印度城市化城市沿海沉积物中细菌多样性和耐药基因的综合宏基因组分析

IF 1 Q4 GENETICS & HEREDITY

Gene Reports Pub Date : 2025-04-26 DOI:10.1016/j.genrep.2025.102239

Pradip Sahebrao Gawande , Vajravelu Manigandan , R. Sankar Ganesh , V. Rajesh Kannan , K. Ramu , M.V. Ramana Murthy

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引用次数: 0

摘要

本研究对印度7个城市化城市沿海沉积物中的细菌多样性和抗菌素耐药性（AMR）基因进行了综合分析：Paradeep （S1）、Visakhapatnam （S2）、Chennai （S3）、Mangalore （S4）、果阿（S5）、孟买（S6）和Veraval （S7）。沉积物DNA测序使用Illumina NextSeq-500平台，meta-SPAdes组装，基因预测使用Prodigal。根据CARD数据库筛选AMR基因。结果表明，Paradeep （S1）和Mumbai （S6）的细菌种群和AMR基因（ARGs）丰度均最高。细菌多样性显示，大多数样品中以Marinobacter最为丰富，而qipenyuanania和Salegentibacter各在一个地点流行。共鉴定出75种ARGs（510例），其中54种耐多药基因（MDR），以Saur_23S_LZD和Ecol_23S_CHL最为常见。ARGs和网络分析的BLASTn结果显示，Ecol_23S_CHL与42种细菌相关，包括人类病原体。本研究为了解ARGs在印度沿海水域的分布建立了基线，并为未来的研究提供了有价值的见解。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

Comprehensive metagenomic analysis of bacterial diversity and antimicrobial resistance genes in coastal sediments from urbanized Indian cities

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Comprehensive metagenomic analysis of bacterial diversity and antimicrobial resistance genes in coastal sediments from urbanized Indian cities

This study presents the comprehensive analysis of bacterial diversity and antimicrobial resistance (AMR) genes in coastal sediments from seven urbanized cities in India: Paradeep (S1), Visakhapatnam (S2), Chennai (S3), Mangalore (S4), Goa (S5), Mumbai (S6), and Veraval (S7). Sediment DNA was sequenced using the Illumina NextSeq-500 platform, assembled with meta-SPAdes, and gene predicted using Prodigal. AMR genes were identified by screening against the CARD database. The results show that Paradeep (S1) and Mumbai (S6) exhibited the highest abundance of both bacterial populations and AMR genes (ARGs). Bacterial diversity revealed that Marinobacter was the most abundant genus in most of the samples, while Qipengyuania and Salegentibacter were prevalent at one location each. A total of 75 types of ARGs (510 counts), including 54 multidrug resistance (MDR) genes, were identified, with Saur_23S_LZD and Ecol_23S_CHL being the most prevalent. BLASTn results of ARGs and network analysis revealed that Ecol_23S_CHL was associated with 42 bacterial species, including human pathogens. This study establishes a baseline for understanding the distribution of ARGs in coastal waters of India and provides valuable insights for future research.

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来源期刊

Gene Reports Biochemistry, Genetics and Molecular Biology-Genetics

CiteScore

3.30

自引率

7.70%

发文量

246

审稿时长

49 days

期刊介绍： Gene Reports publishes papers that focus on the regulation, expression, function and evolution of genes in all biological contexts, including all prokaryotic and eukaryotic organisms, as well as viruses. Gene Reports strives to be a very diverse journal and topics in all fields will be considered for publication. Although not limited to the following, some general topics include: DNA Organization, Replication & Evolution -Focus on genomic DNA (chromosomal organization, comparative genomics, DNA replication, DNA repair, mobile DNA, mitochondrial DNA, chloroplast DNA). Expression & Function - Focus on functional RNAs (microRNAs, tRNAs, rRNAs, mRNA splicing, alternative polyadenylation) Regulation - Focus on processes that mediate gene-read out (epigenetics, chromatin, histone code, transcription, translation, protein degradation). Cell Signaling - Focus on mechanisms that control information flow into the nucleus to control gene expression (kinase and phosphatase pathways controlled by extra-cellular ligands, Wnt, Notch, TGFbeta/BMPs, FGFs, IGFs etc.) Profiling of gene expression and genetic variation - Focus on high throughput approaches (e.g., DeepSeq, ChIP-Seq, Affymetrix microarrays, proteomics) that define gene regulatory circuitry, molecular pathways and protein/protein networks. Genetics - Focus on development in model organisms (e.g., mouse, frog, fruit fly, worm), human genetic variation, population genetics, as well as agricultural and veterinary genetics. Molecular Pathology & Regenerative Medicine - Focus on the deregulation of molecular processes in human diseases and mechanisms supporting regeneration of tissues through pluripotent or multipotent stem cells.