Mining biomass-degrading genes through Illumina-based de novo sequencing and metagenomic analysis of free-living bacteria in the gut of the lower termite Coptotermes gestroi harvested in Vietnam

Journal of Bioscience and Bioengineering

Volumn 118, Issue 6, 2014, Pages 665-671

  Do, Thi Huyen ^a   Nguyen, Thi Thao ^b   Nguyen, Thanh Ngoc ^a   Le, Quynh Giang ^a   Nguyen, Cuong ^a   Kimura, Keitarou ^c   Truong, Nam Hai ^a  

^a GRADUATE UNIVERSITY OF SCIENCE AND TECHNOLOGY   (Viet Nam)

^b VINH UNIVERSITY   (Viet Nam)

^c NATIONAL FOOD RESEARCH INSTITUTE   (Japan)

Author keywords

Cellulase; Coptotermes gestroi; Free living gut bacterial community; Hemicellulase; Illumina de novo sequencing; Metagenome; Pectinesterase

Indexed keywords

BACTERIA; BIOMASS; CELLULOSE; ENCODING (SYMBOLS); ENZYMES; GENES; SIGNAL ENCODING;

BACTERIAL COMMUNITY; CELLULASE; COPTOTERMES GESTROI; DE NOVO SEQUENCING; HEMICELLULASES; METAGENOMES; PECTINESTERASE;

BIODEGRADATION;

ALPHA ARABINOFURANOSIDASE; ALPHA GALACTOSIDASE; BACTERIAL DNA; BETA GLUCOSIDASE; BETA MANNOSIDASE; CELLOBIOSE PHOSPHORYLASE; CELLULOSE; CELLULOSE 1,4 BETA CELLOBIOSIDASE; GLUCAN ENDO 1,3 BETA GLUCOSIDASE; GLUCOSIDASE; HEMICELLULOSE; HYDROLASE; PECTATE LYASE; PECTIN; PECTINESTERASE; PHOSPHORYLASE; UNCLASSIFIED DRUG; XYLAN 1,4 BETA XYLOSIDASE; XYLAN ENDO 1,3 BETA XYLOSIDASE; CARBOXYLESTERASE; CELLULASE; LIGNIN; LIGNOCELLULOSE;

ACTINOBACTERIA; ACTINOMYCETALES; ALGORITHM; AMINO ACID SEQUENCE; ARTICLE; BACILLALES; BACTERIAL GENE; BACTEROIDALES; BACTEROIDES; BACTEROIDETES; BIOFUEL PRODUCTION; BIOMASS; BURKHOLDERIALES; CARBOHYDRATE METABOLISM; CHROMATIN STRUCTURE; CLOSTRIDIALES; CLOSTRIDIUM; COPTOTERMES; COPTOTERMES GESTROI; DEGRADATION; DESULFOVIBRIONALES; ENTEROBACTER; ENTEROBACTERIALES; ENZYME ACTIVE SITE; FIRMICUTES; GENE SEQUENCE; HYDROLYSIS; INTESTINE FLORA; LACTOBACILLALES; LACTOCOCCUS; METAGENOME; METAGENOMICS; MICROBIAL COMMUNITY; MYCOPLASMATALES; NONHUMAN; PLANCTOMYCETES; PROTEOBACTERIA; PSEUDOMONAS; SPIROCHETE; TREPONEMA; VIET NAM; XANTHOMONADALES; ANIMAL; BACTERIUM; CLASSIFICATION; DNA SEQUENCE; ENZYMOLOGY; GASTROINTESTINAL TRACT; GENETICS; ISOLATION AND PURIFICATION; ISOPTERA; METABOLISM; MICROBIOLOGY; NUCLEOTIDE SEQUENCE; OPEN READING FRAME;

ACTINOMYCETALES; BACILLALES; BACTERIA (MICROORGANISMS); BACTEROIDALES; BURKHOLDERIALES; CLOSTRIDIALES; COPTOTERMES GESTROI; DESULFOVIBRIONALES; ENTEROBACTERIALES; ISOPTERA; LACTOBACILLALES; SPIROCHAETALES; XANTHOMONADALES;

ANIMALS; BACTERIA; BASE SEQUENCE; BIOMASS; CARBOXYLIC ESTER HYDROLASES; CELLULASES; GASTROINTESTINAL TRACT; GENES, BACTERIAL; ISOPTERA; LIGNIN; METAGENOME; METAGENOMICS; OPEN READING FRAMES; SEQUENCE ANALYSIS, DNA; VIETNAM;

EID: 84922794825     PISSN: 13891723     EISSN: 13474421     Source Type: Journal    
DOI: 10.1016/j.jbiosc.2014.05.010     Document Type: Article

References (47)

1. Hongoh Y. Toward the functional analysis of uncultivable, symbiotic microorganisms in the termite gut. Cell. Mol. Life Sci. 2011, 68:1311-1325.
2. Kudo T. Termite-microbe symbiotic system and its efficient degradation of lignocellulose. Biosci. Biotechnol. Biochem. 2009, 73:2561-2567.
3. Chaffron S., von Mering C. Termites in the woodwork. Genome Biol. 2007, 8:229.
4. Scharf M.E., Tartar A. Termite digestomes as sources for novel lignocellulases. Biofuels Bioprod. Biorefining 2008, 2:540-552.
5. Katsumata K.S., Jin Z., Hori K., Iiyama K. Structural changes in lignin of tropical woods during digestion by termite, Cryptotermes brevis. J.Wood Sci. 2007, 53:419-426.
6. Scharf M.E., Karl Z.J., Sethi A., Boucias D.G. Multiple levels of synergistic collaboration in termite lignocellulose digestion. PLoS One 2011, 6:e21709.
7. Hongoh Y. Diversity and genomes of uncultured microbial symbionts in the termite gut. Biosci. Biotechnol. Biochem. 2010, 74:1145-1151.
8. He S., Ivanova N., Kirton E., Allgaier M., Bergin C., Scheffrahn R.H., Kyrpides N.C., Warnecke F., Tringe S.G., Hugenholtz P. Comparative metagenomic and metatranscriptomic analysis of hindgut paunch microbiota in wood- and dung-feeding higher termites. PloS One 2013, 8:e61126.
9. Warnecke F., Luginbühl P., Ivanova N., Ghassemian M., Richardson T.H., Stege J.T., Cayouette M., McHardy A.C., Djordjevic G., Aboushadi N., other 29 authors Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite. Nature 2007, 450:560-565.
10. Breznak J.A., Brune A. Role of microorganisms in the digestion of lignocellulose by termites. Annu. Rev. Entomol. 1994, 39:453-487.
11. Evans T.A., Forschler B.T., Grace J.K. Biology of invasive termites: a worldwide review. Annu. Rev. Entomol. 2013, 58:455-474.
12. Li H.F., Fujisaki I., Su N.Y. Predicting habitat suitability of Coptotermes gestroi (Isoptera: Rhinotermitidae) with species distribution models. J.Econ. Entomol. 2013, 106:311-321.
13. Franco Cairo J.P.L., Leonardo F.C., Alvarez T.M., Ribeiro D.A., Buchli F., Costa-Leonardo A.M., Carazzolle M.F., Costa F.F., Paes Leme A.F., Pereira G.A., Squina F.M. Functional characterization and target discovery of glycoside hydrolases from the digestome of the lower termite Coptotermes gestroi. Biotechnol. Biofuels 2011, 4:50.
14. Köhler T., Dietrich C., Scheffrahn R.H., Brune A. High-resolution analysis of gut environment and bacterial microbiota reveals functional compartmentation of the gut in wood-feeding higher termites (Nasutitermes spp.). Appl. Environ. Microbiol. 2012, 78:4691-4701.
15. Tartar A., Wheeler M.M., Zhou X., Coy M.R., Boucias D.G., Scharf M.E. Parallel metatranscriptome analyses of host and symbiont gene expression in the gut of the termite Reticulitermes flavipes. Biotechnol. Biofuels 2009, 2:25.
16. Xie L., Zhang L., Zhong Y., Liu N., Long Y., Wang S., Zhou X., Zhou Z., Huang Y., Wang Q. Profiling the metatranscriptome of the protistan community in Coptotermes formosanus with emphasis on the lignocellulolytic system. Genomics 2012, 99:246-255.
17. Todaka N., Inoue T., Saita K., Ohkuma M., Nalepa C.A., Lenz M., Kudo T., Moriya S. Phylogenetic analysis of cellulolytic enzyme genes from representative lineages of termites and a related cockroach. PLoS ONE 2010, 5:e8636.
18. Noda S., Iida T., Kitade O., Nakajima H., Kudo T., Ohkuma M. Endosymbiotic Bacteroidales bacteria of the flagellated protist Pseudotrichonympha grassii in the gut of the termite Coptotermes formosanus. Appl. Environ. Microbiol. 2005, 71:8811-8817.
19. Nakajima H., Hongoh Y., Usami R., Kudo T., Ohkuma M. Spatial distribution of bacterial phylotypes in the gut of the termite Reticulitermes speratus and the bacterial community colonizing the gut epithelium. FEMS Microbiol. Ecol. 2005, 54:247-255.
20. Nakajima H., Hongoh Y., Noda S., Yoshida Y., Usami R., Kudo T., Ohkuma M. Phylogenetic and morphological diversity of Bacteroidales members associated with the gut wall of termites. Biosci. Biotechnol. Biochem. 2006, 70:211-218.
21. Szalanski A.L., Austin J.W., Scheffrahn R.H., Messenger M.T. Molecular diagnostics of the formosan subterranean termite (Isoptera: Rhinotermitidae). Fla. Entomol. 2004, 87:145-151.
22. Sambrook J., Russell D.W. Molecular cloning: a laboratory manual 1989, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
23. Harnpicharnchai P., Thongaram T., Sriprang R., Champreda V., Tanapongpipat S., Eurwilaichitr L. An efficient purification and fractionation of genomic DNA from soil by modified troughing method. Lett. Appl. Microbiol. 2007, 45:387-391.
24. Luo R., Liu B., Xie Y., Li Z., Huang W., Yuan J., He G., Chen Y., Pan Q., Liu Y., other 20 authors SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. GigaScience 2012, 1:18.
25. Cole J.R., Wang Q., Cardenas E., Fish J., Chai B., Farris R.J., Kulam-Syed-Mohideen A.S., McGarrell D.M., Marsh T., Garrity G.M., Tiedje J.M. The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res. 2009, 37:D141-D145.
26. Noguchi H., Taniguchi T., Itoh T. MetaGeneAnnotator: detecting species-specific patterns of ribosomal binding site for precise gene prediction in anonymous prokaryotic and phage genomes. DNA Res. 2008, 15:387-396.
27. Kanehisa M., Araki M., Goto S., Hattori M., Hirakawa M., Itoh M., Katayama T., Kawashima S., Okuda S., Tokimatsu T., Yamanishi Y. KEGG for linking genomes to life and the environment. Nucleic Acids Res. 2008, 36:D480-D484.
28. Powell S., Szklarczyk D., Trachana K., Roth A., Kuhn M., Muller J., Arnold R., Rattei T., Letunic I., Doerks T., other 3 authors eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges. Nucleic Acids Res. 2011, 40:D284-D289.
29. Mitra S., Rupek P., Richter D.C., Urich T., Gilbert J.A., Meyer F., Wilke A., Huson D.H. Functional analysis of metagenomes and metatranscriptomes using SEED and KEGG. BMC Bioinformatics 2011, 12:S21.
30. Huson D.H., Auch A.F., Qi J., Schuster S.C. MEGAN analysis of metagenomic data. Genome Res. 2007, 17:377-386.
31. Hongoh Y., Ohkuma M., Kudo T. Molecular analysis of bacterial microbiota in the gut of the termite Reticulitermes speratus (Isoptera: Rhinotermitidae). FEMS Microbiol. Ecol. 2003, 44:231-242.
32. Hongoh Y., Deevong P., Inoue T., Moriya S., Trakulnaleamsai S., Ohkuma M., Vongkaluang C., Noparatnaraporn N., Kudo T. Intra- and interspecific comparisons of bacterial diversity and community structure support coevolution of gut microbiota and termite host. Appl. Environ. Microbiol. 2005, 71:6590-6599.
33. Hongoh Y., Yuzawa H., Ohkuma M., Kudo T. Evaluation of primers and PCR conditions for the analysis of 16S rRNA genes from a natural environment. FEMS Microbiol. Lett. 2003, 221:299-304.
34. Ohkuma M., Sato T., Noda S., Ui S., Kudo T., Hongoh Y. The candidate phylum "Termite Group 1" of bacteria: phylogenetic diversity, distribution, and endosymbiont members of various gut flagellated protists. FEMS Microbiol. Ecol. 2007, 60:467-476.
35. Shinzato N., Muramatsu M., Matsui T., Watanabe Y. Molecular phylogenetic diversity of the bacterial community in the gut of the termiteCoptotermes formosanus. Biosci. Biotechnol. Biochem. 2005, 69:1145-1155.
36. Dietrich C., Köhler T., Brune A. The cockroach origin of the termite gut microbiota: patterns in bacterial community structure reflect major evolutionary events. Appl. Environ. Microbiol. 2014, 80:2261-2269.
37. Breznak J.A. Phylogenetic diversity and physiology of termite gut spirochetes. Integr. Comp. Biol. 2002, 42:313-318.
38. Martins L.F., Antunes L.P., Pascon R.C., de Oliveira J.C.F., Digiampietri L.A., Barbosa D., Peixoto B.M., Vallim M.A., Viana-Niero C., Ostroski E.H., other 7 authors Metagenomic analysis of a tropical composting operation at the São Paulo Zoo Park reveals diversity of biomass degradation functions and organisms. PLoS ONE 2013, 8:e61928.
39. Partanen P., Hultman J., Paulin L., Auvinen P., Romantschuk M. Bacterial diversity at different stages of the composting process. BMC Microbiol. 2010, 10:94.
40. Guo Y., Zhu N., Zhu S., Deng C. Molecular phylogenetic diversity of bacteria and its spatial distribution in composts. J.Appl. Microbiol. 2007, 103:1344-1354.
41. Kato S., Haruta S., Cui Z.J., Ishii M., Igarashi Y. Effective cellulose degradation by a mixed-culture system composed of a cellulolytic Clostridium and aerobic non-cellulolytic bacteria. FEMS Microbiol. Ecol. 2004, 51:133-142.
42. Paster B.J. Phylum XV. Spirochaetes Garrity and Holt 2001. Bergey's manual of systematic bacteriology 2010, 471-566. Springer, New York. N.R. Krieg, J.T. Staley, D.R. Brown, B.P. Hedlund, B.J. Paster, N.L. Ward, W. Ludwig, W.B. Whitman (Eds.).
43. Davies G.J., Henrissat B. Structural enzymology of carbohydrate-active enzymes: implications for the post-genomic era. Biochem. Soc. Trans. 2002, 30:291-297.
44. Todaka N., Moriya S., Saita K., Hondo T., Kiuchi I., Takasu H., Ohkuma M., Piero C., Hayashizaki Y., Kudo T. Environmental cDNA analysis of the genes involved in lignocellulose digestion in the symbiotic protist community of Reticulitermes speratus. FEMS Microbiol. Ecol. 2007, 59:592-599.
45. Zhou X., Smith J.A., Oi F.M., Koehler P.G., Bennett G.W., Scharf M.E. Correlation of cellulase gene expression and cellulolytic activity throughout the gut of the termite Reticulitermes flavipes. Gene 2007, 395:29-39.
46. Golan A.E. Cellulase types and action, mechanism, and uses 2011, Nova Science Publishers, New York.
47. Berlemont R., Martiny A.C. Phylogenetic distribution of potential cellulases in bacteria. Appl. Environ. Microbiol. 2013, 79:1545-1554.