Metagenomic insights into lignocellulose-degrading genes through Illuminabased de novo sequencing of the microbiome in vietnamese native goats’ rumen

Thi Huyen Do; Ngoc Giang Le; Trong Khoa Dao; Thi Mai Phuong Nguyen; Tung Lam Le; Han Ly Luu; Khanh Hoang Viet Nguyen; Van Lam Nguyen; Lan Anh Le; Thu Nguyet Phung; Nico M van Straalen; Dick Roelofs; Nam Hai Truong

doi:10.2323/jgam.2017.08.004

Metagenomic insights into lignocellulose-degrading genes through Illuminabased de novo sequencing of the microbiome in vietnamese native goats’ rumen

Thi Huyen Do, Ngoc Giang Le, Trong Khoa Dao, Thi Mai Phuong Nguyen, Tung Lam Le, Han Ly Luu, Khanh Hoang Viet Nguyen, Van Lam Nguyen, Lan Anh Le, Thu Nguyet Phung, Nico M van Straalen, Dick Roelofs, Nam Hai Truong^*

^*Corresponding author for this work

Research output: Contribution to Journal › Article › Academic › peer-review

Abstract

The scarcity of enzymes having an optimal activity in lignocellulose deconstruction is an obstacle for industrial-scale conversion of cellulosic biomass into biofuels. With the aim of mining novel lignocellulolytic enzymes, a ~9 Gb metagenome of bacteria in Vietnamese native goats’ rumen was sequenced by Illumina platform. From the data, 821 ORFs encoding carbohydrate esterases (CEs) and polysaccharide lyases (PLs) serving for lignocellulose pre-treatment, 816 ORFs encoding 11 glycoside hydrolase families (GHs) of cellulases, and 2252 ORFs encoding 22 GHs of hemicellulases, were mined. The carbohydrate binding module (CBM) was also abundant with 763 ORFs, of which 480 ORFs are located with lignocellulolytic enzymes. The enzyme modularity analysis showed that CBMs are usually present in endoglucanase, endo 1,3-beta-D-glucosidase, and endoxylanase, whereas fibronectin 3-like module (FN3) mainly represents in GH3 and immunoglobulin-like domain (Ig) was located in GH9 only. Every domain located in each ORF was analyzed in detail to contribute enzymes’ modularity which is valuable for modelling, to study the structure, and for recombinant production. With the aim of confirming the annotated results, a mined ORF encoding CBM63 was highly expressed in E. coli in soluble form. The purified recombinant CBM63 exhibited no cellulase activity, but enhanced a commercial cellulase activity in the destruction of a paper filter.

Original language	English
Pages (from-to)	108-116
Number of pages	9
Journal	The Journal of general and applied microbiology
Volume	64
Issue number	3
Early online date	12 Mar 2018
DOIs	https://doi.org/10.2323/jgam.2017.08.004
Publication status	Published - Mar 2018

Funding

We would like to acknowledge Dr. S. V. N. Vijayendra (Food Microbiology Dept., Central Food Technological Research Institute, Mysore-570020, India) for proofreading and correcting the English of this manuscript. The study was carried out with the financial support of the Project “Metagenome of some potential mini-ecologies for mining novel genes encoding effective lignocellulolytic enzymes” code DTDLCN.15/14, managed by the Ministry of Science and Technology, Vietnam, in collaboration with the Department of Ecological Science, Vrije Universiteit Amsterdam, The Netherlands, supported by the BE-BASIC consortium project numbers F07.003.05 and F07.003.07. We thank the National Key Laboratory of Gene Technology, Institute of Biotechnology, VAST, Vietnam, for the use of their facilities. We are also grateful to the Editor of JGAM for valuable comments to improve the manuscript.

Funders	Funder number
Ministry of Science and Technology
Vietnam Academy of Science and Technology
Vrije Universiteit Amsterdam	F07.003.05, F07.003.07
Ministerio de Ciencia y Tecnología

Keywords

Carbohydrate binding model
Cellulase
Hemicellulase
Illumina de novo sequencing
Metagenome
Pretreatment
Vietnamese native goat

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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Do, T. H., Le, N. G., Dao, T. K., Nguyen, T. M. P., Le, T. L., Luu, H. L., Nguyen, K. H. V., Nguyen, V. L., Le, L. A., Phung, T. N., van Straalen, N. M., Roelofs, D., & Truong, N. H. (2018). Metagenomic insights into lignocellulose-degrading genes through Illuminabased de novo sequencing of the microbiome in vietnamese native goats’ rumen. The Journal of general and applied microbiology, 64(3), 108-116. https://doi.org/10.2323/jgam.2017.08.004

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title = "Metagenomic insights into lignocellulose-degrading genes through Illuminabased de novo sequencing of the microbiome in vietnamese native goats{\textquoteright} rumen",

abstract = "The scarcity of enzymes having an optimal activity in lignocellulose deconstruction is an obstacle for industrial-scale conversion of cellulosic biomass into biofuels. With the aim of mining novel lignocellulolytic enzymes, a ~9 Gb metagenome of bacteria in Vietnamese native goats{\textquoteright} rumen was sequenced by Illumina platform. From the data, 821 ORFs encoding carbohydrate esterases (CEs) and polysaccharide lyases (PLs) serving for lignocellulose pre-treatment, 816 ORFs encoding 11 glycoside hydrolase families (GHs) of cellulases, and 2252 ORFs encoding 22 GHs of hemicellulases, were mined. The carbohydrate binding module (CBM) was also abundant with 763 ORFs, of which 480 ORFs are located with lignocellulolytic enzymes. The enzyme modularity analysis showed that CBMs are usually present in endoglucanase, endo 1,3-beta-D-glucosidase, and endoxylanase, whereas fibronectin 3-like module (FN3) mainly represents in GH3 and immunoglobulin-like domain (Ig) was located in GH9 only. Every domain located in each ORF was analyzed in detail to contribute enzymes{\textquoteright} modularity which is valuable for modelling, to study the structure, and for recombinant production. With the aim of confirming the annotated results, a mined ORF encoding CBM63 was highly expressed in E. coli in soluble form. The purified recombinant CBM63 exhibited no cellulase activity, but enhanced a commercial cellulase activity in the destruction of a paper filter.",

keywords = "Carbohydrate binding model, Cellulase, Hemicellulase, Illumina de novo sequencing, Metagenome, Pretreatment, Vietnamese native goat",

author = "Do, {Thi Huyen} and Le, {Ngoc Giang} and Dao, {Trong Khoa} and Nguyen, {Thi Mai Phuong} and Le, {Tung Lam} and Luu, {Han Ly} and Nguyen, {Khanh Hoang Viet} and Nguyen, {Van Lam} and Le, {Lan Anh} and Phung, {Thu Nguyet} and {van Straalen}, {Nico M} and Dick Roelofs and Truong, {Nam Hai}",

year = "2018",

month = mar,

doi = "10.2323/jgam.2017.08.004",

language = "English",

volume = "64",

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Do, TH, Le, NG, Dao, TK, Nguyen, TMP, Le, TL, Luu, HL, Nguyen, KHV, Nguyen, VL, Le, LA, Phung, TN, van Straalen, NM, Roelofs, D & Truong, NH 2018, 'Metagenomic insights into lignocellulose-degrading genes through Illuminabased de novo sequencing of the microbiome in vietnamese native goats’ rumen', The Journal of general and applied microbiology, vol. 64, no. 3, pp. 108-116. https://doi.org/10.2323/jgam.2017.08.004

Metagenomic insights into lignocellulose-degrading genes through Illuminabased de novo sequencing of the microbiome in vietnamese native goats’ rumen. / Do, Thi Huyen; Le, Ngoc Giang; Dao, Trong Khoa et al.
In: The Journal of general and applied microbiology, Vol. 64, No. 3, 03.2018, p. 108-116.

Research output: Contribution to Journal › Article › Academic › peer-review

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T1 - Metagenomic insights into lignocellulose-degrading genes through Illuminabased de novo sequencing of the microbiome in vietnamese native goats’ rumen

AU - Do, Thi Huyen

AU - Le, Ngoc Giang

AU - Dao, Trong Khoa

AU - Nguyen, Thi Mai Phuong

AU - Le, Tung Lam

AU - Luu, Han Ly

AU - Nguyen, Khanh Hoang Viet

AU - Nguyen, Van Lam

AU - Le, Lan Anh

AU - Phung, Thu Nguyet

AU - van Straalen, Nico M

AU - Roelofs, Dick

AU - Truong, Nam Hai

PY - 2018/3

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AB - The scarcity of enzymes having an optimal activity in lignocellulose deconstruction is an obstacle for industrial-scale conversion of cellulosic biomass into biofuels. With the aim of mining novel lignocellulolytic enzymes, a ~9 Gb metagenome of bacteria in Vietnamese native goats’ rumen was sequenced by Illumina platform. From the data, 821 ORFs encoding carbohydrate esterases (CEs) and polysaccharide lyases (PLs) serving for lignocellulose pre-treatment, 816 ORFs encoding 11 glycoside hydrolase families (GHs) of cellulases, and 2252 ORFs encoding 22 GHs of hemicellulases, were mined. The carbohydrate binding module (CBM) was also abundant with 763 ORFs, of which 480 ORFs are located with lignocellulolytic enzymes. The enzyme modularity analysis showed that CBMs are usually present in endoglucanase, endo 1,3-beta-D-glucosidase, and endoxylanase, whereas fibronectin 3-like module (FN3) mainly represents in GH3 and immunoglobulin-like domain (Ig) was located in GH9 only. Every domain located in each ORF was analyzed in detail to contribute enzymes’ modularity which is valuable for modelling, to study the structure, and for recombinant production. With the aim of confirming the annotated results, a mined ORF encoding CBM63 was highly expressed in E. coli in soluble form. The purified recombinant CBM63 exhibited no cellulase activity, but enhanced a commercial cellulase activity in the destruction of a paper filter.

KW - Carbohydrate binding model

KW - Cellulase

KW - Hemicellulase

KW - Illumina de novo sequencing

KW - Metagenome

KW - Pretreatment

KW - Vietnamese native goat

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Metagenomic insights into lignocellulose-degrading genes through Illuminabased de novo sequencing of the microbiome in vietnamese native goats’ rumen

Abstract

Funding

Keywords

UN SDGs

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