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

Comparing bioinformatic pipelines for microbial 16S rRNA amplicon sequencing

(2020) Andrei Prodan et al.   PLoS One

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

(2020) Kun Sun   BIOINFORMATICS

Functional Microbial Responses to Alcohol Abstinence in Patients With Alcohol Use Disorder

(2020) Bei Gao et al.   Frontiers in Physiology

PEMA: a flexible Pipeline for Environmental DNA Metabarcoding Analysis of the 16S/18S ribosomal RNA, ITS, and COI marker genes

(2020) Haris Zafeiropoulos et al.   GigaScience

Inference-based accuracy of metagenome prediction tools varies across sample types and functional categories

(2020) Shan Sun et al.   Microbiome

Intestinal Virome Signature Associated With Severity of Nonalcoholic Fatty Liver Disease

(2020) Sonja Lang et al.   GASTROENTEROLOGY

Intestinal virome in patients with alcoholic hepatitis

(2020) Lu Jiang et al.   HEPATOLOGY

Tax4Fun2: prediction of habitat-specific functional profiles and functional redundancy based on 16S rRNA gene sequences

(2020) Franziska Wemheuer et al.   Environmental Microbiome

Distinct gut virome profile of pregnant women with type 1 diabetes in the ENDIA study

(2019) Ki Wook Kim et al.   Open Forum Infectious Diseases

The Gut Microbiome Signatures Discriminate Healthy From Pulmonary Tuberculosis Patients

(2019) Yongfei Hu et al.   Frontiers in Cellular and Infection Microbiology

Microbiome Signatures Associated with Steatohepatitis and Moderate to Severe Fibrosis in Children With Nonalcoholic Fatty Liver Disease

(2019) Jeffrey B. Schwimmer et al.   GASTROENTEROLOGY

Intestinal fungal dysbiosis and systemic immune response to fungi in patients with alcoholic hepatitis

(2019) Sonja Lang et al.   HEPATOLOGY

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

(2019) Evan Bolyen et al.   NATURE BIOTECHNOLOGY

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

(2019) Mikkel Malham et al.   SCANDINAVIAN JOURNAL OF GASTROENTEROLOGY

Combining the 5.8S and ITS 2 to improve classification of fungi

(2019) Felix Heeger et al.   Methods in Ecology and Evolution

To assemble or not to resemble—A validated Comparative Metatranscriptomics Workflow (CoMW)

(2019) Muhammad Zohaib Anwar et al.   GigaScience

Advances and Challenges in Metatranscriptomic Analysis

(2019) Migun Shakya et al.   Frontiers in Genetics

Studying the gut virome in the metagenomic era: challenges and perspectives

(2019) Sanzhima Garmaeva et al.   BMC BIOLOGY

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

(2018) Seungbum Kim et al.   CLINICAL SCIENCE

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

(2018) Geicho Nakatsu et al.   GASTROENTEROLOGY

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

(2018) Seunghyun Park et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

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

(2018) Lesley Hoyles et al.   NATURE MEDICINE

Best practices for analysing microbiomes

(2018) Rob Knight et al.   NATURE REVIEWS MICROBIOLOGY

Human Gut Microbiome: Function Matters

(2018) Anna Heintz-Buschart et al.   TRENDS IN MICROBIOLOGY

Dynamics of metatranscription in the inflammatory bowel disease gut microbiome

(2018) Melanie Schirmer et al.   Nature Microbiology

EukRef: Phylogenetic curation of ribosomal RNA to enhance understanding of eukaryotic diversity and distribution

(2018) Javier del Campo et al.   PLOS BIOLOGY

Enterobacteriaceae are essential for the modulation of colitis severity by fungi

(2018) Bruno Sovran et al.   Microbiome

Enteric fungal microbiota dysbiosis and ecological alterations in colorectal cancer

(2018) Olabisi Oluwabukola Coker et al.   GUT

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

(2018) Adam Carstens et al.   Journal of Digestive Diseases

Species-level functional profiling of metagenomes and metatranscriptomes

(2018) Eric A. Franzosa et al.   NATURE METHODS

Mycobiome diversity: high-throughput sequencing and identification of fungi

(2018) R. Henrik Nilsson et al.   NATURE REVIEWS MICROBIOLOGY

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

(2018) Huaiyu Mi et al.   NUCLEIC ACIDS RESEARCH

eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses

(2018) Jaime Huerta-Cepas et al.   NUCLEIC ACIDS RESEARCH

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

(2018) Rolf Henrik Nilsson et al.   NUCLEIC ACIDS RESEARCH

Gut microbiota composition and functional changes in inflammatory bowel disease and irritable bowel syndrome

(2018) Arnau Vich Vila et al.   Science Translational Medicine

Diagnostic Potential and Interactive Dynamics of the Colorectal Cancer Virome

(2018) Geoffrey D. Hannigan et al.   mBio

Comparison of Mothur and QIIME for the Analysis of Rumen Microbiota Composition Based on 16S rRNA Amplicon Sequences

(2018) Adrian López-García et al.   Frontiers in Microbiology

Gut microbiome structure and metabolic activity in inflammatory bowel disease

(2018) Eric A. Franzosa et al.   Nature Microbiology

Exact sequence variants should replace operational taxonomic units in marker-gene data analysis

(2017) Benjamin J Callahan et al.   ISME Journal

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

(2017) Sebastian Jünemann et al.   JOURNAL OF BIOTECHNOLOGY

Intestinal fungi contribute to development of alcoholic liver disease

(2017) An-Ming Yang et al.   JOURNAL OF CLINICAL INVESTIGATION

The nasal and gut microbiome in Parkinson's disease and idiopathic rapid eye movement sleep behavior disorder

(2017) Anna Heintz-Buschart et al.   MOVEMENT DISORDERS

Shotgun metagenomics, from sampling to analysis

(2017) Christopher Quince et al.   NATURE BIOTECHNOLOGY

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

(2017) Monica Santamaria et al.   NUCLEIC ACIDS RESEARCH

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

(2017) Guoyan Zhao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2017) Josephine Ni et al.   Science Translational Medicine

Gut microbiome: a new player in gastrointestinal disease

(2017) Gregor Gorkiewicz et al.   VIRCHOWS ARCHIV

Functional implications of microbial and viral gut metagenome changes in early stage L-DOPA-naïve Parkinson’s disease patients

(2017) J. R. Bedarf et al.   Genome Medicine

A Bayesian method for detecting pairwise associations in compositional data

(2017) Emma Schwager et al.   PLoS Computational Biology

New evidences on the altered gut microbiota in autism spectrum disorders

(2017) Francesco Strati et al.   Microbiome

The gut mycobiome of the Human Microbiome Project healthy cohort

(2017) Andrea K. Nash et al.   Microbiome

Metagenomic Shotgun Sequencing and Unbiased Metabolomic Profiling Identify Specific Human Gut Microbiota and Metabolites Associated with Immune Checkpoint Therapy Efficacy in Melanoma Patients

(2017) Arthur E. Frankel et al.   NEOPLASIA

Deblur Rapidly Resolves Single-Nucleotide Community Sequence Patterns

(2017) Amnon Amir et al.   mSystems

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

(2016) Philip Ewels et al.   BIOINFORMATICS

Altered Virome and Bacterial Microbiome in Human Immunodeficiency Virus-Associated Acquired Immunodeficiency Syndrome

(2016) Cynthia L. Monaco et al.   Cell Host & Microbe

DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

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

(2016) I-Min A. Chen et al.   NUCLEIC ACIDS RESEARCH

Vikodak - A Modular Framework for Inferring Functional Potential of Microbial Communities from 16S Metagenomic Datasets

(2016) Sunil Nagpal et al.   PLoS One

Piphillin: Improved Prediction of Metagenomic Content by Direct Inference from Human Microbiomes

(2016) Shoko Iwai et al.   PLoS One

Tax4Fun: predicting functional profiles from metagenomic 16S rRNA data: Fig. 1.

(2015) Kathrin P. Aßhauer et al.   BIOINFORMATICS

MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

(2015) Dinghua Li et al.   BIOINFORMATICS

MetaQUAST: evaluation of metagenome assemblies

(2015) Alla Mikheenko et al.   BIOINFORMATICS

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

(2015) Jason M. Norman et al.   CELL

Inflammation, Antibiotics, and Diet as Environmental Stressors of the Gut Microbiome in Pediatric Crohn’s Disease

(2015) James D. Lewis et al.   Cell Host & Microbe

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

(2015) Christel Chehoud et al.   INFLAMMATORY BOWEL DISEASES

The fungal microbiota of de-novo paediatric inflammatory bowel disease

(2015) I. Mukhopadhya et al.   MICROBES AND INFECTION

Comparative study of the validity of three regions of the 18S-rRNA gene for massively parallel sequencing-based monitoring of the planktonic eukaryote community

(2015) Akifumi S. Tanabe et al.   Molecular Ecology Resources

Gut Microbiome

(2015) Gail A. Cresci et al.   NUTRITION IN CLINICAL PRACTICE

Application of metagenomics in the human gut microbiome

(2015) Wei-Lin Wang et al.   WORLD JOURNAL OF GASTROENTEROLOGY

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

(2015) Davide Albanese et al.   Scientific Reports

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

(2015) Chunguang Luan et al.   Scientific Reports

Sparse and Compositionally Robust Inference of Microbial Ecological Networks

(2015) Zachary D. Kurtz et al.   PLoS Computational Biology

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

(2015) Shirley Bikel et al.   Computational and Structural Biotechnology Journal

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

(2014) B. E. Suzek et al.   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

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

(2014) Simon Roux et al.   BMC BIOINFORMATICS

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

Assessment of quality control approaches for metagenomic data analysis

(2014) Qian Zhou et al.   Scientific Reports

LotuS: an efficient and user-friendly OTU processing pipeline

(2014) Falk Hildebrand et al.   Microbiome

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

(2013) Morgan G I Langille et al.   NATURE BIOTECHNOLOGY

UPARSE: highly accurate OTU sequences from microbial amplicon reads

(2013) Robert C Edgar   NATURE METHODS

The Long-Term Stability of the Human Gut Microbiota

(2013) J. J. Faith et al.   SCIENCE

Improved software detection and extraction of ITS1 and ITS2 from ribosomal ITS sequences of fungi and other eukaryotes for analysis of environmental sequencing data

(2013) Johan Bengtsson-Palme et al.   Methods in Ecology and Evolution

Functional profiling of the gut microbiome in disease-associated inflammation

(2013) Daniela Börnigen et al.   Genome Medicine

IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth

(2012) Y. Peng et al.   BIOINFORMATICS

De novo assembly of highly diverse viral populations

(2012) Xiao Yang et al.   BMC GENOMICS

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

(2012) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

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

(2012) Toshiaki Namiki et al.   NUCLEIC ACIDS RESEARCH

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

(2012) C. L. Schoch et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Inferring Correlation Networks from Genomic Survey Data

(2012) Jonathan Friedman et al.   PLoS Computational Biology

Meta-IDBA: a de Novo assembler for metagenomic data

(2011) Y. Peng et al.   BIOINFORMATICS

Metavir: a web server dedicated to virome analysis

(2011) Simon Roux et al.   BIOINFORMATICS

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

(2011) Yunpeng Cai et al.   NUCLEIC ACIDS RESEARCH

TheViral MetaGenome Annotation Pipeline (VMGAP):an automated tool for the functional annotation of viral Metagenomic shotgun sequencing data

(2011) Hernan A. Lorenzi et al.   Standards in Genomic Sciences

Structural diversity of eukaryotic 18S rRNA and its impact on alignment and phylogenetic reconstruction

(2011) Qiang Xie et al.   Protein & Cell

Metagenomic biomarker discovery and explanation

(2011) Nicola Segata et al.   GENOME BIOLOGY

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

(2010) Johannes Goll et al.   BIOINFORMATICS

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Fast evolving 18S rRNA sequences from Solenogastres (Mollusca) resist standard PCR amplification and give new insights into mollusk substitution rate heterogeneity

(2010) Achim Meyer et al.   BMC EVOLUTIONARY BIOLOGY

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

(2010) Yu Chen et al.   DIAGNOSTIC MICROBIOLOGY AND INFECTIOUS DISEASE

Assembly algorithms for next-generation sequencing data

(2010) Jason R. Miller et al.   GENOMICS

A human gut microbial gene catalogue established by metagenomic sequencing

(2010) Junjie Qin et al.   NATURE

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

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

(2009) P. D. Schloss et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Internal Transcribed Spacer Region Sequence Heterogeneity inRhizopus microsporus: Implications for Molecular Diagnosis in Clinical Microbiology Laboratories

(2009) Patrick C. Y. Woo et al.   JOURNAL OF CLINICAL MICROBIOLOGY

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

(2009) Yijun Sun et al.   NUCLEIC ACIDS RESEARCH