Understanding the Role of <i>Prevotella</i> Genus in the Digestion of Lignocellulose and Other Substrates in Vietnamese Native Goats’ Rumen by Metagenomic Deep Sequencing

Bacteria in rumen play pivotal roles in the digestion of nutrients to support energy for the host. In this study, metagenomic deep sequencing of bacterial metagenome extracted from the goats’ rumen generated 48.66 GB of data with 3,411,867 contigs and 5,367,270 genes. The genes were mainly functiona...

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Autores principales:	Trong-Khoa Dao, Thi-Huyen Do, Ngoc-Giang Le, Hong-Duong Nguyen, Thi-Quy Nguyen, Thi-Thu-Hong Le, Nam-Hai Truong
Formato:	article
Lenguaje:	EN
Publicado:	MDPI AG 2021
Materias:	Illumina <i>de novo</i> deep sequencing lignocellulose digestion <i>Prevotella</i> starch digestion Vietnamese goats’ rumen Veterinary medicine SF600-1100 Zoology QL1-991
Acceso en línea:	https://doaj.org/article/63e252dee1b34667bfb98a4f312415ed
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spelling	oai:doaj.org-article:63e252dee1b34667bfb98a4f312415ed2021-11-25T16:19:54ZUnderstanding the Role of <i>Prevotella</i> Genus in the Digestion of Lignocellulose and Other Substrates in Vietnamese Native Goats’ Rumen by Metagenomic Deep Sequencing10.3390/ani111132572076-2615https://doaj.org/article/63e252dee1b34667bfb98a4f312415ed2021-11-01T00:00:00Zhttps://www.mdpi.com/2076-2615/11/11/3257https://doaj.org/toc/2076-2615Bacteria in rumen play pivotal roles in the digestion of nutrients to support energy for the host. In this study, metagenomic deep sequencing of bacterial metagenome extracted from the goats’ rumen generated 48.66 GB of data with 3,411,867 contigs and 5,367,270 genes. The genes were mainly functionally annotated by Kyoto Encyclopedia of Genes and Genomes (KEGG) Carbohydrate-Active enZYmes (CAZy), and HMMER database, and taxonomically classified by MEGAN. As a result, 65,554 genes encoding for 30 enzymes/proteins related to lignocellulose conversion were exploited, in which nine enzymes were seen for the first time in goat rumen. <i>Prevotella</i> was the most abundant genus, contributing 30% hemicellulases and 36% enzymes/proteins for lignocellulose pretreatment, and supporting 98.8% of feruloyl esterases and 71.7% acetylxylan esterases. In addition, 18 of the 22 most lignocellulose digesting- potential contigs belonged to <i>Prevotella.</i> Besides, <i>Prevotella</i> possessed many genes coding for amylolytic enzymes. One gene encoding for endoxylanase was successfully expressed in <i>E. coli</i>. The recombinant enzyme had high Vmax, was tolerant to some salts and detergents, worked better at pH 5.5–6.5, temperature 40–50 °C, and was capable to be used in practices. Based on these findings, we confirm that <i>Prevotella</i> plays a pivotal role for hemicellulose digestion and significantly participates in starch, cellulose, hemicellulose, and pectin digestion in the goat rumen.Trong-Khoa DaoThi-Huyen DoNgoc-Giang LeHong-Duong NguyenThi-Quy NguyenThi-Thu-Hong LeNam-Hai TruongMDPI AGarticleIllumina <i>de novo</i> deep sequencinglignocellulose digestion<i>Prevotella</i>starch digestionVietnamese goats’ rumenVeterinary medicineSF600-1100ZoologyQL1-991ENAnimals, Vol 11, Iss 3257, p 3257 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Illumina <i>de novo</i> deep sequencing lignocellulose digestion <i>Prevotella</i> starch digestion Vietnamese goats’ rumen Veterinary medicine SF600-1100 Zoology QL1-991
spellingShingle	Illumina <i>de novo</i> deep sequencing lignocellulose digestion <i>Prevotella</i> starch digestion Vietnamese goats’ rumen Veterinary medicine SF600-1100 Zoology QL1-991 Trong-Khoa Dao Thi-Huyen Do Ngoc-Giang Le Hong-Duong Nguyen Thi-Quy Nguyen Thi-Thu-Hong Le Nam-Hai Truong Understanding the Role of <i>Prevotella</i> Genus in the Digestion of Lignocellulose and Other Substrates in Vietnamese Native Goats’ Rumen by Metagenomic Deep Sequencing
description	Bacteria in rumen play pivotal roles in the digestion of nutrients to support energy for the host. In this study, metagenomic deep sequencing of bacterial metagenome extracted from the goats’ rumen generated 48.66 GB of data with 3,411,867 contigs and 5,367,270 genes. The genes were mainly functionally annotated by Kyoto Encyclopedia of Genes and Genomes (KEGG) Carbohydrate-Active enZYmes (CAZy), and HMMER database, and taxonomically classified by MEGAN. As a result, 65,554 genes encoding for 30 enzymes/proteins related to lignocellulose conversion were exploited, in which nine enzymes were seen for the first time in goat rumen. <i>Prevotella</i> was the most abundant genus, contributing 30% hemicellulases and 36% enzymes/proteins for lignocellulose pretreatment, and supporting 98.8% of feruloyl esterases and 71.7% acetylxylan esterases. In addition, 18 of the 22 most lignocellulose digesting- potential contigs belonged to <i>Prevotella.</i> Besides, <i>Prevotella</i> possessed many genes coding for amylolytic enzymes. One gene encoding for endoxylanase was successfully expressed in <i>E. coli</i>. The recombinant enzyme had high Vmax, was tolerant to some salts and detergents, worked better at pH 5.5–6.5, temperature 40–50 °C, and was capable to be used in practices. Based on these findings, we confirm that <i>Prevotella</i> plays a pivotal role for hemicellulose digestion and significantly participates in starch, cellulose, hemicellulose, and pectin digestion in the goat rumen.
format	article
author	Trong-Khoa Dao Thi-Huyen Do Ngoc-Giang Le Hong-Duong Nguyen Thi-Quy Nguyen Thi-Thu-Hong Le Nam-Hai Truong
author_facet	Trong-Khoa Dao Thi-Huyen Do Ngoc-Giang Le Hong-Duong Nguyen Thi-Quy Nguyen Thi-Thu-Hong Le Nam-Hai Truong
author_sort	Trong-Khoa Dao
title	Understanding the Role of <i>Prevotella</i> Genus in the Digestion of Lignocellulose and Other Substrates in Vietnamese Native Goats’ Rumen by Metagenomic Deep Sequencing
title_short	Understanding the Role of <i>Prevotella</i> Genus in the Digestion of Lignocellulose and Other Substrates in Vietnamese Native Goats’ Rumen by Metagenomic Deep Sequencing
title_full	Understanding the Role of <i>Prevotella</i> Genus in the Digestion of Lignocellulose and Other Substrates in Vietnamese Native Goats’ Rumen by Metagenomic Deep Sequencing
title_fullStr	Understanding the Role of <i>Prevotella</i> Genus in the Digestion of Lignocellulose and Other Substrates in Vietnamese Native Goats’ Rumen by Metagenomic Deep Sequencing
title_full_unstemmed	Understanding the Role of <i>Prevotella</i> Genus in the Digestion of Lignocellulose and Other Substrates in Vietnamese Native Goats’ Rumen by Metagenomic Deep Sequencing
title_sort	understanding the role of <i>prevotella</i> genus in the digestion of lignocellulose and other substrates in vietnamese native goats’ rumen by metagenomic deep sequencing
publisher	MDPI AG
publishDate	2021
url	https://doaj.org/article/63e252dee1b34667bfb98a4f312415ed
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Understanding the Role of <i>Prevotella</i> Genus in the Digestion of Lignocellulose and Other Substrates in Vietnamese Native Goats’ Rumen by Metagenomic Deep Sequencing

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