{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,10]],"date-time":"2026-07-10T21:30:57Z","timestamp":1783719057444,"version":"3.55.0"},"reference-count":179,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2019,12,18]],"date-time":"2019-12-18T00:00:00Z","timestamp":1576627200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,1,18]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Analyzing the microbiome of diverse species and environments using next-generation sequencing techniques has significantly enhanced our understanding on metabolic, physiological and ecological roles of environmental microorganisms. However, the analysis of the microbiome is affected by experimental conditions (e.g. sequencing errors and genomic repeats) and computationally intensive and cumbersome downstream analysis (e.g. quality control, assembly, binning and statistical analyses). Moreover, the introduction of new sequencing technologies and protocols led to a flood of new methodologies, which also have an immediate effect on the results of the analyses. The aim of this work is to review the most important workflows for 16S rRNA sequencing and shotgun and long-read metagenomics, as well as to provide best-practice protocols on experimental design, sample processing, sequencing, assembly, binning, annotation and visualization. To simplify and standardize the computational analysis, we provide a set of best-practice workflows for 16S rRNA and metagenomic sequencing data (available at https:\/\/github.com\/grimmlab\/MicrobiomeBestPracticeReview).<\/jats:p>","DOI":"10.1093\/bib\/bbz155","type":"journal-article","created":{"date-parts":[[2019,11,7]],"date-time":"2019-11-07T12:10:35Z","timestamp":1573128635000},"page":"178-193","source":"Crossref","is-referenced-by-count":523,"title":["Current challenges and best-practice protocols for microbiome analysis"],"prefix":"10.1093","volume":"22","author":[{"given":"Richa","family":"Bharti","sequence":"first","affiliation":[{"name":"Weihenstephan-Triesdorf University of Applied Sciences and Technical University of Munich, TUM Campus Straubing for Biotechnology and Sustainability, Straubing, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2085-4591","authenticated-orcid":false,"given":"Dominik G","family":"Grimm","sequence":"additional","affiliation":[{"name":"Weihenstephan-Triesdorf University of Applied Sciences and Technical University of Munich, TUM Campus Straubing for Biotechnology and Sustainability, Straubing, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2019,12,18]]},"reference":[{"key":"2021012203303173400_ref1","doi-asserted-by":"crossref","first-page":"e01294-18","DOI":"10.1128\/mBio.01294-18","article-title":"Drivers of microbiome biodiversity: a review of general rules, feces, and ignorance","volume":"9","author":"Reese","year":"2018","journal-title":"MBio"},{"key":"2021012203303173400_ref2","doi-asserted-by":"crossref","first-page":"804","DOI":"10.1038\/nature06244","article-title":"The human microbiome project","volume":"449","author":"Turnbaugh","year":"2007","journal-title":"Nature"},{"key":"2021012203303173400_ref3","doi-asserted-by":"crossref","first-page":"321","DOI":"10.1038\/nri3430","article-title":"Role of the gut microbiota in immunity and inflammatory disease","volume":"13","author":"Kamada","year":"2013","journal-title":"Nat Rev Immunol"},{"key":"2021012203303173400_ref4","doi-asserted-by":"crossref","first-page":"789","DOI":"10.1038\/nrmicro3109","article-title":"Going back to the roots: the microbial ecology of the rhizosphere","volume":"11","author":"Philippot","year":"2013","journal-title":"Nat Rev Microbiol"},{"key":"2021012203303173400_ref5","doi-asserted-by":"crossref","first-page":"723","DOI":"10.1111\/j.1574-6976.2008.00123.x","article-title":"Role of microorganisms in the evolution of animals and plants: the hologenome theory of evolution","volume":"32","author":"Zilber-Rosenberg","year":"2008","journal-title":"FEMS Microbiol Rev"},{"key":"2021012203303173400_ref6","doi-asserted-by":"crossref","first-page":"5","DOI":"10.1186\/s40168-019-0619-4","article-title":"Host-microbiota interactions: from holobiont theory to analysis","volume":"7","author":"Simon","year":"2019","journal-title":"Microbiome"},{"key":"2021012203303173400_ref7","doi-asserted-by":"crossref","first-page":"507","DOI":"10.1126\/science.aac8480","article-title":"MICROBIOME. 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reads","volume":"40","author":"Namiki","year":"2012","journal-title":"Nucleic Acids Res"},{"key":"2021012203303173400_ref85","doi-asserted-by":"crossref","first-page":"R122","DOI":"10.1186\/gb-2012-13-12-r122","article-title":"Ray meta: scalable de novo metagenome assembly and profiling","volume":"13","author":"Boisvert","year":"2012","journal-title":"Genome Biol"},{"key":"2021012203303173400_ref86","doi-asserted-by":"crossref","first-page":"824","DOI":"10.1101\/gr.213959.116","article-title":"metaSPAdes: a new versatile metagenomic assembler","volume":"27","author":"Nurk","year":"2017","journal-title":"Genome Res"},{"key":"2021012203303173400_ref87","doi-asserted-by":"crossref","first-page":"1674","DOI":"10.1093\/bioinformatics\/btv033","article-title":"MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph","volume":"31","author":"Li","year":"2015","journal-title":"Bioinformatics"},{"key":"2021012203303173400_ref88","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0169662","article-title":"Comparing and evaluating metagenome assembly tools from a microbiologist\u2019s perspective - not only size matters!","volume":"12","author":"Vollmers","year":"2017","journal-title":"PLoS One"},{"key":"2021012203303173400_ref89","first-page":"Nr. bbz020","article-title":"New approaches for metagenome assembly with short reads","author":"Ayling","year":"2019","journal-title":"Brief Bioinform"},{"key":"2021012203303173400_ref90","doi-asserted-by":"crossref","first-page":"987","DOI":"10.1038\/nbt.2023","article-title":"How to apply de Bruijn graphs to genome assembly","volume":"29","author":"Compeau","year":"2011","journal-title":"Nat Biotechnol"},{"key":"2021012203303173400_ref91","doi-asserted-by":"crossref","first-page":"521","DOI":"10.1186\/s12864-017-3918-9","article-title":"Assembling metagenomes, one community at a time","volume":"18","author":"van der Walt","year":"2017","journal-title":"BMC Genomics"},{"key":"2021012203303173400_ref92","doi-asserted-by":"crossref","DOI":"10.1155\/2017\/4740354","article-title":"Gene prediction in metagenomic fragments with deep learning","volume":"2017","author":"Zhang","year":"2017","journal-title":"Biomed Res Int"},{"key":"2021012203303173400_ref93","doi-asserted-by":"crossref","first-page":"119","DOI":"10.1186\/1471-2105-11-119","article-title":"Prodigal: prokaryotic gene recognition and translation initiation site identification","volume":"11","author":"Hyatt","year":"2010","journal-title":"BMC Bioinformatics"},{"key":"2021012203303173400_ref94","doi-asserted-by":"crossref","first-page":"673","DOI":"10.1093\/bioinformatics\/btm009","article-title":"Identifying bacterial genes and endosymbiont DNA with glimmer","volume":"23","author":"Delcher","year":"2007","journal-title":"Bioinformatics"},{"key":"2021012203303173400_ref95","doi-asserted-by":"crossref","first-page":"2607","DOI":"10.1093\/nar\/29.12.2607","article-title":"GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions","volume":"29","author":"Besemer","year":"2001","journal-title":"Nucleic Acids Res"},{"key":"2021012203303173400_ref96","doi-asserted-by":"crossref","first-page":"3554","DOI":"10.1093\/nar\/23.17.3554","article-title":"Detection of new genes in a bacterial genome using Markov models for three gene classes","volume":"23","author":"Borodovsky","year":"1995","journal-title":"Nucleic Acids Res"},{"key":"2021012203303173400_ref97","doi-asserted-by":"crossref","first-page":"1079","DOI":"10.1101\/gr.230615.117","article-title":"Modeling leaderless transcription and atypical genes results in more accurate gene prediction in prokaryotes","volume":"28","author":"Lomsadze","year":"2018","journal-title":"Genome Res"},{"key":"2021012203303173400_ref98","doi-asserted-by":"crossref","first-page":"677","DOI":"10.2741\/2711","article-title":"Emergent unsupervised clustering paradigms with potential application to 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Bioinformatics"},{"key":"2021012203303173400_ref108","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1038\/nmeth.1923","article-title":"Fast gapped-read alignment with Bowtie 2","volume":"9","author":"Langmead","year":"2012","journal-title":"Nat Methods"},{"key":"2021012203303173400_ref109","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pcbi.1002195","article-title":"Accelerated profile HMM searches","volume":"7","author":"Eddy","year":"2011","journal-title":"PLoS Comput Biol"},{"key":"2021012203303173400_ref110","doi-asserted-by":"crossref","first-page":"811","DOI":"10.1038\/nmeth.2066","article-title":"Metagenomic microbial community profiling using unique clade-specific marker genes","volume":"9","author":"Segata","year":"2012","journal-title":"Nat Methods"},{"key":"2021012203303173400_ref111","doi-asserted-by":"crossref","first-page":"e243","DOI":"10.7717\/peerj.243","article-title":"PhyloSift: phylogenetic analysis of genomes and metagenomes","volume":"2","author":"Darling","year":"2014","journal-title":"PeerJ"},{"key":"2021012203303173400_ref112","doi-asserted-by":"crossref","first-page":"1014","DOI":"10.1038\/s41467-019-08844-4","article-title":"Microbial abundance, activity and population genomic profiling with mOTUs2","volume":"10","author":"Milanese","year":"2019","journal-title":"Nat Commun"},{"key":"2021012203303173400_ref113","doi-asserted-by":"crossref","first-page":"e69","DOI":"10.1093\/nar\/gkv180","article-title":"Accurate read-based metagenome characterization using a hierarchical suite of unique signatures","volume":"43","author":"Freitas","year":"2015","journal-title":"Nucleic Acids Res"},{"key":"2021012203303173400_ref114","doi-asserted-by":"crossref","first-page":"R46","DOI":"10.1186\/gb-2014-15-3-r46","article-title":"Kraken: ultrafast metagenomic sequence classification using exact alignments","volume":"15","author":"Wood","year":"2014","journal-title":"Genome Biol"},{"key":"2021012203303173400_ref115","doi-asserted-by":"crossref","first-page":"236","DOI":"10.1186\/s12864-015-1419-2","article-title":"CLARK: fast and accurate classification of metagenomic and genomic sequences using discriminative k-mers","volume":"16","author":"Ounit","year":"2015","journal-title":"BMC Genomics"},{"key":"2021012203303173400_ref116","doi-asserted-by":"crossref","first-page":"1721","DOI":"10.1101\/gr.210641.116","article-title":"Centrifuge: rapid and sensitive classification of metagenomic sequences","volume":"26","author":"Kim","year":"2016","journal-title":"Genome Res"},{"key":"2021012203303173400_ref117","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pcbi.1004957","article-title":"MEGAN Community edition - interactive exploration and analysis of large-scale microbiome sequencing data","volume":"12","author":"Huson","year":"2016","journal-title":"PLoS Comput Biol"},{"key":"2021012203303173400_ref118","doi-asserted-by":"crossref","first-page":"2272","DOI":"10.1093\/bioinformatics\/btw150","article-title":"DUDes: a top-down taxonomic profiler for metagenomics","volume":"32","author":"Piro","year":"2016","journal-title":"Bioinformatics"},{"key":"2021012203303173400_ref119","doi-asserted-by":"crossref","first-page":"111","DOI":"10.1186\/s13059-016-0969-1","article-title":"Taxonomer: an interactive metagenomics analysis portal for universal pathogen detection and host mRNA expression profiling","volume":"17","author":"Flygare","year":"2016","journal-title":"Genome Biol"},{"key":"2021012203303173400_ref120","doi-asserted-by":"crossref","first-page":"W29","DOI":"10.1093\/nar\/gkt282","article-title":"BLAST: a more efficient report with usability improvements","volume":"41","author":"Boratyn","year":"2013","journal-title":"Nucleic Acids Res"},{"key":"2021012203303173400_ref121","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1038\/nmeth.3176","article-title":"Fast and sensitive protein alignment using DIAMOND","volume":"12","author":"Buchfink","year":"2015","journal-title":"Nat Methods"},{"key":"2021012203303173400_ref122","doi-asserted-by":"crossref","first-page":"487","DOI":"10.1101\/gr.113985.110","article-title":"Adaptive seeds tame genomic sequence comparison","volume":"21","author":"Kielbasa","year":"2011","journal-title":"Genome Res"},{"key":"2021012203303173400_ref123","doi-asserted-by":"crossref","first-page":"D733","DOI":"10.1093\/nar\/gkv1189","article-title":"Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion and functional annotation","volume":"44","author":"O'Leary","year":"2016","journal-title":"Nucleic Acids Res"},{"key":"2021012203303173400_ref124","first-page":"D190","article-title":"The universal protein resource (UniProt)","volume":"36","author":"UniProt","year":"2008","journal-title":"Nucleic Acids Res"},{"key":"2021012203303173400_ref125","doi-asserted-by":"crossref","first-page":"231","DOI":"10.1093\/nar\/28.1.231","article-title":"SMART: a web-based tool for the study of genetically mobile domains","volume":"28","author":"Schultz","year":"2000","journal-title":"Nucleic Acids Res"},{"key":"2021012203303173400_ref126","doi-asserted-by":"crossref","first-page":"D507","DOI":"10.1093\/nar\/gkw929","article-title":"IMG\/M: integrated genome and metagenome comparative data analysis system","volume":"45","author":"Chen","year":"2017","journal-title":"Nucleic Acids Res"},{"key":"2021012203303173400_ref127","doi-asserted-by":"crossref","first-page":"207","DOI":"10.1007\/978-1-4939-3369-3_13","article-title":"MG-RAST, a Metagenomics Service for Analysis of microbial community structure and function","volume":"1399","author":"Keegan","year":"2016","journal-title":"Methods Mol Biol"},{"key":"2021012203303173400_ref128","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1093\/nar\/28.1.33","article-title":"The COG database: a tool for genome-scale analysis of protein functions and evolution","volume":"28","author":"Tatusov","year":"2000","journal-title":"Nucleic Acids Res"},{"key":"2021012203303173400_ref129","doi-asserted-by":"crossref","first-page":"D222","DOI":"10.1093\/nar\/gkt1223","article-title":"Pfam: the protein families database","volume":"42","author":"Finn","year":"2014","journal-title":"Nucleic Acids Res"},{"key":"2021012203303173400_ref130","doi-asserted-by":"crossref","first-page":"371","DOI":"10.1093\/nar\/gkg128","article-title":"The TIGRFAMs database of protein families","volume":"31","author":"Haft","year":"2003","journal-title":"Nucleic Acids Res"},{"key":"2021012203303173400_ref131","doi-asserted-by":"crossref","first-page":"W362","DOI":"10.1093\/nar\/gkl124","article-title":"ScanProsite: detection of PROSITE signature matches and ProRule-associated functional and structural residues in proteins","volume":"34","author":"de Castro","year":"2006","journal-title":"Nucleic Acids Res"},{"key":"2021012203303173400_ref132","doi-asserted-by":"crossref","first-page":"252","DOI":"10.1093\/bib\/3.3.252","article-title":"The PRINTS database: a resource for identification of protein families","volume":"3","author":"Attwood","year":"2002","journal-title":"Brief Bioinform"},{"key":"2021012203303173400_ref133","doi-asserted-by":"crossref","first-page":"2977","DOI":"10.1093\/bioinformatics\/btq536","article-title":"SmashCommunity: a metagenomic annotation and analysis tool","volume":"26","author":"Arumugam","year":"2010","journal-title":"Bioinformatics"},{"key":"2021012203303173400_ref134","doi-asserted-by":"crossref","first-page":"D490","DOI":"10.1093\/nar\/gkt1178","article-title":"The carbohydrate-active enzymes database (CAZy) in 2013","volume":"42","author":"Lombard","year":"2014","journal-title":"Nucleic Acids Res"},{"key":"2021012203303173400_ref135","doi-asserted-by":"crossref","first-page":"D391","DOI":"10.1093\/nar\/gkl791","article-title":"MvirDB--a microbial database of protein toxins, virulence factors and antibiotic resistance genes for bio-defence applications","volume":"35","author":"Zhou","year":"2007","journal-title":"Nucleic Acids Res"},{"key":"2021012203303173400_ref136","doi-asserted-by":"crossref","first-page":"1107","DOI":"10.1002\/prot.20821","article-title":"Prediction of protein secondary structure content using amino acid composition and evolutionary information","volume":"62","author":"Lee","year":"2006","journal-title":"Proteins"},{"key":"2021012203303173400_ref137","doi-asserted-by":"crossref","first-page":"34","DOI":"10.1016\/S0968-0004(98)01336-X","article-title":"PSORT: a program for detecting sorting signals in proteins and predicting their subcellular localization","volume":"24","author":"Nakai","year":"1999","journal-title":"Trends Biochem Sci"},{"key":"2021012203303173400_ref138","doi-asserted-by":"crossref","first-page":"1177","DOI":"10.1038\/nmeth.2714","article-title":"Assessment of transcript reconstruction methods for RNA-seq","volume":"10","author":"Steijger","year":"2013","journal-title":"Nat Methods"},{"key":"2021012203303173400_ref139","doi-asserted-by":"crossref","first-page":"405","DOI":"10.1186\/gb-2013-14-6-405","article-title":"The advantages of SMRT sequencing","volume":"14","author":"Roberts","year":"2013","journal-title":"Genome Biol"},{"key":"2021012203303173400_ref140","doi-asserted-by":"crossref","first-page":"133","DOI":"10.1126\/science.1162986","article-title":"Real-time DNA sequencing from single polymerase molecules","volume":"323","author":"Eid","year":"2009","journal-title":"Science"},{"key":"2021012203303173400_ref141","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0144305","article-title":"Evaluation and validation of assembling corrected PacBio long reads for microbial genome completion via hybrid approaches","volume":"10","author":"Lin","year":"2015","journal-title":"PLoS One"},{"key":"2021012203303173400_ref142","doi-asserted-by":"crossref","first-page":"563","DOI":"10.1038\/nmeth.2474","article-title":"Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data","volume":"10","author":"Chin","year":"2013","journal-title":"Nat Methods"},{"key":"2021012203303173400_ref143","doi-asserted-by":"crossref","first-page":"435","DOI":"10.1186\/s12859-016-1288-y","article-title":"BIGMAC: breaking inaccurate genomes and merging assembled contigs for long read metagenomic assembly","volume":"17","author":"Lam","year":"2016","journal-title":"BMC Bioinformatics"},{"key":"2021012203303173400_ref144","doi-asserted-by":"crossref","first-page":"820","DOI":"10.1080\/15476286.2016.1197481","article-title":"PacBio full-length transcriptome profiling of insect mitochondrial gene expression","volume":"13","author":"Gao","year":"2016","journal-title":"RNA Biol"},{"key":"2021012203303173400_ref145","doi-asserted-by":"crossref","first-page":"190","DOI":"10.1186\/s40168-018-0569-2","article-title":"Species-level bacterial community profiling of the healthy sinonasal microbiome using Pacific biosciences sequencing of full-length 16S rRNA genes","volume":"6","author":"Earl","year":"2018","journal-title":"Microbiome"},{"key":"2021012203303173400_ref146","doi-asserted-by":"crossref","first-page":"2465","DOI":"10.1038\/ismej.2017.101","article-title":"Metagenomic binning of a marine sponge microbiome reveals unity in defense but metabolic specialization","volume":"11","author":"Slaby","year":"2017","journal-title":"ISME J"},{"key":"2021012203303173400_ref147","doi-asserted-by":"crossref","first-page":"e01948","DOI":"10.1128\/mBio.01948-15","article-title":"Resolving the complexity of human skin metagenomes using single-molecule sequencing","volume":"7","author":"Tsai","year":"2016","journal-title":"MBio"},{"key":"2021012203303173400_ref148","doi-asserted-by":"crossref","first-page":"40","DOI":"10.1186\/s40793-017-0255-1","article-title":"Insights into Cedecea neteri strain M006 through complete genome sequence, a rare bacterium from aquatic environment","volume":"12","author":"Chan","year":"2017","journal-title":"Stand Genomic Sci"},{"key":"2021012203303173400_ref149","doi-asserted-by":"crossref","first-page":"9","DOI":"10.1186\/s40793-017-0224-8","article-title":"Towards long-read metagenomics: complete assembly of three novel genomes from bacteria dependent on a diazotrophic cyanobacterium in a freshwater lake co-culture","volume":"12","author":"Driscoll","year":"2017","journal-title":"Stand Genomic Sci"},{"key":"2021012203303173400_ref150","doi-asserted-by":"crossref","first-page":"338","DOI":"10.1038\/nbt.4060","article-title":"Nanopore sequencing and assembly of a human genome with ultra-long reads","volume":"36","author":"Jain","year":"2018","journal-title":"Nat Biotechnol"},{"key":"2021012203303173400_ref151","doi-asserted-by":"crossref","first-page":"296","DOI":"10.1016\/j.jhin.2017.02.020","article-title":"Use of the Oxford Nanopore MinION sequencer for MLST genotyping of vancomycin-resistant enterococci","volume":"96","author":"Tarumoto","year":"2017","journal-title":"J Hosp Infect"},{"key":"2021012203303173400_ref152","doi-asserted-by":"crossref","first-page":"733","DOI":"10.1038\/nmeth.3444","article-title":"A complete bacterial genome assembled de novo using only nanopore sequencing data","volume":"12","author":"Loman","year":"2015","journal-title":"Nat Methods"},{"key":"2021012203303173400_ref153","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1093\/gigascience\/gix137","article-title":"Finding Nemo: hybrid assembly with Oxford Nanopore and Illumina reads greatly improves the clownfish (Amphiprion ocellaris) genome assembly","volume":"7","author":"Tan","year":"2018","journal-title":"Gigascience"},{"key":"2021012203303173400_ref154","doi-asserted-by":"crossref","first-page":"e38","DOI":"10.1093\/nar\/gky014","article-title":"Complete genomic and transcriptional landscape analysis using third-generation sequencing: a case study of Saccharomyces cerevisiae CEN.PK113-7D","volume":"46","author":"Jenjaroenpun","year":"2018","journal-title":"Nucleic Acids Res"},{"key":"2021012203303173400_ref155","doi-asserted-by":"crossref","first-page":"260","DOI":"10.3389\/fmicb.2019.00260","article-title":"Rapid sequencing of multiple RNA viruses in their native form","volume":"10","author":"Wongsurawat","year":"2019","journal-title":"Front Microbiol"},{"key":"2021012203303173400_ref156","doi-asserted-by":"crossref","first-page":"548","DOI":"10.1002\/2211-5463.12590","article-title":"Rapid bacterial identification by direct PCR amplification of 16S rRNA genes using the MinION nanopore sequencer","volume":"9","author":"Kai","year":"2019","journal-title":"FEBS Open Bio"},{"key":"2021012203303173400_ref157","doi-asserted-by":"crossref","first-page":"W171","DOI":"10.1093\/nar\/gkx348","article-title":"BusyBee Web: metagenomic data analysis by bootstrapped supervised binning and annotation","volume":"45","author":"Laczny","year":"2017","journal-title":"Nucleic Acids Res"},{"key":"2021012203303173400_ref158","doi-asserted-by":"crossref","first-page":"581","DOI":"10.1038\/nmeth.3869","article-title":"DADA2: high-resolution sample inference from Illumina amplicon data","volume":"13","author":"Callahan","year":"2016","journal-title":"Nat Methods"},{"key":"2021012203303173400_ref159","doi-asserted-by":"crossref","first-page":"7537","DOI":"10.1128\/AEM.01541-09","article-title":"Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities","volume":"75","author":"Schloss","year":"2009","journal-title":"Appl Environ Microbiol"},{"key":"2021012203303173400_ref160","first-page":"37","article-title":"Author correction: reproducible, interactive, scalable and extensible microbiome data science using QIIME 2","volume":"2019","author":"Bolyen","year":"1091","journal-title":"Nat Biotechnol"},{"key":"2021012203303173400_ref161","doi-asserted-by":"crossref","first-page":"169","DOI":"10.1007\/978-1-4939-8728-3_11","article-title":"Predicting the functional potential of the microbiome from marker genes using PICRUSt","volume":"1849","author":"Douglas","year":"2018","journal-title":"Methods Mol Biol"},{"key":"2021012203303173400_ref162","doi-asserted-by":"crossref","first-page":"2882","DOI":"10.1093\/bioinformatics\/btv287","article-title":"Tax4Fun: predicting functional profiles from metagenomic 16S rRNA 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