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Complete genome sequence and comparative genome analysis of Klebsiella oxytoca HKOPL1 isolated from giant panda feces
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 cellulo...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2014
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4289185/ https://www.ncbi.nlm.nih.gov/pubmed/25417012 http://dx.doi.org/10.1186/1756-0500-7-827 |
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author | Jiang, Jingwei Tun, Hein Min Mauroo, Nathalie France Ma, Angel Po Yee Chan, San Yuen Leung, Frederick C |
author_facet | Jiang, Jingwei Tun, Hein Min Mauroo, Nathalie France Ma, Angel Po Yee Chan, San Yuen Leung, Frederick C |
author_sort | Jiang, Jingwei |
collection | PubMed |
description | 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). ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/1756-0500-7-827) contains supplementary material, which is available to authorized users. |
format | Online Article Text |
id | pubmed-4289185 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2014 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-42891852015-01-11 Complete genome sequence and comparative genome analysis of Klebsiella oxytoca HKOPL1 isolated from giant panda feces Jiang, Jingwei Tun, Hein Min Mauroo, Nathalie France Ma, Angel Po Yee Chan, San Yuen Leung, Frederick C BMC Res Notes Research Article 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). ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/1756-0500-7-827) contains supplementary material, which is available to authorized users. BioMed Central 2014-11-23 /pmc/articles/PMC4289185/ /pubmed/25417012 http://dx.doi.org/10.1186/1756-0500-7-827 Text en © Jiang et al.; licensee BioMed Central Ltd. 2014 This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
spellingShingle | Research Article Jiang, Jingwei Tun, Hein Min Mauroo, Nathalie France Ma, Angel Po Yee Chan, San Yuen Leung, Frederick C Complete genome sequence and comparative genome analysis of Klebsiella oxytoca HKOPL1 isolated from giant panda feces |
title | Complete genome sequence and comparative genome analysis of Klebsiella oxytoca HKOPL1 isolated from giant panda feces |
title_full | Complete genome sequence and comparative genome analysis of Klebsiella oxytoca HKOPL1 isolated from giant panda feces |
title_fullStr | Complete genome sequence and comparative genome analysis of Klebsiella oxytoca HKOPL1 isolated from giant panda feces |
title_full_unstemmed | Complete genome sequence and comparative genome analysis of Klebsiella oxytoca HKOPL1 isolated from giant panda feces |
title_short | Complete genome sequence and comparative genome analysis of Klebsiella oxytoca HKOPL1 isolated from giant panda feces |
title_sort | complete genome sequence and comparative genome analysis of klebsiella oxytoca hkopl1 isolated from giant panda feces |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4289185/ https://www.ncbi.nlm.nih.gov/pubmed/25417012 http://dx.doi.org/10.1186/1756-0500-7-827 |
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