The Ribosomal Database Project: improved alignments and new tools for rRNA analysis

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Cole, J. R., Wang, Q., Cardenas, E., Fish, J., Chai, B., Farris, R. J., Kulam-Syed-Mohideen, A. S., McGarrell, D. M., Marsh, T., Garrity, G. M., Tiedje, J. M.·2009·Nucleic Acids Research

DOI 10.1093/nar/gkn879

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Abstract

The Ribosomal Database Project (RDP) provides researchers with quality-controlled bacterial and archaeal small subunit rRNA alignments and analysis tools. An improved alignment strategy uses the Infernal secondary structure aware aligner to provide a more consistent higher quality alignment and faster processing of user sequences. Substantial new analysis features include a new Pyrosequencing Pipeline that provides tools to support analysis of ultra high-throughput rRNA sequencing data. This pipeline offers a collection of tools that automate the data processing and simplify the computationally intensive analysis of large sequencing libraries. In addition, a new Taxomatic visualization tool allows rapid visualization of taxonomic inconsistencies and suggests corrections, and a new class Assignment Generator provides instructors with a lesson plan and individualized teaching materials. Details about RDP data and analytical functions can be found at http://rdp.cme.msu.edu/.

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Wang, Y., Li, N., Yang, J.-J., Zhao, D.-M., Chen, B., Zhang, G.-Q., Chen, S., Cao, R.-F., Yu, H., Zhao, C.-Y., et al. (2020) · Pharmacological Research · doi:10.1016/j.phrs.2020.104784 · Cited by 324
Microbiome profiling by Illumina sequencing of combinatorial sequence-tagged PCR products
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Probiotic Administration Attenuates Myocardial Hypertrophy and Heart Failure After Myocardial Infarction in the Rat
Gan, X. T., Ettinger, G., Huang, C. X., Burton, J. P., Haist, J. V., Rajapurohitam, V., Sidaway, J. E., Martin, G., Gloor, G. B., Swann, J. R., et al. (2014) · Circulation: Heart Failure · doi:10.1161/circheartfailure.113.000978 · Cited by 329
High-throughput DNA sequence analysis reveals stable engraftment of gut microbiota following transplantation of previously frozen fecal bacteria
Hamilton, M. J., Weingarden, A. R., Unno, T., Khoruts, A., & Sadowsky, M. J. (2013) · Gut Microbes · doi:10.4161/gmic.23571 · Cited by 315
Establishment of ruminal bacterial community in dairy calves from birth to weaning is sequential
Rey, M., Enjalbert, F., Combes, S., Cauquil, L., Bouchez, O., & Monteils, V. (2014) · Journal of Applied Microbiology · doi:10.1111/jam.12405 · Cited by 314
Mapping the Tree of Life: Progress and Prospects
Pace, N. R. (2009) · Microbiology and Molecular Biology Reviews · doi:10.1128/mmbr.00033-09 · Cited by 286
Relationship between Milk Microbiota, Bacterial Load, Macronutrients, and Human Cells during Lactation
Boix-Amorós, A., Collado, M. C., & Mira, A. (2016) · Frontiers in Microbiology · doi:10.3389/fmicb.2016.00492 · Cited by 283
Microbiome dynamics of human epidermis following skin barrier disruption
Zeeuwen, P. L., Boekhorst, J., van den Bogaard, E. H., de Koning, H. D., van de Kerkhof, P. M., Saulnier, D. M., van Swam, I. I., van Hijum, S. A., Kleerebezem, M., Schalkwijk, J., et al. (2012) · Genome Biology · doi:10.1186/gb-2012-13-11-r101 · Cited by 274
Staphylococcus aureus and the ecology of the nasal microbiome
Liu, C. M., Price, L. B., Hungate, B. A., Abraham, A. G., Larsen, L. A., Christensen, K., Stegger, M., Skov, R., & Andersen, P. S. (2015) · Science Advances · doi:10.1126/sciadv.1400216 · Cited by 253
The microbiome in respiratory medicine: current challenges and future perspectives
Faner, R., Sibila, O., Agustí, A., Bernasconi, E., Chalmers, J. D., Huffnagle, G. B., Manichanh, C., Molyneaux, P. L., Paredes, R., Pérez Brocal, V., et al. (2017) · European Respiratory Journal · doi:10.1183/13993003.02086-2016 · Cited by 247
Community Analysis of Chronic Wound Bacteria Using 16S rRNA Gene-Based Pyrosequencing: Impact of Diabetes and Antibiotics on Chronic Wound Microbiota
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Alteration of intestinal dysbiosis by fecal microbiota transplantation does not induce remission in patients with chronic active ulcerative colitis
Kump, P. K., Gröchenig, H.-P., Lackner, S., Trajanoski, S., Reicht, G., Hoffmann, K. M., Deutschmann, A., Wenzl, H. H., Petritsch, W., Krejs, G. J., et al. (2013) · Inflammatory Bowel Diseases · doi:10.1097/mib.0b013e31829ea325 · Cited by 235
APOE genotype influences the gut microbiome structure and function in humans and mice: relevance for Alzheimer's disease pathophysiology
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Impact of Pelvic Radiotherapy on Gut Microbiota of Gynecological Cancer Patients Revealed by Massive Pyrosequencing
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Isolation of vaginal lactobacilli and characterization of anti-candida activity
Parolin, C., Marangoni, A., Laghi, L., Foschi, C., Ñahui Palomino, R. A., Calonghi, N., Cevenini, R., & Vitali, B. (2015) · PLOS ONE · doi:10.1371/journal.pone.0131220 · Cited by 228
Microbial Communities of the Upper Respiratory Tract and Otitis Media in Children
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“calculate the Shannon diversity and evenness indices (25, 26, 52, 53).”
Method
Metagenomics uncovers a new group of low GC and ultra-small marine Actinobacteria
Ghai, R., Mizuno, C. M., Picazo, A., Camacho, A., & Rodriguez-Valera, F. (2013) · Scientific Reports · doi:10.1038/srep02471 · Cited by 224
Impact of polyphenols from black tea and red wine/grape juice on a gut model microbiome
Kemperman, R. A., Gross, G., Mondot, S., Possemiers, S., Marzorati, M., Van de Wiele, T., Doré, J., & Vaughan, E. E. (2013) · Food Research International · doi:10.1016/j.foodres.2013.01.034 · Cited by 223
Heritable Bovine Rumen Bacteria Are Phylogenetically Related and Correlated with the Cow’s Capacity To Harvest Energy from Its Feed
Sasson, G., Kruger Ben-Shabat, S., Seroussi, E., Doron-Faigenboim, A., Shterzer, N., Yaacoby, S., Berg Miller, M. E., White, B. A., Halperin, E., & Mizrahi, I. (2017) · mBio · doi:10.1128/mbio.00703-17 · Cited by 219
Differential Effects of Antibiotic Therapy on the Structure and Function of Human Gut Microbiota
Pérez-Cobas, A. E., Artacho, A., Knecht, H., Ferrús, M. L., Friedrichs, A., Ott, S. J., Moya, A., Latorre, A., & Gosalbes, M. J. (2013) · PLoS ONE · doi:10.1371/journal.pone.0080201 · Cited by 212
Next-Generation Sequencing for Infectious Disease Diagnosis and Management
Lefterova, M. I., Suarez, C. J., Banaei, N., & Pinsky, B. A. (2015) · The Journal of Molecular Diagnostics · doi:10.1016/j.jmoldx.2015.07.004 · Cited by 207
Aerobic Respiration Metabolism in Lactic Acid Bacteria and Uses in Biotechnology
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Toward an understanding of changes in diversity associated with fecal microbiome transplantation based on 16S rRNA gene deep sequencing
Shahinas, D., Silverman, M., Sittler, T., Chiu, C., Kim, P., Allen-Vercoe, E., Weese, S., Wong, A., Low, D. E., & Pillai, D. R. (2012) · mBio · doi:10.1128/mbio.00338-12 · Cited by 191
Microbial Enterotypes, Inferred by the Prevotella-to-Bacteroides Ratio, Remained Stable during a 6-Month Randomized Controlled Diet Intervention with the New Nordic Diet
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Impact of next generation sequencing techniques in food microbiology.
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Developing a metagenomic view of xenobiotic metabolism
Haiser, H. J., & Turnbaugh, P. J. (2013) · Pharmacological Research · doi:10.1016/j.phrs.2012.07.009 · Cited by 186
Variation in Raw Milk Microbiota Throughout 12 Months and the Impact of Weather Conditions
Li, N., Wang, Y., You, C., Ren, J., Chen, W., Zheng, H., & Liu, Z. (2018) · Scientific Reports · doi:10.1038/s41598-018-20862-8 · Cited by 187
Upper Respiratory Tract Microbial Communities, Acute Otitis Media Pathogens, and Antibiotic Use in Healthy and Sick Children
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Long-term temporal analysis of the human fecal microbiota revealed a stable core of dominant bacterial species
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Inflammation and Airway Microbiota during Cystic Fibrosis Pulmonary Exacerbations
Zemanick, E. T., Harris, J. K., Wagner, B. D., Robertson, C. E., Sagel, S. D., Stevens, M. J., Accurso, F. J., & Laguna, T. A. (2013) · PLoS ONE · doi:10.1371/journal.pone.0062917 · Cited by 180
A comprehensive assessment of demographic, environmental, and host genetic associations with gut microbiome diversity in healthy individuals
The Milieu Intérieur Consortium, Scepanovic, P., Hodel, F., Mondot, S., Partula, V., Byrd, A., Hammer, C., Alanio, C., Bergstedt, J., Patin, E., et al. (2019) · Microbiome · doi:10.1186/s40168-019-0747-x · Cited by 171

Authors: Cole, J. R., Wang, Q., Cardenas, E., Fish, J., Chai, B., Farris, R. J., Kulam-Syed-Mohideen, A. S., McGarrell, D. M., Marsh, T., Garrity, G. M., & Tiedje, J. M.
Venue: Nucleic Acids Research
Publisher: Oxford University Press (OUP)
Published: 2009-01-01
Volume: 37
Issue: Database
Pages: D141-D145
ISSN: 0305-1048 (ISSN-L)
1362-4962
DOI: 10.1093/nar/gkn879
OpenAlex: W2155066423
Cited by: 4,762
References: 0
FWCI: 84.99
Type: journal article
Language: en
Open access: gold
Licence: creativecommons.org/licenses/by-nc/2.0/uk/ (vor, 2833 d)

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The Ribosomal Database Project: improved alignments and new tools for rRNA analysis

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