Highly comparable metabarcoding results from MGI-Tech and Illumina sequencing platforms

Abstract

With the developments in DNA nanoball sequencing technologies and the emergence of new platforms, there is an increasing interest in their performance in comparison with the widely used sequencing-by-synthesis methods. Here, we test the consistency of metabarcoding results from DNBSEQ-G400RS (DNA nanoball sequencing platform by MGI-Tech) and NovaSeq 6000 (sequencing-by-synthesis platform by Illumina) platforms using technical replicates of DNA libraries that consist of COI gene amplicons from 120 soil DNA samples. By subjecting raw sequencing data from both platforms to a uniform bioinformatics processing, we found that the proportion of high-quality reads passing through the filtering steps was similar in both datasets. Per-sample operational taxonomic unit (OTU) and amplicon sequence variant (ASV) richness patterns were highly correlated, but sequencing data from DNBSEQ-G400RS harbored a higher number of OTUs. This may be related to the lower dominance of most common OTUs in DNBSEQ data set (thus revealing higher richness by detecting rare taxa) and/or to a lower effective read quality leading to generation of spurious OTUs. However, there was no statistical difference in the ASV and post-clustered ASV richness between platforms, suggesting that additional denoising step in the ASV workflow had effectively removed the ‘noisy’ reads. Both OTU-based and ASV-based composition were strongly correlated between the sequencing platforms, with essentially interchangeable results. Therefore, we conclude that DNBSEQ-G400RS and NovaSeq 6000 are both equally efficient high-throughput sequencing platforms to be utilized in studies aiming to apply the metabarcoding approach, but the main benefit of the former is related to lower sequencing cost.

Benchmarking second and third-generation sequencing platforms for microbial metagenomics

“…Notably, correlations were slightly lower for mock communities with higher microbial richness, partially due to cross-matching events during mapping procedures. Whilst second generation sequencers were equivalent for taxonomic profiling 28 , we found more pronounced decreases for MinION and PacBio correlations, even if reads were almost entirely uniquely mapped. Although the PacBio sequencer presented the lowest error rate, these results could be explained by the DNA size filtering step performed during library preparation, which was calibrated to maximize the read length.…”

Responses of the Soil Microbial Community to Salinity Stress in Maize Fields

“…Principal coordinate analysis (PCoA) based on Bray−Curtis similarity distances were carried out in the R package vegan [ 28 ]. Mantel tests with 999 permutations were used to examine the correlation between environmental distance and microbial community distance within the R vegan package [ 29 ]. The relationships between the soil dominant environmental factors (Ca 2+ , AP, EC e , AK and urease) and the soil microbial community were analyzed by using redundancy analysis (RDA).…”

Attenuation by Time-Restricted Feeding of High-Fat and High-Fructose Diet-Induced NASH in Mice Is Related to Per2 and Ferroptosis

“…RNA-Seq experiments and data analysis were performed using fresh-frozen liver tissues from the FA+Veh and FA+Lip-1 mice ( n = 3 per group) or Per2 △hep and Per2 fl/fl mice ( n = 3 − 4 per group). After total RNA was extracted and quantified, RNA sequencing was implemented using an Illumina Novaseq 6000 sequencer [ 33 ] to obtain the raw data.…”