Evidence map›Paper›PMID 39358791›Full record

ArticleBMC research notes2024

Prokaryotic communities profiling of Indonesian hot springs using long-read Oxford Nanopore sequencing.

I Nengah Wirajana, Ni Putu Ariantari, Douglas J H Shyu, Nilam Vaghamshi, Komal Antaliya, Pravin Dudhagara

Abstract read
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Article in BMC research notes, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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1 · What the graph read from it

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2 · The registry

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3 · Its place in the literature

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4 · The record

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5 · Who and what money

Authors and funding

6 authors.

I Nengah WirajanaDepartment of Chemistry, Faculty of Mathematics and Natural Science, Udayana University, Jimbaran-Badung, Bali, 18036, Indonesia.
Ni Putu AriantariDepartment of Pharmacy, Faculty of Mathematics and Natural Science, Udayana University, Jimbaran-Badung, Bali, 80361, Indonesia.
Douglas J H ShyuDepartment of Biological Science and Technology, National Pingtung University of Science and Technology, Neipu, Pingtung, 912301, Taiwan.
Nilam VaghamshiDepartment of Biosciences, Veer Narmad South Gujarat University, Surat, 395007, India.
Komal AntaliyaDepartment of Biosciences, Veer Narmad South Gujarat University, Surat, 395007, India.
Pravin DudhagaraDepartment of Chemistry, Faculty of Mathematics and Natural Science, Udayana University, Jimbaran-Badung, Bali, 18036, Indonesia. pravindudhagara@vnsgu.ac.in.

Funding

Udayana University International Senior Fellowship (UNISERF) grant for year 2023 (Grant Number: B/530-4/UN14.4A/PT.01.03/2023), Udayana University, Bali, Indonesia B/530-4/UN14.4A/PT.01.03/2023
6 · The paper itself

Abstract

objectivesIndonesia's location at the convergence of multiple tectonic plates results in a unique geomorphological feature with abundant hot springs. This study pioneers the metagenomic exploration of Indonesian hot springs, harbouring unique life forms despite high temperatures. The microbial community of hot springs is taxonomically versatile and biotechnologically valuable. 16s rRNA amplicon sequencing of the metagenome is a viable option for the microbiome investigation. This study utilized Oxford Nanopore's long-read 16 S rRNA sequencing for enhanced species identification, improved detection of rare members, and a more detailed community composition profile. DATA DESCRIPTION: Water samples were taken from three hot springs of the Bali, Indonesia (i) Angseri, 8.362503 S, 115.133452 E; (ii) Banjar, 8.210270 S, 114.967063 E; and (iii) Batur, 8.228806 S, 115.404829 E. BioLit Genomic DNA Extraction Kit (SRL, Mumbai, India) was used to isolate DNA from water samples. The quantity and quality of the DNA were determined using a NanoDrop™ spectrophotometer and a Qubit fluorometer (Thermo Fisher Scientific, USA). The library was created using Oxford Nanopore Technology kits, and the sequencing was done using Oxford Nanopore's GridION platform. All sequencing data was obtained in FASTQ files and filtered using NanoFilt software. This dataset is valuable for searching novel bacteria diversity and their existence.

Indexed as

Hot SpringsNanopore SequencingRNA, Ribosomal, 16SBacteriaDNA, BacterialIndonesiaMetagenomeMetagenomicsMicrobiotaPhylogenySequence Analysis, DNAWater MicrobiologyDNA, BacterialRNA, Ribosomal, 16S16s rRNA ampliconHot springsMetagenomeNanopore sequencing

Identifiers

PMID39358791
PMCPMC11446079

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.