A clinician's guide to microbiome analysis

Basic local alignment search tool

Altschul, S. F., Gish, W., Miller, W., Myers, E. W., & Lipman, D. J. (1990) · Journal of Molecular Biology · doi:10.1006/jmbi.1990.9999 · Cited by 98,669 · see citing works

Trimmomatic: a flexible trimmer for Illumina sequence data

Bolger, A. M., Lohse, M., & Usadel, B. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu170 · Cited by 65,548 · see citing works

KEGG: Kyoto Encyclopedia of Genes and Genomes

Kanehisa, M. (2000) · Nucleic Acids Research · doi:10.1093/nar/28.1.27 · Cited by 37,077 · see citing works

DADA2: High–resolution sample inference from Illumina amplicon data

Callahan, B. J., McMurdie, P. J., Rosen, M. J., Han, A. W., Johnson, A. J. A., & Holmes, S. P. (2016) · Nature Methods · doi:10.1038/nmeth.3869 · Cited by 35,698 · see citing works

QIIME allows analysis of high-throughput community sequencing data

Caporaso, J. G., Kuczynski, J., Stombaugh, J., Bittinger, K., Bushman, F. D., Costello, E. K., Fierer, N., Peña, A. G., Goodrich, J. K., Gordon, J. I., et al. (2010) · Nature Methods · doi:10.1038/nmeth.f.303 · Cited by 34,887 · see citing works

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

Quast, C., Pruesse, E., Yilmaz, P., Gerken, J., Schweer, T., Yarza, P., Peplies, J., & Glöckner, F. O. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks1219 · Cited by 33,055 · see citing works

KEGG: Kyoto Encyclopedia of Genes and Genomes

Ogata, H., Goto, S., Sato, K., Fujibuchi, W., Bono, H., & Kanehisa, M. (1999) · Nucleic Acids Research · doi:10.1093/nar/27.1.29 · Cited by 31,232 · see citing works

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

McMurdie, P. J., & Holmes, S. (2013) · PLoS ONE · doi:10.1371/journal.pone.0061217 · Cited by 21,013 · see citing works

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

Schloss, P. D., Westcott, S. L., Ryabin, T., Hall, J. R., Hartmann, M., Hollister, E. B., Lesniewski, R. A., Oakley, B. B., Parks, D. H., Robinson, C. J., et al. (2009) · Applied and Environmental Microbiology · doi:10.1128/aem.01541-09 · Cited by 20,966 · see citing works

Search and clustering orders of magnitude faster than BLAST

Edgar, R. C. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq461 · Cited by 20,617 · see citing works

Naive Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy

Wang, Q., Garrity, G. M., Tiedje, J. M., & Cole, J. R. (2007) · Applied and Environmental Microbiology · doi:10.1128/aem.00062-07 · Cited by 19,770 · see citing works

UPARSE: highly accurate OTU sequences from microbial amplicon reads

Edgar, R. C. (2013) · Nature Methods · doi:10.1038/nmeth.2604 · Cited by 16,587 · see citing works

Metagenomic biomarker discovery and explanation

Segata, N., Izard, J., Waldron, L., Gevers, D., Miropolsky, L., Garrett, W. S., & Huttenhower, C. (2011) · Genome Biology · doi:10.1186/gb-2011-12-6-r60 · Cited by 16,192 · see citing works

UCHIME improves sensitivity and speed of chimera detection

Edgar, R. C., Haas, B. J., Clemente, J. C., Quince, C., & Knight, R. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr381 · Cited by 15,114 · see citing works

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

Li, W.-Z., & Godzik, A. (2006) · Bioinform. · doi:10.1093/bioinformatics/btl158 · Cited by 10,994 · see citing works

Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB

DeSantis, T. Z., Hugenholtz, P., Larsen, N., Rojas, M., Brodie, E. L., Keller, K., Huber, T., Dalevi, D., Hu, P., & Andersen, G. L. (2006) · Applied and Environmental Microbiology · doi:10.1128/aem.03006-05 · Cited by 10,891 · see citing works

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

Li, D., Liu, C.-M., Luo, R., Sadakane, K., & Lam, T. (2015) · Bioinformatics · doi:10.1093/bioinformatics/btv033 · Cited by 9,781 · see citing works

Velvet: Algorithms for de novo short read assembly using de Bruijn graphsPreprint

Zerbino, D. R., & Birney, E. (2008) · Genome Research · doi:10.1101/gr.074492.107 · Cited by 9,387 · see citing works

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

Langille, M. G. I., Zaneveld, J., Caporaso, J. G., McDonald, D., Knights, D., Reyes, J. A., Clemente, J. C., Burkepile, D. E., Vega Thurber, R. L., Knight, R., et al. (2013) · Nature Biotechnology · doi:10.1038/nbt.2676 · Cited by 9,116 · see citing works

Pfam: the protein families database

Finn, R. D., Bateman, A., Clements, J., Coggill, P., Eberhardt, R. Y., Eddy, S. R., Heger, A., Hetherington, K., Holm, L., Mistry, J., et al. (2014) · Nucleic Acids Research · doi:10.1093/nar/gkt1223 · Cited by 6,148 · see citing works

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

Luo, R., Liu, B., Xie, Y., Li, Z., Huang, W., Yuan, J., He, G., Chen, Y., Pan, Q., Liu, Y., et al. (2012) · GigaScience · doi:10.1186/2047-217x-1-18 · Cited by 5,270 · see citing works

Quality control and preprocessing of metagenomic datasets

Schmieder, R., & Edwards, R. A. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr026 · Cited by 4,989 · see citing works

Richness of human gut microbiome correlates with metabolic markers

Le Chatelier, E., Nielsen, T., Qin, J., Prifti, E., Hildebrand, F., Falony, G., Almeida, M., Arumugam, M., Batto, J.-M., Kennedy, S., et al. (2013) · Nature · doi:10.1038/nature12506 · Cited by 4,662 · see citing works

Kraken: ultrafast metagenomic sequence classification using exact alignments

Wood, D. E., & Salzberg, S. L. (2014) · Genome Biology · doi:10.1186/gb-2014-15-3-r46 · Cited by 4,521 · see citing works

The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST)

Overbeek, R., Olson, R., Pusch, G. D., Olsen, G. J., Davis, J. J., Disz, T. L., Edwards, R. A., Gerdes, S., Parrello, B., Shukla, M. P., et al. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt1226 · Cited by 4,509 · see citing works

The COG database: an updated version includes eukaryotes

Tatusov, R. L., Fedorova, N. D., Jackson, J. D., Jacobs, A. R., Kiryutin, B., Koonin, E. V., Krylov, D. M., Mazumder, R., Mekhedov, S., Nikolskaya, A. N., et al. (2003) · BMC Bioinformatics · doi:10.1186/1471-2105-4-41 · Cited by 4,410 · see citing works

Coming of age: ten years of next-generation sequencing technologies

Goodwin, S., McPherson, J. D., & McCombie, W. R. (2016) · Nature Reviews Genetics · doi:10.1038/nrg.2016.49 · Cited by 4,352 · see citing works

Duodenal Infusion of Donor Feces for Recurrent <i>Clostridium difficile</i>

van Nood, E., Vrieze, A., Nieuwdorp, M., Fuentes, S., Zoetendal, E. G., de Vos, W. M., Visser, C. E., Kuijper, E. J., Bartelsman, J. F. W. M., Tijssen, J. G. P., et al. (2013) · New England Journal of Medicine · doi:10.1056/nejmoa1205037 · Cited by 3,708 · see citing works

ABySS: A parallel assembler for short read sequence dataPreprint

Simpson, J. T., Wong, K., Jackman, S. D., Schein, J. E., Jones, S. J. M., & Birol, İ. (2009) · Genome Research · doi:10.1101/gr.089532.108 · Cited by 3,583 · see citing works

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

Meyer, F., Paarmann, D., D'Souza, M., Olson, R., Glass, E., Kubal, M., Paczian, T., Rodriguez, A., Stevens, R. L., Wilke, A., et al. (2008) · BMC Bioinformatics · doi:10.1186/1471-2105-9-386 · Cited by 3,565 · see citing works

Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR ampliconsPreprint

Haas, B. J., Gevers, D., Earl, A. M., Feldgarden, M., Ward, D. V., Giannoukos, G., Ciulla, D., Tabbaa, D., Highlander, S. K., Sodergren, E. J., et al. (2011) · Genome Research · doi:10.1101/gr.112730.110 · Cited by 3,480 · see citing works

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

Salter, S. J., Cox, M. J., Turek, E. M., Calus, S. T., Cookson, W. O., Moffatt, M. F., Turner, P., Parkhill, J., Loman, N. J., & Walker, A. W. (2014) · BMC Biology · doi:10.1186/s12915-014-0087-z · Cited by 3,463 · see citing works

Intestinal microbial metabolism of phosphatidylcholine and cardiovascular risk

Tang, W. H. W., Wang, Z., Levison, B. S., Koeth, R. A., Britt, E. B., Fu, X., Wu, Y., & Hazen, S. L. (2013) · New England Journal of Medicine · doi:10.1056/nejmoa1109400 · Cited by 3,402 · see citing works

Gut microbiota composition correlates with diet and health in the elderly

Claesson, M. J., Jeffery, I. B., Conde, S., Power, S. E., O’Connor, E. M., Cusack, S., Harris, H. M. B., Coakley, M., Lakshminarayanan, B., O’Sullivan, O., et al. (2012) · Nature · doi:10.1038/nature11319 · Cited by 3,314 · see citing works

The Treatment-Naive Microbiome in New-Onset Crohn’s Disease

Gevers, D., Kugathasan, S., Denson, L. A., Vázquez-Baeza, Y., Van Treuren, W., Ren, B., Schwager, E., Knights, D., Song, S. J., Yassour, M., et al. (2014) · Cell Host &amp; Microbe · doi:10.1016/j.chom.2014.02.005 · Cited by 3,220 · see citing works

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

Peng, Y., Leung, H. C. M., Yiu, S., & Chin, F. Y. L. (2012) · Bioinformatics · doi:10.1093/bioinformatics/bts174 · Cited by 2,997 · see citing works

Personalized nutrition by prediction of glycemic responses

Zeevi, D., Korem, T., Zmora, N., Israeli, D., Rothschild, D., Weinberger, A., Ben-Yacov, O., Lador, D., Avnit-Sagi, T., Lotan-Pompan, M., et al. (2015) · Cell · doi:10.1016/j.cell.2015.11.001 · Cited by 2,929 · see citing works

NGS QC Toolkit: A Toolkit for Quality Control of Next Generation Sequencing Data

Patel, R. K., & Jain, M. (2012) · PLoS ONE · doi:10.1371/journal.pone.0030619 · Cited by 2,921 · see citing works

Introducing DOTUR, a Computer Program for Defining Operational Taxonomic Units and Estimating Species Richness

Schloss, P. D., & Handelsman, J. (2005) · Applied and Environmental Microbiology · doi:10.1128/aem.71.3.1501-1506.2005 · Cited by 2,503 · see citing works

Differential abundance analysis for microbial marker-gene surveys

Paulson, J. N., Stine, O. C., Bravo, H. C., & Pop, M. (2013) · Nature Methods · doi:10.1038/nmeth.2658 · Cited by 2,437 · see citing works

The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S rRNA sequencing

Dethlefsen, L., Huse, S., Sogin, M. L., & Relman, D. A. (2008) · PLoS Biology · doi:10.1371/journal.pbio.0060280 · Cited by 2,361 · see citing works

MetaPhlAn2 for enhanced metagenomic taxonomic profiling

Truong, D. T., Franzosa, E. A., Tickle, T. L., Scholz, M., Weingart, G., Pasolli, E., Tett, A., Huttenhower, C., & Segata, N. (2015) · Nature Methods · doi:10.1038/nmeth.3589 · Cited by 2,185 · see citing works

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update

Afgan, E., Baker, D., van den Beek, M., Blankenberg, D. J., Bouvier, D., Čech, M., Chilton, J. M., Clements, D., Coraor, N., Eberhard, C., et al. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw343 · Cited by 2,150 · see citing works

Human gut microbes impact host serum metabolome and insulin sensitivity

Pedersen, H. K., Gudmundsdottir, V., Nielsen, H. B., Hyotylainen, T., Nielsen, T., Jensen, B. A. H., Forslund, K., Hildebrand, F., Prifti, E., Falony, G., et al. (2016) · Nature · doi:10.1038/nature18646 · Cited by 2,116 · see citing works

InterPro: the integrative protein signature database

Hunter, S., Apweiler, R., Attwood, T. K., Bairoch, A., Bateman, A., Binns, D., Bork, P., Das, U., Daugherty, L., Duquenne, L., et al. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkn785 · Cited by 2,107 · see citing works

Fast and sensitive taxonomic classification for metagenomics with Kaiju

Menzel, P., Ng, K. L., & Krogh, A. (2016) · Nature Communications · doi:10.1038/ncomms11257 · Cited by 2,101 · see citing works

eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences

Huerta‐Cepas, J., Szklarczyk, D., Forslund, S. K., Cook, H., Heller, D., Walter, M. C., Rattei, T., Mende, D. R., Sunagawa, S., Kuhn, M., et al. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv1248 · Cited by 2,062 · see citing works

The RDP (Ribosomal Database Project)

Maidak, B. L., Olsen, G. J., Larsen, N. E., Overbeek, R., McCaughey, M. J., & Woese, C. R. (1997) · Nucleic Acids Research · doi:10.1093/nar/25.1.109 · Cited by 2,018 · see citing works

Variations in the Prevalence of Obesity Among European Countries, and a Consideration of Possible Causes

Blundell, J. E., Baker, J. L., Boyland, E. J., Blaak, E. E., Charzewska, J., Henauw, S. D., Frühbeck, G., González‐Gross, M., Hebebrand, J., Holm, L., et al. (2017) · Obesity Facts · doi:10.1159/000455952 · Cited by 1,980 · see citing works

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

(2015) · doi:10.7717/peerj.1165 · Cited by 1,960 · see citing works

Ab initio gene identification in metagenomic sequences

Zhu, W., Lomsadze, A., & Borodovsky, M. Y. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq275 · Cited by 1,793 · see citing works

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

Huson, D. H., Beier, S., Flade, I., Górska, A., El-Hadidi, M., Mitra, S., Ruscheweyh, H.-J., & Tappu, R. (2016) · PLOS Computational Biology · doi:10.1371/journal.pcbi.1004957 · Cited by 1,761 · see citing works

Antibiotics in early life alter the murine colonic microbiome and adiposity

Cho, I., Yamanishi, S., Cox, L., Methé, B. A., Zavadil, J., Li, K., Gao, Z., Mahana, D., Raju, K., Teitler, I., et al. (2012) · Nature · doi:10.1038/nature11400 · Cited by 1,613 · see citing works

Tax4Fun: predicting functional profiles from metagenomic 16S rRNA data

Aßhauer, K. P., Wemheuer, B., Daniel, R., & Meinicke, P. (2015) · Bioinformatics · doi:10.1093/bioinformatics/btv287 · Cited by 1,583 · see citing works

UniFrac – An online tool for comparing microbial community diversity in a phylogenetic context

Lozupone, C., Hamady, M., & Knight, R. D. (2006) · BMC Bioinformatics · doi:10.1186/1471-2105-7-371 · Cited by 1,454 · see citing works

The Application of Ecological Theory Toward an Understanding of the Human Microbiome

Costello, E. K., Stagaman, K., Dethlefsen, L., Bohannan, B. J. M., & Relman, D. A. (2012) · Science · doi:10.1126/science.1224203 · Cited by 1,437 · see citing works

Topographic diversity of fungal and bacterial communities in human skin

NIH Intramural Sequencing Center Comparative Sequencing Program, Findley, K., Oh, J., Yang, J., Conlan, S., Deming, C., Meyer, J. A., Schoenfeld, D., Nomicos, E., Park, M., et al. (2013) · Nature · doi:10.1038/nature12171 · Cited by 1,206 · see citing works

The RDP-II (Ribosomal Database Project)

Maidak, B. L. (2001) · Nucleic Acids Research · doi:10.1093/nar/29.1.173 · Cited by 1,182 · see citing works

UNITE: a database providing web‐based methods for the molecular identification of ectomycorrhizal fungi

Kõljalg, U., Larsson, K., Abarenkov, K., Nilsson, R. H., Alexander, I. J., Eberhardt, U., Erland, S., Høiland, K., Kjøller, R., Larsson, E., et al. (2005) · New Phytologist · doi:10.1111/j.1469-8137.2005.01376.x · Cited by 1,162 · see citing works

The gut microbiota in IBD

Manichanh, C., Borruel, N., Casellas, F., & Guarner, F. (2012) · Nature Reviews Gastroenterology &amp; Hepatology · doi:10.1038/nrgastro.2012.152 · Cited by 1,160 · see citing works

rrnDB: improved tools for interpreting rRNA gene abundance in bacteria and archaea and a new foundation for future development

Stoddard, S. F., Smith, B. J., Hein, R., Roller, B. R. K., & Schmidt, T. M. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku1201 · Cited by 1,096 · see citing works

A critical assessment of the “sterile womb” and “in utero colonization” hypotheses: implications for research on the pioneer infant microbiome

Perez-Muñoz, M. E., Arrieta, M.-C., Ramer-Tait, A. E., & Walter, J. (2017) · Microbiome · doi:10.1186/s40168-017-0268-4 · Cited by 1,096 · see citing works

Metabolic Reconstruction for Metagenomic Data and Its Application to the Human Microbiome

Abubucker, S., Segata, N., Goll, J. B., Schubert, A. M., Izard, J., Cantarel, B. L., Rodriguez-Mueller, B., Zucker, J., Thiagarajan, M., Henrissat, B., et al. (2012) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1002358 · Cited by 1,050 · see citing works

The vocabulary of microbiome research: a proposal

Marchesi, J., & Ravel, J. (2015) · Microbiome · doi:10.1186/s40168-015-0094-5 · Cited by 1,016 · see citing works

The TIGRFAMs database of protein families

Haft, D. H. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkg128 · Cited by 984 · see citing works

Comparison of two next-generation sequencing technologies for resolving highly complex microbiota composition using tandem variable 16S rRNA gene regions

Claesson, M. J., Wang, Q., O’Sullivan, Ó., Greene-Diniz, R., Cole, J. R., Ross, R. P., & O’Toole, P. W. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq873 · Cited by 981 · see citing works

FragGeneScan: predicting genes in short and error-prone reads

Rho, M., Tang, H., & Ye, Y. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq747 · Cited by 838 · see citing works

Microbes, Microbiota, and Colon Cancer

Sears, C. L., & Garrett, W. S. (2014) · Cell Host & Microbe · doi:10.1016/j.chom.2014.02.007 · Cited by 820 · see citing works

Tumour-associated and non-tumour-associated microbiota in colorectal cancer

Flemer, B., Lynch, D. B., Brown, J. M. R., Jeffery, I. B., Ryan, F. J., Claesson, M. J., O'Riordain, M., Shanahan, F., & O'Toole, P. W. (2017) · Gut · doi:10.1136/gutjnl-2015-309595 · Cited by 804 · see citing works

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

Wu, Y., Tang, Y.-H., Tringe, S. G., Simmons, B. A., & Singer, S. W. (2014) · Microbiome · doi:10.1186/2049-2618-2-26 · Cited by 708 · see citing works

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

Namiki, T., Hachiya, T., Tanaka, H. L., & Sakakibara, Y. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks678 · Cited by 677 · see citing works

How to apply de Bruijn graphs to genome assembly

Compeau, P. E. C., Pevzner, P. A., & Tesler, G. (2011) · Nature Biotechnology · doi:10.1038/nbt.2023 · Cited by 673 · see citing works

Gene and translation initiation site prediction in metagenomic sequences

Hyatt, D., LoCascio, P. F., Hauser, L., & Uberbacher, E. C. (2012) · Bioinformatics · doi:10.1093/bioinformatics/bts429 · Cited by 655 · see citing works

eggNOG v4.0: nested orthology inference across 3686 organisms

Powell, S., Forslund, K., Szklarczyk, D., Trachana, K., Roth, A., Huerta-Cepas, J., Gabaldón, T., Rattei, T., Creevey, C., Kuhn, M., et al. (2014) · Nucleic Acids Research · doi:10.1093/nar/gkt1253 · Cited by 652 · see citing works

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

Ounit, R., Wanamaker, S. I., Close, T. J., & Lonardi, S. (2015) · BMC Genomics · doi:10.1186/s12864-015-1419-2 · Cited by 624 · see citing works

WebMGA: a customizable web server for fast metagenomic sequence analysis

Wu, S., Zhu, Z., Fu, L., Niu, B., & Li, W. (2011) · BMC Genomics · doi:10.1186/1471-2164-12-444 · Cited by 612 · see citing works

Divergence and Redundancy of 16S rRNA Sequences in Genomes with Multiple rrn Operons

Acinas, S. G., Marcelino, L. A., Klepac‐Ceraj, V., & Polz, M. F. (2004) · Journal of Bacteriology · doi:10.1128/jb.186.9.2629-2635.2004 · Cited by 604 · see citing works

Ray Meta: scalable de novo metagenome assembly and profiling

Boisvert, S., Raymond, F., Godzaridis, É., Laviolette, F., & Corbeil, J. (2012) · Genome biology · doi:10.1186/gb-2012-13-12-r122 · Cited by 593 · see citing works

MyTaxa: an advanced taxonomic classifier for genomic and metagenomic sequences

Luo, C., Rodriguez‐R, L. M., & Konstantinidis, K. T. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku169 · Cited by 574 · see citing works

Swarm v2: highly-scalable and high-resolution amplicon clustering

Mahé, F., Rognes, T., Quince, C., de Vargas, C., & Dunthorn, M. (2015) · PeerJ · doi:10.7717/peerj.1420 · Cited by 572 · see citing works

Comparison of placenta samples with contamination controls does not provide evidence for a distinct placenta microbiota

Lauder, A. P., Roche, A. M., Sherrill-Mix, S., Bailey, A., Laughlin, A. L., Bittinger, K., Leite, R., Elovitz, M. A., Parry, S., & Bushman, F. D. (2016) · Microbiome · doi:10.1186/s40168-016-0172-3 · Cited by 539 · see citing works

Metagenomic Pyrosequencing and Microbial Identification

Petrosino, J. F., Highlander, S. K., Luna, R. A., Gibbs, R. A., & Versalovic, J. A. (2009) · Clinical Chemistry · doi:10.1373/clinchem.2008.107565 · Cited by 536 · see citing works

Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov models

Brady, A., & Salzberg, S. L. (2009) · Nature Methods · doi:10.1038/nmeth.1358 · Cited by 526 · see citing works

Metagenomic species profiling using universal phylogenetic marker genes

Sunagawa, S., Mende, D. R., Zeller, G., Izquierdo-Carrasco, F., Berger, S. A., Kultima, J. R., Coelho, L. P., Arumugam, M., Tap, J., Nielsen, H. B., et al. (2013) · Nature Methods · doi:10.1038/nmeth.2693 · Cited by 517 · see citing works

Evaluation of Methods for the Extraction and Purification of DNA from the Human Microbiome

Yuan, S., Cohen, D. B., Ravel, J., Abdo, Z., & Forney, L. J. (2012) · PLoS ONE · doi:10.1371/journal.pone.0033865 · Cited by 511 · see citing works

Sample storage conditions significantly influence faecal microbiome profiles

Choo, J. M., Leong, L. E. X., & Rogers, G. B. (2015) · Scientific Reports · doi:10.1038/srep16350 · Cited by 506 · see citing works

Compilation of small ribosomal subunit RNA structures

Neefs, J., de Peer, Y. V., Rijk, P. D., Chapelle, S., & Wächter, R. D. (1993) · Nucleic Acids Research · doi:10.1093/nar/21.13.3025 · Cited by 478 · see citing works

Phylogenomic analysis of bacterial and archaeal sequences with AMPHORA2

Wu, M., & Scott, A. J. (2012) · Bioinformatics · doi:10.1093/bioinformatics/bts079 · Cited by 453 · see citing works

TETRA: a web-service and a stand-alone program for the analysis and comparison of tetranucleotide usage patterns in DNA sequences

Teeling, H., Waldmann, J., Lombardot, T., Bauer, M., & Glöckner, F. (2004) · BMC Bioinformatics · doi:10.1186/1471-2105-5-163 · Cited by 405 · see citing works

CAMERA: A Community Resource for Metagenomics

Seshadri, R., Kravitz, S. A., Smarr, L. L., Gilna, P., & Frazier, M. E. (2007) · PLoS Biology · doi:10.1371/journal.pbio.0050075 · Cited by 394 · see citing works

Selection of primers for optimal taxonomic classification of environmental 16S rRNA gene sequences

Soergel, D. A. W., Dey, N., Knight, R. D., & Brenner, S. E. (2012) · The ISME Journal · doi:10.1038/ismej.2011.208 · Cited by 376 · see citing works

Making the Leap from Research Laboratory to Clinic: Challenges and Opportunities for Next-Generation Sequencing in Infectious Disease Diagnostics

Goldberg, B., Sichtig, H., Geyer, C., Ledeboer, N., & Weinstock, G. M. (2015) · mBio · doi:10.1128/mbio.01888-15 · Cited by 360 · see citing works

Meta-IDBA: a de Novo assembler for metagenomic data

Peng, Y., Leung, H. C. M., Yiu, S., & Chin, F. Y. L. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr216 · Cited by 326 · see citing works

An evaluation of the accuracy and speed of metagenome analysis tools

Lindgreen, S., Adair, K. L., & Gardner, P. P. (2016) · Scientific Reports · doi:10.1038/srep19233 · Cited by 324 · see citing works

The Impact of Different DNA Extraction Kits and Laboratories upon the Assessment of Human Gut Microbiota Composition by 16S rRNA Gene Sequencing

Kennedy, N. A., Walker, A. W., Berry, S. H., Duncan, S. H., Farquarson, F. M., Louis, P., Thomson, J., surname):, O. M. N. N. W. T. M. A. L. (. B., Satsangi, J. J., Flint, H. J., et al. (2014) · PLoS ONE · doi:10.1371/journal.pone.0088982 · Cited by 311 · see citing works

Methods for Improving Human Gut Microbiome Data by Reducing Variability through Sample Processing and Storage of Stool

Gorzelak, M. A., Gill, S. K., Tasnim, N., Zahra, A.-V., Jay, M., & Gibson, D. L. (2015) · PLoS ONE · doi:10.1371/journal.pone.0134802 · Cited by 307 · see citing works

De novo clustering methods outperform reference-based methods for assigning 16S rRNA gene sequences to operational taxonomic units

Westcott, S. L., & Schloss, P. D. (2015) · PeerJ · doi:10.7717/peerj.1487 · Cited by 296 · see citing works

CopyRighter: a rapid tool for improving the accuracy of microbial community profiles through lineage-specific gene copy number correction

Angly, F. E., Dennis, P. G., Skarshewski, A., Vanwonterghem, I., Hugenholtz, P., & Tyson, G. W. (2014) · Microbiome · doi:10.1186/2049-2618-2-11 · Cited by 293 · see citing works

Choice of bacterial DNA extraction method from fecal material influences community structure as evaluated by metagenomic analysis

Wesolowska-Andersen, A., Bahl, M. I., Carvalho, V., Kristiansen, K., Sicheritz-Pontén, T., Gupta, R., & Licht, T. R. (2014) · Microbiome · doi:10.1186/2049-2618-2-19 · Cited by 277 · see citing works

Storage conditions of intestinal microbiota matter in metagenomic analysis

Cardona, S. T., Eck, A., Cassellas, M., Gallart, M., Alastrue, C., Dore, J. M., Azpiroz, F., Roca, J., Guarner, F., & Manichanh, C. (2012) · BMC Microbiology · doi:10.1186/1471-2180-12-158 · Cited by 275 · see citing works

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

Lin, H.-H., & Liao, Y.-C. (2016) · Scientific Reports · doi:10.1038/srep24175 · Cited by 274 · see citing works

Comparing Apples and Oranges?: Next Generation Sequencing and Its Impact on Microbiome Analysis

Clooney, A. G., Fouhy, F., Sleator, R. D., O’ Driscoll, A., Stanton, C., Cotter, P. D., & Claesson, M. J. (2016) · PLOS ONE · doi:10.1371/journal.pone.0148028 · Cited by 270 · see citing works

IMG/M 4 version of the integrated metagenome comparative analysis system

Markowitz, V. M., Chen, I.-M. A., Chu, K., Szeto, E., Palaniappan, K., Pillay, M., Ratner, A., Huang, J., Pagani, I., Tringe, S. G., et al. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt919 · Cited by 264 · see citing works

Gastrointestinal microbiota in irritable bowel syndrome: present state and perspectives

Salonen, A., de Vos, W. M., & Palva, A. (2010) · Microbiology · doi:10.1099/mic.0.043257-0 · Cited by 264 · see citing works

Clustering 16S rRNA for OTU prediction: a method of unsupervised Bayesian clustering

Hao, X., Jiang, R., & Chen, T. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btq725 · Cited by 264 · see citing works

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

Albanese, D., Fontana, P., Filippo, C. D., Cavalieri, D., & Donati, C. (2015) · Scientific Reports · doi:10.1038/srep09743 · Cited by 264 · see citing works

Spatial variation of the colonic microbiota in patients with ulcerative colitis and control volunteers

Lavelle, A., Lennon, G., O'Sullivan, Ó., Docherty, N., Balfe, Á., Maguire, A., Mulcahy, H., Doherty, G., O'Donoghue, D., Hyland, J., et al. (2015) · Gut · doi:10.1136/gutjnl-2014-307873 · Cited by 259 · see citing works

Freezing fecal samples prior to DNA extraction affects the Firmicutes to Bacteroidetes ratio determined by downstream quantitative PCR analysis

Bahl, M. I., Bergström, A., & Licht, T. R. (2012) · FEMS Microbiology Letters · doi:10.1111/j.1574-6968.2012.02523.x · Cited by 245 · see citing works

NBC: the Naïve Bayes Classification tool webserver for taxonomic classification of metagenomic reads

ROSEN, G. L., Reichenberger, E. R., & Rosenfeld, A. M. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq619 · Cited by 225 · see citing works

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

Treangen, T. J., Koren, S., Sommer, D. D., Liu, B., Astrovskaya, I., Ondov, B., Darling, A. E., Phillippy, A. M., & Pop, M. (2013) · Genome biology · doi:10.1186/gb-2013-14-1-r2 · Cited by 225 · see citing works

DNACLUST: accurate and efficient clustering of phylogenetic marker genes

Ghodsi, M., Liu, B., & Pop, M. (2011) · BMC Bioinformatics · doi:10.1186/1471-2105-12-271 · Cited by 208 · see citing works

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

Diaz, N. N., Krause, L., Goesmann, A., Niehaus, K., & Nattkemper, T. (2009) · BMC Bioinformatics · doi:10.1186/1471-2105-10-56 · Cited by 207 · see citing works

A Comparison of Methods for Clustering 16S rRNA Sequences into OTUs

Chen, W., Zhang, H., Cheng, Y., Zhang, S., & Zhao, H. (2013) · PLoS ONE · doi:10.1371/journal.pone.0070837 · Cited by 207 · see citing works

Open-Source Sequence Clustering Methods Improve the State Of the Art

Kopylova, E., Navas-Molina, J. A., Mercier, C., Xu, Z. Z., Mahé, F., He, Y., Zhou, H.-W., Rognes, T., Caporaso, J. G., & Knight, R. D. (2016) · mSystems · doi:10.1128/msystems.00003-15 · Cited by 205 · see citing works

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

Kelley, D. R., Liu, B., Delcher, A. L., Pop, M., & Salzberg, S. L. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkr1067 · Cited by 204 · see citing works

Accurate and fast estimation of taxonomic profiles from metagenomic shotgun sequences

Liu, B., Gibbons, T., Ghodsi, M., Treangen, T. J., & Pop, M. (2011) · BMC Genomics · doi:10.1186/1471-2164-12-s2-s4 · Cited by 203 · see citing works

PHACCS, an online tool for estimating the structure and diversity of uncultured viral communities using metagenomic information

Angly, F. E., Rodriguez-Brito, B., Bangor, D., McNairnie, P., Breitbart, M., Salamon, P., Felts, B., Nulton, J., Mahaffy, J. M., & Rohwer, F. L. (2005) · BMC Bioinformatics · doi:10.1186/1471-2105-6-41 · Cited by 202 · see citing works

Scalable metagenomic taxonomy classification using a reference genome database

Ames, S. K., Hysom, D., Gardner, S. N., Lloyd, G. S., Gokhale, M. B., & Allen, J. (2013) · Bioinformatics · doi:10.1093/bioinformatics/btt389 · Cited by 201 · see citing works

MOCAT: A Metagenomics Assembly and Gene Prediction Toolkit

Kultima, J. R., Sunagawa, S., Li, J., Chen, W., Chen, H., Mende, D. R., Arumugam, M., Pan, Q., Liu, B., Qin, J., et al. (2012) · PLoS ONE · doi:10.1371/journal.pone.0047656 · Cited by 199 · see citing works

Deriving accurate microbiota profiles from human samples with low bacterial content through post-sequencing processing of Illumina MiSeq data

Jervis-Bardy, J., Leong, L. E. X., Marri, S., Smith, R. J., Choo, J. M., Smith-Vaughan, H. C., Nosworthy, E., Morris, P. S., O’Leary, S., Rogers, G. B., et al. (2015) · Microbiome · doi:10.1186/s40168-015-0083-8 · Cited by 192 · see citing works

Accurate read-based metagenome characterization using a hierarchical suite of unique signatures

Freitas, T. A. K., Li, P., Scholz, M. B., & Chain, P. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv180 · Cited by 179 · see citing works

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

Ritari, J., Salojärvi, J., Lahti, L., & de Vos, W. M. (2015) · BMC Genomics · doi:10.1186/s12864-015-2265-y · Cited by 175 · see citing works

Comparison of Collection Methods for Fecal Samples in Microbiome Studies

Vogtmann, E., Chen, J., Amir, A., Shi, J., Abnet, C. C., Nelson, H., Knight, R. D., Chia, N., & Sinha, R. R. (2016) · American Journal of Epidemiology · doi:10.1093/aje/kww177 · Cited by 163 · see citing works

Microbial Population Differentials between Mucosal and Submucosal Intestinal Tissues in Advanced Crohn's Disease of the Ileum

Chiodini, R. J., Dowd, S. E., Chamberlin, W., Galandiuk, S., Davis, B. R., & Glassing, A. (2015) · PLoS ONE · doi:10.1371/journal.pone.0134382 · Cited by 160 · see citing works

SPINGO: a rapid species-classifier for microbial amplicon sequences

Allard, G., Ryan, F. J., Jeffery, I. B., & Claesson, M. J. (2015) · BMC Bioinformatics · doi:10.1186/s12859-015-0747-1 · Cited by 160 · see citing works

Evaluation of shotgun metagenomics sequence classification methods using in silico and in vitro simulated communities

Peabody, M. A., Rossum, T. V., Lo, R., & Brinkman, F. (2015) · BMC Bioinformatics · doi:10.1186/s12859-015-0788-5 · Cited by 159 · see citing works

Comparative Evaluation of DNA Extraction Methods from Feces of Multiple Host Species for Downstream Next-Generation Sequencing

Hart, M. L., Meyer, A. M., Johnson, P. J., & Ericsson, A. C. (2015) · PLoS ONE · doi:10.1371/journal.pone.0143334 · Cited by 157 · see citing works

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

Dröge, J., Gregor, I., & McHardy, A. C. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu745 · Cited by 156 · see citing works

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

Cai, Y., & Sun, Y. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkr349 · Cited by 156 · see citing works

Rectal Swabs for Analysis of the Intestinal Microbiota

Budding, A. E., Grasman, M. E., Eck, A., Bogaards, J. A., Vandenbroucke‐Grauls, C. M. J. E., Bodegraven, A. A. V., & Savelkoul, P. H. M. (2014) · PLoS ONE · doi:10.1371/journal.pone.0101344 · Cited by 152 · see citing works

EBI metagenomics—a new resource for the analysis and archiving of metagenomic data

Hunter, S., Corbett, M., Denise, H., Fraser, M., Gonzalez-Beltran, A. N., Hunter, C., JONES, P. M., Leinonen, R., McAnulla, C., Maguire, E., et al. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt961 · Cited by 149 · see citing works

Orphelia: predicting genes in metagenomic sequencing reads

Hoff, K. J., Lingner, T., Meinicke, P., & Tech, M. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkp327 · Cited by 142 · see citing works

Comparison of DNA extraction kits for PCR-DGGE analysis of human intestinal microbial communities from fecal specimens

Ariefdjohan, M. W., Savaiano, D. A., & Nakatsu, C. H. (2010) · Nutrition Journal · doi:10.1186/1475-2891-9-23 · Cited by 142 · see citing works

A Comparison of Three Bioinformatics Pipelines for the Analysis of Preterm Gut Microbiota using 16S rRNA Gene Sequencing Data

Plummer, E. L., & Twin, J. (2015) · Journal of Proteomics & Bioinformatics · doi:10.4172/jpb.1000381 · Cited by 142 · see citing works

Medicines from microbiota

Olle, B. (2013) · Nature Biotechnology · doi:10.1038/nbt.2548 · Cited by 140 · see citing works

Collection media and delayed freezing effects on microbial composition of human stool

Flores, R., Shi, J., Yu, G., Ma, B., Ravel, J., Goedert, J. J., & Sinha, R. R. (2015) · Microbiome · doi:10.1186/s40168-015-0092-7 · Cited by 138 · see citing works

ShotgunFunctionalizeR: an R-package for functional comparison of metagenomes

Kristiansson, E., Hugenholtz, P., & Dalevi, D. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp508 · Cited by 138 · see citing works

SOrt-ITEMS: Sequence orthology based approach for improved taxonomic estimation of metagenomic sequences

Haque, M. M., Ghosh, T. S., Komanduri, D., et al. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp317 · Cited by 136 · see citing works

The PhyloPythiaS Web Server for Taxonomic Assignment of Metagenome Sequences

Patil, K. R., Roune, L., & McHardy, A. C. (2012) · PLoS ONE · doi:10.1371/journal.pone.0038581 · Cited by 133 · see citing works

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

Goll, J. B., Rusch, D. B., Tanenbaum, D. M., Thiagarajan, M., Li, K., Methé, B. A., & Yooseph, S. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq455 · Cited by 131 · see citing works

Higher classification sensitivity of short metagenomic reads with CLARK- S

Ounit, R., & Lonardi, S. (2016) · Bioinformatics · doi:10.1093/bioinformatics/btw542 · Cited by 130 · see citing works

Analysis and comparison of very large metagenomes with fast clustering and functional annotation

Li, W. (2009) · BMC Bioinformatics · doi:10.1186/1471-2105-10-359 · Cited by 129 · see citing works

Optimization of terminal restriction fragment polymorphism (TRFLP) analysis of human gut microbiota

Li, F., Hullar, M. A. J., & Lampe, J. W. (2006) · Journal of Microbiological Methods · doi:10.1016/j.mimet.2006.09.006 · Cited by 126 · see citing works

RAIphy: Phylogenetic classification of metagenomics samples using iterative refinement of relative abundance index profiles

Nalbantoğlu, Ö. U., Way, S. F., Hinrichs, S. H., & Sayood, K. (2011) · BMC Bioinformatics · doi:10.1186/1471-2105-12-41 · Cited by 124 · see citing works

MLTreeMap - accurate Maximum Likelihood placement of environmental DNA sequences into taxonomic and functional reference phylogenies

Stark, M., Berger, S. A., Stamatakis, A., & von Mering, C. (2010) · BMC Genomics · doi:10.1186/1471-2164-11-461 · Cited by 122 · see citing works

Taxonomic classification of metagenomic shotgun sequences with CARMA3

Gerlach, W., & Stoye, J. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkr225 · Cited by 121 · see citing works

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

Afiahayati, Sato, K., & Sakakibara, Y. (2014) · DNA Research · doi:10.1093/dnares/dsu041 · Cited by 118 · see citing works

PANGEA: pipeline for analysis of next generation amplicons

Giongo, A., Crabb, D. B., Davis‐Richardson, A. G., Chauliac, D., Mobberley, J. M., Gano, K. A., Mukherjee, N., Casella, G., Roesch, L. F. W., Walts, B., et al. (2010) · The ISME Journal · doi:10.1038/ismej.2010.16 · Cited by 115 · see citing works

Acute West Nile Virus Meningoencephalitis Diagnosed Via Metagenomic Deep Sequencing of Cerebrospinal Fluid in a Renal Transplant Patient

Wilson, M. R., Zimmermann, L. L., Crawford, E. D., et al. (2016) · American Journal of Transplantation · doi:10.1111/ajt.14058 · Cited by 114 · see citing works

Comparison of brush and biopsy sampling methods of the ileal pouch for assessment of mucosa-associated microbiota of human subjects

Huse, S. M., Young, V. B., Morrison, H. G., Antonopoulos, D. A., Kwon, J. H., Dalal, S. R., Arrieta, R. L., Hubert, N. A., Shen, L., Vineis, J. H., et al. (2014) · Microbiome · doi:10.1186/2049-2618-2-5 · Cited by 112 · see citing works

Gene prediction in metagenomic fragments based on the SVM algorithm

Liu, Y., Guo, J., Hu, G., & Zhu, H. (2013) · BMC Bioinformatics · doi:10.1186/1471-2105-14-s5-s12 · Cited by 111 · see citing works

The Effects of Bowel Preparation on Microbiota-Related Metrics Differ in Health and in Inflammatory Bowel Disease and for the Mucosal and Luminal Microbiota Compartments

Shobar, R., Velineni, S., Keshavarzian, A., Swanson, G. R., DeMeo, M. T., Melson, J. E., Losurdo, J., Engen, P. A., Sun, Y., Koenig, L., et al. (2016) · Clinical and Translational Gastroenterology · doi:10.1038/ctg.2015.54 · Cited by 108 · see citing works

SmashCommunity: a metagenomic annotation and analysis tool

Arumugam, M., Harrington, E. D., Förstner, K. U., Raes, J., & Peer Bork, B. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq536 · Cited by 103 · see citing works

Improved OTU-picking using long-read 16S rRNA gene amplicon sequencing and generic hierarchical clustering

Franzén, O., Hu, J., Bao, X., Itzkowitz, S. H., Peter, I., & Bashir, A. (2015) · Microbiome · doi:10.1186/s40168-015-0105-6 · Cited by 98 · see citing works

Systems biology of host–microbe metabolomics

Heinken, A., & Thiele, I. (2015) · WIREs Systems Biology and Medicine · doi:10.1002/wsbm.1301 · Cited by 96 · see citing works

Omega: an Overlap-graphde novoAssembler for Metagenomics

Haider, B., Ahn, T.-H., Bushnell, B., Chai, J., Copeland, A., & Pan, C. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu395 · Cited by 96 · see citing works

Binning sequences using very sparse labels within a metagenome

Chan, C. K., Hsu, A. L., Halgamuge, S. K., & Tang, S. (2008) · BMC Bioinformatics · doi:10.1186/1471-2105-9-215 · Cited by 87 · see citing works

16S Classifier: A Tool for Fast and Accurate Taxonomic Classification of 16S rRNA Hypervariable Regions in Metagenomic Datasets

Chaudhary, N., Sharma, A. K., Agarwal, P. C., et al. (2015) · PLoS ONE · doi:10.1371/journal.pone.0116106 · Cited by 86 · see citing works

The effect of DNA extraction methodology on gut microbiota research applications

Gerasimidis, K., Bertz, M., Quince, C., Brunner, K., Bruce, A., Combet, E., Calus, S., Loman, N. J., & Ijaz, U. Z. (2016) · BMC Research Notes · doi:10.1186/s13104-016-2171-7 · Cited by 83 · see citing works

Latitude in sample handling and storage for infant faecal microbiota studies: the elephant in the room?

Shaw, A., Sim, K., Powell, E. A., Cornwell, E., Cramer, T. L. M., McClure, Z. E., Li, M., & Kroll, J. S. (2016) · Microbiome · doi:10.1186/s40168-016-0186-x · Cited by 83 · see citing works

Microbial diversity in fecal samples depends on DNA extraction method: easyMag DNA extraction compared to QIAamp DNA stool mini kit extraction

Mirsepasi‐Lauridsen, H. C., Persson, S., Struve, C., Andersen, L. O., Petersen, A. M., & Krogfelt, K. A. (2014) · BMC Research Notes · doi:10.1186/1756-0500-7-50 · Cited by 82 · see citing works

The 120 kilodalton outer membrane protein (rOmp B) of Rickettsia rickettsii is encoded by an unusually long open reading frame: evidence for protein processing from a large precursor

Gilmore, R. D., Cieplak, W., Policastro, P. F., et al. (1991) · Molecular Microbiology · doi:10.1111/j.1365-2958.1991.tb02082.x · Cited by 76 · see citing works

CLOTU: An online pipeline for processing and clustering of 454 amplicon reads into OTUs followed by taxonomic annotation

Kumar, S., Carlsen, T., Mevik, B., Enger, P., Blaalid, R., Shalchian‐Tabrizi, K., & Kauserud, H. (2011) · BMC Bioinformatics · doi:10.1186/1471-2105-12-182 · Cited by 76 · see citing works

Rapid identification of high-confidence taxonomic assignments for metagenomic data

MACDONALD, N. J., Parks, D. H., & Beiko, R. G. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks335 · Cited by 75 · see citing works

Parallel-META 2.0: Enhanced Metagenomic Data Analysis with Functional Annotation, High Performance Computing and Advanced Visualization

Su, X., Pan, W., Song, B., Xu, J., & Ning, K. (2014) · PLoS ONE · doi:10.1371/journal.pone.0089323 · Cited by 75 · see citing works

SPHINX—an algorithm for taxonomic binning of metagenomic sequences

Mohammed, M. H., Ghosh, T. S., Singh, N. K., & Mande, S. S. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq608 · Cited by 71 · see citing works

Extending colonic mucosal microbiome analysis—assessment of colonic lavage as a proxy for endoscopic colonic biopsies

Watt, E., Gemmell, M., Berry, S., Glaire, M. A., Farquharson, F. M., Louis, P., Murray, G. I., El-Omar, E. M., & Hold, G. L. (2016) · Microbiome · doi:10.1186/s40168-016-0207-9 · Cited by 67 · see citing works

CATCh, an Ensemble Classifier for Chimera Detection in 16S rRNA Sequencing Studies

Mysara, M., Saeys, Y., Leys, N., et al. (2014) · Applied and Environmental Microbiology · doi:10.1128/aem.02896-14 · Cited by 65 · see citing works

Composition-based classification of short metagenomic sequences elucidates the landscapes of taxonomic and functional enrichment of microorganisms

Liu, J., Wang, H., Yang, H., et al. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks828 · Cited by 64 · see citing works

Effect of room temperature transport vials on DNA quality and phylogenetic composition of faecal microbiota of elderly adults and infants

Hill, C. J., Brown, J. R.-M., Lynch, D. B., Jeffery, I. B., Ryan, C. A., Ross, R. P., Stanton, C., & O’Toole, P. W. (2016) · Microbiome · doi:10.1186/s40168-016-0164-3 · Cited by 63 · see citing works

Comparison of six commercial kits to extract bacterial chromosome and plasmid DNA for MiSeq sequencing

Becker, L., Steglich, M., Fuchs, S., Werner, G., & Nübel, U. (2016) · Scientific Reports · doi:10.1038/srep28063 · Cited by 62 · see citing works

A robust ambient temperature collection and stabilization strategy: Enabling worldwide functional studies of the human microbiome

Anderson, E. L., Li, W., Klitgord, N., Highlander, S. K., Dayrit, M., Seguritan, V., Yooseph, S., Biggs, W., Venter, J. C., Nelson, K. E., et al. (2016) · Scientific Reports · doi:10.1038/srep31731 · Cited by 59 · see citing works

BioMaS: a modular pipeline for Bioinformatic analysis of Metagenomic AmpliconS

Fosso, B., Santamaría, M., Marzano, M., et al. (2015) · BMC Bioinformatics · doi:10.1186/s12859-015-0595-z · Cited by 58 · see citing works

Practical application of self-organizing maps to interrelate biodiversity and functional data in NGS-based metagenomics

Weber, M., Teeling, H., Huang, S., Waldmann, J., Kassabgy, M., Fuchs, B. M., Klindworth, A., Klockow, C., Wichels, A., Gerdts, G., et al. (2010) · The ISME Journal · doi:10.1038/ismej.2010.180 · Cited by 57 · see citing works

MetaCluster-TA: taxonomic annotation for metagenomic data based on assembly-assisted binning

Wang, Y., Leung, H. C. M., Yiu, S. M., et al. (2014) · BMC Genomics · doi:10.1186/1471-2164-15-s1-s12 · Cited by 56 · see citing works

DUDes: a top-down taxonomic profiler for metagenomics

Piro, V. C., Lindner, M. S., & Renard, B. Y. (2016) · Bioinformatics · doi:10.1093/bioinformatics/btw150 · Cited by 55 · see citing works

Treephyler: fast taxonomic profiling of metagenomes

Schreiber, F., Gumrich, P., Daniel, R., et al. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq070 · Cited by 54 · see citing works

FastGroup: A program to dereplicate libraries of 16S rDNA sequences

Seguritan, V., & Rohwer, F. L. (2001) · BMC Bioinformatics · doi:10.1186/1471-2105-2-9 · Cited by 53 · see citing works

MetaPath: identifying differentially abundant metabolic pathways in metagenomic datasets

Liu, B., & Pop, M. (2011) · BMC Proceedings · doi:10.1186/1753-6561-5-s2-s9 · Cited by 49 · see citing works

ClaMS: A Classifier for Metagenomic Sequences

Pati, A., Heath, L. S., Kyrpides, N. C., et al. (2011) · Standards in Genomic Sciences · doi:10.4056/sigs.2075298 · Cited by 48 · see citing works

Woods: A fast and accurate functional annotator and classifier of genomic and metagenomic sequences

Sharma, A. K., Gupta, A., Kumar, S., Dhakan, D. B., & Sharma, V. K. (2015) · Genomics · doi:10.1016/j.ygeno.2015.04.001 · Cited by 45 · see citing works

WGSQuikr: Fast Whole-Genome Shotgun Metagenomic Classification

Koslicki, D., Foucart, S., & Rosen, G. L. (2014) · PLoS ONE · doi:10.1371/journal.pone.0091784 · Cited by 44 · see citing works

Phenotypic differentiation of gastrointestinal microbes is reflected in their encoded metabolic repertoires

Bauer, E., Laczny, C. C., Magnúsdóttir, S., Wilmes, P., & Thiele, I. (2015) · Microbiome · doi:10.1186/s40168-015-0121-6 · Cited by 44 · see citing works

Genometa - A Fast and Accurate Classifier for Short Metagenomic Shotgun Reads

Davenport, C., Neugebauer, J., Beckmann, N., Friedrich, B., Kameri, B., Kokott, S., Paetow, M., Siekmann, B., Wieding-Drewes, M., Wienhöfer, M., et al. (2012) · PLoS ONE · doi:10.1371/journal.pone.0041224 · Cited by 43 · see citing works

A grammar-based distance metric enables fast and accurate clustering of large sets of 16S sequences

Russell, D. J., Way, S. F., Benson, A. K., et al. (2010) · BMC Bioinformatics · doi:10.1186/1471-2105-11-601 · Cited by 42 · see citing works

JAGUC — A SOFTWARE PACKAGE FOR ENVIRONMENTAL DIVERSITY ANALYSES

Nebel, M. E., Wild, S., Holzhauser, M., Huettenberger, L., Reitzig, R., Sperber, M., & Stoeck, T. (2011) · Journal of Bioinformatics and Computational Biology · doi:10.1142/s0219720011005781 · Cited by 42 · see citing works

MetAnnotate: function-specific taxonomic profiling and comparison of metagenomes

Petrenko, P., Lobb, B., Kurtz, D. A., Neufeld, J. D., & Doxey, A. C. (2015) · BMC Biology · doi:10.1186/s12915-015-0195-4 · Cited by 42 · see citing works

DiScRIBinATE: a rapid method for accurate taxonomic classification of metagenomic sequences

Ghosh, T. S., Monzoorul Haque, M., & Mande, S. S. (2010) · BMC Bioinformatics · doi:10.1186/1471-2105-11-s7-s14 · Cited by 40 · see citing works

M-pick, a modularity-based method for OTU picking of 16S rRNA sequences

Wang, X., Jin, Y., Sun, Y., & Mai, V. (2013) · BMC Bioinformatics · doi:10.1186/1471-2105-14-43 · Cited by 39 · see citing works

Quantifying the Effect of Ribosomal Density on mRNA Stability

Edri, S., & Tuller, T. (2014) · PLoS ONE · doi:10.1371/journal.pone.0102308 · Cited by 39 · see citing works

AN ORFOME ASSEMBLY APPROACH TO METAGENOMICS SEQUENCES ANALYSIS

Ye, Y., & Tang, H. (2009) · Journal of Bioinformatics and Computational Biology · doi:10.1142/s0219720009004151 · Cited by 37 · see citing works

Protein signature-based estimation of metagenomic abundances including all domains of life and viruses

Klingenberg, H., Aßhauer, K. P., Lingner, T., & Meinicke, P. (2013) · Bioinformatics · doi:10.1093/bioinformatics/btt077 · Cited by 35 · see citing works

Five commercial DNA extraction systems tested and compared on a stool sample collection

Persson, S., de Boer, R. F., Kooistra-Smid, A. M. D., et al. (2011) · Diagnostic Microbiology and Infectious Disease · doi:10.1016/j.diagmicrobio.2010.09.023 · Cited by 34 · see citing works

Fast and Accurate Taxonomic Assignments of Metagenomic Sequences Using MetaBin

Sharma, V. K., Kumar, N., Prakash, T., et al. (2012) · PLoS ONE · doi:10.1371/journal.pone.0034030 · Cited by 32 · see citing works

METAGENOMIC TAXONOMIC CLASSIFICATION USING EXTREME LEARNING MACHINES

Rasheed, Z., & Rangwala, H. (2012) · Journal of Bioinformatics and Computational Biology · doi:10.1142/s0219720012500151 · Cited by 30 · see citing works

A Statistical Framework for Accurate Taxonomic Assignment of Metagenomic Sequencing Reads

Jiang, H., An, L., Lin, S. M., et al. (2012) · PLoS ONE · doi:10.1371/journal.pone.0046450 · Cited by 29 · see citing works

MtHc: a motif-based hierarchical method for clustering massive 16S rRNA sequences into OTUs

Wei, Z., & Zhang, S. (2015) · Molecular BioSystems · doi:10.1039/c5mb00089k · Cited by 24 · see citing works

PhylOPDb: a 16S rRNA oligonucleotide probe database for prokaryotic identification

Jaziri, F., Parisot, N., Abid, A., Denonfoux, J., Ribière, C., Gasc, C., Boucher, D., Brugère, J., Mahul, A., Hill, D. R. C., et al. (2014) · Database · doi:10.1093/database/bau036 · Cited by 24 · see citing works

INDUS - a composition-based approach for rapid and accurate taxonomic classification of metagenomic sequences

Mohammed, M. H., Ghosh, T. S., Reddy, R. M., et al. (2011) · BMC Genomics · doi:10.1186/1471-2164-12-s3-s4 · Cited by 24 · see citing works

Meta-QC-Chain: Comprehensive and Fast Quality Control Method for Metagenomic Data

Zhou, Q., Su, X., Jing, G., et al. (2014) · Genomics Proteomics & Bioinformatics · doi:10.1016/j.gpb.2014.01.002 · Cited by 21 · see citing works

The Microbiota-Gut-Brain Axis

Cryan, J. F., O'Riordan, K. J., Cowan, C. S. M., Sandhu, K. V., Bastiaanssen, T. F. S., Boehme, M., Codagnone, M. G., Cussotto, S., Fulling, C., Golubeva, A. V., et al. (2019) · Physiological Reviews · doi:10.1152/physrev.00018.2018 · Cited by 5,286 · see citing works

Gut reactions: Breaking down xenobiotic–microbiome interactions

Clarke, G., Sandhu, K. V., Griffin, B. T., Dinan, T. G., Cryan, J. F., & Hyland, N. P. (2019) · Pharmacological Reviews · doi:10.1124/pr.118.015768 · Cited by 319 · see citing works

Systematic review: human gut dysbiosis induced by non-antibiotic prescription medications

Le Bastard, Q., Al‐Ghalith, G. A., Grégoire, M., Chapelet, G., Javaudin, F., Dailly, E., Batard, E., Knights, D., & Montassier, E. (2018) · Alimentary Pharmacology &amp; Therapeutics · doi:10.1111/apt.14451 · Cited by 263 · see citing works

Age-dependent changes in GI physiology and microbiota: time to reconsider?

An, R., Wilms, E., Masclee, A. A. M., Smidt, H., Zoetendal, E. G., & Jonkers, D. (2018) · Gut · doi:10.1136/gutjnl-2017-315542 · Cited by 209 · see citing works

Annual Research Review: Critical windows – the microbiota-gut-brain axis in neurocognitive development

Cowan, C. S. M., Dinan, T. G., & Cryan, J. F. (2020) · Journal of Child Psychology and Psychiatry · doi:10.1111/jcpp.13156 · Cited by 176 · see citing works

BMC322- A RATIONALLY-DESIGNED LIVE BACTERIAL CONSORTIUM BASED ON MICROBIOME FUNCTIONAL GENOMIC ANALYSIS FOR TREATMENT OF IBD

Polonsky, O., Meshner, S., Eshar, S., et al. (2021) · Gastroenterology · doi:10.1053/j.gastro.2021.01.140 · Cited by 1 · see citing works

Why targeting the microbiome is not so successful: can randomness overcome the adaptation that occurs following gut manipulation?

Ilan, Y. (2019) · Clinical and Experimental Gastroenterology · doi:10.2147/ceg.s203823 · Cited by 76 · see citing works

Microbiome-based stratification to guide dietary interventions to improve human health

Liu, Z., de Vries, B., Gerritsen, J., Smidt, H., & Zoetendal, E. G. (2020) · Nutrition Research · doi:10.1016/j.nutres.2020.07.004 · Cited by 42 · see citing works

Pediatric intestinal failure and the microbiome

Josyabhatla, R., & Imseis, E. M. (2021) · Seminars in Perinatology · doi:10.1016/j.semperi.2021.151453 · Cited by 4 · see citing works

Sa1911 – Analysis of the Small Intestinal Microbiome Reveals Marked Differences from Stool Microbiome in a Large Scale Human Cohort: Redefining the “Gut Microbiome”

Leite, G., Weitsman, S. R., Celly, S., et al. (2019) · Gastroenterology · doi:10.1016/s0016-5085(19)37977-6 · Cited by 5 · see citing works