Metagenomic approaches in microbial ecology: an update on whole-genome and marker gene sequencing analyses

Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle

(2019) Edoardo Pasolli et al.   CELL

Characterizing both bacteria and fungi improves understanding of the Arabidopsis root microbiome

(2019) Joy Bergelson et al.   Scientific Reports

Infectious Complications Are Associated With Alterations in the Gut Microbiome in Pediatric Patients With Acute Lymphoblastic Leukemia

(2019) Jacob T. Nearing et al.   Frontiers in Cellular and Infection Microbiology

Autometa: automated extraction of microbial genomes from individual shotgun metagenomes

(2019) Ian J Miller et al.   NUCLEIC ACIDS RESEARCH

A new genomic blueprint of the human gut microbiota

(2019) Alexandre Almeida et al.   NATURE

SolidBin: improving metagenome binning with semi-supervised normalized cut

(2019) Ziye Wang et al.   BIOINFORMATICS

Application of Machine Learning in Microbiology

(2019) Kaiyang Qu et al.   Frontiers in Microbiology

The Water Microbiome Through a Pilot Scale Advanced Treatment Facility for Direct Potable Reuse

(2019) Rose S. Kantor et al.   Frontiers in Microbiology

MGS-Fast: Metagenomic shotgun data fast annotation using microbial gene catalogs

(2019) Stuart M Brown et al.   GigaScience

MetaBMF: A Scalable Binning Algorithm for Large-scale Reference-free Metagenomic Studies

(2019) Terry Ma et al.   BIOINFORMATICS

GRASP2: fast and memory-efficient gene-centric assembly and homolog search for metagenomic sequencing data

(2019) Cuncong Zhong et al.   BMC BIOINFORMATICS

Hybrid metagenomic assembly enables high-resolution analysis of resistance determinants and mobile elements in human microbiomes

(2019) Denis Bertrand et al.   NATURE BIOTECHNOLOGY

Machine learning to predict microbial community functions: An analysis of dissolved organic carbon from litter decomposition

(2019) Jaron Thompson et al.   PLoS One

MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies

(2019) Dongwan D. Kang et al.   PeerJ

A Review and Tutorial of Machine Learning Methods for Microbiome Host Trait Prediction

(2019) Yi-Hui Zhou et al.   Frontiers in Genetics

Metagenomic assembly provides a deep insight into the antibiotic resistome alteration induced by drinking water chlorination and its correlations with bacterial host changes

(2019) Shuyu Jia et al.   JOURNAL OF HAZARDOUS MATERIALS

An Integrated Pipeline for Annotation and Visualization of Metagenomic Contigs

(2019) Xiaoli Dong et al.   Frontiers in Genetics

Taxonomy-aware feature engineering for microbiome classification

(2018) Mai Oudah et al.   BMC BIOINFORMATICS

Comparison of normalization methods for the analysis of metagenomic gene abundance data

(2018) Mariana Buongermino Pereira et al.   BMC GENOMICS

Modeling leaderless transcription and atypical genes results in more accurate gene prediction in prokaryotes

(2018) Alexandre Lomsadze et al.   GENOME RESEARCH

Practical evaluation of 11 de novo assemblers in metagenome assembly

(2018) Esmaeil Forouzan et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Best practices for analysing microbiomes

(2018) Rob Knight et al.   NATURE REVIEWS MICROBIOLOGY

Host contributes to longitudinal diversity of fecal microbiota in swine selected for lean growth

(2018) Duc Lu et al.   Microbiome

Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2’s q2-feature-classifier plugin

(2018) Nicholas A. Bokulich et al.   Microbiome

Recovery of genomes from metagenomes via a dereplication, aggregation and scoring strategy

(2018) Christian M. K. Sieber et al.   Nature Microbiology

On the Road to Strain-Resolved Comparative Metagenomics

(2018) Nicola Segata   mSystems

OUP accepted manuscript

(2018)   NUCLEIC ACIDS RESEARCH

Denoising the Denoisers: an independent evaluation of microbiome sequence error-correction approaches

(2018) Jacob T. Nearing et al.   PeerJ

MetaWRAP—a flexible pipeline for genome-resolved metagenomic data analysis

(2018) Gherman V. Uritskiy et al.   Microbiome

MAGpy: a reproducible pipeline for the downstream analysis of metagenome-assembled genomes (MAGs)

(2018) Robert D Stewart et al.   BIOINFORMATICS

Species-level functional profiling of metagenomes and metatranscriptomes

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

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

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

Biofilm Microbiome (Re)Growth Dynamics in Drinking Water Distribution Systems Are Impacted by Chlorine Concentration

(2018) Katherine E. Fish et al.   Frontiers in Microbiology

Changes in the Drinking Water Microbiome: Effects of Water Treatments Along the Flow of Two Drinking Water Treatment Plants in a Urbanized Area, Milan (Italy)

(2018) Antonia Bruno et al.   Frontiers in Microbiology

metaSPAdes: a new versatile metagenomic assembler

(2017) Sergey Nurk et al.   GENOME RESEARCH

Impact of sequence processing and taxonomic classification approaches on eukaryotic community structure from environmental samples with emphasis on diatoms

(2017) Kristin Hardge et al.   Molecular Ecology Resources

Shotgun metagenomics, from sampling to analysis

(2017) Christopher Quince et al.   NATURE BIOTECHNOLOGY

Critical Assessment of Metagenome Interpretation—a benchmark of metagenomics software

(2017) Alexander Sczyrba et al.   NATURE METHODS

Comparing and Evaluating Metagenome Assembly Tools from a Microbiologist’s Perspective - Not Only Size Matters!

(2017) John Vollmers et al.   PLoS One

Critical Issues in Mycobiota Analysis

(2017) Bettina Halwachs et al.   Frontiers in Microbiology

Normalization and microbial differential abundance strategies depend upon data characteristics

(2017) Sophie Weiss et al.   Microbiome

Bioinformatics strategies for taxonomy independent binning and visualization of sequences in shotgun metagenomics

(2017) Karel Sedlar et al.   Computational and Structural Biotechnology Journal

metaSNV: A tool for metagenomic strain level analysis

(2017) Paul Igor Costea et al.   PLoS One

MOCAT2: a metagenomic assembly, annotation and profiling framework

(2016) Jens Roat Kultima et al.   BIOINFORMATICS

Fungal identification using a Bayesian classifier and the Warcup training set of internal transcribed spacer sequences

(2016) Vinita Deshpande et al.   MYCOLOGIA

MetaMLST: multi-locus strain-level bacterial typing from metagenomic samples

(2016) Moreno Zolfo et al.   NUCLEIC ACIDS RESEARCH

NCBI prokaryotic genome annotation pipeline

(2016) Tatiana Tatusova et al.   NUCLEIC ACIDS RESEARCH

The standard operating procedure of the DOE-JGI Metagenome Annotation Pipeline (MAP v.4)

(2016) Marcel Huntemann et al.   Standards in Genomic Sciences

MEGAN Community Edition - Interactive Exploration and Analysis of Large-Scale Microbiome Sequencing Data

(2016) Daniel H. Huson et al.   PLoS Computational Biology

Identification, Recovery, and Refinement of Hitherto Undescribed Population-Level Genomes from the Human Gastrointestinal Tract

(2016) Cedric C. Laczny et al.   Frontiers in Microbiology

PhyloPythiaS+: a self-training method for the rapid reconstruction of low-ranking taxonomic bins from metagenomes

(2016) Ivan Gregor et al.   PeerJ

VSEARCH: a versatile open source tool for metagenomics

(2016) Torbjørn Rognes et al.   PeerJ

Skin fungal community and its correlation with bacterial community of urban Chinese individuals

(2016) Marcus H. Y. Leung et al.   Microbiome

MetaStorm: A Public Resource for Customizable Metagenomics Annotation

(2016) Gustavo Arango-Argoty et al.   PLoS One

Accurate binning of metagenomic contigs via automated clustering sequences using information of genomic signatures and marker genes

(2016) Hsin-Hung Lin et al.   Scientific Reports

MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets

(2015) Yu-Wei Wu 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

Improved taxonomic assignment of human intestinal 16S rRNA sequences by a dedicated reference database

(2015) Jarmo Ritari et al.   BMC GENOMICS

CLARK: fast and accurate classification of metagenomic and genomic sequences using discriminative k-mers

(2015) Rachid Ounit et al.   BMC GENOMICS

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

(2015) Donovan H. Parks et al.   GENOME RESEARCH

Methods for virus classification and the challenge of incorporating metagenomic sequence data

(2015) Peter Simmonds   JOURNAL OF GENERAL VIROLOGY

MetaPhlAn2 for enhanced metagenomic taxonomic profiling

(2015) Duy Tin Truong et al.   NATURE METHODS

Proportionality: A Valid Alternative to Correlation for Relative Data

(2015) David Lovell et al.   PLoS Computational Biology

Taxator-tk: precise taxonomic assignment of metagenomes by fast approximation of evolutionary neighborhoods

(2014) J. Dröge et al.   BIOINFORMATICS

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

MetaVelvet-SL: an extension of the Velvet assembler to a de novo metagenomic assembler utilizing supervised learning

(2014) Afiahayati et al.   DNA RESEARCH

Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes

(2014) H Bjørn Nielsen et al.   NATURE BIOTECHNOLOGY

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

Binning metagenomic contigs by coverage and composition

(2014) Johannes Alneberg et al.   NATURE METHODS

Improved Assemblies Using a Source-Agnostic Pipeline for MetaGenomic Assembly by Merging (MeGAMerge) of Contigs

(2014) Matthew Scholz et al.   Scientific Reports

Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible

(2014) Paul J. McMurdie et al.   PLoS Computational Biology

voom: precision weights unlock linear model analysis tools for RNA-seq read counts

(2014) Charity W Law et al.   GENOME BIOLOGY

Space-efficient and exact de Bruijn graph representation based on a Bloom filter

(2013) Rayan Chikhi et al.   Algorithms for Molecular Biology

The MaSuRCA genome assembler

(2013) Aleksey V. Zimin et al.   BIOINFORMATICS

GAM-NGS: genomic assemblies merger for next generation sequencing

(2013) Riccardo Vicedomini et al.   BMC BIOINFORMATICS

PERMANOVA, ANOSIM, and the Mantel test in the face of heterogeneous dispersions: What null hypothesis are you testing?

(2013) Marti J. Anderson et al.   ECOLOGICAL MONOGRAPHS

Differential abundance analysis for microbial marker-gene surveys

(2013) Joseph N Paulson et al.   NATURE METHODS

Ribosomal Database Project: data and tools for high throughput rRNA analysis

(2013) James R. Cole et al.   NUCLEIC ACIDS RESEARCH

BacMet: antibacterial biocide and metal resistance genes database

(2013) Chandan Pal et al.   NUCLEIC ACIDS RESEARCH

Pfam: the protein families database

(2013) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data

(2013) Paul J. McMurdie et al.   PLoS One

A Guide to Enterotypes across the Human Body: Meta-Analysis of Microbial Community Structures in Human Microbiome Datasets

(2013) Omry Koren et al.   PLoS Computational Biology

MetAMOS: a modular and open source metagenomic assembly and analysis pipeline

(2013) Todd J Treangen et al.   GENOME BIOLOGY

Characterizing and measuring bias in sequence data

(2013) Michael G Ross et al.   GENOME BIOLOGY

Gene and translation initiation site prediction in metagenomic sequences

(2012) Doug Hyatt et al.   BIOINFORMATICS

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

(2012) Y. Peng et al.   BIOINFORMATICS

Denoising PCR-amplified metagenome data

(2012) Michael J Rosen et al.   BMC BIOINFORMATICS

Short-read reading-frame predictors are not created equal: sequence error causes loss of signal

(2012) William L Trimble et al.   BMC BIOINFORMATICS

MetaCluster 4.0: A Novel Binning Algorithm for NGS Reads and Huge Number of Species

(2012) Yi Wang et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

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

Incorporating 16S Gene Copy Number Information Improves Estimates of Microbial Diversity and Abundance

(2012) Steven W. Kembel et al.   PLoS Computational Biology

The Binning of Metagenomic Contigs for Microbial Physiology of Mixed Cultures

(2012) Marc Strous et al.   Frontiers in Microbiology

Ray Meta: scalable de novo metagenome assembly and profiling

(2012) Sébastien Boisvert et al.   GENOME BIOLOGY

SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler

(2012) Ruibang Luo et al.   GigaScience

Marine Protistan Diversity

(2011) David A. Caron et al.   Annual Review of Marine Science

RAPSearch2: a fast and memory-efficient protein similarity search tool for next-generation sequencing data

(2011) Y. Zhao et al.   BIOINFORMATICS

MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects

(2011) Carson Holt et al.   BMC BIOINFORMATICS

Combining gene prediction methods to improve metagenomic gene annotation

(2011) Non G Yok et al.   BMC BIOINFORMATICS

Assessing the complex sponge microbiota: core, variable and species-specific bacterial communities in marine sponges

(2011) Susanne Schmitt et al.   ISME Journal

Using network analysis to explore co-occurrence patterns in soil microbial communities

(2011) Albert Barberán et al.   ISME Journal

A Novel Abundance-Based Algorithm for Binning Metagenomic Sequences Using l-tuples

(2011) Yu-Wei Wu et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Gene prediction with Glimmer for metagenomic sequences augmented by classification and clustering

(2011) David R. Kelley et al.   NUCLEIC ACIDS RESEARCH

Meraculous: De Novo Genome Assembly with Short Paired-End Reads

(2011) Jarrod A. Chapman et al.   PLoS One

Metagenomic biomarker discovery and explanation

(2011) Nicola Segata et al.   GENOME BIOLOGY

SPHINX—an algorithm for taxonomic binning of metagenomic sequences

(2010) Monzoorul Haque Mohammed et al.   BIOINFORMATICS

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

Clustering metagenomic sequences with interpolated Markov models

(2010) David R Kelley et al.   BMC BIOINFORMATICS

pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree

(2010) Frederick A Matsen et al.   BMC BIOINFORMATICS

Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments

(2010) James H Bullard et al.   BMC BIOINFORMATICS

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

Assembly algorithms for next-generation sequencing data

(2010) Jason R. Miller et al.   GENOMICS

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

Ab initio gene identification in metagenomic sequences

(2010) Wenhan Zhu et al.   NUCLEIC ACIDS RESEARCH

FragGeneScan: predicting genes in short and error-prone reads

(2010) Mina Rho et al.   NUCLEIC ACIDS RESEARCH

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

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

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

TACOA – Taxonomic classification of environmental genomic fragments using a kernelized nearest neighbor approach

(2009) Naryttza N Diaz et al.   BMC BIOINFORMATICS

Unsupervised statistical clustering of environmental shotgun sequences

(2009) Andrey Kislyuk et al.   BMC BIOINFORMATICS

Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov models

(2009) Arthur Brady et al.   NATURE METHODS

A Parsimony Approach to Biological Pathway Reconstruction/Inference for Genomes and Metagenomes

(2009) Yuzhen Ye et al.   PLoS Computational Biology

Community-wide analysis of microbial genome sequence signatures

(2009) Gregory J Dick et al.   GENOME BIOLOGY

The metagenomics RAST server – a public resource for the automatic phylogenetic and functional analysis of metagenomes

(2008) F Meyer et al.   BMC BIOINFORMATICS

MetaGeneAnnotator: Detecting Species-Specific Patterns of Ribosomal Binding Site for Precise Gene Prediction in Anonymous Prokaryotic and Phage Genomes

(2008) H. Noguchi et al.   DNA RESEARCH

Gene prediction in novel fungal genomes using an ab initio algorithm with unsupervised training

(2008) V. Ter-Hovhannisyan et al.   GENOME RESEARCH

Metabonomic and Microbiological Analysis of the Dynamic Effect of Vancomycin-Induced Gut Microbiota Modification in the Mouse

(2008) Ivan K. S. Yap et al.   JOURNAL OF PROTEOME RESEARCH

InterPro: the integrative protein signature database

(2008) S. Hunter et al.   NUCLEIC ACIDS RESEARCH