Contamination in Low Microbial Biomass Microbiome Studies: Issues and Recommendations

Structure, function and diversity of the healthy human microbiome

The Human Microbiome Project Consortium (2012) · Nature · doi:10.1038/nature11234 · Cited by 11,726 · see citing works

Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms

Caporaso, J. G., Lauber, C. L., Walters, W. A., Berg-Lyons, D., Huntley, J., Fierer, N., Owens, S. M., Betley, J., Fraser, L., Bauer, M., et al. (2012) · The ISME Journal · doi:10.1038/ismej.2012.8 · Cited by 8,839 · see citing works

UniFrac: a New Phylogenetic Method for Comparing Microbial Communities

Lozupone, C., & Knight, R. (2005) · Applied and Environmental Microbiology · doi:10.1128/aem.71.12.8228-8235.2005 · Cited by 8,227 · see citing works

Simple statistical identification and removal of contaminant sequences in marker-gene and metagenomics data

Davis, N. M., Proctor, D. M., Holmes, S. P., Relman, D. A., & Callahan, B. J. (2018) · Microbiome · doi:10.1186/s40168-018-0605-2 · Cited by 3,493 · 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

The Placenta Harbors a Unique Microbiome

Aagaard, K., Ma, J., Antony, K. M., Ganu, R., Petrosino, J., & Versalovic, J. (2014) · Science Translational Medicine · doi:10.1126/scitranslmed.3008599 · Cited by 2,494 · see citing works

Illumina Sequencing Library Preparation for Highly Multiplexed Target Capture and SequencingPreprint

Meyer, M., & Kircher, M. (2010) · Cold Spring Harbor Protocols · doi:10.1101/pdb.prot5448 · Cited by 2,233 · see citing works

Genomic analysis identifies association of <i>Fusobacterium</i> with colorectal carcinoma

Kostic, A. D., Gevers, D., Pedamallu, C. S., Michaud, M., Duke, F., Earl, A. M., Ojesina, A. I., Jung, J., Bass, A. J., Tabernero, J., et al. (2012) · Genome Research · doi:10.1101/gr.126573.111 · Cited by 1,960 · see citing works

Ancient DNA: Do It Right or Not at All

Cooper, A., & Poinar, H. N. (2000) · Science · doi:10.1126/science.289.5482.1139b · Cited by 1,270 · see citing works

Strains, functions and dynamics in the expanded Human Microbiome Project

Lloyd-Price, J., Mahurkar, A., Rahnavard, G., Crabtree, J., Orvis, J., Hall, A. B., Brady, A., Creasy, H. H., McCracken, C., Giglio, M. G., et al. (2017) · Nature · doi:10.1038/nature23889 · Cited by 1,267 · see citing works

Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries

Aird, D., Ross, M. G., Chen, W.-S., Danielsson, M., Fennell, T., Russ, C., Jaffe, D. B., Nusbaum, C., & Gnirke, A. (2011) · Genome Biology · doi:10.1186/gb-2011-12-2-r18 · Cited by 1,174 · see citing works

The influence of sex, handedness, and washing on the diversity of hand surface bacteria

Fierer, N., Hamady, M., Lauber, C. L., & Knight, R. D. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0807920105 · Cited by 1,100 · 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

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

Fecal microbiota transplantation for Clostridium difficile infection: systematic review and meta-analysis

Kassam, Z., Lee, C. H., Yuan, Y., & Hunt, R. H. (2013) · American Journal of Gastroenterology · doi:10.1038/ajg.2013.59 · Cited by 904 · see citing works

Revival and identification of bacterial spores in 25- to 40-million-year-old Dominican amber

Cano, R. J., & Borucki, M. K. (1995) · Science · doi:10.1126/science.7538699 · Cited by 641 · see citing works

The half-life of DNA in bone: measuring decay kinetics in 158 dated fossils

Allentoft, M. E., Collins, M., Harker, D., Haile, J., Oskam, C. L., Hale, M. L., Campos, P. F., Samaniego, J. A., Gilbert, M. T. P., Willerslev, E., et al. (2012) · Proceedings of the Royal Society B: Biological Sciences · doi:10.1098/rspb.2012.1745 · Cited by 633 · see citing works

Forensic identification using skin bacterial communities

Fierer, N., Lauber, C. L., Zhou, N., McDonald, D. T., Costello, E. K., & Knight, R. D. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1000162107 · Cited by 610 · see citing works

Neanderthal behaviour, diet, and disease inferred from ancient DNA in dental calculus

Weyrich, L. S., Duchêne, S., Soubrier, J., Arriola, L. A., Llamas, B., Breen, J., Morris, A. G., Alt, K. W., Caramelli, D., Dresely, V., et al. (2017) · Nature · doi:10.1038/nature21674 · Cited by 584 · see citing works

Inherent bacterial DNA contamination of extraction and sequencing reagents may affect interpretation of microbiota in low bacterial biomass samples

Glassing, A., Dowd, S. E., Galandiuk, S., Davis, B. R., & Chiodini, R. J. (2016) · Gut Pathogens · doi:10.1186/s13099-016-0103-7 · Cited by 569 · see citing works

Microbial Dysbiosis Is Associated with Human Breast Cancer

Xuan, C., Shamonki, J. M., Chung, A., DiNome, M. L., Chung, M., Sieling, P. A., & Lee, D. J. (2014) · PLoS ONE · doi:10.1371/journal.pone.0083744 · Cited by 543 · 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

The Microbiome of Aseptically Collected Human Breast Tissue in Benign and Malignant Disease

Hieken, T. J., Chen, J., Hoskin, T. L., Walther-Antonio, M. R. S., Johnson, S. P., Ramaker, S., Xiao, J. Y., Radisky, D. C., Knutson, K. L., Kalari, K. R., et al. (2016) · Scientific Reports · doi:10.1038/srep30751 · Cited by 495 · see citing works

Home Life: Factors Structuring the Bacterial Diversity Found within and between Homes

Dunn, R. R., Fierer, N., Henley, J. B., Leff, J., & Menninger, H. (2013) · PLoS ONE · doi:10.1371/journal.pone.0064133 · Cited by 345 · see citing works

Controlling for Contaminants in Low-Biomass 16S rRNA Gene Sequencing Experiments

Karstens, L., Asquith, M. J., Davin, S., Fair, D. A., Gregory, W. T., Wolfe, A. J., Braun, J. G., & McWeeney, S. K. (2019) · mSystems · doi:10.1128/msystems.00290-19 · Cited by 327 · see citing works

Parsing ecological signal from noise in next generation amplicon sequencing

Nguyen, N., Smith, D. P., Peay, K., & Kennedy, P. G. (2014) · New Phytologist · doi:10.1111/nph.12923 · Cited by 320 · see citing works

Common Contaminants in Next-Generation Sequencing That Hinder Discovery of Low-Abundance Microbes

Laurence, M., Hatzis, C., & Brash, D. E. (2014) · PLoS ONE · doi:10.1371/journal.pone.0097876 · Cited by 314 · see citing works

DNA Sequence from Cretaceous Period Bone Fragments

Woodward, S. R., Weyand, N. J., & Bunnell, M. D. (1994) · Science · doi:10.1126/science.7973705 · Cited by 314 · see citing works

A microbial ecosystem beneath the West Antarctic ice sheet

Christner, B. C., Priscu, J. C., Achberger, A. M., Barbante, C., Carter, S. P., Christianson, K., Michaud, A. B., Mikucki, J. A., Mitchell, A. C., Skidmore, M. L., et al. (2014) · Nature · doi:10.1038/nature13667 · Cited by 313 · see citing works

The Microbiome of Animals: Implications for Conservation Biology

Bahrndorff, S., Alemu, T., Alemneh, T., & Nielsen, J. L. (2016) · International Journal of Genomics · doi:10.1155/2016/5304028 · Cited by 305 · see citing works

Simple statistical identification and removal of contaminant sequences in marker-gene and metagenomics dataPreprint

Davis, N. M., Proctor, D. M., Holmes, S., et al. (2017) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/221499 · Cited by 304 · see citing works

Bioaerosol generation by raindrops on soil

Joung, Y. S., Ge, Z., & Buie, C. (2017) · Nature Communications · doi:10.1038/ncomms14668 · Cited by 300 · see citing works

An Efficient Multistrategy DNA Decontamination Procedure of PCR Reagents for Hypersensitive PCR Applications

Champlot, S., Berthelot, C., Pruvost, M., Bennett, E. A., Grange, T., & Geigl, E.-M. (2010) · PLoS ONE · doi:10.1371/journal.pone.0013042 · Cited by 297 · see citing works

Microbiota of the indoor environment: a meta-analysis

Adams, R. I., Bateman, A. C., Bik, H. M., & Meadow, J. F. (2015) · Microbiome · doi:10.1186/s40168-015-0108-3 · Cited by 288 · see citing works

Isolation of nucleic acids and cultures from fossil ice and permafrost

Willerslev, E., Hansen, A. J., & Poinar, H. N. (2003) · Trends in Ecology & Evolution · doi:10.1016/j.tree.2003.11.010 · Cited by 279 · see citing works

Characterization and remediation of sample index swaps by non-redundant dual indexing on massively parallel sequencing platforms

Costello, M., Fleharty, M., Abreu, J., Farjoun, Y., Ferriera, S., Holmes, L., Granger, B. R., Green, L., Howd, T., Mason, T., et al. (2018) · BMC Genomics · doi:10.1186/s12864-018-4703-0 · Cited by 276 · see citing works

Amplification and sequencing of DNA from a 120–135-million-year-old weevil

Cano, R. J., Poinar, H. N., Pieniążek, N. J., Acra, A. N., & Poinar, G. O. (1993) · Nature · doi:10.1038/363536a0 · Cited by 273 · see citing works

Specific Ribosomal DNA Sequences from Diverse Environmental Settings Correlate with Experimental Contaminants

Tanner, M. A., Goebel, B. M., Dojka, M. A., & Pace, N. R. (1998) · Applied and Environmental Microbiology · doi:10.1128/aem.64.8.3110-3113.1998 · Cited by 270 · see citing works

Laboratory contamination over time during low‐biomass sample analysis

(2018) · doi:10.1101/460212 · Cited by 252 · see citing works

Laboratory contamination over time during low‐biomass sample analysis

Weyrich, L. S., Farrer, A. G., Eisenhofer, R., Arriola, L. A., Young, J. M., Selway, C. A., Handsley‐Davis, M., Adler, C. J., Breen, J., & Cooper, A. (2019) · Molecular Ecology Resources · doi:10.1111/1755-0998.13011 · Cited by 252 · see citing works

The Perils of Pathogen Discovery: Origin of a Novel Parvovirus-Like Hybrid Genome Traced to Nucleic Acid Extraction Spin Columns

Naccache, S. N., Greninger, A. L., Lee, D., Coffey, L. L., Phan, T. G., Rein‐Weston, A., Aronsohn, A. I., Hackett, J., Delwart, E., & Chiu, C. Y. (2013) · Journal of Virology · doi:10.1128/jvi.02323-13 · Cited by 251 · see citing works

Temporal Stability and Composition of the Ocular Surface Microbiome

Ozkan, J., Nielsen, S. J., Díez‐Vives, C., Coroneo, M. T., Thomas, T., & Willcox, M. D. P. (2017) · Scientific Reports · doi:10.1038/s41598-017-10494-9 · Cited by 244 · see citing works

Microbiomes of the dust particles collected from the International Space Station and Spacecraft Assembly Facilities

Checinska, A., Probst, A. J., Vaishampayan, P., White, J. R., Kumar, D., Stepanov, V. G., Fox, G. E., Nilsson, R. H., Pierson, D. L., Perry, J. L., et al. (2015) · Microbiome · doi:10.1186/s40168-015-0116-3 · Cited by 236 · see citing works

Local genomic adaptation of coral reef-associated microbiomes to gradients of natural variability and anthropogenic stressors

Kelly, L. W., Williams, G. J., Barott, K. L., Carlson, C. A., Dinsdale, E. A., Edwards, R. A., Haas, A. F., Haynes, M. R., Lim, Y. W., Somera, T. M., et al. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1403319111 · Cited by 232 · see citing works

Characterization of the microbiome of nipple aspirate fluid of breast cancer survivors

Chan, A. A., Bashir, M., Rivas, M. N., Duvall, K., Sieling, P. A., Pieber, T. R., Vaishampayan, P., Love, S. M., & Lee, D. J. (2016) · Scientific Reports · doi:10.1038/srep28061 · Cited by 223 · see citing works

From the field to the laboratory: Controlling DNA contamination in human ancient DNA research in the high-throughput sequencing era

Llamas, B., Valverde, G., Fehren‐Schmitz, L., Weyrich, L. S., Cooper, A., & Haak, W. (2016) · STAR Science & Technology of Archaeological Research · doi:10.1080/20548923.2016.1258824 · Cited by 217 · see citing works

The preterm placental microbiome varies in association with excess maternal gestational weight gain

Antony, K. M., Ma, J., Mitchell, K. B., Racusin, D., Versalovic, J. A., & Aagaard, K. M. (2015) · American Journal of Obstetrics and Gynecology · doi:10.1016/j.ajog.2014.12.041 · Cited by 212 · see citing works

Decontamination of MDA Reagents for Single Cell Whole Genome Amplification

Woyke, T., Sczyrba, A., Lee, J., Rinke, C., Tighe, D., Clingenpeel, S. R., Malmstrom, R. R., Stepanauskas, R., & Cheng, J. (2011) · PLoS ONE · doi:10.1371/journal.pone.0026161 · Cited by 206 · see citing works

Diverse and Widespread Contamination Evident in the Unmapped Depths of High Throughput Sequencing Data

Lusk, R. W. (2014) · PLoS ONE · doi:10.1371/journal.pone.0110808 · Cited by 201 · see citing works

The Placental Microbiome Varies in Association with Low Birth Weight in Full-Term Neonates

Zheng, J., Xiao, X., Zhang, Q., Mao, L., Yu, M., & Xu, J. (2015) · Nutrients · doi:10.3390/nu7085315 · Cited by 200 · 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

Detecting Dinosaur DNA

Zischler, H., Höss, M., Handt, O., von Haeseler, A., van der Kuyl, A. C., Goudsmit, J., & Pääbo, S. (1995) · Science · doi:10.1126/science.7605504 · Cited by 184 · see citing works

Tracking down the sources of experimental contamination in microbiome studies

Weiss, S. J., Amir, A., Hyde, E. R., Metcalf, J. L., Song, S. J., & Knight, R. D. (2014) · Genome biology · doi:10.1186/s13059-014-0564-2 · Cited by 182 · see citing works

Don't make a mista(g)ke: is tag switching an overlooked source of error in amplicon pyrosequencing studies?

Carlsen, T., Aas, A. B., Lindner, D. L., Vrålstad, T., Schumacher, T. K., & Kauserud, H. (2012) · Fungal ecology · doi:10.1016/j.funeco.2012.06.003 · Cited by 180 · see citing works

New perspectives on viable microbial communities in low-biomass cleanroom environments

Vaishampayan, P., Probst, A. J., Duc, M. T. L., Bargoma, E., Benardini, J. N., Andersen, G. L., & Venkateswaran, K. J. (2012) · The ISME Journal · doi:10.1038/ismej.2012.114 · Cited by 170 · see citing works

Problems of reproducibility – does geologically ancient DNA survive in amber–preserved insects?

Austin, J. J., Ross, A. J., Smith, A. B., Fortey, R. A., & Thomas, R. H. (1997) · Proceedings of the Royal Society B Biological Sciences · doi:10.1098/rspb.1997.0067 · Cited by 163 · see citing works

Microbiome of the placenta in pre‐eclampsia supports the role of bacteria in the multifactorial cause of pre‐eclampsia

Amarasekara, R., Jayasekara, R. W., Senanayake, H. M., & Dissanayake, V. H. W. (2014) · Journal of obstetrics and gynaecology research · doi:10.1111/jog.12619 · Cited by 152 · see citing works

Airborne Bacterial Communities in Residences: Similarities and Differences with Fungi

Adams, R. I., Miletto, M., Lindow, S. E., Taylor, J. W., & Bruns, T. D. (2014) · PLoS ONE · doi:10.1371/journal.pone.0091283 · Cited by 152 · see citing works

DNA extraction from low-biomass carbonate rock: An improved method with reduced contamination and the low-biomass contaminant database

Barton, H. A., Taylor, N. M., Lübbers, B., & Pemberton, A. C. (2005) · Journal of Microbiological Methods · doi:10.1016/j.mimet.2005.10.005 · Cited by 150 · see citing works

Brain microbial populations in HIV/AIDS: α-proteobacteria predominate independent of host immune status

Branton, W. G., Ellestad, K. K., Maingat, F., Wheatley, B. M., Rud, E., Warren, R. L., Holt, R. A., Surette, M. G., & Power, C. (2013) · PLoS ONE · doi:10.1371/journal.pone.0054673 · Cited by 149 · see citing works

Metagenomic resolution of microbial functions in deep-sea hydrothermal plumes across the Eastern Lau Spreading Center

Anantharaman, K., Breier, J. A., & Dick, G. J. (2015) · The ISME Journal · doi:10.1038/ismej.2015.81 · Cited by 146 · see citing works

Identification of mixed bacterial DNA contamination in broad-range PCR amplification of 16S rDNA V1 and V3 variable regions by pyrosequencing of cloned amplicons

Grahn, N., Olofsson, M., Ellnebo‐Svedlund, K., Monstein, H.-J. ⁄. R., & Jonasson, J. (2003) · FEMS Microbiology Letters · doi:10.1016/s0378-1097(02)01190-4 · Cited by 143 · see citing works

KatharoSeq Enables High-Throughput Microbiome Analysis from Low-Biomass Samples

Minich, J. J., Zhu, Q., Janssen, S., Hendrickson, R., Amir, A., Vetter, R., Hyde, J. R., Doty, M. M., Stillwell, K., Benardini, J. N., et al. (2018) · mSystems · doi:10.1128/msystems.00218-17 · Cited by 135 · see citing works

Barcoded sequencing reveals diverse intrauterine microbiomes in patients suffering with endometrial polyps.

Fang, R., Chen, L.-X., Shu, W., Yao, S., Wang, S., & Chen, Y. (2016) · PubMed Central · Cited by 132 · see citing works

21st century agriculture: integration of plant microbiomes for improved crop production and food security

Sessitsch, A., & Mitter, B. (2014) · Microbial Biotechnology · doi:10.1111/1751-7915.12180 · Cited by 129 · see citing works

Gestational diabetes is associated with changes in placental microbiota and microbiome

Bassols, J., Sérino, M., Carreras‐Badosa, G., Burcelin, R., Blasco‐Baqué, V., López‐Bermejo, A., & Fernández‐Real, J. M. (2016) · Pediatric Research · doi:10.1038/pr.2016.155 · Cited by 123 · see citing works

Patterns of cross-contamination in a multispecies population genomic project: detection, quantification, impact, and solutions

Ballenghien, M., Faivre, N., & Galtier, N. (2017) · BMC Biology · doi:10.1186/s12915-017-0366-6 · Cited by 115 · see citing works

Detecting Dinosaur DNA

Hedges, S. B., & Schweitzer, M. H. (1995) · Science · doi:10.1126/science.7761839 · Cited by 115 · see citing works

The Application of Ultraviolet Irradiation to Exogenous Sources of DNA in Plasticware and Water for the Amplification of Low Copy Number DNA

Tamariz, J., Voynarovska, K., Prinz, M., & Caragine, T. A. (2006) · Journal of Forensic Sciences · doi:10.1111/j.1556-4029.2006.00172.x · Cited by 88 · see citing works

Computational correction of index switching in multiplexed sequencing libraries

Larsson, A. J. M., Stanley, G., Sinha, R., Weissman, I. L., & Sandberg, R. (2018) · Nature Methods · doi:10.1038/nmeth.4666 · Cited by 83 · see citing works

Discovery of a Novel Seminal Fluid Microbiome and Influence of Estrogen Receptor Alpha Genetic Status

Javurek, A. B., Spollen, W. G., Ali, A. M. M., Johnson, S., Lubahn, D. B., Bivens, N. J., Bromert, K. H., Ellersieck, M. R., Givan, S. A., & Rosenfeld, C. S. (2016) · Scientific Reports · doi:10.1038/srep23027 · Cited by 81 · see citing works

Comment on “The placenta harbors a unique microbiome”

Kliman, H. J. (2014) · Science Translational Medicine · doi:10.1126/scitranslmed.3009864 · Cited by 77 · see citing works

Survival and nutritional requirements of three bacteria isolated from ultrapure water

McAlister, M., Kulakov, L. A., O'Hanlon, J., Larkin, M., & Ogden, K. L. (2002) · Journal of Industrial Microbiology & Biotechnology · doi:10.1038/sj.jim.7000273 · Cited by 75 · see citing works

Sensitive, real-time PCR detects low-levels of contamination by Legionella pneumophila in commercial reagents

Shen, H., Rogelj, S., & Kieft, T. L. (2006) · Molecular and Cellular Probes · doi:10.1016/j.mcp.2005.09.007 · Cited by 63 · see citing works

Distribution of bacteria within operating laboratory water purification systems

McFeters, G. A., Broadaway, S. C., Pyle, B. H., & Egozy, Y. (1993) · Applied and Environmental Microbiology · doi:10.1128/aem.59.5.1410-1415.1993 · Cited by 55 · see citing works

Improved Multiple Displacement Amplification (iMDA) and Ultraclean Reagents

Motley, S. T., Picuri, J. M., Crowder, C. D., Minich, J. J., Hofstadler, S. A., & Eshoo, M. W. (2014) · BMC Genomics · doi:10.1186/1471-2164-15-443 · Cited by 50 · see citing works

An assessment of air as a source of DNA contamination encountered when performing PCR.

Witt, N., Rodger, G., Vandesompele, J., Beneš, V., Zumla, A. I., Rook, G. A. W., & Huggett, J. F. (2009) · PubMed Central · Cited by 43 · see citing works

A new method to prevent carry-over contaminations in two-step PCR NGS library preparations

Seitz, V., Schaper, S., Dröge, A., Lenze, D., Hummel, M., & Hennig, S. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv694 · Cited by 42 · see citing works

Controlling for contaminants in low biomass 16S rRNA gene sequencing experimentsPreprint

Karstens, L. A., Asquith, M. J., Davin, S., et al. (2018) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/329854 · Cited by 31 · see citing works

Contamination-pipetting: relative efficiency of filter tips compared to Microman® positive displacement pipette

Rouzic, E. L. (2006) · Nature Methods · doi:10.1038/nmeth887 · Cited by 24 · see citing works

DNA similarity analysis of a putative ancient bacterial isolate obtained from amber

Yousten, A. A., & Rippere, K. E. (2006) · FEMS Microbiology Letters · doi:10.1111/j.1574-6968.1997.tb10450.x · Cited by 22 · see citing works

Detecting Dinosaur DNA

Henikoff, S. (1995) · Science · doi:10.1126/science.7761841 · Cited by 19 · see citing works

Reply to Santiago-Rodriguez et al.: proper authentication of ancient DNA is essential

Eisenhofer, R., Cooper, A., & Weyrich, L. S. (2017) · FEMS Microbiology Ecology · doi:10.1093/femsec/fix042 · Cited by 17 · see citing works

Estimation of Bacterial Contamination in Ultrapure Water: Application of the Anti-DNA Antibody

Nogami, T., Ohto, T., Kawaguchi, O., Zaitsu, Y., & Sasaki, S. (1998) · Analytical Chemistry · doi:10.1021/ac9805854 · Cited by 16 · see citing works

Bacterial regulatory RNA : methods and protocols

Keiler, K. C. (2012) · Cited by 15 · see citing works

Improving the genetic representation of rare taxa within complex microbial communities using DNA normalization methods

Gagić, D., Maclean, P. H., Li, D., Attwood, G. T., & Moon, C. D. (2014) · Molecular Ecology Resources · doi:10.1111/1755-0998.12321 · Cited by 14 · see citing works

Improving the sensitivity of negative controls in ancient DNA extractions

Xu, Z., Zhang, F., Xu, B., Tan, J., Li, S., & Li, J. (2009) · Electrophoresis · doi:10.1002/elps.200800473 · Cited by 12 · see citing works

RNA Visualization in Bacteria by Fluorescence In Situ Hybridization

Russell, J. H., & Keiler, K. C. (2012) · Methods in molecular biology · doi:10.1007/978-1-61779-949-5_7 · Cited by 3 · see citing works

Reducing Run-to-Run Carryover on the MiSeq Using Dilute Sodium Hypochlorite Solution

Illumina Inc. (2018) · Figshare · doi:10.25909/5b85eb0b95552

Interaction between microbiota and immunity in health and disease

Zheng, D., Liwinski, T., & Elinav, E. (2020) · Cell Research · doi:10.1038/s41422-020-0332-7 · Cited by 3,947 · see citing works

The human tumor microbiome is composed of tumor type–specific intracellular bacteria

Nejman, D., Livyatan, I., Fuks, G., Gavert, N., Zwang, Y., Geller, L. T., Rotter-Maskowitz, A., Weiser, R., Mallel, G., Gigi, E., et al. (2020) · Science · doi:10.1126/science.aay9189 · Cited by 2,464 · see citing works

The microbiome and human cancer

Sepich-Poore, G. D., Zitvogel, L., Straussman, R., Hasty, J., Wargo, J. A., & Knight, R. (2021) · Science · doi:10.1126/science.abc4552 · Cited by 1,332 · see citing works

Tumor-resident intracellular microbiota promotes metastatic colonization in breast cancer

Fu, A., Yao, B., Dong, T., Chen, Y., Yao, J., Liu, Y., Li, H., Bai, H., Liu, X., Zhang, Y., et al. (2022) · Cell · doi:10.1016/j.cell.2022.02.027 · Cited by 981 · see citing works

Comparison between 16S rRNA and shotgun sequencing data for the taxonomic characterization of the gut microbiota

Durazzi, F., Sala, C., Castellani, G., Manfreda, G., Remondini, D., & Cesare, A. D. (2021) · Scientific Reports · doi:10.1038/s41598-021-82726-y · Cited by 599 · see citing works

Targeting the gut and tumor microbiota in cancer

Park, E. M., Chelvanambi, M., Bhutiani, N., Kroemer, G., Zitvogel, L., & Wargo, J. A. (2022) · Nature Medicine · doi:10.1038/s41591-022-01779-2 · Cited by 496 · see citing works

Consistent and correctable bias in metagenomic sequencing experiments

McLaren, M. R., Willis, A. D., & Callahan, B. J. (2019) · eLife · doi:10.7554/elife.46923 · Cited by 424 · see citing works

Bioremediation of environmental wastes: the role of microorganisms

Ayilara, M. S., & Babalola, O. O. (2023) · Frontiers in Agronomy · doi:10.3389/fagro.2023.1183691 · Cited by 437 · see citing works

Questioning the fetal microbiome illustrates pitfalls of low-biomass microbial studies

Kennedy, K. M., de Goffau, M. C., Pérez-Muñoz, M. E., Arrieta, M., Bäckhed, F., Peer Bork, B., Braun, T., Bushman, F. D., Dore, J. M., de Vos, W. M., et al. (2023) · Nature · doi:10.1038/s41586-022-05546-8 · Cited by 375 · see citing works

Best practices in metabarcoding of fungi: From experimental design to results

Tedersoo, L., Bahram, M., Zinger, L., Nilsson, R. H., Kennedy, P. G., Yang, T., Anslan, S., & Mikryukov, V. S. (2022) · Molecular Ecology · doi:10.1111/mec.16460 · Cited by 351 · see citing works

Role of the gut microbiota in anticancer therapy: from molecular mechanisms to clinical applications

Zhao, L.-Y., Mei, J.-X., Yu, G., Lei, L., Zhang, W.-H., Liu, K., Chen, X.-L., Kołat, D., Yang, K., & Hu, J.-K. (2023) · Signal Transduction and Targeted Therapy · doi:10.1038/s41392-023-01406-7 · Cited by 359 · see citing works

Endometrial microbiota composition is associated with reproductive outcome in infertile patients

Moreno, I., Garcia-Grau, I., Perez-Villaroya, D., Gonzalez-Monfort, M., Bahçeci, M., Barrionuevo, M. J., Taguchi, S., Puente, E., Dimattina, M., Lim, M. W., et al. (2022) · Microbiome · doi:10.1186/s40168-021-01184-w · Cited by 325 · see citing works

Not all animals need a microbiome

Hammer, T. J., Sanders, J. G., & Fierer, N. (2019) · FEMS Microbiology Letters · doi:10.1093/femsle/fnz117 · Cited by 301 · see citing works

The cancer microbiome atlas: a pan-cancer comparative analysis to distinguish tissue-resident microbiota from contaminants

Dohlman, A. B., Mendoza, D. A., Ding, S., Gao, M. C., Dressman, H. K., Iliev, I. D., Lipkin, S. M., & Shen, X. (2021) · Cell Host & Microbe · doi:10.1016/j.chom.2020.12.001 · Cited by 279 · see citing works

Evolutionary and Ecological Consequences of Gut Microbial Communities

Moran, N. A., Ochman, H., & Hammer, T. J. (2019) · Annual Review of Ecology Evolution and Systematics · doi:10.1146/annurev-ecolsys-110617-062453 · Cited by 271 · see citing works

Human breast microbiome correlates with prognostic features and immunological signatures in breast cancer

Tzeng, A., Sangwan, N., Jia, M. R., Liu, C.-C., Keslar, K. S., Downs-Kelly, E. P., Fairchild, R. L., Al‐Hilli, Z., Grobmyer, S. R., & Eng, C. (2021) · Genome Medicine · doi:10.1186/s13073-021-00874-2 · Cited by 282 · see citing works

The role of gut and genital microbiota and the estrobolome in endometriosis, infertility and chronic pelvic pain

Salliss, M. E., Farland, L. V., Mahnert, N. D., & Herbst‐Kralovetz, M. M. (2021) · Human Reproduction Update · doi:10.1093/humupd/dmab035 · Cited by 287 · see citing works

Tumor-resident Lactobacillus iners confer chemoradiation resistance through lactate-induced metabolic rewiring

Colbert, L. E., Alam, M. B. E., Wang, R., Karpinets, T. V., Lo, D., Lynn, E. J., Harris, T. A., Elnaggar, J. H., Yoshida-Court, K., Tomasic, K., et al. (2023) · Cancer Cell · doi:10.1016/j.ccell.2023.09.012 · Cited by 279 · see citing works

Abundance-occupancy distributions to prioritize plant core microbiome membership

Shade, A. L., & Stopnišek, N. (2019) · Current Opinion in Microbiology · doi:10.1016/j.mib.2019.09.008 · Cited by 268 · see citing works

Laboratory contamination over time during low‐biomass sample analysis

Weyrich, L. S., Farrer, A. G., Eisenhofer, R., Arriola, L. A., Young, J. M., Selway, C. A., Handsley‐Davis, M., Adler, C. J., Breen, J., & Cooper, A. (2019) · Molecular Ecology Resources · doi:10.1111/1755-0998.13011 · Cited by 252 · see citing works

Issues and current standards of controls in microbiome research

Hornung, B., Zwittink, R. D., & Kuijper, E. J. (2019) · FEMS Microbiology Ecology · doi:10.1093/femsec/fiz045 · Cited by 249 · see citing works

Urinary Microbiome: Yin and Yang of the Urinary Tract

Pérez‐Carrasco, V., Soriano‐Lerma, A., Soriano, M., Fernández, J. G., & Garcia-Salcedo, J. A. (2021) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2021.617002 · Cited by 241 · see citing works

Nanopore Targeted Sequencing for the Accurate and Comprehensive Detection of SARS‐CoV‐2 and Other Respiratory Viruses

Wang, M., Fu, A., Hu, B., Tong, Y., Liu, R., Liu, Z., Gu, J., Xiang, B., Liu, J., Jiang, W., et al. (2020) · Small · doi:10.1002/smll.202002169 · Cited by 229 · see citing works

The intratumor mycobiome promotes lung cancer progression via myeloid-derived suppressor cells

Liu, N., Yi, C., Wei, L., Zhou, J., Jiang, T., Hu, C.-C., Wang, L., Wang, Y.-Y., Zou, Y., Zhao, Y.-K., et al. (2023) · Cancer Cell · doi:10.1016/j.ccell.2023.08.012 · Cited by 229 · see citing works

The composition of the perinatal intestinal microbiota in cattle

Alipour, M. J., Jalanka, J., Pessa‐Morikawa, T., Kokkonen, T., Satokari, R. M., Hynönen, U., Iivanainen, A., & Niku, M. (2018) · Scientific Reports · doi:10.1038/s41598-018-28733-y · Cited by 216 · see citing works

Microbiota in Tumors: From Understanding to Application

Xie, Y., Xie, F., Zhou, X., Zhang, L., Yang, B., Huang, J., Wang, F., Yan, H., Zhang, L., Zhang, L., et al. (2022) · Advanced Science · doi:10.1002/advs.202200470 · Cited by 211 · see citing works

The seminal microbiome in health and disease

Altmäe, S., Franasiak, J. M., & Mändar, R. (2019) · Nature Reviews Urology · doi:10.1038/s41585-019-0250-y · Cited by 192 · see citing works

Tumor microbiome links cellular programs and immunity in pancreatic cancer

Ghaddar, B., Biswas, A., Harris, C., Omary, M. B., Carpizo, D. R., Blaser, M. J., & De, S. (2022) · Cancer Cell · doi:10.1016/j.ccell.2022.09.009 · Cited by 181 · see citing works

New Opportunities for Endometrial Health by Modifying Uterine Microbial Composition: Present or Future?

Molina, N. M., Sola‐Leyva, A., Sáez‐Lara, M. J., Plaza‐Díaz, J., Tubić-Pavlović, A., Romero, B., Clavero, A., Mozas‐Moreno, J., Fontes, J., & Altmäe, S. (2020) · Biomolecules · doi:10.3390/biom10040593 · Cited by 189 · see citing works

Quantifying and Understanding Well-to-Well Contamination in Microbiome Research

Minich, J. J., Sanders, J. G., Amir, A., Humphrey, G. C., Gilbert, J. A., & Knight, R. D. (2019) · mSystems · doi:10.1128/msystems.00186-19 · Cited by 178 · see citing works

Microbial ecology of the atmosphere

Šantl‐Temkiv, T., Amato, P., Casamayor, E. O., Lee, P. K. H., & Pointing, S. B. (2022) · FEMS Microbiology Reviews · doi:10.1093/femsre/fuac009 · Cited by 174 · see citing works

Microbial transmission, colonisation and succession: from pregnancy to infancy

Xiao, L., & Zhao, F. (2023) · Gut · doi:10.1136/gutjnl-2022-328970 · Cited by 183 · see citing works

Liquid biopsy for infectious diseases: a focus on microbial cell-free DNA sequencing

Han, D., Li, R., Shi, J., Tan, P., Zhang, R., & Li, J. (2020) · Theranostics · doi:10.7150/thno.45554 · Cited by 171 · see citing works

Crypt- and Mucosa-Associated Core Microbiotas in Humans and Their Alteration in Colon Cancer Patients

Saffarian, A., Mulet, C., Regnault, B., Amiot, A., Nhieu, J. T. V., Ravel, J., Sobhani, I., Sansonetti, P. J., & Pédron, T. (2019) · mBio · doi:10.1128/mbio.01315-19 · Cited by 160 · see citing works

Continuous Cropping Alters Multiple Biotic and Abiotic Indicators of Soil Health

Pervaiz, Z. H., Iqbal, J., Zhang, Q., Chen, D., Wei, H., & Saleem, M. (2020) · Soil Systems · doi:10.3390/soilsystems4040059 · Cited by 163 · see citing works

Elimination of “kitome” and “splashome” contamination results in lack of detection of a unique placental microbiome

Olomu, I. N., Cortes, L. C. P., Long, R. A., Vyas, A. K., Krichevskiy, O., Luellwitz, R., Singh, P., & Mulks, M. H. (2020) · BMC Microbiology · doi:10.1186/s12866-020-01839-y · Cited by 162 · see citing works

Guidelines for preventing and reporting contamination in low-biomass microbiome studies

Fierer, N., Leung, P. M., Lappan, R. J., Eisenhofer, R., Ricci, F., Holland, S. I., Dragone, N. B., Blackall, L. L., Dong, X., Dorador, C., et al. (2025) · Nature Microbiology · doi:10.1038/s41564-025-02035-2 · Cited by 162 · see citing works

Neoadjuvant Chemotherapy Shifts Breast Tumor Microbiota Populations to Regulate Drug Responsiveness and the Development of Metastasis

Chiba, A., Bawaneh, A., Velázquez, C., Clear, K. Y. J., Wilson, A. S., Howard-McNatt, M. M., Levine, E. A., Levi‐Polyachenko, N. H., Yates-Alston, S. A., Diggle, S. P., et al. (2019) · Molecular Cancer Research · doi:10.1158/1541-7786.mcr-19-0451 · Cited by 145 · see citing works

Studying the gut virome in the metagenomic era: challenges and perspectives

Garmaeva, S., Sinha, T., Kurilshikov, A., Fu, J., Wijmenga, C., & Zhernakova, A. (2019) · BMC Biology · doi:10.1186/s12915-019-0704-y · Cited by 139 · see citing works

A guide to human microbiome research: study design, sample collection, and bioinformatics analysis

Qian, X., Chen, T., Xu, Y., Chen, L., Fu-xiang, S., Lu, M., & Liu, Y. (2020) · Chinese Medical Journal · doi:10.1097/cm9.0000000000000871 · Cited by 140 · see citing works

DNA extraction for human microbiome studies: the issue of standardization

Greathouse, K. L., Sinha, R., & Vogtmann, E. (2019) · Genome Biology · doi:10.1186/s13059-019-1843-8 · Cited by 138 · see citing works

Considerations and best practices in animal science 16S ribosomal RNA gene sequencing microbiome studies

Weinroth, M. D., Belk, A. D., Dean, C. J., Noyes, N. R., Dittoe, D. K., Rothrock, M. J., Ricke, S. C., Myer, P. R., Henniger, M. T., Ramírez, G. A., et al. (2022) · Journal of Animal Science · doi:10.1093/jas/skab346 · Cited by 134 · see citing works

Differential response of digesta- and mucosa-associated intestinal microbiota to dietary insect meal during the seawater phase of Atlantic salmon

Li, Y., Bruni, L., Jaramillo-Torres, A., Gajardo, K., Kortner, T. M., & Krogdahl, Å. (2021) · Animal Microbiome · doi:10.1186/s42523-020-00071-3 · Cited by 128 · see citing works

The role of the tumor microbe microenvironment in the tumor immune microenvironment: bystander, activator, or inhibitor?

Ma, J., Huang, L., Hu, D., Zeng, S., Han, Y., & Shen, H. (2021) · Journal of Experimental & Clinical Cancer Research · doi:10.1186/s13046-021-02128-w · Cited by 138 · see citing works

What is new and relevant for sequencing-based microbiome research? A mini-review

Fricker, A. M., Podlesny, D., & Fricke, W. F. (2019) · Journal of Advanced Research · doi:10.1016/j.jare.2019.03.006 · Cited by 121 · see citing works

Capturing the Resistome: a Targeted Capture Method To Reveal Antibiotic Resistance Determinants in Metagenomes

Guitor, A. K., Raphenya, A. R., Klunk, J., Kuch, M., Alcock, B. P., Surette, M. G., McArthur, A. G., Poinar, H. N., & Wright, G. D. (2019) · Antimicrobial Agents and Chemotherapy · doi:10.1128/aac.01324-19 · Cited by 116 · see citing works

Immune-Microbiota Interplay and Colonization Resistance in Infection

Leshem, A., Liwinski, T., & Elinav, E. (2020) · Molecular Cell · doi:10.1016/j.molcel.2020.03.001 · Cited by 113 · see citing works

Optimizing extraction and targeted capture of ancient environmental DNA for reconstructing past environments using the PalaeoChip Arctic-1.0 bait-set

Murchie, T. J., Kuch, M., Duggan, A. T., Ledger, M. L., Roche, K., Klunk, J., Karpinski, E., Hackenberger, D., Sadoway, T. R., MacPhee, R. D. E., et al. (2020) · Quaternary Research · doi:10.1017/qua.2020.59 · Cited by 98 · see citing works

Optimizing the quality of clinical studies on oral microbiome: A practical guide for planning, performing, and reporting

Zaura, E., Pappalardo, V. Y., Buijs, M. J., Volgenant, C. M. C., & Brandt, B. W. (2020) · Periodontology 2000 · doi:10.1111/prd.12359 · Cited by 105 · see citing works

The human milk microbiome: who, what, when, where, why, and how?

Stinson, L. F., Sindi, A. S., Cheema, A. S., Lai, C. T., Mühlhäusler, B. S., Wlodek, M. E., Payne, M. S., & Geddes, D. T. (2020) · Nutrition Reviews · doi:10.1093/nutrit/nuaa029 · Cited by 100 · see citing works

Mapping the entire functionally active endometrial microbiota

Sola‐Leyva, A., Andrés‐León, E., Molina, N. M., Terron-Camero, L. C., Plaza‐Díaz, J., Sáez‐Lara, M. J., Gonzalvo, M. C., Sánchez, R., Ruiz, S., Martínez, L., et al. (2020) · Human Reproduction · doi:10.1093/humrep/deaa372 · Cited by 100 · see citing works

Microbiome and Prostate Cancer: A Novel Target for Prevention and Treatment

Kuštrimović, N. Z., Bombelli, R., Baci, D., & Mortara, L. (2023) · International Journal of Molecular Sciences · doi:10.3390/ijms24021511 · Cited by 98 · see citing works

Altered Skin and Gut Microbiome in Hidradenitis Suppurativa

McCarthy, S., Barrett, M., Kirthi, S., Pellanda, P., Vlckova, K., Tobin, A.-M., Murphy, M., Shanahan, F., & O’Toole, P. W. (2022) · Journal of Investigative Dermatology · doi:10.1016/j.jid.2021.05.036 · Cited by 98 · see citing works

Contribution of the Mucosal Microbiota to Bovine Respiratory Health

Zeineldin, M. M., Lowe, J. F., & Aldridge, B. M. (2019) · Trends in Microbiology · doi:10.1016/j.tim.2019.04.005 · Cited by 97 · see citing works

Diet induces parallel changes to the gut microbiota and problem solving performance in a wild bird

Davidson, G. L., Wiley, N., Cooke, A. C., Johnson, C. N., Fouhy, F., Reichert, M. S., de la Hera, I., Crane, J. M. S., Kulahci, I. G., Ross, R. P., et al. (2020) · Scientific Reports · doi:10.1038/s41598-020-77256-y · Cited by 97 · see citing works

Analysing endometrial microbiome: methodological considerations and recommendations for good practice

Molina, N. M., Sola‐Leyva, A., Haahr, T., Aghajanova, L., Laudański, P., Castilla, J. A., & Altmäe, S. (2021) · Human Reproduction · doi:10.1093/humrep/deab009 · Cited by 97 · see citing works

A Janus-Faced Bacterium: Host-Beneficial and -Detrimental Roles of Cutibacterium acnes

Brüggemann, H., Salar‐Vidal, L., Gollnick, H. P. M., & Lood, R. (2021) · Frontiers in Microbiology · doi:10.3389/fmicb.2021.673845 · Cited by 98 · see citing works

Interactions between reproductive biology and microbiomes in wild animal species

Comizzoli, P., Power, M. L., Bornbusch, S. L., & Muletz‐Wolz, C. R. (2021) · Animal Microbiome · doi:10.1186/s42523-021-00156-7 · Cited by 93 · see citing works

Long-term biodiversity intervention shapes health-associated commensal microbiota among urban day-care children

Roslund, M. I., Puhakka, R., Nurminen, N., Oikarinen, S., Siter, N., Grönroos, M., Cinek, O., Kramná, L., Jumpponen, A., Laitinen, O. H., et al. (2021) · Environment International · doi:10.1016/j.envint.2021.106811 · Cited by 97 · see citing works

Multicenter assessment of microbial community profiling using 16S rRNA gene sequencing and shotgun metagenomic sequencing

Han, D., Gao, P., Li, R., Tan, P., Xie, J., Zhang, R., & Li, J. (2020) · Journal of Advanced Research · doi:10.1016/j.jare.2020.07.010 · Cited by 93 · see citing works

DNA extraction approaches substantially influence the assessment of the human breast milk microbiome

Douglas, C. A., Ivey, K. L., Papanicolas, L. E., Best, K. P., Mühlhäusler, B. S., & Rogers, G. B. (2020) · Scientific Reports · doi:10.1038/s41598-019-55568-y · Cited by 89 · see citing works

Analysis of metagenomic data

Liu, S., Rodriguez, J. S., Munteanu, V., Ronkowski, C., Sharma, N. K., Alser, M., Andreace, F., Blekhman, R., Błaszczyk, D., Chikhi, R., et al. (2025) · Nature Reviews Methods Primers · doi:10.1038/s43586-024-00376-6 · Cited by 92 · see citing works

Composition and co-occurrence patterns of the microbiota of different niches of the bovine mammary gland: potential associations with mastitis susceptibility, udder inflammation, and teat-end hyperkeratosis

Derakhshani, H., Plaizier, J. C., Buck, J. D., Barkema, H. W., & Khafipour, E. (2020) · Animal Microbiome · doi:10.1186/s42523-020-00028-6 · Cited by 87 · see citing works

The Human Respiratory Microbiome: Current Understandings and Future Directions

Zhao, L., Luo, J., Ali, M. K., Spiekerkoetter, E. F., & Nicolls, M. R. (2022) · American Journal of Respiratory Cell and Molecular Biology · doi:10.1165/rcmb.2022-0208tr · Cited by 92 · see citing works

Towards precision quantification of contamination in metagenomic sequencing experiments

Zinter, M. S., Mayday, M. Y., Ryckman, K. K., Jelliffe‐Pawlowski, L. L., & DeRisi, J. L. (2019) · Microbiome · doi:10.1186/s40168-019-0678-6 · Cited by 86 · see citing works

Sequence-Based Characterization of Intratumoral Bacteria—A Guide to Best Practice

Walker, S. P., Tangney, M., & Claesson, M. J. (2020) · Frontiers in Oncology · doi:10.3389/fonc.2020.00179 · Cited by 85 · see citing works

Contamination Issue in Viral Metagenomics: Problems, Solutions, and Clinical Perspectives

Jurasz, H., Pawłowski, T., & Perlejewski, K. (2021) · Frontiers in Microbiology · doi:10.3389/fmicb.2021.745076 · Cited by 83 · see citing works

Generating amplicon reads for microbial community assessment with next‐generation sequencing

Gołębiewski, M., & Tretyn, A. (2019) · Journal of Applied Microbiology · doi:10.1111/jam.14380 · Cited by 83 · see citing works

Exploring breast tissue microbial composition and the association with breast cancer risk factors

German, R., Marino, N., Hemmerich, C. M., Podicheti, R., Rusch, D. B., Stiemsma, L. T., Gao, H., Xuei, X., Rockey, P., & Storniolo, A. M. (2023) · Breast Cancer Research · doi:10.1186/s13058-023-01677-6 · Cited by 82 · see citing works

Pre-digest of unprotected DNA by Benzonase improves the representation of living skin bacteria and efficiently depletes host DNA

Amar, Y., Lagkouvardos, I., Silva, R. L., Ishola, O. A., Foesel, B. U., Kublik, S., Schöler, A., Niedermeier, S., Bleuel, R., Zink, A., et al. (2021) · Microbiome · doi:10.1186/s40168-021-01067-0 · Cited by 82 · see citing works

Contamination detection in genomic data: more is not enough

Cornet, L., & Baurain, D. (2022) · Genome biology · doi:10.1186/s13059-022-02619-9 · Cited by 80 · see citing works

Contamination source modeling with SCRuB improves cancer phenotype prediction from microbiome data

Austin, G. I., Park, H., Meydan, Y., Seeram, D., Sezin, T., Lou, Y. C., Firek, B., Morowitz, M. J., Banfield, J. F., Christiano, A. M., et al. (2023) · Nature Biotechnology · doi:10.1038/s41587-023-01696-w · Cited by 80 · see citing works

Re‐assessing microbiomes in the low‐biomass reproductive niche

O’Callaghan, J. L., Turner, R., Nitert, M. D., Barrett, H. L., Clifton, V. L., & Pelzer, E. (2019) · BJOG An International Journal of Obstetrics & Gynaecology · doi:10.1111/1471-0528.15974 · Cited by 77 · see citing works

Guidelines for Transparency on Gut Microbiome Studies in Essential and Experimental Hypertension

Marques, F. Z., Jama, H. A., Tsyganov, K., Gill, P. A., Rhys-Jones, D. R., Muralitharan, R. R., Muir, J. G., Holmes, A. J., & Mackay, C. R. (2019) · Hypertension · doi:10.1161/hypertensionaha.119.13079 · Cited by 77 · see citing works

Approaches to Improve Endometrial Receptivity in Case of Repeated Implantation Failures

Makrigiannakis, A., Makrygiannakis, F., & Vrekoussis, T. (2021) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2021.613277 · Cited by 75 · see citing works

The subway microbiome: seasonal dynamics and direct comparison of air and surface bacterial communities

Gohli, J., Bøifot, K. O., Moen, L. V., Pastuszek, P., Skogan, G., Udekwu, K. I., & Dybwad, M. (2019) · Microbiome · doi:10.1186/s40168-019-0772-9 · Cited by 73 · see citing works

Non-specific amplification of human DNA is a major challenge for 16S rRNA gene sequence analysis

Walker, S. P., Barrett, M., Hogan, G. E., Bueso, Y. F., Claesson, M. J., & Tangney, M. (2020) · Scientific Reports · doi:10.1038/s41598-020-73403-7 · Cited by 72 · see citing works

A critical analysis of research methods and experimental models to study the root canal microbiome

Siqueira, J. F., Jr., & Rôças, I. N. (2021) · International Endodontic Journal · doi:10.1111/iej.13656 · Cited by 72 · see citing works

Microbiomes of Urine and the Prostate Are Linked to Human Prostate Cancer Risk Groups

Hurst, R., Meader, E. J., Gihawi, A., Rallapalli, G., Clark, J., Kay, G. L., Webb, M., Manley, K., Curley, H. M., Walker, H., et al. (2022) · European Urology Oncology · doi:10.1016/j.euo.2022.03.006 · Cited by 72 · see citing works

Cancer type classification using plasma cell-free RNAs derived from human and microbes

Chen, S., Jin, Y., Wang, S., Xing, S., Wu, Y., Tao, Y., Ma, Y., Zuo, S., Liu, X., Hu, Y., et al. (2022) · eLife · doi:10.7554/elife.75181 · Cited by 71 · see citing works

Identification of an intraocular microbiota

Deng, Y., Ge, X., Yan, L., Zou, B., Wen, X., Chen, W., Lü, L., Zhang, M., Zhang, X., Li, C., et al. (2021) · Cell Discovery · doi:10.1038/s41421-021-00245-6 · Cited by 73 · see citing works

A Comparison of Six DNA Extraction Protocols for 16S, ITS and Shotgun Metagenomic Sequencing of Microbial Communities

Shaffer, J. P., Carpenter, C. S., Martino, C., Salido, R. A., Minich, J. J., Bryant, M., Sanders, K., Schwartz, T., Humphrey, G., Swafford, A. D.-E., et al. (2022) · BioTechniques · doi:10.2144/btn-2022-0032 · Cited by 73 · see citing works

High Throughput Sequencing for the Detection and Characterization of RNA Viruses

Fitzpatrick, A., Rupnik, A., O’Shea, H., Crispie, F., Keaveney, S., & Cotter, P. D. (2021) · Frontiers in Microbiology · doi:10.3389/fmicb.2021.621719 · Cited by 68 · see citing works

A bird's-eye view of phylosymbiosis: weak signatures of phylosymbiosis among all 15 species of cranes

Trevelline, B. K., Sosa, J., Hartup, B. K., & Kohl, K. D. (2020) · Proceedings of the Royal Society B Biological Sciences · doi:10.1098/rspb.2019.2988 · Cited by 69 · see citing works

The human “contaminome”: bacterial, viral, and computational contamination in whole genome sequences from 1000 families

Chrisman, B., He, C., Jung, J.-Y., Stockham, N., Paskov, K. M., Washington, P. Y., & Wall, D. P. (2022) · Scientific Reports · doi:10.1038/s41598-022-13269-z · Cited by 68 · see citing works

Circulating microbiome in patients with portal hypertension

Gedgaudas, R., Bajaj, J. S., Skiecevičienė, J., Varkalaitė, G., Jurkeviciute, G., Gelman, S., Valantienė, I., Zykus, R., Pranculis, A., Bang, C., et al. (2022) · Gut Microbes · doi:10.1080/19490976.2022.2029674 · Cited by 68 · see citing works

Is There a Brain Microbiome?

Link, C. D. (2021) · Neuroscience Insights · doi:10.1177/26331055211018709 · Cited by 67 · see citing works

Microbial Dark Matter: From Discovery to Applications

Zha, Y., Chong, H., Yang, P., & Ning, K. (2022) · Genomics Proteomics & Bioinformatics · doi:10.1016/j.gpb.2022.02.007 · Cited by 65 · see citing works

Metagenomic Next-Generation Sequencing in Infectious Diseases: Clinical Applications, Translational Challenges, and Future Directions

Elbehiry, A., & Abalkhail, A. (2025) · Diagnostics · doi:10.3390/diagnostics15161991 · Cited by 75 · see citing works

Disordered development of gut microbiome interferes with the establishment of the gut ecosystem during early childhood with atopic dermatitis

Lee, M.-J., Park, Y. M., Kim, B., Tae, I. H., Kim, N.-E., Pranata, M., Kim, T., Won, S., Kang, N. J., Lee, D., et al. (2022) · Gut Microbes · doi:10.1080/19490976.2022.2068366 · Cited by 66 · see citing works

Microbiome applications for pathology: challenges of low microbial biomass samples during diagnostic testing

Selway, C. A., Eisenhofer, R., & Weyrich, L. S. (2020) · The Journal of Pathology Clinical Research · doi:10.1002/cjp2.151 · Cited by 67 · see citing works

Broadening oncological boundaries: the intratumoral microbiota

Lu, Y.-Q., Qiao, H., Tan, X.-R., & Liu, N. (2024) · Trends in Microbiology · doi:10.1016/j.tim.2024.01.007 · Cited by 66 · see citing works

The microbiome and prostate cancer

Javier-DesLoges, J. F., McKay, R. R., Swafford, A. D.-E., Sepich‐Poore, G. D., Knight, R. D., & Parsons, J. K. (2021) · Prostate Cancer and Prostatic Diseases · doi:10.1038/s41391-021-00413-5 · Cited by 64 · see citing works

The composition of the perinatal intestinal microbiota in horse

Husso, A., Jalanka, J., Alipour, M. J., Huhti, P., Kareskoski, M., Pessa‐Morikawa, T., Iivanainen, A., & Niku, M. (2020) · Scientific Reports · doi:10.1038/s41598-019-57003-8 · Cited by 63 · see citing works

Association of Bacteroides acidifaciens relative abundance with high-fibre diet-associated radiosensitisation

Then, C. K., Paillas, S., Wang, X., Hampson, A., & Kiltie, A. E. (2020) · BMC Biology · doi:10.1186/s12915-020-00836-x · Cited by 61 · see citing works

Investigation of direct and indirect transfer of microbiomes between individuals

Neckovic, A., van Oorschot, R. A. H., Szkuta, B., & Durdle, A. (2019) · Forensic Science International Genetics · doi:10.1016/j.fsigen.2019.102212 · Cited by 62 · see citing works

Female reproductive tract microbiota and recurrent pregnancy loss: a nested case-control study

Peuranpää, P., Holster, T., Saqib, S., Kalliala, I. E. J., Tiitinen, A. E., Salonen, A., & Hautamäki, H. (2022) · Reproductive BioMedicine Online · doi:10.1016/j.rbmo.2022.06.008 · Cited by 66 · see citing works

Endometrial Microbiota and Immune Tolerance in Pregnancy

Inversetti, A., Zambella, E., Guarano, A., Dell’avanzo, M., & Simone, N. D. (2023) · International Journal of Molecular Sciences · doi:10.3390/ijms24032995 · Cited by 62 · see citing works

Toward Standards in Clinical Microbiota Studies: Comparison of Three DNA Extraction Methods and Two Bioinformatic Pipelines

Ducarmon, Q. R., Hornung, B., Geelen, A. R., Kuijper, E. J., & Zwittink, R. D. (2020) · mSystems · doi:10.1128/msystems.00547-19 · Cited by 61 · see citing works

Guidelines for preventing and reporting contamination in low-biomass microbiome studies

Fierer, N., Leung, P. M., Lappan, R. J., Eisenhofer, R., Ricci, F., Holland, S. I., Dragone, N. B., Blackall, L. L., Dong, X., Dorador, C., et al. (2025) · Nature Microbiology · doi:10.1038/s41564-025-02035-2 · Cited by 162 · see citing works

Scrubbing contaminated microbiomes

Shao, Y. (2023) · Nature Reviews Microbiology · doi:10.1038/s41579-023-00941-y

A Lot on Your Plate? Well-to-Well Contamination as an Additional Confounder in Microbiome Sequence Analyses

Walker, A. W. (2019) · mSystems · doi:10.1128/msystems.00362-19 · Cited by 16 · 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

Tracking down the sources of experimental contamination in microbiome studies

Weiss, S. J., Amir, A., Hyde, E. R., Metcalf, J. L., Song, S. J., & Knight, R. D. (2014) · Genome biology · doi:10.1186/s13059-014-0564-2 · Cited by 182 · see citing works