Current challenges and best-practice protocols for microbiome analysis

Trimmomatic: a flexible trimmer for Illumina sequence data

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Fast and accurate short read alignment with Burrows-Wheeler transform

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Fast gapped-read alignment with Bowtie 2

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DADA2: High–resolution sample inference from Illumina amplicon data

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

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

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

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Prokka: rapid prokaryotic genome annotation

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Fast and sensitive protein alignment using DIAMOND

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CheckM: Assessing the Quality of Microbial Genomes Recovered from Isolates, Single Cells, and Metagenomes

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Prodigal: prokaryotic gene recognition and translation initiation site identification

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16S ribosomal DNA amplification for phylogenetic study

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A human gut microbial gene catalogue established by metagenomic sequencing

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

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Accelerated Profile HMM Searches

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A metagenome-wide association study of gut microbiota in type 2 diabetes

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Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation

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The carbohydrate-active enzymes database (CAZy) in 2013

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Pfam: the protein families database

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The human microbiome project

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

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Kraken: ultrafast metagenomic sequence classification using exact alignments

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metaSPAdes: a new versatile metagenomic assembler

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The COG database: a tool for genome-scale analysis of protein functions and evolution

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

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Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data

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Going back to the roots: the microbial ecology of the rhizosphere

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The Universal Protein Resource (UniProt)

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Real-Time DNA Sequencing from Single Polymerase Molecules

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Reagent and laboratory contamination can critically impact sequence-based microbiome analyses

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

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Identifying bacterial genes and endosymbiont DNA with Glimmer

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

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Binning metagenomic contigs by coverage and composition

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A communal catalogue reveals Earth's multiscale microbial diversity

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Metagenomics: Application of Genomics to Uncultured Microorganisms

Handelsman, J. (2004) · Microbiology and Molecular Biology Reviews · doi:10.1128/mmbr.68.4.669-685.2004 · Cited by 2,454 · see citing works

GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions.

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Role of the gut microbiota in immunity and inflammatory disease

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16S rRNA Gene Sequencing for Bacterial Identification in the Diagnostic Laboratory: Pluses, Perils, and Pitfalls

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Shotgun metagenomics, from sampling to analysis

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PSORT: a program for detecting sorting signals in proteins and predicting their subcellular localization

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MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities

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Nanopore sequencing and assembly of a human genome with ultra-long reads

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MicrobiomeAnalyst: a web-based tool for comprehensive statistical, visual and meta-analysis of microbiome data

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Deblur Rapidly Resolves Single-Nucleotide Community Sequence Patterns

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Review and re-analysis of domain-specific 16S primers

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UNOISE2: improved error-correction for Illumina 16S and ITS amplicon sequencingPreprint

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Metagenomic microbial community profiling using unique clade-specific marker genes

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

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Role of microorganisms in the evolution of animals and plants: the hologenome theory of evolution

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Repetitive DNA and next-generation sequencing: computational challenges and solutions

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ScanProsite: detection of PROSITE signature matches and ProRule-associated functional and structural residues in proteins

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Challenges in homology search: HMMER3 and convergent evolution of coiled-coil regions

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The Oxford Nanopore MinION: delivery of nanopore sequencing to the genomics community

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Tax4Fun: predicting functional profiles from metagenomic 16S rRNA data

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The role of microorganisms in coral health, disease and evolution

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Centrifuge: rapid and sensitive classification of metagenomic sequences

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The Universal Protein Resource (UniProt) in 2010

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SMART: a web-based tool for the study of genetically mobile domains

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BLAST: a more efficient report with usability improvements

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Adaptive seeds tame genomic sequence comparisonPreprint

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A complete bacterial genome assembled de novo using only nanopore sequencing data

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Quantitative microbiome profiling links gut community variation to microbial load

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Metagenomics: Genomic Analysis of Microbial Communities

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Metagenomics - a guide from sampling to data analysis

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The TIGRFAMs database of protein families

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Fungal Identification Using Molecular Tools: A Primer for the Natural Products Research Community

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Critical Assessment of Metagenome Interpretation—a benchmark of metagenomics software

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

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The Universal Protein Resource (UniProt)

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Then and now: use of 16S rDNA gene sequencing for bacterial identification and discovery of novel bacteria in clinical microbiology laboratories

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Sample size calculation

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Single molecule real-time (SMRT) sequencing comes of age: applications and utilities for medical diagnostics

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Fast Identification and Removal of Sequence Contamination from Genomic and Metagenomic Datasets

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Paneth cells as a site of origin for intestinal inflammation

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Conducting a microbiome study

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MetaQUAST: evaluation of metagenome assemblies

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Experimental and analytical tools for studying the human microbiome

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MaxBin: an automated binning method to recover individual genomes from metagenomes using an expectation-maximization algorithm

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Assessment of transcript reconstruction methods for RNA-seq

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Gastric microbial community profiling reveals a dysbiotic cancer-associated microbiota

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Efficacy of Sterile Fecal Filtrate Transfer for Treating Patients With Clostridium difficile Infection

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

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

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How to apply de Bruijn graphs to genome assembly

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Longitudinal studies.

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

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PhyloSift: phylogenetic analysis of genomes and metagenomes

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Advancements in Next-Generation Sequencing

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Minimum entropy decomposition: Unsupervised oligotyping for sensitive partitioning of high-throughput marker gene sequences

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Ray Meta: scalable de novo metagenome assembly and profiling

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The advantages of SMRT sequencing

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Calypso: a user-friendly web-server for mining and visualizing microbiome–environment interactions

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The Hologenome Concept: Helpful or Hollow?

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Sample storage conditions significantly influence faecal microbiome profiles

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Host-microbiota interactions: from holobiont theory to analysis

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A Perspective on the Role of Microbiome for Colorectal Cancer Treatment

Kalasabail, S., Engelman, J., Zhang, L. Y., El-Omar, E. M., & Yim, H. C. H. (2021) · Cancers · doi:10.3390/cancers13184623 · Cited by 35 · see citing works

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

Hoang, M. T. V., Irinyi, L., Hu, Y., Schwessinger, B., & Meyer, W. (2022) · Frontiers in Microbiology · doi:10.3389/fmicb.2021.708550 · Cited by 35 · see citing works

Impact of Antibiotic Therapies on Resistance Genes Dynamic and Composition of the Animal Gut Microbiota

Rochegüe, T., Haenni, M., Mondot, S., Astruc, C., Cazeau, G., Ferry, T., Madec, J.-Y., & Lupo, A. (2021) · Animals · doi:10.3390/ani11113280 · Cited by 34 · see citing works

VIRify: An integrated detection, annotation and taxonomic classification pipeline using virus-specific protein profile hidden Markov models

Rangel-Piñeros, G., Almeida, A., Beracochea, M., Sakharova, E., Marz, M., Reyes, A., Hölzer, M., & Finn, R. D. (2023) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1011422 · Cited by 34 · see citing works

Shotgun Metagenomics of Gastric Biopsies Reveals Compositional and Functional Microbiome Shifts in High- and Low-Gastric-Cancer-Risk Populations from Colombia, South America

Mannion, A. J., Sheh, A., Shen, Z., Dzink-Fox, J., Piazuelo, M. B., Wilson, K. T., Peek, R. M., & Fox, J. G. (2023) · Gut Microbes · doi:10.1080/19490976.2023.2186677 · Cited by 33 · see citing works

Mild and Severe SARS-CoV-2 Infection Induces Respiratory and Intestinal Microbiome Changes in the K18-hACE2 Transgenic Mouse Model

Seibert, B., Cáceres, C. J., Garcia, S. C., Carnaccini, S., Geiger, G., Rajão, D. S., Ottesen, E. A., & Perez, D. R. (2021) · Microbiology Spectrum · doi:10.1128/spectrum.00536-21 · Cited by 33 · see citing works

Microbiome Research and Multi-Omics Integration for Personalized Medicine in Asthma

Logotheti, M., Agioutantis, P. C., Katsaounou, P. A., & Loutrari, H. V. (2021) · Journal of Personalized Medicine · doi:10.3390/jpm11121299 · Cited by 32 · see citing works

Computational challenges of sequence classification in microbiomic data

Ribeca, P., & Valiente, G. (2011) · Briefings in Bioinformatics · doi:10.1093/bib/bbr019 · Cited by 18 · see citing works

The Madness of Microbiome: Attempting To Find Consensus “Best Practice” for 16S Microbiome Studies

Pollock, J., Glendinning, L., Wisedchanwet, T., & Watson, M. (2018) · Applied and Environmental Microbiology · doi:10.1128/aem.02627-17 · Cited by 575 · see citing works

Considerations For Optimizing Microbiome Analysis Using a Marker Gene

de la Cuesta‐Zuluaga, J., & Escobar, J. S. (2016) · Frontiers in Nutrition · doi:10.3389/fnut.2016.00026 · Cited by 46 · see citing works

Instruction of microbiome taxonomic profiling based on 16S rRNA sequencing

Kim, H.-J., Kim, S., & Jung, S. (2020) · The Journal of Microbiology · doi:10.1007/s12275-020-9556-y · Cited by 47 · see citing works

Pearls and pitfalls of genomics-based microbiome analysis

Carlos, N., Tang, Y., & Pei, Z. (2012) · Emerging Microbes & Infections · doi:10.1038/emi.2012.41 · Cited by 31 · see citing works