Phylotype-Level Characterization of Complex Communities of Lactobacilli Using a High-Throughput, High-Resolution Phenylalanyl-tRNA Synthetase (pheS) Gene Amplicon Sequencing Approach
文献类型：期刊论文
| 作者 | Silvaraju, Shaktheeshwari; Menon, Nandita; Fan, Huan1 ; Lim, Kevin; Kittelmann, Sandra
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| 刊名 | APPLIED AND ENVIRONMENTAL MICROBIOLOGY
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| 出版日期 | 2021 |
| 卷号 | 87期号:1页码:- |
| ISSN号 | 0099-2240 |
| 关键词 | LACTIC-ACID BACTERIA PHYLOGENETIC ANALYSIS SP-NOV. IDENTIFICATION RPOA METABOLISM GENOMICS ECOLOGY SILVA |
| DOI | 10.1128/AEM.02191-20 |
| 英文摘要 | The lactobacilli identified to date encompass more than 270 closely related species that were recently reclassified into 26 genera. Because of their relevance to industry, there is a need to distinguish between closely related and yet metabolically and regulatory distinct species, e.g., during monitoring of biotechnological processes or screening of samples of unknown composition. Current available methods, such as shotgun metagenomics or rRNA gene-based amplicon sequencing, have significant limitations (high cost, low resolution, etc.). Here, we generated a phylogeny of lactobacilli based on phenylalanyl-tRNA synthetase (pheS) genes and, from it, developed a high-resolution taxonomic framework which allows for comprehensive and confident characterization of the community diversity and structure of lactobacilli at the species level. This framework is based on a total of 445 pheS gene sequences, including sequences of 276 validly described species and subspecies (of a total of 282, including the proposed L. timonensis species and the reproposed L. zeae species; coverage of 98%), and allows differentiation between 265 species-level clades of lactobacilli and the subspecies of L. sakei. The methodology was validated through next-generation sequencing of mock communities. At a sequencing depth of similar to 30,000 sequences, the minimum level of detection was approximately 0.02 pg per mu l DNA (equaling approximately 10 genome copies per mu l template DNA). The pheS approach, along with parallel sequencing of partial 16S rRNA genes, revealed considerable diversity of lactobacilli and distinct community structures across a broad range of samples from different environmental niches. This novel complementary approach may be applicable to industry and academia alike. IMPORTANCE Species formerly classified within the genera Lactobacillus and Pediococcus have been studied extensively at the genomic level. To accommodate their exceptional functional diversity, the over 270 species were recently reclassified into 26 distinct genera. Despite their relevance to both academia and industry, methods that allow detailed exploration of their ecology are still limited by low resolution, high cost, or copy number variations. The approach described here makes use of a single-copy marker gene which outperforms other markers with regard to species-level resolution and availability of reference sequences (98% coverage). The tool was validated against a mock community and used to address diversity of lactobacilli and community structure in various environmental matrices. Such analyses can now be performed at a broader scale to assess and monitor the assembly, structure, and function of communities of lactobacilli at the species level (and, in some cases, even at the subspecies level) across a wide range of academic and commercial applications. |
| 学科主题 | Biotechnology & Applied Microbiology ; Microbiology |
| 语种 | 英语 |
| WOS记录号 | WOS:000605458700022 |
| 源URL | [http://ir.xtbg.org.cn/handle/353005/11932]  |
| 专题 | 西双版纳热带植物园_其他 |
| 作者单位 | 1.Natl Univ Singapore, Ctr Translat Med, WIL NUS Corp Lab, Wilmar Int Ltd, Singapore, Singapore 2.Chinese Acad Sci, Ctr Integrat Conservat, Xishuangbanna Trop Bot Garden, Menglun, Yunnan, Peoples R China |
| 推荐引用方式 GB/T 7714 | Silvaraju, Shaktheeshwari,Menon, Nandita,Fan, Huan,et al. Phylotype-Level Characterization of Complex Communities of Lactobacilli Using a High-Throughput, High-Resolution Phenylalanyl-tRNA Synthetase (pheS) Gene Amplicon Sequencing Approach[J]. APPLIED AND ENVIRONMENTAL MICROBIOLOGY,2021,87(1):-. |
| APA | Silvaraju, Shaktheeshwari,Menon, Nandita,Fan, Huan,Lim, Kevin,&Kittelmann, Sandra.(2021).Phylotype-Level Characterization of Complex Communities of Lactobacilli Using a High-Throughput, High-Resolution Phenylalanyl-tRNA Synthetase (pheS) Gene Amplicon Sequencing Approach.APPLIED AND ENVIRONMENTAL MICROBIOLOGY,87(1),-. |
| MLA | Silvaraju, Shaktheeshwari,et al."Phylotype-Level Characterization of Complex Communities of Lactobacilli Using a High-Throughput, High-Resolution Phenylalanyl-tRNA Synthetase (pheS) Gene Amplicon Sequencing Approach".APPLIED AND ENVIRONMENTAL MICROBIOLOGY 87.1(2021):-. |
入库方式： OAI收割
来源：西双版纳热带植物园
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