John Daisy Vanitha, Purushottam Meera
Department of Neuromicrobiology, National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore, Karnataka, India.
Molecular Genetics Laboratory, Department of Psychiatry, National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore, Karnataka, India.
Data Brief. 2023 Jan 11;46:108893. doi: 10.1016/j.dib.2023.108893. eCollection 2023 Feb.
A brain abscess is a focal collection of pus in the brain parenchyma surrounded by a well-vascularized collagenous capsule in response to an infection. The microbiome of brain abscesses has been shown to be polymicrobial, dominated by uncultivable and anaerobic organisms of odontogenic origin. The data provided in this article includes the sequences of bacterial 16S rRNA gene from three culture-negative brain abscess samples suspected to have poly-microbial aetiology based on Sanger sequencing. DNA was extracted from brain abscess samples, and targeted-metagenomics sequencing was done by amplifying the full-length bacterial 16S rRNA followed by a nested PCR for V3-V4 regions using universal and specific primers. The barcoded amplicons were sequenced on Illumina MiSeq V2 instrument to generate 0.5M, 250bp paired-end reads/sample. The total sequencing reads were 455966, 345746, and 438658 for samples P32, P49, and P8, respectively. Bioinformatics tools such as FLASH, VSEARCH, and QIIME1 were used to process the reads generated for Operational Taxonomic Unit analysis (OTU). Bacterial species belonging to phyla Firmicutes, Bacteroidetes, and Fusobacteria were abundant in samples P49 and P8, which are mainly anaerobic and microaerophilic bacteria. These are typical of the human oral/gut microbiota and are implicated in brain abscess formation. Sample P32 showed the abundance of bacterial species belonging to phyla Proteobacteria and Actinobacteria, which are commonly found in the environment. Raw data files are available at the Sequence Read Archive (SRA), National Center for Biotechnology Information (NCBI), and data information can be found at the BioProject, PRJNA785100 under the accession numbers SRX13271109, SRX13271110, SRX13295897. The data shows the microbiome constitution, including several anaerobic and unculturable bacterial species from culture-negative brain abscess samples. This dataset will be useful for future research on comparative genomics and management of patients with culture-negative brain abscesses.
脑脓肿是脑实质内的局限性脓液聚集，周围有血管丰富的胶原包膜，是对感染的反应。脑脓肿的微生物群已被证明是多微生物的，以牙源性不可培养和厌氧生物为主。本文提供的数据包括来自三个培养阴性脑脓肿样本的细菌16S rRNA基因序列，这些样本基于桑格测序怀疑有多微生物病因。从脑脓肿样本中提取DNA，并通过扩增全长细菌16S rRNA，然后使用通用引物和特异性引物对V3-V4区域进行巢式PCR，进行靶向宏基因组测序。带条形码的扩增子在Illumina MiSeq V2仪器上进行测序，以产生每个样本0.5M、250bp的双端读数。样本P32、P49和P8的总测序读数分别为455966、345746和438658。使用FLASH、VSEARCH和QIIME1等生物信息学工具处理生成的读数，用于操作分类单元分析（OTU）。属于厚壁菌门、拟杆菌门和梭杆菌门的细菌物种在样本P49和P8中丰富，这些主要是厌氧和微需氧细菌。这些是人类口腔/肠道微生物群的典型特征，并与脑脓肿的形成有关。样本P32显示属于变形菌门和放线菌门的细菌物种丰富，这些在环境中常见。原始数据文件可在国家生物技术信息中心（NCBI）的序列读数存档（SRA）中获取，数据信息可在生物项目PRJNA785100下找到，登录号为SRX13271109、SRX13271110、SRX13295897。数据显示了微生物群组成，包括来自培养阴性脑脓肿样本的几种厌氧和不可培养细菌物种。该数据集将有助于未来对培养阴性脑脓肿患者的比较基因组学和管理的研究。
