16S rRNA全基因和ITS区域扩增子测序对结肠束微生物组的高分辨率分析。

IF 3.6 4区 生物学 Q2 ENVIRONMENTAL SCIENCES
Pia Marter, Heike M. Freese, Victoria Ringel, Henner Brinkmann, Silke Pradella, Manfred Rohde, Michal Jarek, Cathrin Spröer, Irene Wagner-Döbler, Jörg Overmann, Boyke Bunk, Jörn Petersen
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引用次数: 0

摘要

丝状蓝藻结束藻是海洋微生物席的主要生产者。我们利用基于pacbio的16S rRNA全基因扩增子测序和内部转录间隔(16S- its)测序技术,对32株非无菌结肠束菌分离株的微生物组进行了鉴定。真实扩增子序列变异(asv)的长度为1827 ~ 3044个核苷酸(中位数:2267 nt)。通过宏基因组分析和培养方法,发现Coleofasciculus sp. WW12培养中存在70多种相关异养菌。蓝藻圈细菌多样性以假单胞菌属(59%)和拟杆菌属(23%)为主。在18株结肠束菌株中检测到等位基因核糖体操纵子变异,我们的分析表明至少存在四个不同的物种。蓝藻微生物组的比较分析证明了扩增子测序与宏基因组学在(i)核糖体靶序列质量、(ii)污染物检测和(iii)稀有细菌鉴定方面的互补优势,以及16S-ITS方法的个体强度。Coleofasciculus微生物组的表征表明,16S-ITS区域的长读扩增子测序是快速分析非无菌蓝藻的首选方法。其优越的分辨率允许一个可靠的分化,甚至非常密切相关的菌株。
本文章由计算机程序翻译,如有差异,请以英文原文为准。

Superior Resolution Profiling of the Coleofasciculus Microbiome by Amplicon Sequencing of the Complete 16S rRNA Gene and ITS Region

Superior Resolution Profiling of the Coleofasciculus Microbiome by Amplicon Sequencing of the Complete 16S rRNA Gene and ITS Region

The filamentous cyanobacterium Coleofasciculus chthonoplastes is the key primary producer of marine microbial mats. We elucidated the microbiomes of 32 non-axenic Coleofasciculus isolates using PacBio-based amplicon sequencing of the complete 16S rRNA gene and the internally transcribed spacer (16S-ITS). The length of authentic amplicon sequence variants (ASVs) ranged from 1827 to 3044 nucleotides (median: 2267 nt). The results, which were complemented by metagenome analyses and cultivation approaches, revealed the presence of more than 70 associated heterotrophs in the culture of Coleofasciculus sp. WW12. The great bacterial diversity in the cyanosphere is dominated by Pseudomonadota (59%) and Bacteroidota (23%). Allelic ribosomal operon variants were detected in 18 Coleofasciculus strains and our analyses proposed the presence of at least four different species. A comparative analysis of cyanobacterial microbiomes documented complementary advantages of amplicon sequencing versus metagenomics with an individual strength of the 16S-ITS approach in terms of (i) ribosomal target sequence quality, (ii) contaminant detection and (iii) identification of rare bacteria. The characterisation of the Coleofasciculus microbiome showed that long-read amplicon sequencing of the 16S-ITS region is the method of choice for rapid profiling of non-axenic cyanobacteria. Its superior resolution allows a reliable differentiation of even very closely related strains.

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来源期刊
Environmental Microbiology Reports
Environmental Microbiology Reports ENVIRONMENTAL SCIENCES-MICROBIOLOGY
CiteScore
6.00
自引率
3.00%
发文量
91
审稿时长
3.0 months
期刊介绍: The journal is identical in scope to Environmental Microbiology, shares the same editorial team and submission site, and will apply the same high level acceptance criteria. The two journals will be mutually supportive and evolve side-by-side. Environmental Microbiology Reports provides a high profile vehicle for publication of the most innovative, original and rigorous research in the field. The scope of the Journal encompasses the diversity of current research on microbial processes in the environment, microbial communities, interactions and evolution and includes, but is not limited to, the following: the structure, activities and communal behaviour of microbial communities microbial community genetics and evolutionary processes microbial symbioses, microbial interactions and interactions with plants, animals and abiotic factors microbes in the tree of life, microbial diversification and evolution population biology and clonal structure microbial metabolic and structural diversity microbial physiology, growth and survival microbes and surfaces, adhesion and biofouling responses to environmental signals and stress factors modelling and theory development pollution microbiology extremophiles and life in extreme and unusual little-explored habitats element cycles and biogeochemical processes, primary and secondary production microbes in a changing world, microbially-influenced global changes evolution and diversity of archaeal and bacterial viruses new technological developments in microbial ecology and evolution, in particular for the study of activities of microbial communities, non-culturable microorganisms and emerging pathogens.
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