The National Ecological Observatory Network’s soil metagenomes: assembly and basic analysis

Werbin, Zoey R.; Hackos, Briana; Dietze, Michael C.; Bhatnagar, Jennifer

doi:10.12688/f1000research.51494.1

Cited by 3 publications

(1 citation statement)

References 49 publications

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“…The challenges associated with the standardization of workflows in mNGS have a significant impact on the turnaround time and costs [ 30 , 31 ], data quality, reproducibility [ 32 ], comparability [ 33 ], and biological interpretation [ 34 , 35 , 36 ]. Therefore, recent studies have made significant progress in standardizing metagenomics workflows both in the wet laboratory (wet lab) [ 37 , 38 ] and the dry laboratory (dry lab) [ 39 , 40 , 41 ]. For instance, Parker et al (2023) developed a sample-to-answer workflow called PanGIA that includes simplified, standardized wet lab procedures and data analysis with an easy-to-use bioinformatics tool [ 38 ].…”

Section: Introductionmentioning

confidence: 99%

Enhancing Clinical Utility: Utilization of International Standards and Guidelines for Metagenomic Sequencing in Infectious Disease Diagnosis

Kan,

Tsang,

Pei

et al. 2024

IJMS

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Metagenomic sequencing has emerged as a transformative tool in infectious disease diagnosis, offering a comprehensive and unbiased approach to pathogen detection. Leveraging international standards and guidelines is essential for ensuring the quality and reliability of metagenomic sequencing in clinical practice. This review explores the implications of international standards and guidelines for the application of metagenomic sequencing in infectious disease diagnosis. By adhering to established standards, such as those outlined by regulatory bodies and expert consensus, healthcare providers can enhance the accuracy and clinical utility of metagenomic sequencing. The integration of international standards and guidelines into metagenomic sequencing workflows can streamline diagnostic processes, improve pathogen identification, and optimize patient care. Strategies in implementing these standards for infectious disease diagnosis using metagenomic sequencing are discussed, highlighting the importance of standardized approaches in advancing precision infectious disease diagnosis initiatives.

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Section: Introductionmentioning

confidence: 99%

Enhancing Clinical Utility: Utilization of International Standards and Guidelines for Metagenomic Sequencing in Infectious Disease Diagnosis

Kan,

Tsang,

Pei

et al. 2024

IJMS

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From DNA sequences to microbial ecology: Wrangling NEON soil microbe data with the neonMicrobe R package

et al. 2021

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Soil microbial communities play critical roles in various ecosystem processes, but studies at a large spatial and temporal scale have been challenging due to the difficulty in finding the relevant samples in available data sets as well as the lack of standardization in sample collection and processing. The National Ecological Observatory Network (NEON) has been collecting soil microbial community data multiple times per year for 47 terrestrial sites in 20 eco-climatic domains, producing one of the most extensive standardized sampling efforts for soil microbial biodiversity to date. Here, we introduce the neonMicrobe R package-a suite of downloading, preprocessing, data set assembly, and sensitivity analysis tools for NEON's newly published 16S and ITS amplicon sequencing data products which characterize soil bacterial and fungal communities, respectively. neonMicrobe is designed to make these data more accessible to ecologists without assuming prior experience with bioinformatic pipelines. We describe quality control steps used to remove quality-flagged samples, report on sensitivity analyses used to determine appropriate quality filtering parameters for the DADA2 workflow, and demonstrate the immediate usability of the output data by conducting standard analyses of soil microbial diversity. The sequence abundance tables produced by neonMicrobe can be linked to NEON's other data products (e.g., soil physical and chemical properties, plant community composition) and soil subsamples archived in the NEON Biorepository. We provide recommendations for incorporating neonMicrobe into reproducible scientific workflows, discuss technical considerations for large-scale amplicon sequence analysis, and outline future directions for NEON-enabled microbial ecology. In particular, we believe that NEON marker gene sequence data will allow researchers to answer outstanding questions about the spatial and temporal dynamics of soil microbial communities while explicitly accounting for scale dependence. We expect that the data produced by NEON and the neonMicrobe R package will act as a valuable ecological baseline to inform and contextualize future experimental and modeling endeavors.

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Metagenomics: An Effective Approach for Exploring Microbial Diversity and Functions

Nam

Khoa

Trinh

et al. 2023

Foods

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Various fields have been identified in the “omics” era, such as genomics, proteomics, transcriptomics, metabolomics, phenomics, and metagenomics. Among these, metagenomics has enabled a significant increase in discoveries related to the microbial world. Newly discovered microbiomes in different ecologies provide meaningful information on the diversity and functions of microorganisms on the Earth. Therefore, the results of metagenomic studies have enabled new microbe-based applications in human health, agriculture, and the food industry, among others. This review summarizes the fundamental procedures on recent advances in bioinformatic tools. It also explores up-to-date applications of metagenomics in human health, food study, plant research, environmental sciences, and other fields. Finally, metagenomics is a powerful tool for studying the microbial world, and it still has numerous applications that are currently hidden and awaiting discovery. Therefore, this review also discusses the future perspectives of metagenomics.

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The National Ecological Observatory Network’s soil metagenomes: assembly and basic analysis

Cited by 3 publications

References 49 publications

Enhancing Clinical Utility: Utilization of International Standards and Guidelines for Metagenomic Sequencing in Infectious Disease Diagnosis

Enhancing Clinical Utility: Utilization of International Standards and Guidelines for Metagenomic Sequencing in Infectious Disease Diagnosis

From DNA sequences to microbial ecology: Wrangling NEON soil microbe data with the neonMicrobe R package

Metagenomics: An Effective Approach for Exploring Microbial Diversity and Functions

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