Complete genome sequence and comparative genome analysis of Klebsiella oxytoca HKOPL1 isolated from giant panda feces

BMC Research Notes

Frederick C Leung⁴  San Yuen Chan¹  Angel Po Yee Ma⁴  Nathalie France Mauroo³  Hein Min Tun²  Jingwei Jiang⁴ 

[1] Clinical Laboratory, Veterinary Center, Ocean Park Corporation, Hong Kong SAR, China;Present address: Gut Microbiome and Large Animal Biosecurity Laboratories, Department of Animal Science, University of Manitoba, Winnipeg, MB, Canada;Department of Pathology, The University of Hong Kong, Hong Kong SAR, China;School of Biological Sciences, The University of Hong Kong, Hong Kong SAR, China

关键词: Biofuel;    Cellulose degradation;    Gut microbiota;    Complete genome sequence;    Giant panda;    Klebsiella oxytoca;   

Others  :  1118349
DOI  :  10.1186/1756-0500-7-827

 received in 2014-01-20, accepted in 2014-10-10,  发布年份 2014

【 摘 要 】

Background

The giant panda (Ailuropoda melanoleuca) is an endangered species well-known for ingesting bamboo as a major part of their diet despite the fact that it belongs to order Carnivora. However, the giant panda’s draft genome shows no direct evidence of enzymatic genes responsible for cellulose digestion. To explore this phenomenon, we study the giant panda’s gut microbiota using genomic approaches in order to better understand their physiological processes as well as any potential microbial cellulose digestion processes.

Results

A complete genome of isolated Klebsiella oxytoca HKOPL1 of 5.9 Mb has been successfully sequenced, closed and comprehensively annotated against various databases. Genome comparisons within the Klebsiella genus and K. oxytoca species have also been performed. A total of 5,772 genes were predicted, and among them, 211 potential virulence genes, 35 pathogenicity island-like regions, 1,615 potential horizontal transferring genes, 23 potential antibiotics resistant genes, a potential prophage integrated region, 8 genes in 2,3-Butanediol production pathway and 3 genes in the cellulose degradation pathway could be identified and discussed based on the comparative genomic studies between the complete genome sequence of K. oxytoca HKOPL1 and other Klebsiella strains. A functional study shows that K. oxytoca HKOPL1 can degrade cellulose within 72 hours. Phylogenomic studies indicate that K. oxytoca HKOPL1 is clustered with K. oxytoca strains 1686 and E718.

Conclusions

K. oxytoca HKOPL1 is a gram-negative bacterium able to degrade cellulose. We report here the first complete genome sequence of K. oxytoca isolated from giant panda feces. These studies have provided further insight into the role of gut microbiota in giant panda digestive physiology. In addition, K. oxytoca HKOPL1 has the potential for biofuel application in terms of cellulose degradation and potential for the production of 2,3-Butanediol (an important industrial raw material).

【 授权许可】

   
2014 Jiang et al.; licensee BioMed Central Ltd.

【 图 表 】

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【 参考文献 】

• [1]Zhan X, Li M, Zhang Z, Goossens B, Chen Y, Wang H, Bruford MW, Wei F: Molecular censusing doubles giant panda population estimate in a key nature reserve. Curr Biol 2006, 16(12):R451-R452.
• [2]Li R, Fan W, Tian G, Zhu H, He L, Cai J, Huang Q, Cai Q, Li B, Bai Y, Zhang Z, Zhang Y, Wang W, Li J, Wei F, Li H, Jian M, Li J, Zhang Z, Nielsen R, Li D, Gu W, Yang Z, Xuan Z, Ryder OA, Leung FC, Zhou Y, Cao J, Sun X, Fu Y, et al.: The sequence and de novo assembly of the giant panda genome. Nature 2010, 463(7279):311-317.
• [3]Zhu L, Wu Q, Dai J, Zhang S, Wei F: Evidence of cellulose metabolism by the giant panda gut microbiome. Proc Natl Acad Sci 2011, 108(43):17714-17719.
• [4]Tun HM, Mauroo NF, Yuen CS, Ho JCW, Wong MT, Leung FC-C: Microbial diversity and evidence of novel homoacetogens in the gut of both geriatric and adult giant pandas (Ailuropoda melanoleuca). PLoS One 2014, 9(1):e79902.
• [5]Liu P, Li P, Jiang X, Bi D, Xie Y, Tai C, Deng Z, Rajakumar K, Ou H-Y: Complete genome sequence of klebsiella pneumoniae subsp. pneumoniae HS11286, a multidrug-resistant strain isolated from human sputum. J Bacteriol 2012, 194(7):1841-1842.
• [6]Wu K-M, Li L-H, Yan J-J, Tsao N, Liao T-L, Tsai H-C, Fung C-P, Chen H-J, Liu Y-M, Wang J-T, Fang CT, Chang SC, Shu HY, Liu TT, Chen YT, Shiau YR, Lauderdale TL, Su IJ, Kirby R, Tsai SF: Genome sequencing and comparative analysis of klebsiella pneumoniae NTUH-K2044, a strain causing liver abscess and meningitis. J Bacteriol 2009, 191(14):4492-4501.
• [7]Shin SH, Kim S, Kim JY, Lee S, Um Y, Oh M-K, Kim Y-R, Lee J, Yang K-S: Complete genome sequence of the 2,3-butanediol-producing klebsiella pneumoniae strain KCTC 2242. J Bacteriol 2012, 194(10):2736-2737.
• [8]Derrick EF, Heather LT, Robert TD, Sean D, Qinghu R, Jonathan HB, Anthony SD, Heather H, Susmita S, Sagar K, Dodson RJ, Mohamoud Y, Khouri H, Roesch LF, Krogfelt KA, Struve C, Triplett EW, Methé BA: Complete genome sequence of the N2-fixing broad host range endophyte klebsiella pneumoniae 342 and virulence predictions verified in mice. PLoS Genet 2008, 4(7):e1000141.
• [9]Pinto-Tomás AA, Anderson MA, Suen G, Stevenson DM, Chu FST, Cleland WW, Weimer PJ, Currie CR: Symbiotic nitrogen fixation in the fungus gardens of leaf-cutter ants. Science 2009, 326(5956):1120-1123.
• [10]Podschun R, Ullmann U: Klebsiella spp. as nosocomial pathogens: epidemiology, taxonomy, typing methods, and pathogenicity factors. Clin Microbiol Rev 1998, 11(4):589-603.
• [11]Morozkina EV, Zvyagilskaya RA: Nitrate reductases: structure, functions, and effect of stress factors. Biochemistry (Mosc) 2007, 72(10):1151-1160.
• [12]Doran JB, Ingram LO: Fermentation of crystalline cellulose to ethanol by Klebsiella oxytoca containing chromosomally integrated Zymomonas mobilis genes. Biotechnol Prog 1993, 9(5):533-538.
• [13]Högenauer C, Langner C, Beubler E, Lippe IT, Schicho R, Gorkiewicz G, Krause R, Gerstgrasser N, Krejs GJ, Hinterleitner TA: Klebsiella oxytoca as a causative organism of antibiotic-associated hemorrhagic colitis. N Engl J Med 2006, 355(23):2418-2426.
• [14]Halary S, Leigh JW, Cheaib B, Lopez P, Bapteste E: Network analyses structure genetic diversity in independent genetic worlds. Proc Natl Acad Sci 2010, 107(1):127-132.
• [15]Bacterial Genomic DNA Isolation Using CTAB. http://1ofdmq2n8tc36m6i46scovo2e.wpengine.netdnacdn.com/wp-content/uploads/2014/02/JGI-Bacterial-DNA-isolation-CTAB-Protocol-2012.pdf webcite
• [16]Delcher AL, Bratke KA, Powers EC, Salzberg SL: Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics 2007, 23(6):673-679.
• [17]Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997, 25(17):3389-3402.
• [18]RepeatMasker. http://www.repeatmasker.org/ webcite
• [19]Kent WJ: BLAT—The BLAST-Like Alignment Tool. Genome Res 2002, 12(4):656-664.
• [20]Edgar RC: MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004, 32(5):1792-1797.
• [21]Ronquist F, Huelsenbeck JP: MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 2003, 19(12):1572-1574.
• [22]Tracer. http://tree.bio.ed.ac.uk/software/tracer/ webcite
• [23]Krzywinski MI, Schein JE, Birol I, Connors J, Gascoyne R, Horsman D, Jones SJ, Marra MA: Circos: an information aesthetic for comparative genomics. Genome Res 2009, 19(9):1639-1645.
• [24]Tatusov R, Fedorova N, Jackson J, Jacobs A, Kiryutin B, Koonin E, Krylov D, Mazumder R, Mekhedov S, Nikolskaya A, Rao BS, Smirnov S, Sverdlov AV, Vasudevan S, Wolf YI, Yin JJ, Natale DA: The COG database: an updated version includes eukaryotes. BMC Bioinformatics 2003, 4(1):41. BioMed Central Full Text
• [25]Chen L, Yang J, Yu J, Yao Z, Sun L, Shen Y, Jin Q: VFDB: a reference database for bacterial virulence factors. Nucleic Acids Res 2005, 33(suppl 1):D325-D328.
• [26]Yoon SH, Park Y-K, Lee S, Choi D, Oh TK, Hur C-G, Kim JF: Towards pathogenomics: a web-based resource for pathogenicity islands. Nucleic Acids Res 2007, 35(suppl 1):D395-D400.
• [27]Liu B, Pop M: ARDB—Antibiotic Resistance Genes Database. Nucleic Acids Res 2009, 37(suppl 1):D443-D447.
• [28]Leplae R, Hebrant A, Wodak SJ, Toussaint A: ACLAME: A CLAssification of Mobile Genetic Elements. Nucleic Acids Res 2004, 32(suppl 1):D45-D49.
• [29]Zhou Y, Liang Y, Lynch KH, Dennis JJ, Wishart DS: PHAST: a fast phage search tool. Nucleic Acids Res 2011, 39(Web Server issue):W347-W352.
• [30]Kanehisa M, Goto S, Sato Y, Furumichi M, Tanabe M: KEGG for integration and interpretation of large-scale molecular data sets. Nucleic Acids Res 2012, 40(D1):D109-D114.
• [31]Kasana R, Salwan R, Dhar H, Dutt S, Gulati A: A rapid and easy method for the detection of microbial cellulases on agar plates using gram’s iodine. Curr Microbiol 2008, 57(5):503-507.