4.6 Article

Amplicon-Based Microbiome Profiling: From Second- to Third-Generation Sequencing for Higher Taxonomic Resolution

Related references

Note: Only part of the references are listed.
Article Multidisciplinary Sciences

Reliability of species detection in 16S microbiome analysis: Comparison of five widely used pipelines and recommendations for a more standardized approach

Andreas Hiergeist et al.

Summary: The use of NGS-based testing of the bacterial microbiota often leads to inconsistent and non-reproducible results due to variations in analysis pipelines and reference databases. Through comparing five frequently used software packages, we identified that the inconsistencies were caused by the pipelines or the reference databases used. Based on these findings, we recommend certain standards to improve the consistency and reproducibility of microbiome testing in clinical practice.

PLOS ONE (2023)

Article Microbiology

Lactobacillus paracasei CNCM I-5220-derived postbiotic protects from the leaky-gut

Francesca Algieri et al.

Summary: The maintenance of intestinal barrier function is crucial for preventing diseases. The gut microbiota plays a key role in regulating the integrity of the intestinal barrier. This study demonstrates that a postbiotic called LP-PBF, derived from Lactobacillus paracasei CNCM I-5220, can restore tight junction morphology and protect against Salmonella typhimurium infection by interacting with the host cells and inhibiting biofilm formation. These findings suggest that LP-PBF could be a potential therapeutic option for diseases with impaired intestinal barrier function.

FRONTIERS IN MICROBIOLOGY (2023)

Review Microbiology

Long-Reads-Based Metagenomics in Clinical Diagnosis With a Special Focus on Fungal Infections

Minh Thuy Vi Hoang et al.

Summary: Identification of the causative infectious agent is crucial for the management of infectious diseases. Traditional diagnostic techniques have limitations in terms of time and specificity, while long-read sequencing has the potential to provide accurate identification of pathogens directly from clinical samples and additional clinical information.

FRONTIERS IN MICROBIOLOGY (2022)

Article Biology

Third-Generation Sequencing: The Spearhead towards the Radical Transformation of Modern Genomics

Konstantina Athanasopoulou et al.

Summary: The introduction of third-generation sequencing (TGS) technologies has made genome sequencing easier and faster. The long-read sequences produced by TGS methods have enabled advances in transcriptome profiling and epitranscriptomics research.

LIFE-BASEL (2022)

Article Medicine, Research & Experimental

Farnesoid X receptor activation by the novel agonist TC-100 (3?, 7?, 11?-Trihydroxy-6?-ethyl-5?-cholan-24-oic Acid) preserves the intestinal barrier integrity and promotes intestinal microbial reshaping in a mouse model of obstructed bile acid flow

M. Marzano et al.

Summary: This study investigated the effects of TC-100 on intestinal mucosa integrity and cecal microbiome composition in a rodent model of bile flow obstruction. The results showed that TC-100 activates FXR and regulates bile acid homeostasis and gut microbiota composition, preventing early signs of intestinal mucosal damage.

BIOMEDICINE & PHARMACOTHERAPY (2022)

Article Multidisciplinary Sciences

Drastic reduction of false positive species in samples of insects by intersecting the default output of two popular metagenomic classifiers

Lidia Garrido-Sanz et al.

Summary: This study focuses on reducing false positive species caused by classifiers, and benchmarks two popular classifiers for accurate identification of target species. The intersection approach effectively reduces the number of false positive species when combining the results of the two classifiers. In addition, applying an analytical detection limit further decreases the number of false positive species.

PLOS ONE (2022)

Article Multidisciplinary Sciences

Natural and after colon washing fecal samples: the two sides of the coin for investigating the human gut microbiome

Elisabetta Piancone et al.

Summary: This study compared the effectiveness and accuracy of feces and colon washing feces as sampling matrices for representing the complexity of the human gut microbiome. The results showed inter-individual variability among paired feces and colon washing feces samples, but overall high similarity. Both types of samples exhibited comparable microbial load. This comparative study highlights the potential of using both types of sampling matrices for a more comprehensive understanding of the human gut microbiota.

SCIENTIFIC REPORTS (2022)

Article Biochemical Research Methods

Evaluation of taxonomic classification and profiling methods for long-read shotgun metagenomic sequencing datasets

Daniel M. Portik et al.

Summary: In this study, we evaluated and compared the performance of 11 methods for taxonomic classification and profiling in long-read shotgun metagenomic sequencing. The results showed that long-read classifiers performed better, while short-read methods had lower precision and recall. Some long-read methods required moderate filtering for optimal performance. Long-read datasets outperformed short-read datasets in classification methods, demonstrating clear advantages for long-read metagenomic sequencing.

BMC BIOINFORMATICS (2022)

Article Mathematical & Computational Biology

16S-ITGDB: An Integrated Database for Improving Species Classification of Prokaryotic 16S Ribosomal RNA Sequences

Yu-Peng Hsieh et al.

Summary: Analyzing 16S ribosomal RNA sequences allows researchers to understand the makeup of prokaryotes in an environment. However, existing 16S rRNA databases have limitations in accurately classifying species. In order to improve taxonomic resolution at the species level, researchers manually curated three databases and created an integrated database, which was validated using a mock community.

FRONTIERS IN BIOINFORMATICS (2022)

Article Medicine, Research & Experimental

Next-generation sequencing: insights to advance clinical investigations of the microbiome

Caroline R. Wensel et al.

Summary: This Review discusses the advancements in NGS technology for studying the human microbiome, including the pros and cons of different NGS methodologies and important concepts in data variability and study design. Examples of NGS studies on the human microbiome in diverse clinical contexts are provided, as well as insights into the future integration and advancement of NGS in microbiome research and clinical care.

JOURNAL OF CLINICAL INVESTIGATION (2022)

Review Biochemistry & Molecular Biology

Microbiota in health and diseases

Kaijian Hou et al.

Summary: The role of microbiota in health and disease is significant, contributing to homeostasis and immune regulation. Dysbiosis of microbiota can lead to disease progression, associated with dysregulation of community composition, modulation of host immune response, and induction of chronic inflammation. Clinical approaches utilizing microbiota, such as microbiota modulation and fecal microbial transplantation, can be effective for disease treatment.

SIGNAL TRANSDUCTION AND TARGETED THERAPY (2022)

Review Immunology

Introduction to host microbiome symbiosis in health and disease

Florent Malard et al.

Summary: Humans share a core intestinal microbiome but differ in genes, species, enterotypes, and gene count. Microbiome gene count is a key factor for health in immune disorders and clinical conditions. Metagenomic analysis helps define the host-microbe symbiosis associated with a healthy status, and disruption of this symbiosis may lead to chronic diseases or iatrogenic conditions. Möglichkeiten zur Anwendung einer Mikrobiota-Modulation für personalisierte Ernährung und Therapie zur Erhaltung, Konservierung oder Wiederherstellung der Gast-Mikrobe-Symbiose werden diskutiert.

MUCOSAL IMMUNOLOGY (2021)

Article Biology

Twelve years of SAMtools and BCFtools

Petr Danecek et al.

Summary: SAMtools and BCFtools are widely used tools for processing high-throughput sequencing data, with a history of 12 years of continuous development and improvement. These packages have been utilized in various software projects and genomic pipelines and are freely available on GitHub.

GIGASCIENCE (2021)

Review Biochemistry & Molecular Biology

Nanopore sequencing and its application to the study of microbial communities

Laura Ciuffreda et al.

Summary: The introduction of nanopore sequencing technology has significantly improved our ability to study complex microbial samples, allowing real-time sequencing of long reads with low cost and portability. This technology plays a crucial role in resolving complex genomic structures, accessing metagenome assembled genomes, and shows great potential in environmental microbial analysis.

COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL (2021)

Review Microbiology

Advances in Metagenomics and Its Application in Environmental Microorganisms

Lu Zhang et al.

Summary: Metagenomics is a new approach to studying microorganisms from a specific environment, focusing on microbial diversity, community constitute, genetic and evolutionary relationships, functional activities, as well as interactions and relationships with the environment. Sequencing technologies have evolved to high-throughput next-generation sequencing (NGS) and third-generation sequencing (TGS), showing advantages in rapid detection of pathogenic microorganisms. With the help of new algorithms, taxonomic profiling and gene prediction of microbial species can be better performed. Functional metagenomics is helpful for screening new bioactive substances and functional genes from microorganisms and their metabolites.

FRONTIERS IN MICROBIOLOGY (2021)

Article Multidisciplinary Sciences

Evaluation of 16S rRNA primer sets for characterisation of microbiota in paediatric patients with autism spectrum disorder

L. Palkova et al.

Summary: Intestinal microbiota serves as a significant marker for reflecting differences in health and disease states, as well as gut-brain axis communication. The choice of DNA amplification primers was found to influence the outcomes of microbiota investigation, highlighting the importance of standardized protocols in research. Different primer sets can detect varying bacterial compositions, suggesting the need for caution when interpreting microbiota sequencing results.

SCIENTIFIC REPORTS (2021)

Review Microbiology

Rapid Genomic Diagnosis of Fungal Infections in the Age of Next-Generation Sequencing

Chi-Ching Tsang et al.

Summary: NGS technology has matured into clinical applications, showing potential advantages in diagnosing difficult-to-grow fungi and cases with low fungal loads. Studies have revealed that fungal infections diagnosed by NGS present some different characteristics from general epidemiology, such as a low HIV-positive rate among patients with P.jirovecii infections.

JOURNAL OF FUNGI (2021)

Review Biochemical Research Methods

Current challenges and best-practice protocols for microbiome analysis

Richa Bharti et al.

Summary: Analyzing the microbiome using next-generation sequencing techniques has improved our understanding of environmental microorganisms. However, analysis is affected by experimental conditions and downstream analysis, and new sequencing technologies can impact results. This work aims to review important workflows for sequencing data and provide best-practice protocols.

BRIEFINGS IN BIOINFORMATICS (2021)

Article Multidisciplinary Sciences

The human tumor microbiome is composed of tumor type-specific intracellular bacteria

Deborah Nejman et al.

SCIENCE (2020)

Letter Microbiology

Microbiome definition re-visited: old concepts and new challenges

Gabriele Berg et al.

MICROBIOME (2020)

Article Multidisciplinary Sciences

Analysis of compositions of microbiomes with bias correction

Huang Lin et al.

NATURE COMMUNICATIONS (2020)

Review Biotechnology & Applied Microbiology

Opportunities and challenges in long-read sequencing data analysis

Shanika L. Amarasinghe et al.

GENOME BIOLOGY (2020)

Review Pediatrics

The third generation sequencing: the advanced approach to genetic diseases

Tiantian Xiao et al.

TRANSLATIONAL PEDIATRICS (2020)

Editorial Material Biology

Multiple levels of the unknown in microbiome research

Andrew Maltez Thomas et al.

BMC BIOLOGY (2019)

Letter Biotechnology & Applied Microbiology

Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

Evan Bolyen et al.

NATURE BIOTECHNOLOGY (2019)

Article Biochemistry & Molecular Biology

High-throughput amplicon sequencing of the full-length 16S rRNA gene with single-nucleotide resolution

Benjamin J. Callahan et al.

NUCLEIC ACIDS RESEARCH (2019)

Article Multidisciplinary Sciences

Evaluation of 16S rRNA gene sequencing for species and strain-level microbiome analysis

Jethro S. Johnson et al.

NATURE COMMUNICATIONS (2019)

Review Immunology

The gut microbiome: Relationships with disease and opportunities for therapy

Juliana Durack et al.

JOURNAL OF EXPERIMENTAL MEDICINE (2019)

Article Biochemical Research Methods

Minimap2: pairwise alignment for nucleotide sequences

Heng Li

BIOINFORMATICS (2018)

Review Oncology

Quantifying tumor-infiltrating immune cells from transcriptomics data

Francesca Finotello et al.

CANCER IMMUNOLOGY IMMUNOTHERAPY (2018)

Article Multidisciplinary Sciences

Metabarcoding analysis of eukaryotic microbiota in the gut of HIV-infected patients

Ibrahim Hamad et al.

PLOS ONE (2018)

Review Biotechnology & Applied Microbiology

Conducting metagenomic studies in microbiology and clinical research

Tiphaine C. Martin et al.

APPLIED MICROBIOLOGY AND BIOTECHNOLOGY (2018)

Article Multidisciplinary Sciences

Strains, functions and dynamics in the expanded Human Microbiome Project

Jason Lloyd-Price et al.

NATURE (2017)

Article Microbiology

Microbiome Datasets Are Compositional: And This Is Not Optional

Gregory B. Gloor et al.

FRONTIERS IN MICROBIOLOGY (2017)

News Item Biochemistry & Molecular Biology

How to limit false positives in environmental DNA and metabarcoding?

Gentile Francesco Ficetola et al.

MOLECULAR ECOLOGY RESOURCES (2016)

Article Biochemical Research Methods

DADA2: High-resolution sample inference from Illumina amplicon data

Benjamin J. Callahan et al.

NATURE METHODS (2016)

Article Biochemical Research Methods

Error filtering, pair assembly and error correction for next-generation sequencing reads

Robert C. Edgar et al.

BIOINFORMATICS (2015)

Article Microbiology

Primer and platform effects on 16S rRNA tag sequencing

Julien Tremblay et al.

FRONTIERS IN MICROBIOLOGY (2015)

Article Biochemistry & Molecular Biology

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

Christian Quast et al.

NUCLEIC ACIDS RESEARCH (2013)

Article Multidisciplinary Sciences

Structure, function and diversity of the healthy human microbiome

Curtis Huttenhower et al.

NATURE (2012)

Article Multidisciplinary Sciences

Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample

J. Gregory Caporaso et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2011)

Article Biochemistry & Molecular Biology

SILVA:: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB

Elmar Pruesse et al.

NUCLEIC ACIDS RESEARCH (2007)

Article Biotechnology & Applied Microbiology

Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy

Qiong Wang et al.

APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2007)

Article Biochemistry & Molecular Biology

BLAST: at the core of a powerful and diverse set of sequence analysis tools

S McGinnis et al.

NUCLEIC ACIDS RESEARCH (2004)