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A detailed workflow to develop QIIME2-formatted reference databases for taxonomic analysis of DNA metabarcoding data
BackgroundThe DNA metabarcoding approach has become one of the most used techniques to study the taxa composition of various sample types. To deal...
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Hitac: a hierarchical taxonomic classifier for fungal ITS sequences compatible with QIIME2
BackgroundFungi play a key role in several important ecological functions, ranging from organic matter decomposition to symbiotic associations with...
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Inventorizing marine biodiversity using eDNA data from Indonesian coral reefs: comparative high throughput analysis using different bioinformatic pipelines
The selection of specific bioinformatic pipelines to analyse Next Generation Sequencing (NGS) data is instrumental for generating accurate biological...
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A Practical Guide to 16S rRNA Microbiome Analysis in Musculoskeletal Disorders
Microbial taxonomic assignment based on 16S marker gene amplification requires multiple data transformations, often encompassing the use of a variety...
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Computational Omics Protocol for the Comparative Study of Microbiome Analysis
Exploring the microbiome involves an integrative approach of metagenomics, metabolomics, metatranscriptomics, and meta-proteomics combined with...
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Rhizosphere and Endosphere Bacterial Communities Survey by Metagenomics Approach
The diversity of microbes associated with plant roots is in the order of tens of thousands of species. It is estimated that only 0.1–1.0% of the...
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Impact of quality trimming on the efficiency of reads joining and diversity analysis of Illumina paired-end reads in the context of QIIME1 and QIIME2 microbiome analysis frameworks
BackgroundTo increase the accuracy of microbiome data analysis, solving the technical limitations of the existing sequencing machines is required....
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Mare-MAGE curated reference database of fish mitochondrial genes
Biodiversity assessment approaches based on molecular biology techniques such as metabarcoding, RAD-seq, or SnaPshot sequencing are increasingly...
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Multi-factorial examination of amplicon sequencing workflows from sample preparation to bioinformatic analysis
BackgroundThe development of sequencing technologies to evaluate bacterial microbiota composition has allowed new insights into the importance of...
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Evaluating cpn60 for high-resolution profiling of the mammalian skin microbiome and detection of phylosymbiosis
Despite being the most widely used phylogenetic marker for amplicon-based profiling of microbial communities, limited phylogenetic resolution of the...
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Holo-omics analysis reveals the influence of gut microbiota on obesity indicators in **hua pigs
BackgroundThe mechanisms behind obesity are complex and multi-faceted, involving the interplay of both host genomics and gut microbiome. In recent...
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Technologies Promoting Genome-Based Taxonomy
Whole-genome sequencing (WGS) has proven to be a reliable method. Additionally, it is a commonly used approach in research and surveillance...
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16S rRNA Amplicon Sequencing
The 16S rRNA amplicon sequencing technique is a microbiome analysis where different samples are analyzed at the same time using multiplexing. The...
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Cloud Computing for Metagenomics: Building a Personalized Computational Platform for Pipeline Analyses
Cloud Computing services such as Microsoft Azure, Amazon Web Services, and Google Cloud provide a range of tools and services that enable scientists...
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16S-rRNA-Amplicon-Sequenzierung für Metagenomik
Die 16S-rRNA-Amplicon-Sequenzierungstechnik ist eine Mikrobiomanalyse, bei der verschiedene Proben gleichzeitig mit Hilfe von Multiplexing analysiert...
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Garlic (Allium sativum) as a dietary ingredient can cause dysbiosis in the microbiota of the California yellowtail (Seriola dorsalis) at high concentrations
Garlic ( Allium sativum ) can improve the fish’s immune system and modulate the gut microbiota composition, vital in host nutrition and health. This...
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Integrating Multi-Omics Data to Construct Reliable Interconnected Models of Signaling, Gene Regulatory, and Metabolic Pathways
Alteration of the status of the metabolic enzymes could be a probable way to regulate metabolic reprogramming, which is a critical cellular...
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Introduction to QIIME 2
This chapter describes the foundations of the QIIME 2 approach for bioinformatic and biostatistical analyses of microbiome data. It first provides an...
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EzMAP: Easy Microbiome Analysis Platform
BackgroundThe rapid advances in next-generation sequencing technologies have revolutionized the microbiome research by greatly increasing our ability...
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Biological observations in microbiota analysis are robust to the choice of 16S rRNA gene sequencing processing algorithm: case study on human milk microbiota
BackgroundIn recent years, the microbiome field has undergone a shift from clustering-based methods of operational taxonomic unit (OTU) designation...
