The use of iconPCR for 16S library preparation improves data quality and workflow DOI Open Access

Yann Jouvenot,

Caroline Obert,

Brett Hale

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Dec. 21, 2024

Abstract Polymerase Chain Reaction (PCR) is a cornerstone of contemporary biological research, enabling the amplification specific DNA sequences for various applications. However, suboptimal cycling conditions often undermine its efficacy, which can generate chimeric products, exacerbate PCR duplication rates, and skew species representation in metabarcoding experiments due to preferential dominant populations. To address these limitations, we present iconPCR—Individually Controlled PCR—a novel technology that allows each reaction 96-well plate be cycled independently programmatically. By setting predefined fluorescence threshold, iconPCR ensures all Next Generation Sequencing (NGS) libraries are amplified equivalent levels, thereby eliminating risks over- or under-amplification through process known as “Auto-Normalization.” In this study, applied V3, V4, full-length 16S rRNA gene using Avidite sequencing. The V1-V9 variable region were also evaluated with HiFi sequencing, significantly demonstrated potential improve microbial community analysis accuracy reliability.

Language: Английский

iMetaOmics: Advancing human and environmental health through integrated meta‐omics DOI Creative Commons
Chun‐Lin Shi, Tong Chen, Canhui Lan

et al.

iMetaOmics., Journal Year: 2024, Volume and Issue: 1(1)

Published: Aug. 8, 2024

iMetaOmics is a quarterly international journal with the priority of publishing research work within scope One Health, featured well-designed omics. The also welcomes systematic integration extensive public datasets, new and meaningful perspectives, re-analysis high-impact data yielding different/valuable conclusions. microbiome plays critical roles in human [1], animal [2], plant nutrition health [3], food [4], environment [5], as well other aspects society (Figure 1). Metaomics, including metabarcoding, metagenomics, metatranscriptomics, metaproteomics, metabolomics, provide unique powerful tools to better understand taxonomy functions microbiome, biology, [6]. Aiming fill gap lacking top journals field Asia, iMeta Science Society its thousands Chinese scientist members found young but journal—iMeta (ISSN: 2770-5986; eISSN: 2770-596X). It has published more than 200 high-quality papers since 2022, original articles, reproducible methods protocols, systemic reviews peers updated novel findings, easy-to-use analytic tools, knowledge [7]. These publications include are not limited gut pertaining diseases [8], microbiota animals (e.g., chicken [9], pig [10], panda [11]), pan-cancer [12] pan-genome [13], soil associated diversity defense [14, 15], popular for metaomics analyses [16-18]. With great efforts contributions our stakeholders, like publisher, editorial board members, authors, reviewers, received first impact factor 23.7 2024, gradually accumulating broad diverse audiences readership, especially attracting explosive growth submissions recent days. To cope significantly increased submissions, we have from bimonthly journal. However, publication space maintaining high standard iMeta, still reject 90% although many them did an excellent work. Due success officially launching sister (eISSN: 2996-9514, ISSN: 2996-9506), further publish articles [19-23], [24-28], state-of-the-art methodologies [29, 30] satisfy increasing submission demand iMeta. Taking advantage same team, rejected manuscripts valuable/meaningful findings will be transferred iMetaOmics, together detailed comments reviewers. In this context, following review process shortened promote rapid publishing. Before official launch, 12 already been upon approval by authors issue. Currently, featuring reanalysis expected that establish reputation soon, attract wide range interest readers, contribute progress Human Environmental Health studies. Authors' own priority, while utilization analysis robust experimental validation can considered. Multiple evidence required support conclusion. New strategies advantage, indispensable. All used without reasonable concerns should publicly/temporally accessible reviewers editors. A video tutorial, software download, installation, operation, result displaying, highly recommended bioinformatic tools. Additionally, necessary ethics numbers, clear layouts, figures, significant expected. Chun-Lin Shi: Writing—original draft; writing—review editing. Tong Chen: Writing—review Canhui Lan: Ren-You Gan: Jun Yu: Fangqing Zhao: Yong-Xin Liu: editing; conceptualization. Zhao Yu hold position Editor-in-Chief iMetaOmics. Liu, Chen, Lan, Shi Gan Executive Editors

Language: Английский

Citations

6
Metagenomic approaches and opportunities in arid soil research DOI
Muhammad Ejaz, Kareem Rady Badr, Zahoor Ul Hassan

et al.

The Science of The Total Environment, Journal Year: 2024, Volume and Issue: 953, P. 176173 - 176173

Published: Sept. 10, 2024

Language: Английский

Citations

5
Impacts of Biodegradable Microplastics on Rhizosphere Bacterial Communities of Arabidopsis thaliana: Insights into Root Hair-Dependent Colonization DOI
Keyi Chen, Zhihong Jin, Qing Zhu

et al.

Environmental Research, Journal Year: 2025, Volume and Issue: unknown, P. 121496 - 121496

Published: March 1, 2025

Language: Английский

Citations

0
A long-read sequencing approach to high-resolution profiling of bacterioplankton diversity in a shallow freshwater lake DOI Creative Commons
Stephanie O. Castro Márquez, Viktor R. Tóth, Sofia M. Kolchanova

et al.

Scientific Reports, Journal Year: 2025, Volume and Issue: 15(1)

Published: April 10, 2025

Lake Balaton, a large shallow freshwater lake in Hungary, exhibits diverse bacterioplankton communities influenced by various environmental factors. This study aims to evaluate the bacterial diversity Balaton using long-read approach 16 S rRNA gene sequencing. Water samples were collected from wide network of 33 locations across lake's four basins and analyzed for community composition. Sequencing results revealed high taxonomic with significant zonal variations. Dominant families included Comamonadaceae, Burkholderiaceae, Methylophilaceae. Environmental parameters such as temperature, pH, CDOM found significantly correlate abundance diversity. The underscores utility portability sequencing technology assessing microbial provides insights into ecological dynamics lakes.

Language: Английский

Citations

0
Green land in a landscape bolsters the dietary diversity of reared yellow-legged hornet Vespa velutina Lepeletier (Hymenoptera: Vespidae) DOI
Zhenghua Xie, X. Feng, Jianmin Wang

et al.

Bulletin of Entomological Research, Journal Year: 2025, Volume and Issue: unknown, P. 1 - 11

Published: April 21, 2025

Abstract Land use change has significantly altered most ecosystem functioning, such as nutrition provisioning, water flows and pollination services. So far, the impact of land on dietary diversity predatory insects remained largely unexplored. In this study, we explored prey composition reared yellow-legged hornets Vespa velutina Lepeletier (Hymenoptera: Vespidae) in landscapes with a gradient surrounding green lands, using metabarcoding feces eliminated by larvae. The primarily fed upon insects, dipterans, coleopterans, lepidopterans, hemipterans, hymenopterans, orthopterans being dominant groups. percentage lands had positive effect richness at spatial scale 1500 m, but no Shannnon index community. Meanwhile, effects coleopteran lepidopteran prey, significant dipteran hemipteran hymenopteran or orthopteran prey. terms beta diversity, explained dissimilarity communities among landscapes, whereas local factors, distance to buildings, did not explain dissimilarity. Our study indicated that landscape positively affected hornets, varied different taxonomic groups

Language: Английский

Citations

0
Dix-seq: An integrated pipeline for fast amplicon data analysis DOI
Pengsheng Dong, Yubin Chen, Yongjun Wei

et al.

The Innovation Life, Journal Year: 2025, Volume and Issue: unknown, P. 100120 - 100120

Published: Jan. 1, 2025

<p>Rapid advancements in sequencing technologies the past decade have driven widespread adoption of amplicon metagenome. However, current data analysis software/pipelines often require manual intervention spanning multiple steps, necessitating a clear understanding parameters and hindering inexperienced users from automating their workflows. Here, we introduce Dix-seq, fully containerized tool for rapid, automated, scalable analysis. With one single command, Dix-seq can process raw sequences down to various statistical visualization results, generate html-based reports, retrospective logfiles. utilizes parameter sheet file drastically simplify its command line interface, making it much more approachable by while improving study reproducibility. The modular design enables rapid new methods databases into software frame. Currently, than 21 algorithms, software, third-party procedures been integrated eight modules are coming line. This approach also allows experienced fine-tune workflow, facilitating customized Benchmarks performed on datasets real-world case studies demonstrated Dix-seq’s capabilities generating publish-ready figures with information extracting biologically meaningful patterns. Furthermore, remained highly effective at detecting variance upon simulated depth drop, results robust <styled-content style-type="number">11000</styled-content> style-type="number">1000</styled-content> all certain fronts, such as phylogenetic diversity Pearson correlation, respectively. In summary, is convenient yet customizable analysis, an ideal choice both entry-level users.</p>

Language: Английский

Citations

0
The use of iconPCR for 16S library preparation improves data quality and workflow DOI Open Access

Yann Jouvenot,

Caroline Obert,

Brett Hale

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Dec. 21, 2024

Abstract Polymerase Chain Reaction (PCR) is a cornerstone of contemporary biological research, enabling the amplification specific DNA sequences for various applications. However, suboptimal cycling conditions often undermine its efficacy, which can generate chimeric products, exacerbate PCR duplication rates, and skew species representation in metabarcoding experiments due to preferential dominant populations. To address these limitations, we present iconPCR—Individually Controlled PCR—a novel technology that allows each reaction 96-well plate be cycled independently programmatically. By setting predefined fluorescence threshold, iconPCR ensures all Next Generation Sequencing (NGS) libraries are amplified equivalent levels, thereby eliminating risks over- or under-amplification through process known as “Auto-Normalization.” In this study, applied V3, V4, full-length 16S rRNA gene using Avidite sequencing. The V1-V9 variable region were also evaluated with HiFi sequencing, significantly demonstrated potential improve microbial community analysis accuracy reliability.

Language: Английский

Citations

0