M, "Bioethanol- Brazil, 30 years of Proalcool", Int. Sugar. J., 109, pp.195~200 (2007)
- Basso LC, "Yeast selection for fuel ethanol production in Brazil", FEMS Yeast Res., 8, pp.1155~1163 (2008)[DOI]
- Sootsuwan K, "Sorbitol required for cell growth and ethanol production by Zymomonas mobilis under heat, ethanol, and osmotic stresses", Biotechnol. Biofuels., 6, pp.180~ (2013)[DOI]
- Ma R, "Improved osmotic tolerance and ethanol production of ethanologenic Escherichia coli by IrrE, a global regulator of radiationresistance of Deinococcus radiodurans", Curr. Microbiol., 62, pp.659~664 (2011)[DOI]
- Comporti M, "Ethanol-induced oxidative stress: basic knowledge", Genes Nutr., 5, pp.101~109 (2010)
- Stanley D, "The ethanol stress response and ethanol tolerance of Saccharomyces cerevisiae", J. Appl. Microbiol., 109, pp.13~24 (2010)
- Todorov SD, "Bacteriocins from Lactobacillus plantarum production, genetic organization and mode of action: producao, organizacao genetica e modo de acao", Braz J. Microbiol., 40, pp.209~221 (2009)[DOI]
- Bonelli RR, "Insights into in vivo activities of lantibiotics from gallidermin and epidermin mode-of-action studies", Antimicrob. Agents Chemother., 50, pp.1449~1457 (2006)[DOI]
- Knerr PJ, "Discovery, biosynthesis, and engineering of lantipeptides", Annu. Rev. Biochem., 81, pp.479~505 (2012)[DOI]
- Peng J, "The role of nisin in fuel ethanol production with Saccharomyces cerevisiae", Lett. Appl. Microbiol., 55, pp.128~134 (2012)[DOI]
- Ravcheev DA, "Polysaccharides utilization in human gut bacterium Bacteroides thetaiotaomicron: comparative genomics reconstruction of metabolic and regulatory networks", BMC Genomics, 14, pp.873~ (2013)
- Kopecny J, "The effect of rumen chitinolytic bacteria on cellulolytic anaerobic fungi", Lett. Appl. Microbiol., 23, pp.199~202 (1996)
- Bennett GN, "Microbial formation, biotechnological production and applications of 1, 2-propanediol", Appl. Microbiol. Biotechnol., 55, pp.1~9 (2001)[DOI]
- de Albuquerque TL, "Biotechnological production of xylitol from lignocellulosic wastes: a review", Process Biochem., 49, pp.1779~1789 (2014)[DOI]
- Garcia-Quintans N, "Activation of the diacetyl", acetoin pathway in Lactococcus lactis subsp. lactis bv. diacetylactis CRL264 by acidic growth, 2008, pp.74, 1988~1996
- Joo J, "Improved fermentation of lignocellulosic hydrolysates to 2, 3-butanediol through investigation of effects of inhibitory compounds by Enterobacter aerogenes", Chem. Eng. J., 306, pp.916~924 (2016)[DOI]
