Illumina iSeq 100 and MiSeq exhibit similar performance in freshwater fish environmental DNA metabarcoding

Abstract

Environmental DNA (eDNA) analysis is a method of detecting DNA from environmental samples and is used as a biomonitoring tool. In recent studies, Illumina MiSeq has been the most extensively used tool for eDNA metabarcoding. The Illumina iSeq 100 (hereafter, iSeq), one of the high-throughput sequencers (HTS), has a relatively simple workflow and is potentially more affordable than other HTS. However, its utility in eDNA metabarcoding has still not been investigated. In the present study, we applied fish eDNA metabarcoding to 40 water samples from river and lake ecosystems to assess the difference in species detectability and composition between iSeq and MiSeq. To check differences in sequence quality and errors, we also assessed differences in read changes between the two HTS. There were similar sequence qualities between iSeq and MiSeq. Significant difference was observed in the number of species between two HTS, but no difference was observed in species composition between the two HTS. Additionally, the species compositions in common with the conventional method were the same between the two HTS. According to the results, using the same amplicon library for sequencing, two HTS would exhibit a similar performance of fish species detection using eDNA metabarcoding.

Honeysuckle Berry (Lonicera caerulea L.) Inhibits Lipase Activity and Modulates the Gut Microbiota in High-Fat Diet-Fed Mice

“…Briefly, the QIAamp PowerFecal DNA Kit (QIAGEN, Hilden, Germany) was used to extract the genomic DNA from feces samples. The bacterial 16S rRNA V4 region was amplified with unique 8 bp barcodes and sequenced on the Illumina iSeq 100 system according to standard protocol [ 47 ]. The sequences were processed by the Quantitative Insights into Microbial Ecology (QIIME) pipeline [ 48 ] using the SILVA 128 database [ 49 ].…”

Comparison of iSeq and MiSeq as the two platforms for 16S rRNA sequencing in the study of the gut of rat microbiome

“…They enable the second-generation sequencing, relating to the NGS technologies after the first-generation Sanger sequencing (Das et al 2020 ; Hu et al 2021 ). Illumina’s sequencing systems are currently most popular used in microbiome studies (Gao et al 2021 ; Nakao et al 2021 ).…”

“…However, if we consider the equipment’s size, cost and the sequencing’s time duration (Table 1 ), iSeq seems to be the platform of choice (Colman et al 2019 ; Dohál et al 2020 ; Kazantseva et al 2021 ). Additionally, a close model of the cartridge-made iSeq platform may have a lower cross-contamination risk between sequencing runs than in MiSeq (Nakao et al 2021 ), although future research should evaluate cross-contamination risks as additional system’s maintenance procedures were introduced.…”

“…Nakao et al ( 2021 ) considered that both platforms were equally suitable for evaluating freshwater fish environmental microbiome, and the % PF value for iSeq was slightly lower compared to MiSeq: 80.8% vs. 95.05%, respectively. Uelze L. et al compared the consistency, accuracy, and repeatability of whole-genome short read sequencing.…”

“…The most common taxa identification is based on the amplicon-based NGS of the 16S ribosomal RNA (rRNA) gene. The prokaryotic 16S rRNA gene is approximately 1500 bp long and has conserved and hypervariable nine regions (V1-V9), which are used for phylogenetic classification of genera and in diverse microbial populations (Gao et al 2021 ; Nakao et al 2021 ). Such metagenomic studies require specific infrastructure, trained personnel, appropriate sequencing platforms, and bioinformatics pipelines (Allali et al 2017 ; Gao et al 2021 ).…”