4.7 Review

An Introduction to Next Generation Sequencing Bioinformatic Analysis in Gut Microbiome Studies

Related references

Note: Only part of the references are listed.
Article Biochemistry & Molecular Biology

COG database update: focus on microbial diversity, model organisms, and widespread pathogens

Michael Y. Galperin et al.

Summary: The COG database, created in 1997 and most recently updated in 2014, includes extensive information on bacterial and archaeal genomes. The current version introduces new features and plans for future expansion and refinement of annotations.

NUCLEIC ACIDS RESEARCH (2021)

Article Biochemistry & Molecular Biology

Pfam: The protein families database in 2021

Jaina Mistry et al.

Summary: The Pfam database has recently added a large number of protein families and domains, made revisions for COVID-19 research, and introduced Pfam-B as a supplement. These updates and improvements can help researchers classify protein sequences more effectively and conduct related studies.

NUCLEIC ACIDS RESEARCH (2021)

Article Multidisciplinary Sciences

Comparing bioinformatic pipelines for microbial 16S rRNA amplicon sequencing

Andrei Prodan et al.

PLOS ONE (2020)

Article Biochemical Research Methods

Ktrim: an extra-fast and accurate adapter- and quality-trimmer for sequencing data

Kun Sun

BIOINFORMATICS (2020)

Article Gastroenterology & Hepatology

Intestinal Virome Signature Associated With Severity of Nonalcoholic Fatty Liver Disease

Sonja Lang et al.

GASTROENTEROLOGY (2020)

Article Gastroenterology & Hepatology

Intestinal Virome in Patients With Alcoholic Hepatitis

Lu Jiang et al.

HEPATOLOGY (2020)

Article Immunology

The Gut Microbiome Signatures Discriminate Healthy From Pulmonary Tuberculosis Patients

Yongfei Hu et al.

FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY (2019)

Letter Biotechnology & Applied Microbiology

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

Evan Bolyen et al.

NATURE BIOTECHNOLOGY (2019)

Article Gastroenterology & Hepatology

The microbiome reflects diagnosis and predicts disease severity in paediatric onset inflammatory bowel disease

Mikkel Malham et al.

SCANDINAVIAN JOURNAL OF GASTROENTEROLOGY (2019)

Article Ecology

Combining the 5.8S and ITS2 to improve classification of fungi

Felix Heeger et al.

METHODS IN ECOLOGY AND EVOLUTION (2019)

Review Genetics & Heredity

Advances and Challenges in Metatranscriptomic Analysis

Migun Shakya et al.

FRONTIERS IN GENETICS (2019)

Article Gastroenterology & Hepatology

Enteric fungal microbiota dysbiosis and ecological alterations in colorectal cancer

Olabisi Oluwabukola Coker et al.

Review Microbiology

Mycobiome diversity: high-throughput sequencing and identification of fungi

R. Henrik Nilsson et al.

NATURE REVIEWS MICROBIOLOGY (2019)

Article Biochemistry & Molecular Biology

PANTHER version 14: more genomes, a new PANTHER GO-slim and improvements in enrichment analysis tools

Huaiyu Mi et al.

NUCLEIC ACIDS RESEARCH (2019)

Article Biochemistry & Molecular Biology

The UNITE database for molecular identification of fungi: handling dark taxa and parallel taxonomic classifications

Rolf Henrik Nilsson et al.

NUCLEIC ACIDS RESEARCH (2019)

Article Microbiology

Gut microbiome structure and metabolic activity in inflammatory bowel disease

Eric A. Franzosa et al.

NATURE MICROBIOLOGY (2019)

Article Immunology

Distinct Gut Virome Profile of Pregnant Women With Type 1 Diabetes in the ENDIA Study

Ki Wook Kim et al.

OPEN FORUM INFECTIOUS DISEASES (2019)

Article Biochemistry & Molecular Biology

ITSoneDB: a comprehensive collection of eukaryotic ribosomal RNA Internal Transcribed Spacer 1 (ITS1) sequences

Monica Santamaria et al.

NUCLEIC ACIDS RESEARCH (2018)

Review Pathology

Gut microbiome: a new player in gastrointestinal disease

Gregor Gorkiewicz et al.

VIRCHOWS ARCHIV (2018)

Article Medicine, Research & Experimental

Imbalance of gut microbiome and intestinal epithelial barrier dysfunction in patients with high blood pressure

Seungbum Kim et al.

CLINICAL SCIENCE (2018)

Article Gastroenterology & Hepatology

Alterations in Enteric Virome Are Associated With Colorectal Cancer and Survival Outcomes

Geicho Nakatsu et al.

GASTROENTEROLOGY (2018)

Article Biochemical Research Methods

hc-OTU: A Fast and Accurate Method for Clustering Operational Taxonomic Units Based on Homopolymer Compaction

Seunghyun Park et al.

IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS (2018)

Article Biochemistry & Molecular Biology

Molecular phenomics and metagenomics of hepatic steatosis in non-diabetic obese women

Lesley Hoyles et al.

NATURE MEDICINE (2018)

Review Microbiology

Best practices for analysing microbiomes

Rob Knight et al.

NATURE REVIEWS MICROBIOLOGY (2018)

Review Biochemistry & Molecular Biology

Human Gut Microbiome: Function Matters

Anna Heintz-Buschart et al.

TRENDS IN MICROBIOLOGY (2018)

Article Microbiology

Dynamics of metatranscription in the inflammatory bowel disease gut microbiome

Melanie Schirmer et al.

NATURE MICROBIOLOGY (2018)

Article Gastroenterology & Hepatology

Differential clustering of fecal and mucosa-associated microbiota in 'healthy' individuals

Adam Carstens et al.

JOURNAL OF DIGESTIVE DISEASES (2018)

Article Biochemical Research Methods

Species-level functional profiling of metagenomes and metatranscriptomes

Eric A. Franzosa et al.

NATURE METHODS (2018)

Review Biotechnology & Applied Microbiology

The Gut Microbiome and Mental Health: Implications for Anxiety- and Trauma-Related Disorders

Stefanie Malan-Muller et al.

OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY (2018)

Article Biochemistry & Molecular Biology

IMG/M: integrated genome and metagenome comparative data analysis system

I-Min A. Chen et al.

NUCLEIC ACIDS RESEARCH (2017)

Article Biotechnology & Applied Microbiology

Bioinformatics for NGS-based metagenomics and the application to biogas research

Sebastian Juenemann et al.

JOURNAL OF BIOTECHNOLOGY (2017)

Article Medicine, Research & Experimental

Intestinal fungi contribute to development of alcoholic liver disease

An-Ming Yang et al.

JOURNAL OF CLINICAL INVESTIGATION (2017)

Review Biotechnology & Applied Microbiology

Shotgun metagenomics, from sampling to analysis

Christopher Quince et al.

NATURE BIOTECHNOLOGY (2017)

Article Multidisciplinary Sciences

Intestinal virome changes precede autoimmunity in type I diabetes-susceptible children

Guoyan Zhao et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2017)

Article Cell Biology

A role for bacterial urease in gut dysbiosis and Crohn's disease

Josephine Ni et al.

SCIENCE TRANSLATIONAL MEDICINE (2017)

Article Biochemical Research Methods

A Bayesian method for detecting pairwise associations in compositional data

Emma Schwager et al.

PLOS COMPUTATIONAL BIOLOGY (2017)

Article Microbiology

New evidences on the altered gut microbiota in autism spectrum disorders

Francesco Strati et al.

MICROBIOME (2017)

Article Microbiology

The gut mycobiome of the Human Microbiome Project healthy cohort

Andrea K. Nash et al.

MICROBIOME (2017)

Review Medicine, Research & Experimental

Human Virome

Selene Zarate et al.

ARCHIVES OF MEDICAL RESEARCH (2017)

Review Gastroenterology & Hepatology

Review article: the human intestinal virome in health and disease

S. R. Carding et al.

ALIMENTARY PHARMACOLOGY & THERAPEUTICS (2017)

Article Biotechnology & Applied Microbiology

Assembling metagenomes, one community at a time

Andries Johannes van der Walt et al.

BMC GENOMICS (2017)

Article Biotechnology & Applied Microbiology

Quantitative metagenomics reveals unique gut microbiome biomarkers in ankylosing spondylitis

Chengping Wen et al.

GENOME BIOLOGY (2017)

Article Biochemical Research Methods

MetaQUAST: evaluation of metagenome assemblies

Alla Mikheenko et al.

BIOINFORMATICS (2016)

Article Biochemical Research Methods

MultiQC: summarize analysis results for multiple tools and samples in a single report

Philip Ewels et al.

BIOINFORMATICS (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

Use of Metatranscriptomics in Microbiome Research

Stavros Bashiardes et al.

BIOINFORMATICS AND BIOLOGY INSIGHTS (2016)

Article Biochemical Research Methods

Tax4Fun: predicting functional profiles from metagenomic 16S rRNA data

Kathrin P. Asshauer et al.

BIOINFORMATICS (2015)

Article Biochemistry & Molecular Biology

Disease-Specific Alterations in the Enteric Virome in Inflammatory Bowel Disease

Jason M. Norman et al.

Article Gastroenterology & Hepatology

Fungal Signature in the Gut Microbiota of Pediatric Patients With Inflammatory Bowel Disease

Christel Chehoud et al.

INFLAMMATORY BOWEL DISEASES (2015)

Article Immunology

The fungal microbiota of de-novo paediatric inflammatory bowel disease

I. Mukhopadhya et al.

MICROBES AND INFECTION (2015)

Review Nutrition & Dietetics

Gut Microbiome: What We Do and Don't Know

Gail A. Cresci et al.

NUTRITION IN CLINICAL PRACTICE (2015)

Review Gastroenterology & Hepatology

Application of metagenomics in the human gut microbiome

Wei-Lin Wang et al.

WORLD JOURNAL OF GASTROENTEROLOGY (2015)

Article Multidisciplinary Sciences

MICCA: a complete and accurate software for taxonomic profiling of metagenomic data

Davide Albanese et al.

SCIENTIFIC REPORTS (2015)

Article Multidisciplinary Sciences

Dysbiosis of Fungal Microbiota in the Intestinal Mucosa of Patients with Colorectal Adenomas

Chunguang Luan et al.

SCIENTIFIC REPORTS (2015)

Article Biochemical Research Methods

Sparse and Compositionally Robust Inference of Microbial Ecological Networks

Zachary D. Kurtz et al.

PLOS COMPUTATIONAL BIOLOGY (2015)

Review Biochemistry & Molecular Biology

Combining metagenomics, metatranscriptomics and viromics to explore novel microbial interactions: towards a systems-level understanding of human microbiome

Shirley Bikel et al.

COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL (2015)

Article Biochemical Research Methods

UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches

Baris E. Suzek et al.

BIOINFORMATICS (2015)

Article Biochemical Research Methods

Fast and sensitive protein alignment using DIAMOND

Benjamin Buchfink et al.

NATURE METHODS (2015)

Article Microbiology

Altered gut microbial energy and metabolism in children with non-alcoholic fatty liver disease

Sonia Michail et al.

FEMS MICROBIOLOGY ECOLOGY (2015)

Article Biochemical Research Methods

Trimmomatic: a flexible trimmer for Illumina sequence data

Anthony M. Bolger et al.

BIOINFORMATICS (2014)

Article Biochemical Research Methods

Metavir 2: new tools for viral metagenome comparison and assembled virome analysis

Simon Roux et al.

BMC BIOINFORMATICS (2014)

Article Multidisciplinary Sciences

Assessment of quality control approaches for metagenomic data analysis

Qian Zhou et al.

SCIENTIFIC REPORTS (2014)

Article Microbiology

LotuS: an efficient and user-friendly OTU processing pipeline

Falk Hildebrand et al.

MICROBIOME (2014)

Article Biotechnology & Applied Microbiology

Differential analysis of gene regulation at transcript resolution with RNA-seq

Cole Trapnell et al.

NATURE BIOTECHNOLOGY (2013)

Article Biotechnology & Applied Microbiology

Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences

Morgan G. I. Langille et al.

NATURE BIOTECHNOLOGY (2013)

Article Biochemical Research Methods

UPARSE: highly accurate OTU sequences from microbial amplicon reads

Robert C. Edgar

NATURE METHODS (2013)

Article Multidisciplinary Sciences

The Long-Term Stability of the Human Gut Microbiota

Jeremiah J. Faith et al.

SCIENCE (2013)

Review Genetics & Heredity

Functional profiling of the gut microbiome in disease-associated inflammation

Daniela Boernigen et al.

GENOME MEDICINE (2013)

Article Biotechnology & Applied Microbiology

De novo assembly of highly diverse viral populations

Xiao Yang et al.

BMC GENOMICS (2012)

Article Biochemical Research Methods

Fast gapped-read alignment with Bowtie 2

Ben Langmead et al.

NATURE METHODS (2012)

Article Biochemistry & Molecular Biology

MetaVelvet: an extension of Velvet assembler to de novo metagenome assembly from short sequence reads

Toshiaki Namiki et al.

NUCLEIC ACIDS RESEARCH (2012)

Article Multidisciplinary Sciences

Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi

Conrad L. Schoch et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2012)

Article Biochemical Research Methods

Inferring Correlation Networks from Genomic Survey Data

Jonathan Friedman et al.

PLOS COMPUTATIONAL BIOLOGY (2012)

Article Biochemical Research Methods

Meta-IDBA: a de Novo assembler for metagenomic data

Yu Peng et al.

BIOINFORMATICS (2011)

Article Biochemical Research Methods

Metavir: a web server dedicated to virome analysis

Simon Roux et al.

BIOINFORMATICS (2011)

Article Infectious Diseases

Correlation between gastrointestinal fungi and varying degrees of chronic hepatitis B virus infection

Yu Chen et al.

DIAGNOSTIC MICROBIOLOGY AND INFECTIOUS DISEASE (2011)

Article Biochemistry & Molecular Biology

ESPRIT-Tree: hierarchical clustering analysis of millions of 16S rRNA pyrosequences in quasilinear computational time

Yunpeng Cai et al.

NUCLEIC ACIDS RESEARCH (2011)

Article Biotechnology & Applied Microbiology

Metagenomic biomarker discovery and explanation

Nicola Segata et al.

GENOME BIOLOGY (2011)

Article Biochemical Research Methods

METAREP: JCVI metagenomics reports-an open source tool for high-performance comparative metagenomics

Johannes Goll et al.

BIOINFORMATICS (2010)

Article Biochemical Research Methods

Search and clustering orders of magnitude faster than BLAST

Robert C. Edgar

BIOINFORMATICS (2010)

Review Biotechnology & Applied Microbiology

Assembly algorithms for next-generation sequencing data

Jason R. Miller et al.

GENOMICS (2010)

Article Multidisciplinary Sciences

A human gut microbial gene catalogue established by metagenomic sequencing

Junjie Qin et al.

NATURE (2010)

Letter Biochemical Research Methods

QIIME allows analysis of high-throughput community sequencing data

J. Gregory Caporaso et al.

NATURE METHODS (2010)

Article Biotechnology & Applied Microbiology

Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities

Patrick D. Schloss et al.

APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2009)

Article Biochemistry & Molecular Biology

ESPRIT: estimating species richness using large collections of 16S rRNA pyrosequences

Yijun Sun et al.

NUCLEIC ACIDS RESEARCH (2009)

Article Biochemistry & Molecular Biology

MEGAN analysis of metagenomic data

Daniel H. Huson et al.

GENOME RESEARCH (2007)

Article Biochemical Research Methods

Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences

Weizhong Li et al.

BIOINFORMATICS (2006)

Article Biochemistry & Molecular Biology

KEGG: Kyoto Encyclopedia of Genes and Genomes

M Kanehisa et al.

NUCLEIC ACIDS RESEARCH (2000)