Cited by 33,055Genomics and Phylogenetic StudiesMicrobial Community Ecology and PhysiologyEnvironmental DNA in Biodiversity Studies

The DOI matches its Crossref record; 24 of the 24 references it cites were found in a registry or an index.

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

Open access

Quast, Christian, Pruesse, Elmar, Yilmaz, Pelin, Gerken, Jan, Schweer, Timmy, Yarza, Pablo, Peplies, Jörg, Glöckner, Frank Oliver·2012·Nucleic Acids Research

DOI 10.1093/nar/gks1219PMC PMC3531112

Open this paper in CoChat — free account Open PDF

Abstract

SILVA (from Latin silva, forest, http://www.arb-silva.de) is a comprehensive web resource for up to date, quality-controlled databases of aligned ribosomal RNA (rRNA) gene sequences from the Bacteria, Archaea and Eukaryota domains and supplementary online services. The referred database release 111 (July 2012) contains 3 194 778 small subunit and 288 717 large subunit rRNA gene sequences. Since the initial description of the project, substantial new features have been introduced, including advanced quality control procedures, an improved rRNA gene aligner, online tools for probe and primer evaluation and optimized browsing, searching and downloading on the website. Furthermore, the extensively curated SILVA taxonomy and the new non-redundant SILVA datasets provide an ideal reference for high-throughput classification of data from next-generation sequencing approaches.

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

Integrity signals

Registry

Crossref · 10.1093/nar/gks1219

Cites

24 of 24 references verified0 citation errors · 0 not checkable

Statistics

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

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
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 21,481
Search and clustering orders of magnitude faster than BLAST
Edgar, R. C. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq461 · Cited by 21,098
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
ARB: a software environment for sequence data
Ludwig, W. (2004) · Nucleic Acids Research · doi:10.1093/nar/gkh293 · Cited by 6,714
RNAmmer: consistent and rapid annotation of ribosomal RNA genes
Lagesen, K., Hallin, P., Rødland, E., Stærfeldt, H., Rognes, T., & Ussery, D. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm160 · Cited by 5,965
The Ribosomal Database Project: improved alignments and new tools for rRNA analysis
Cole, J. R., Wang, Q., Cardenas, E., Fish, J., Chai, B., Farris, R. J., Kulam-Syed-Mohideen, A. S., McGarrell, D. M., Marsh, T. L., Garrity, G. M., et al. (2008) · Nucleic Acids Research · doi:10.1093/nar/gkn879 · Cited by 4,873
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
SINA: Accurate high-throughput multiple sequence alignment of ribosomal RNA genes
Pruesse, E., Peplies, J., & Glöckner, F. (2012) · Bioinform. · doi:10.1093/bioinformatics/bts252 · Cited by 2,989
Self-citation
The New Higher Level Classification of Eukaryotes with Emphasis on the Taxonomy of Protists
Adl, S., Simpson, A., Farmer, M. A., Andersen, R., Anderson, O., Barta, J. R., Bowser, S., Brugerolle, G., Fensome, R., Fredericq, S., et al. (2005) · Journal of Eukaryotic Microbiology · doi:10.1111/j.1550-7408.2005.00053.x · Cited by 1,749

Flagged first, then by citations

Show all 24 references

Research works printed but not linked: 2

Schweer, 2011, Qualitätsmanagement ribosomaler RNA sequencen in der SILVA datenbank
Garrity, 2002, Taxonomic Outline of the Prokaryotes

Sorted by citations

Items 101–200 of 257

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
“8) [9] and SILVA (v111) [10], to assign identities to OTUs generated from a multi-template control comprised of known species at defined relative abundance.”
BackgroundMethod
The taxonomic composition of the donor intestinal microbiota is a major factor influencing the efficacy of faecal microbiota transplantation in therapy refractory ulcerative colitis
Kump, P., Wurm, P., Gröchenig, H. P., Wenzl, H., Petritsch, W., Halwachs, B., Wagner, M., Stadlbauer, V., Eherer, A., Hoffmann, K. M., et al. (2018) · Alimentary Pharmacology & Therapeutics · doi:10.1111/apt.14387 · Cited by 196
Adipose tissue derived bacteria are associated with inflammation in obesity and type 2 diabetes
Massier, L., Chakaroun, R., Tabei, S., Crane, A., Didt, K. D., Fallmann, J., von Bergen, M., Haange, S.-B., Heyne, H., Stumvoll, M., et al. (2020) · Gut · doi:10.1136/gutjnl-2019-320118 · Cited by 194
Impact of next generation sequencing techniques in food microbiology.
Mayo, B., Rachid, C., Alegria, A., Leite, A., Peixoto, R., & Delgado, S. (2014) · Current Genomics · doi:10.2174/1389202915666140616233211 · Cited by 188
Supplementation with a probiotic mixture accelerates gut microbiome maturation and reduces intestinal inflammation in extremely preterm infants
Samara, J., Moossavi, S., Alshaikh, B., Ortega, V. A., Pettersen, V. K., Ferdous, T., Hoops, S. L., Soraisham, A., Vayalumkal, J., Dersch-Mills, D., et al. (2022) · Cell Host & Microbe · doi:10.1016/j.chom.2022.04.005 · Cited by 191
Commensal bacteria contribute to insulin resistance in aging by activating innate B1a cells
Bodogai, M., O’Connell, J., Kim, K., Kim, Y., Moritoh, K., Chen, C., Gusev, F., Vaughan, K., Shulzhenko, N., Mattison, J. A., et al. (2018) · Science Translational Medicine · doi:10.1126/scitranslmed.aat4271 · Cited by 182
The eukaryotic life on microplastics in Brackish ecosystems
Kettner, M. T., Oberbeckmann, S., Labrenz, M., & Grossart, H.-P. (2019) · Frontiers in Microbiology · doi:10.3389/fmicb.2019.00538 · Cited by 185
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
Bile salt hydrolase/aminoacyltransferase shapes the microbiome
Guzior, D., Okros, M., Hernandez, C. M., Shivel, M., Armwald, B., Hausinger, R., & Quinn, R. (2022) · doi:10.21203/rs.3.rs-2050406/v1 · Cited by 187
Gut microbiome dysbiosis across early Parkinson’s disease, REM sleep behavior disorder and their first-degree relatives
Huang, B., Chau, S. W. H., Liu, Y., Chan, J. W. Y., Wang, J., Ma, S. L., Zhang, J., Chan, P. K. S., Yeoh, Y. K., Chen, Z., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-38248-4 · Cited by 187
Unveiling the gut microbiota composition and functionality associated with constipation through metagenomic analyses
Mancabelli, L., Milani, C., Lugli, G. A., Turroni, F., Mangifesta, M., Viappiani, A., Ticinesi, A., Nouvenne, A., Meschi, T., van Sinderen, D., et al. (2017) · Scientific Reports · doi:10.1038/s41598-017-10663-w · Cited by 182
Nlrp6- and ASC-Dependent Inflammasomes Do Not Shape the Commensal Gut Microbiota Composition
Mamantopoulos, M., Ronchi, F., Van Hauwermeiren, F., Vieira-Silva, S., Yilmaz, B., Martens, L., Saeys, Y., Drexler, S. K., Yazdi, A. S., Raes, J., et al. (2017) · Immunity · doi:10.1016/j.immuni.2017.07.011 · Cited by 181
Modulation of Metabolome and Bacterial Community in Whole Crop Corn Silage by Inoculating Homofermentative Lactobacillus plantarum and Heterofermentative Lactobacillus buchneri
Xu, D., Ding, W., Ke, W., Li, F., Zhang, P., & Guo, X. (2019) · Frontiers in Microbiology · doi:10.3389/fmicb.2018.03299 · Cited by 177
Niche partitioning of diverse sulfur-oxidizing bacteria at hydrothermal vents.
Meier, D. V., Pjevac, P., Bach, W., Hourdez, S., Girguis, P. R., Vidoudez, C., Amann, R., & Meyerdierks, A. (2017) · The ISME Journal · doi:10.1038/ismej.2017.37 · Cited by 177
Differences in fungi present in induced sputum samples from asthma patients and non-atopic controls: a community based case control study
van Woerden, H. C., Gregory, C., Brown, R., Marchesi, J. R., Hoogendoorn, B., & Matthews, I. P. (2013) · BMC Infectious Diseases · doi:10.1186/1471-2334-13-69 · Cited by 177
Gut Microbiota Differs Between Parkinson’s Disease Patients and Healthy Controls in Northeast China
Li, C., Cui, L., Yang, Y., Miao, J., Zhao, X., Zhang, J., Cui, G., & Zhang, Y. (2019) · Frontiers in Molecular Neuroscience · doi:10.3389/fnmol.2019.00171 · Cited by 178
Gut bacteria Akkermansia is associated with reduced risk of obesity: evidence from the American Gut Project
Zhou, Q., Zhang, Y., Wang, X., Yang, R., Zhu, X., Zhang, Y., Chen, C., Yuan, H., Yang, Z., & Sun, L. (2020) · Nutrition & Metabolism · doi:10.1186/s12986-020-00516-1 · Cited by 175
Aberrant type 1 immunity drives susceptibility to mucosal fungal infections.
Break, T. J., Oikonomou, V., Dutzan, N., Desai, J. V., Swidergall, M., Freiwald, T., Chauss, D., Harrison, O. J., Alejo, J., Williams, D. W., et al. (2021) · Science · doi:10.1126/science.aay5731 · Cited by 175
Gastro-Intestinal and Oral Microbiome Signatures Associated with Healthy Aging
Singh, H., Torralba, M. G., Moncera, K. J., DiLello, L., Petrini, J., Nelson, K. E., & Pieper, R. (2019) · GeroScience · doi:10.1007/s11357-019-00098-8 · Cited by 158
Effect of caloric restriction on gut permeability, inflammation markers, and fecal microbiota in obese women
Ott, B., Skurk, T., Hastreiter, L., Lagkouvardos, I., Fischer, S., Büttner, J., Kellerer, T., Clavel, T., Rychlik, M., Haller, D., et al. (2017) · Scientific Reports · doi:10.1038/s41598-017-12109-9 · Cited by 170
Effect of the Macroalgae Asparagopsis Taxiformis on Methane Production and Rumen Microbiome Assemblage
Roque, B. M., Brooke, C. G., Ladau, J., Polley, T., Marsh, L. J., Najafi, N., Pandey, P., Singh, L., Kinley, R., Salwen, J. K., et al. (2019) · Animal Microbiome · doi:10.1186/s42523-019-0004-4 · Cited by 166
Commensal microbe-derived acetate suppresses NAFLD/NASH development via hepatic FFAR2 signalling in mice
Aoki, R., Onuki, M., Hattori, K., Ito, M., Yamada, T., Kamikado, K., Kim, Y.-G., Nakamoto, N., Kimura, I., Clarke, J. M., et al. (2021) · Microbiome · doi:10.1186/s40168-021-01125-7 · Cited by 167
Gut microbiota profiles in critically ill patients, potential biomarkers and risk variables for sepsis
Agudelo-Ochoa, G. M., Valdés-Duque, B. E., Giraldo-Giraldo, N. A., Jaillier-Ramírez, A. M., Giraldo-Villa, A., Acevedo-Castaño, I., Yepes-Molina, M. A., Barbosa-Barbosa, J., & Benítez-Paéz, A. (2020) · Gut Microbes · doi:10.1080/19490976.2019.1707610 · Cited by 166
Prolonged use of a proton pump inhibitor reduces microbial diversity: implications for Clostridium difficile susceptibility
Seto, C. T., Jeraldo, P., Orenstein, R., Chia, N., & DiBaise, J. K. (2014) · Microbiome · doi:10.1186/2049-2618-2-42 · Cited by 163
Chemical and pathogen-induced inflammation disrupt the murine intestinal microbiome
Borton, M. A., Sabag-Daigle, A., Wu, J., Solden, L. M., O’Banion, B. S., Daly, R. A., Wolfe, R. A., Gonzalez, J. F., Wysocki, V. H., Ahmer, B. M. M., et al. (2017) · Microbiome · doi:10.1186/s40168-017-0264-8 · Cited by 149
Comparative microbiome analysis of a Fusarium wilt suppressive soil and a Fusarium wilt conducive soil from the Châteaurenard region
Siegel-Hertz, K., Edel-Hermann, V., Chapelle, E., Terrat, S., Raaijmakers, J. M., & Steinberg, C. (2018) · Frontiers in Microbiology · doi:10.3389/fmicb.2018.00568 · Cited by 164
“…et al., 2013) using the Basic Local Alignment Search Tool algorithm BLASTn version 2.2.23 (Altschul et al., 1997) with the filter turned off for fungal sequences; (ii) a dedicated reference database from SILVA (Quast et al., 2013), using the USEARCH tool (Edgar, 2010) for bacterial sequences.”
MethodInfluential
Lactobacillus Plantarum PS128 Alleviates Neurodegenerative Progression in 1-Methyl-4-Phenyl-1,2,3,6-Tetrahydropyridine-Induced Mouse Models of Parkinson’s Disease
Liao, J.-F., Cheng, Y.-F., You, S.-T., Kuo, W.-C., Huang, C.-W., Chiou, J.-J., Hsu, C.-C., Hsieh-Li, H.-M., Wang, S., & Tsai, Y.-C. (2020) · Brain, Behavior, and Immunity · doi:10.1016/j.bbi.2020.07.036 · Cited by 159
A clinician's guide to microbiome analysis
Claesson, M. J., Clooney, A. G., & O'Toole, P. W. (2017) · Nature Reviews Gastroenterology & Hepatology · doi:10.1038/nrgastro.2017.97 · Cited by 153
Intratumor microbiome features reveal antitumor potentials of intrahepatic cholangiocarcinoma
Chai, X., Wang, J., Li, H., Gao, C., Li, S., Wei, C., Huang, J., Tian, Y., Yuan, J., Lu, J., et al. (2023) · Gut Microbes · doi:10.1080/19490976.2022.2156255 · Cited by 152
Human gut microbiome composition and tryptophan metabolites were changed differently by fast food and Mediterranean diet in 4 days: a pilot study
Zhu, C., Sawrey-Kubicek, L., Beals, E., Rhodes, C. H., Houts, H. E., Sacchi, R., & Zivkovic, A. M. (2020) · Nutrition Research · doi:10.1016/j.nutres.2020.03.005 · Cited by 153
Effects of the Dietary Protein and Carbohydrate Ratio on Gut Microbiomes in Dogs of Different Body Conditions
Li, Q., Lauber, C. L., Czarnecki-Maulden, G., Pan, Y., & Hannah, S. S. (2017) · mBio · doi:10.1128/mbio.01703-16 · Cited by 148
Microbial mechanisms in the reduction of CH4 emission from double rice cropping system amended by biochar: A four-year study
Wang, C., Shen, J., Liu, J., Qin, H., Yuan, Q., Fan, F., Hu, Y., Wang, J., Wei, W., Li, Y., et al. (2019) · Soil Biology and Biochemistry · doi:10.1016/j.soilbio.2019.05.012 · Cited by 152
A prospective longitudinal study on the microbiota composition in amyotrophic lateral sclerosis
Di Gioia, D., Bozzi Cionci, N., Baffoni, L., Amoruso, A., Pane, M., Mogna, L., Gaggìa, F., Lucenti, M. A., Bersano, E., Cantello, R., et al. (2020) · BMC Medicine · doi:10.1186/s12916-020-01607-9 · Cited by 151
Intestinal transgene delivery with native E. coli chassis allows persistent physiological changes
Russell, B. J., Brown, S. D., Siguenza, N., Mai, I., Saran, A. R., Lingaraju, A., Maissy, E. S., Dantas Machado, A. C., Pinto, A. F. M., Sanchez, C., et al. (2022) · Cell · doi:10.1016/j.cell.2022.06.050 · Cited by 151
Differential effects of monensin and a blend of essential oils on rumen microbiota composition of transition dairy cows
Schären, M., Drong, C., Kiri, K., Riede, S., Gardener, M., Meyer, U., Hummel, J., Urich, T., Breves, G., & Dänicke, S. (2017) · Journal of Dairy Science · doi:10.3168/jds.2016-11994 · Cited by 149
Myelin as a regulator of development of the microbiota-gut-brain axis
Keogh, C. E., Kim, D. H. J., Pusceddu, M. M., Knotts, T. A., Rabasa, G., Sladek, J. A., Hsieh, M. T., Honeycutt, M., Brust-Mascher, I., Barboza, M., et al. (2021) · Brain, Behavior, and Immunity · doi:10.1016/j.bbi.2020.11.001 · Cited by 137
A widespread coral-infecting apicomplexan with chlorophyll biosynthesis genes
Kwong, W. K., del Campo, J., Mathur, V., Vermeij, M. J. A., & Keeling, P. J. (2019) · Nature · doi:10.1038/s41586-019-1072-z · Cited by 145
Human metabolome variation along the upper intestinal tract
Folz, J., Culver, R. N., Morales, J. M., Grembi, J., Triadafilopoulos, G., Relman, D. A., Huang, K. C., Shalon, D., & Fiehn, O. (2023) · Nature Metabolism · doi:10.1038/s42255-023-00777-z · Cited by 143
Short-Chain Fatty Acid-Producing Gut Microbiota Is Decreased in Parkinson’s Disease but Not in Rapid-Eye-Movement Sleep Behavior Disorder
Nishiwaki, H., Hamaguchi, T., Ito, M., Ishida, T., Maeda, T., Kashihara, K., Tsuboi, Y., Ueyama, J., Shimamura, T., Mori, H., et al. (2020) · mSystems · doi:10.1128/msystems.00797-20 · Cited by 133
Gut Microbiome Signatures Are Predictive of Infectious Risk Following Induction Therapy for Acute Myeloid Leukemia
Galloway-Peña, J. R., Shi, Y., Peterson, C. B., Sahasrabhojane, P., Gopalakrishnan, V., Brumlow, C. E., Daver, N. G., Alfayez, M., Boddu, P. C., Khan, M. A. W., et al. (2020) · Clinical Infectious Diseases · doi:10.1093/cid/ciz777 · Cited by 140
Fecal Microbiome Transplantation from Children with Autism Spectrum Disorder Modulates Tryptophan and Serotonergic Synapse Metabolism and Induces Altered Behaviors in Germ-Free Mice
Xiao, L., Yan, J., Yang, T., Zhu, J., Li, T., Wei, H., & Chen, J. (2021) · mSystems · doi:10.1128/msystems.01343-20 · Cited by 141
Bacterial and fungal core microbiomes associated with small grain silages during ensiling and aerobic spoilage
Duniere, L., Xu, S., Long, J., Elekwachi, C., Wang, Y., Turkington, K., Forster, R., & McAllister, T. A. (2017) · BMC Microbiology · doi:10.1186/s12866-017-0947-0 · Cited by 138
Fecal microbiota transplantation reverses antibiotic and chemotherapy-induced gut dysbiosis in mice
Le Bastard, Q., Ward, T., Sidiropoulos, D., Hillmann, B. M., Chun, C. L., Sadowsky, M. J., Knights, D., & Montassier, E. (2018) · Scientific Reports · doi:10.1038/s41598-018-24342-x · Cited by 134
Diverse groups of fungi are associated with plastics in the surface waters of the Western South Atlantic and the Antarctic Peninsula
Lacerda, A. L. D. F., Proietti, M. C., Secchi, E. R., & Taylor, J. D. (2020) · Molecular Ecology · doi:10.1111/mec.15444 · Cited by 129
Assessing the Influence of Vegan, Vegetarian and Omnivore Oriented Westernized Dietary Styles on Human Gut Microbiota: A Cross Sectional Study
Losasso, C., Eckert, E. M., Mastrorilli, E., Villiger, J., Mancin, M., Patuzzi, I., Di Cesare, A., Cibin, V., Barrucci, F., Pernthaler, J., et al. (2018) · Frontiers in Microbiology · doi:10.3389/fmicb.2018.00317 · Cited by 125
Mining microbes for mental health: determining the role of microbial metabolic pathways in human brain health and disease
Spichak, S., Bastiaanssen, T. F. S., Berding, K., Vlckova, K., Clarke, G., Dinan, T. G., & Cryan, J. F. (2021) · Neuroscience & Biobehavioral Reviews · doi:10.1016/j.neubiorev.2021.02.044 · Cited by 127
Endogenous rRNA Sequence Variation Can Regulate Stress Response Gene Expression and Phenotype
Kurylo, C. M., Parks, M. M., Juette, M. F., Zinshteyn, B., Altman, R. B., Thibado, J. K., Vincent, C. T., & Blanchard, S. C. (2018) · Cell Reports · doi:10.1016/j.celrep.2018.08.093 · Cited by 117
Methyl-compound use and slow growth characterize microbial life in 2-km-deep subseafloor coal and shale beds
Trembath-Reichert, E., Morono, Y., Ijiri, A., Hoshino, T., Dawson, K. S., Inagaki, F., & Orphan, V. J. (2017) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1707525114 · Cited by 112
Oral Samples as non-invasive proxies for assessing the composition of the rumen microbial community
Tapio, I., Shingfield, K. J., McKain, N., Bonin, A., Fischer, D., Bayat, A. R., Vilkki, J., Taberlet, P., Snelling, T. J., & Wallace, R. J. (2016) · PLoS ONE · doi:10.1371/journal.pone.0151220 · Cited by 125
The nasopharyngeal microbiota in patients with viral respiratory tract infections is enriched in bacterial pathogens
Edouard, S., Million, M., Bachar, D., Dubourg, G., Michelle, C., Ninove, L., Charrel, R., & Raoult, D. (2018) · European Journal of Clinical Microbiology & Infectious Diseases · doi:10.1007/s10096-018-3305-8 · Cited by 124
Microbial composition of Kombucha determined using amplicon sequencing and shotgun metagenomics
Arıkan, M., Mitchell, A. L., Finn, R. D., & Gürel, F. (2020) · Journal of Food Science · doi:10.1111/1750-3841.14992 · Cited by 123
Orally administered Odoribacter laneus improves glucose control and inflammatory profile in obese mice by depleting circulating succinate
Huber-Ruano, I., Calvo, E., Mayneris-Perxachs, J., Rodríguez-Peña, M.-M., Ceperuelo-Mallafré, V., Cedó, L., Núñez-Roa, C., Miro-Blanch, J., Arnoriaga-Rodríguez, M., Balvay, A., et al. (2022) · Microbiome · doi:10.1186/s40168-022-01306-y · Cited by 122
An open label, non-randomized study assessing a prebiotic fiber intervention in a small cohort of Parkinson’s disease participants
Hall, D. A., Voigt, R. M., Cantu-Jungles, T. M., Hamaker, B., Engen, P. A., Shaikh, M., Raeisi, S., Green, S. J., Naqib, A., Forsyth, C. B., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-36497-x · Cited by 124
Probiotic yogurt and acidified milk similarly reduce postprandial inflammation and both alter the gut microbiota of healthy, young men
Burton, K. J., Rosikiewicz, M., Pimentel, G., Bütikofer, U., von Ah, U., Voirol, M.-J., Croxatto, A., Aeby, S., Drai, J., McTernan, P. G., et al. (2017) · British Journal of Nutrition · doi:10.1017/s0007114517000885 · Cited by 121
Fecal microbial transplantation and a high fiber diet attenuates emphysema development by suppressing inflammation and apoptosis
Jang, Y. O., Lee, S. H., Choi, J. J., Kim, D.-H., Choi, J.-M., Kang, M.-J., Oh, Y.-M., Park, Y.-J., Shin, Y., & Lee, S. W. (2020) · Experimental & Molecular Medicine · doi:10.1038/s12276-020-0469-y · Cited by 121
Tracing the fate of microplastic carbon in the aquatic food web by compound-specific isotope analysis
Taipale, S. J., Peltomaa, E., Kukkonen, J. V. K., Kainz, M. J., Kautonen, P., & Tiirola, M. (2019) · Scientific Reports · doi:10.1038/s41598-019-55990-2 · Cited by 115
Short-term impact of sucralose consumption on the metabolic response and gut microbiome of healthy adults
Thomson, P., Santibañez, R., Aguirre, C., Galgani, J. E., & Garrido, D. (2019) · British Journal Of Nutrition · doi:10.1017/s0007114519001570 · Cited by 117
Photo-produced aromatic compounds stimulate microbial degradation of dissolved organic carbon in thermokarst lakes
Hu, J., Kang, L., Li, Z., Feng, X., Liang, C., Wu, Z., Zhou, W., Liu, X., Yang, Y., & Chen, L. (2023) · Nature Communications · doi:10.1038/s41467-023-39432-2 · Cited by 114
Short chain fatty acids-producing and mucin-degrading intestinal bacteria predict the progression of early Parkinson’s disease
Nishiwaki, H., Ito, M., Hamaguchi, T., Maeda, T., Kashihara, K., Tsuboi, Y., Ueyama, J., Yoshida, T., Hanada, H., Takeuchi, I., et al. (2022) · npj Parkinson's Disease · doi:10.1038/s41531-022-00328-5 · Cited by 116
Heterochronic faecal transplantation boosts gut germinal centres in aged mice
Stebegg, M., Silva-Cayetano, A., Innocentin, S., Jenkins, T. P., Cantacessi, C., Gilbert, C., & Linterman, M. A. (2019) · Nature Communications · doi:10.1038/s41467-019-10430-7 · Cited by 107
Association of the gut microbiota with cognitive function in midlife
Meyer, K., Lulla, A., Debroy, K., Shikany, J. M., Yaffe, K., Meirelles, O., & Launer, L. J. (2022) · JAMA Network Open · doi:10.1001/jamanetworkopen.2021.43941 · Cited by 110
Social isolation alters behavior, the gut-immune-brain axis, and neurochemical circuits in male and female prairie voles
Donovan, M., Mackey, C. S., Platt, G. N., Rounds, J., Brown, A. N., Trickey, D. J., Liu, Y., Jones, K. M., & Wang, Z. (2020) · Neurobiology of Stress · doi:10.1016/j.ynstr.2020.100278 · Cited by 85
Cultured microbes represent a substantial fraction of the human and mouse gut microbiota
Lagkouvardos, I., Overmann, J., & Clavel, T. (2017) · Gut Microbes · doi:10.1080/19490976.2017.1320468 · Cited by 104
Enhancing soil health and nutrient cycling through soil amendments: improving the synergy of bacteria and fungi
Ding, Y., Gao, X., Shu, D., Siddique, K. H. M., Song, X., Wu, P., Li, C., & Zhao, X. (2024) · Science of The Total Environment · doi:10.1016/j.scitotenv.2024.171332 · Cited by 107
Analytical tools and current challenges in the modern era of neuroepigenomics
Maze, I., Shen, L., Zhang, B., Garcia, B. A., Shao, N., Mitchell, A., Sun, H., Akbarian, S., Allis, C. D., & Nestler, E. J. (2014) · Nature Neuroscience · doi:10.1038/nn.3816 · Cited by 100
Reservoirs of antimicrobial resistance genes in retail raw milk
Liu, J., Zhu, Y., Jay-Russell, M., Lemay, D. G., & Mills, D. A. (2020) · Microbiome · doi:10.1186/s40168-020-00861-6 · Cited by 99
The Impact of Intratumoral and Gastrointestinal Microbiota on Systemic Cancer Therapy
Cogdill, A. P., Gaudreau, P. O., Arora, R., Gopalakrishnan, V., & Wargo, J. A. (2018) · Trends in Immunology · doi:10.1016/j.it.2018.09.007 · Cited by 98
Dectin-1 signaling on colonic γδ T cells promotes psychosocial stress responses
Zhu, X., Sakamoto, S., Ishii, C., Smith, M. D., Ito, K., Obayashi, M., Unger, L., Hasegawa, Y., Kurokawa, S., Kishimoto, T., et al. (2023) · Nature Immunology · doi:10.1038/s41590-023-01447-8 · Cited by 99
Temporal evolution of the microbiome, immune system, and epigenome with disease progression in ALS mice
Figueroa-Romero, C., Guo, K., Murdock, B. J., Paez-Colasante, X., Bassis, C. M., Mikhail, K. A., Raue, K. D., Evans, M. C., Taubman, G. F., McDermott, A. J., et al. (2019) · Disease Models & Mechanisms · doi:10.1242/dmm.041947 · Cited by 94
Profiling of tumour-associated microbiota in human hepatocellular carcinoma
Komiyama, S., Yamada, T., Takemura, N., Kokudo, N., Hase, K., & Kawamura, Y. I. (2021) · Scientific Reports · doi:10.1038/s41598-021-89963-1 · Cited by 96
Iron in micronutrient Powder promotes an Unfavorable gut microbiota in Kenyan infants
Tang, M., Frank, D., Hendricks, A., Ir, D., Esamai, F., Liechty, E., Hambidge, K., & Krebs, N. (2017) · Nutrients · doi:10.3390/nu9070776 · Cited by 94
“0-r23838) [23] using the 418,497 bacterial sequences in Silva 115NR99 [24] as reference configured to yield the Silva taxonomy.”
Method
Diet leaves a genetic signature in a keystone member of the gut microbiota
Dapa, T., Ramiro, R. S., Pedro, M. F., Gordo, I., & Xavier, K. B. (2022) · Cell Host & Microbe · doi:10.1016/j.chom.2022.01.002 · Cited by 91
Effects of inoculants Lactobacillus brevis and Lactobacillus parafarraginis on the fermentation characteristics and microbial communities of corn stover silage
Xu, Z., He, H., Zhang, S., & Kong, J. (2017) · Scientific Reports · doi:10.1038/s41598-017-14052-1 · Cited by 94
EIF1AX and RAS Mutations Cooperate to Drive Thyroid Tumorigenesis through ATF4 and c-MYC
Krishnamoorthy, G. P., Davidson, N. R., Leach, S. D., Zhao, Z., Lowe, S. W., Lee, G., Landa, I., Nagarajah, J., Saqcena, M., Singh, K., et al. (2019) · Cancer Discovery · doi:10.1158/2159-8290.cd-18-0606 · Cited by 94
Exercise-induced microbiota metabolite enhances CD8 T cell antitumor immunity promoting immunotherapy efficacy
Phelps, C. M., Willis, N. B., Duan, T., Lee, A. H., Zhang, Y., Rodriguez J, D. M., Pandey, S. P., Laughlin, C. R., Rosen, A. B. I., McPherson, A. C., et al. (2025) · Cell · doi:10.1016/j.cell.2025.06.018 · Cited by 91
Revegetation of urban green space rewilds soil microbiotas with implications for human health and urban design
Mills, J. G., Bissett, A., Gellie, N. J. C., Lowe, A. J., Selway, C. A., Thomas, T., Weinstein, P., Weyrich, L. S., & Breed, M. F. (2020) · Restoration Ecology · doi:10.1111/rec.13175 · Cited by 90
Postnatal colonization with human "infant-type" Bifidobacterium species alters behavior of adult gnotobiotic mice
Luk, B., Veeraragavan, S., Engevik, M., Balderas, M., Major, A., Runge, J., Luna, R. A., & Versalovic, J. (2018) · PLOS ONE · doi:10.1371/journal.pone.0196510 · Cited by 90
Nigral overexpression of α-synuclein in a rat Parkinson's disease model indicates alterations in the enteric nervous system and the gut microbiome
O’Donovan, S. M., Crowley, E. K., Brown, J. R. ‐., O’Sullivan, O., O’Leary, O. F., Timmons, S., Nolan, Y. M., Clarke, D. J., Hyland, N. P., Joyce, S. A., et al. (2020) · Neurogastroenterology & Motility · doi:10.1111/nmo.13726 · Cited by 86
Nitrate reduction capacity of the oral microbiota is impaired in periodontitis: potential implications for systemic nitric oxide availability
Rosier, B. T., Johnston, W., Carda-Diéguez, M., Simpson, A., Cabello-Yeves, E., Piela, K., Reilly, R., Artacho, A., Easton, C., Burleigh, M., et al. (2024) · International Journal of Oral Science · doi:10.1038/s41368-023-00266-9 · Cited by 85
Shaping of Intestinal Microbiota in Nlrp6- and Rag2-Deficient Mice Depends on Community Structure
Gálvez, E. J. C., Iljazovic, A., Gronow, A., Flavell, R., & Strowig, T. (2017) · Cell Reports · doi:10.1016/j.celrep.2017.12.027 · Cited by 81
Analysis of matched skin and gut microbiome of patients with vitiligo reveals deep skin dysbiosis: link with mitochondrial and immune changes
Bzioueche, H., Simonyté Sjödin, K., West, C. E., Khemis, A., Rocchi, S., Passeron, T., & Tulic, M. K. (2021) · Journal of Investigative Dermatology · doi:10.1016/j.jid.2021.01.036 · Cited by 77
Microbial embryonal colonization during pipefish male pregnancy
Beemelmanns, A., Poirier, M., Bayer, T., Kuenzel, S., & Roth, O. (2019) · Scientific Reports · doi:10.1038/s41598-018-37026-3 · Cited by 78
Colonization of the human gut by bovine bacteria present in Parmesan cheese
Milani, C., Duranti, S., Napoli, S., Alessandri, G., Mancabelli, L., Anzalone, R., Longhi, G., Viappiani, A., Mangifesta, M., Lugli, G. A., et al. (2019) · Nature Communications · doi:10.1038/s41467-019-09303-w · Cited by 78
Maternal obese-type gut microbiota differentially impact cognition, anxiety and compulsive behavior in male and female offspring in mice
Bruce-Keller, A. J., Fernandez-Kim, S.-O., Townsend, R. L., Kruger, C., Carmouche, R., Newman, S., Salbaum, J. M., & Berthoud, H.-R. (2017) · PLoS ONE · doi:10.1371/journal.pone.0175577 · Cited by 76
How Really Ancient Is Paulinella Chromatophora?
Delaye, L., Valadez-Cano, C., & Pérez-Zamorano, B. (2016) · PLoS Currents · doi:10.1371/currents.tol.e68a099364bb1a1e129a17b4e06b0c6b · Cited by 72
Integrative analysis of gut microbiota composition, host colonic gene expression and intraluminal metabolites in aging C57BL/6J mice
van der Lugt, B., Rusli, F., Lute, C., Lamprakis, A., Salazar, E., Boekschoten, M. V., Hooiveld, G. J., Müller, M., Vervoort, J., Kersten, S., et al. (2018) · Aging · doi:10.18632/aging.101439 · Cited by 72
Faecal microbiota transplant ameliorates gut dysbiosis and cognitive deficits in Huntington’s disease mice
Gubert, C., Choo, J. M., Love, C. J., Kodikara, S., Masson, B. A., Liew, J. J. M., Wang, Y., Kong, G., Narayana, V. K., Renoir, T., et al. (2022) · Brain Communications · doi:10.1093/braincomms/fcac205 · Cited by 71
Bioremediation of Coastal Aquaculture Effluents Spiked with Florfenicol Using Microalgae-Based Granular Sludge—A Promising Solution for Recirculating Aquaculture Systems
Oliveira, A. S., Alves, M., Leitão, F., Tacão, M., Henriques, I., Castro, P. M. L., & Amorim, C. L. (2023) · Water Research · doi:10.1016/j.watres.2023.119733 · Cited by 67
Microbial ecology of the newly discovered serpentinite-hosted Old City hydrothermal field (southwest Indian ridge)
Lecoeuvre, A., Ménez, B., Cannat, M., Chavagnac, V., & Gérard, E. (2021) · The ISME Journal · doi:10.1038/s41396-020-00816-7 · Cited by 62
Microbiota succession during aerobic stability of maize silage inoculated with Lentilactobacillus buchneri NCIMB 40788 and Lentilactobacillus hilgardii CNCM‐I‐4785
Drouin, P., Tremblay, J., Renaud, J., & Apper, E. (2021) · MicrobiologyOpen · doi:10.1002/mbo3.1153 · Cited by 60
Modulation of pathogenic oral biofilms towards health with nisin probiotic
Radaic, A., Ye, C., Parks, B., Gao, L., Kuraji, R., Malone, E., Kamarajan, P., Zhan, L., & Kapila, Y. L. (2020) · Journal of Oral Microbiology · doi:10.1080/20002297.2020.1809302 · Cited by 59
The Oral Microbiome and Inflammation in Mild Cognitive Impairment
Yang, I., Arthur, R. A., Zhao, L., Clark, J., Hu, Y., Corwin, E. J., & Lah, J. (2021) · Experimental Gerontology · doi:10.1016/j.exger.2021.111273 · Cited by 56
Diversity of Bacterial Community during Ensiling and Subsequent Exposure to Air in Whole-Plant Maize Silage
Hu, Z., Chang, J., Yu, J., Li, S., & Niu, H. (2018) · Asian-Australasian Journal of Animal Sciences · doi:10.5713/ajas.17.0860 · Cited by 55
Development of the gut microbiota in healthy children in the first ten years of life: associations with internalizing and externalizing behavior
Ou, Y., Belzer, C., Smidt, H., & de Weerth, C. (2022) · Gut Microbes · doi:10.1080/19490976.2022.2038853 · Cited by 54
Oral, Nasal, and Gut Microbiota in Parkinson’s Disease
Li, Z., Lu, G., Luo, E., Wu, B., Li, Z., Guo, J., Xia, Z., Zheng, C., Su, Q., Zeng, Y., et al. (2022) · Neuroscience · doi:10.1016/j.neuroscience.2021.10.011 · Cited by 52
Gut microbiota mediated the therapeutic efficacies and the side effects of prednisone in the treatment of MRL/lpr mice
Wang, M., Zhu, Z., Lin, X., Li, H., Wen, C., Bao, J., & He, Z. (2021) · Arthritis Research & Therapy · doi:10.1186/s13075-021-02620-w · Cited by 52
Metabolic landscape of the male mouse gut identifies different niches determined by microbial activities
Meier, K. H. U., Trouillon, J., Li, H., Lang, M., Fuhrer, T., Zamboni, N., Sunagawa, S., Macpherson, A. J., & Sauer, U. (2023) · Nature Metabolism · doi:10.1038/s42255-023-00802-1 · Cited by 48
Revealing the microbial heritage of traditional Brazilian cheeses through metagenomics
Kothe, C. I., Mohellibi, N., & Renault, P. (2022) · Food Research International · doi:10.1016/j.foodres.2022.111265 · Cited by 51
Repurposing Metformin in Nondiabetic People With HIV: Influence on Weight and Gut Microbiota
Isnard, S., Lin, J., Fombuena, B., Ouyang, J., Varin, T. V., Richard, C., Marette, A., Ramendra, R., Planas, D., Raymond Marchand, L., et al. (2020) · Open Forum Infectious Diseases · doi:10.1093/ofid/ofaa338 · Cited by 51
Altered gut microbiota in older adults with mild cognitive impairment: a case-control study
Fan, K.-C., Lin, C.-C., Liu, Y.-C., Chao, Y.-P., Lai, Y.-J., Chiu, Y.-L., & Chuang, Y.-F. (2023) · Frontiers in Aging Neuroscience · doi:10.3389/fnagi.2023.1162057 · Cited by 47

Authors: Quast, C., Pruesse, E., Yilmaz, P., Gerken, J., Schweer, T., Yarza, P., Peplies, J., & Glöckner, F. O.
Affiliations: Max Planck Institute for Marine Microbiology (DE)
Constructor University (DE)
Corresponding author: Glöckner, Frank Oliver
ORCID: Quast, Christian
Pruesse, Elmar
Yilmaz, Pelin
Gerken, Jan
Yarza, Pablo
Peplies, Jörg
Glöckner, Frank Oliver
Venue: Nucleic Acids Research
Publisher: Oxford University Press (OUP)
Published: 2012-11-27
Volume: 41
Issue: D1
Pages: D590-D596
ISSN: 0305-1048 (ISSN-L)
1362-4962
DOI: 10.1093/nar/gks1219
PMC: PMC3531112
OpenAlex: W2034285706
Cited by: 33,055
References: 24
Citations by year: 2026: 3407 · 2025: 4378 · 2024: 4486 · 2023: 4028 · 2022: 4123 · 2021: 3786 · 2020: 2909 · 2019: 1893 · 2018: 1366 · 2017: 959 · 2016: 753 · 2015: 497 · 2014: 317 · 2013: 122 · 2012: 4
FWCI: 121.20
Type: journal article
Language: en
Open access: gold
doi.org
Licence: cc-by-nc
creativecommons.org/licenses/by-nc/3.0 (vor, 1407 d)
Locations: Nucleic Acids Research (publishedVersion, cc-by-nc)
Europe PMC (PubMed Central) (publishedVersion, cc-by-nc)
PubMed Central (publishedVersion, cc-by-nc)
PubMed (publishedVersion)
MPG.PuRe (Max Planck Society) (submittedVersion, other-oa)
Max Planck Digital Library (submittedVersion)
Zenodo (CERN European Organization for Nuclear Research) (cc-by)
Funders: Deutsche Forschungsgemeinschaft
Max-Planck-Gesellschaft
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
Physical Sciences › Environmental Science › Ecology › Environmental DNA in Biodiversity Studies
Keywords: SILVA database, ribosomal RNA gene sequences, small subunit rRNA, large subunit rRNA, sequencing quality control, bacterial classification, web-based tool
MeSH terms: Archaea, Bacteria, Software, Internet, Genes, rRNA, Databases, Nucleic Acid, Eukaryota, High-Throughput Nucleotide Sequencing

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review

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

Abstract

Overview

Integrity signals

Verification

Claims the paper makes

Claims other papers make about this one

Self-check

Citations

Cites

Cited by

Related

Metadata

Record

About these checks