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

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

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

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

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

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

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

Genomic analysis identifies association of Fusobacterium 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

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 1,291

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

Exploring the Relationship between MicroRNAs, Intratumoral Microbiota, and Breast Cancer Progression in Patients with and without Metastasis

Laborda-Illanes, A., Aranega-Martín, L., Sánchez‐Alcoholado, L., Boutriq, S., Plaza-Andrades, I. J., Peralta-Linero, J., Ruiz, G. G., Pajares, B., Álvarez, M., Alba, E., et al. (2024) · International Journal of Molecular Sciences · doi:10.3390/ijms25137091 · Cited by 15

Development and evaluation of statistical and artificial intelligence approaches with microbial shotgun metagenomics data as an untargeted screening tool for use in food production

Beck, K. L., Haiminen, N., Agarwal, A., Carrieri, A. P., Madgwick, M., Kelly, J., Pylro, V. S., Kawas, B., Wiedmann, M., & Ganda, E. (2024) · mSystems · doi:10.1128/msystems.00840-24 · Cited by 19

Review of otitis media microbiome studies: What do they tell us?

Nogues, J. C., Pérez‐Losada, M., & Preciado, D. A. (2020) · Laryngoscope Investigative Otolaryngology · doi:10.1002/lio2.460 · Cited by 14

Low microbial biomass within the reproductive tract of mid-lactation dairy cows: A study approach

Lietaer, L., Pascottini, O. B., Hernandez‐Sanabria, E., Kerckhof, F., Lacoere, T., Boon, N., Vlaminck, L. E. M., OPSOMER, G., & de Wiele, T. V. (2021) · Journal of Dairy Science · doi:10.3168/jds.2020-19554 · Cited by 15

Associations and recovery dynamics of the nasopharyngeal microbiota during influenza-like illness in the aging population

Shetty, S. A., van Beek, J., Bijvank, E., Groot, J. A., Kuiling, S., Bosch, T., van Baarle, D., & Fuentes, S. (2022) · Scientific Reports · doi:10.1038/s41598-022-05618-9 · Cited by 16

Targeting the Tumor Microbiota in Cancer Therapy Basing on Nanomaterials

Niu, Y., Feng, J., Ma, J., Xiao, T., & Yuan, W. (2025) · Exploration · doi:10.1002/exp.20210185 · Cited by 20

The multi-kingdom cancer microbiome

Dohlman, A. B., Pan, X., Zitvogel, L., & Iliev, I. D. (2025) · Nature Microbiology · doi:10.1038/s41564-025-02103-7 · Cited by 16

Diversity of Viridiplantae DNA present on rock surfaces in the Ellsworth Mountains, continental Antarctica

Câmara, P. E. A. S., de Menezes, G. C. A., de Oliveira, F. S., Souza, C. D., de Amorim, E. T., Schaefer, C. E. G. R., Convey, P., Pinto, O. H. B., Carvalho‐Silva, M., & Rosa, L. H. (2022) · Polar Biology · doi:10.1007/s00300-022-03021-8 · Cited by 14

Cascading effects of habitat loss on ectoparasite-associated bacterial microbiomes

Speer, K. A., Teixeira, T. S. M., Brown, A. M., Perkins, S. L., Dittmar, K., Ingala, M. R., Wultsch, C., Krampis, K., Dick, C. W., Galen, S. C., et al. (2022) · ISME Communications · doi:10.1038/s43705-022-00153-0 · Cited by 17

Toward efficient and high-fidelity metagenomic data from sub-nanogram DNA: evaluation of library preparation and decontamination methods

Wang, C., Zhang, L., Jiang, X., Ma, W., Geng, H. Z., Wang, X., & Li, M. (2022) · BMC Biology · doi:10.1186/s12915-022-01418-9 · Cited by 13

Playing Peekaboo with a Master Manipulator: Metagenetic Detection and Phylogenetic Analysis of Wolbachia Supergroups in Freshwater Invertebrates

Mioduchowska, M., Konecka, E., Gołdyn, B., Pinceel, T., Brendonck, L., Lukić, D., Kaczmarek, Ł., Namiotko, T., Zając, K., Zając, T. A., et al. (2023) · International Journal of Molecular Sciences · doi:10.3390/ijms24119400 · Cited by 14

A review on microbiota: relation with diseases and nutrients role

Öz, E., Şimşek, A., Şimşek, M., Tuncer, N., Bayrak, M., Çadırcı, K., Brennan, C. S., Kumar, M., Proestos, C., Brennan, M. A., et al. (2023) · International Journal of Food Science & Technology · doi:10.1111/ijfs.16530 · Cited by 14

Molecular ecology of microbiomes in the wild: Common pitfalls, methodological advances and future directions

Fountain‐Jones, N. M., Giraud, T., Zinger, L., Bik, H. M., Creer, S., & Videvall, E. (2023) · Molecular Ecology · doi:10.1111/mec.17223 · Cited by 14

No microorganism was detected in amniotic fluid of healthy pregnancies from the second trimester to the delivery

Liu, Y., Ma, J., Li, X., Zhao, H., Ai, Q., Zhang, L., Tong, Y., Meng, L., & Yang, H. (2025) · Microbiome · doi:10.1186/s40168-024-02024-3 · Cited by 15

Prostate and urinary microbiomes in prostate cancer development: focus on Cutibacterium acnes

Fu, F., Yu, Y., Wang, B., Zhao, X., Wang, N., Yin, J., Wu, K., & Zhou, Q. (2025) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2025.1562729 · Cited by 15

The jury is still out on the existence of a placental microbiome

Briana, D. D., Papaevangelou, V., & Malamitsi‐Puchner, A. (2021) · Acta Paediatrica · doi:10.1111/apa.16048 · Cited by 15

Analyzing gut microbiota composition in individual Anopheles mosquitoes after experimental treatment

Fofana, A., Gendrin, M., Romoli, O., Yarbanga, G. A. B., Ouédraogo, G. A., Yerbanga, R. S., & Ouédraogo, J. (2021) · iScience · doi:10.1016/j.isci.2021.103416 · Cited by 14

Examining pathogen DNA recovery across the remains of a 14th century Italian friar (Blessed Sante) infected with Brucella melitensis

Hider, J., Duggan, A. T., Klunk, J., Eaton, K., Long, G. S., Karpinski, E., Giuffra, V., Ventura, L., Fornaciari, A., Fornaciari, G., et al. (2022) · International Journal of Paleopathology · doi:10.1016/j.ijpp.2022.08.002 · Cited by 18

Changes in the Ixodes ricinus microbiome associated with artificial tick feeding

Militzer, N., Socias, S. P., & Nijhof, A. M. (2023) · Frontiers in Microbiology · doi:10.3389/fmicb.2022.1050063 · Cited by 14

Bacterial contamination screening and interpretation for biological laboratory environments

Zhu, X. H., Li, X., Wang, W., & Ning, K. (2020) · Medicine in Microecology · doi:10.1016/j.medmic.2020.100021 · Cited by 14

Changes in the Bacterial Diversity of Human Milk during Late Lactation Period (Weeks 21 to 48)

Marín, W. J. B., Burgos, M. J. G., Pulido, R. P., Gálvez, A., & López, R. L. (2020) · Foods · doi:10.3390/foods9091184 · Cited by 14

Response to: ‘Circulating microbiome in blood of different circulatory compartments’ by Schierwagen et al

Hornung, B., Zwittink, R. D., Ducarmon, Q. R., & Kuijper, E. J. (2019) · Gut · doi:10.1136/gutjnl-2019-318601 · Cited by 14

Protocol for microbial profiling of low-biomass upper respiratory tract samples

Odendaal, M.-L., Chu, M. L. J. N., Arp, K., van Beveren, G. J., Biesbroek, G., Binkowska, J. M., Bosch, T., Groot, J. A., Hasrat, R., Kuiling, S., et al. (2025) · STAR Protocols · doi:10.1016/j.xpro.2025.103740 · Cited by 13

Metagenomic co-assembly uncovers mobile antibiotic resistance genes in airborne microbiomes

Erkorkmaz, B. A., Zeevi, D., & Rudich, Y. (2025) · Communications Earth & Environment · doi:10.1038/s43247-025-02381-3 · Cited by 14

From Omics to Applications: How Bioinformatics and Multi-Omics Approaches Are Revolutionizing Metal Bioleaching

Nkuna, R., Mohlomi, N., & Matambo, T. S. (2026) · Minerals · doi:10.3390/min16010056 · Cited by 13

Comparison of Four DNA Extraction Kits Efficiency for 16SrDNA Microbiota Profiling of Diverse Human Samples

Gall‐David, S. L., Boudry, G., & Buffet‐Bataillon, S. (2023) · Future Science OA · doi:10.2144/fsoa-2022-0072 · Cited by 13

Insights into the Human Microbiome and Its Connections with Prostate Cancer

Munteanu, R. A., Feder, R., Onaciu, A., Munteanu, V. C., Iuga, C. A., & Gulei, D. (2023) · Cancers · doi:10.3390/cancers15092539 · Cited by 13

Tissue-resident bacteria in metabolic diseases: emerging evidence and challenges

Massier, L., Musat, N., Stümvoll, M., Tremaroli, V., Chakaroun, R., & Kovacs, P. L. (2024) · Nature Metabolism · doi:10.1038/s42255-024-01065-0 · Cited by 15

Bioinformatics challenges for profiling the microbiome in cancer: pitfalls and opportunities

Bokulich, N. A., & Robeson, M. S. (2024) · Trends in Microbiology · doi:10.1016/j.tim.2024.08.011 · Cited by 13

The interplay between host-specificity and habitat-filtering influences sea cucumber microbiota across an environmental gradient of pollution

Chung, S. S.-W., Cheung, K., Arromrak, B. S., Li, Z., Tse, C. M., & Gaitán‐Espitía, J. D. (2024) · Environmental Microbiome · doi:10.1186/s40793-024-00620-2 · Cited by 14

The lower airways microbiome and antimicrobial peptides in idiopathic pulmonary fibrosis differ from chronic obstructive pulmonary disease

Knudsen, K. S., Lehmann, S., Nielsen, R., Tangedal, S., Haaland, I., Hiemstra, P. S., & Eagan, T. (2022) · PLoS ONE · doi:10.1371/journal.pone.0262082 · Cited by 13

Active Microbial Airborne Dispersal and Biomorphs as Confounding Factors for Life Detection in the Cell-Degrading Brines of the Polyextreme Dallol Geothermal Field

Belilla, J., Iniesto, M., Moreira, D., Benzerara, K., Gérard, E., García, J. M. L., Kotopoulou, E., & López‐García, P. (2022) · mBio · doi:10.1128/mbio.00307-22 · Cited by 12

Interaction between Host and Microbes in the Semen of Patients with Idiopathic Nonobstructive Azoospermia

Chen, P., Li, Y., Zhu, X., Ma, M., Chen, H., He, J., Liang, X., Liu, G., & Yang, X. (2023) · Microbiology Spectrum · doi:10.1128/spectrum.04365-22 · Cited by 13

Potential role of intratumor bacteria outside the gastrointestinal tract: More than passengers

Liu, Z., Hong, L., & Ling, Z. (2023) · Cancer Medicine · doi:10.1002/cam4.6298 · Cited by 12

Microbiome and Metagenome Analyses of a Closed Habitat during Human Occupation

Mohan, G. B. M., Parker, C. W., Urbaniak, C., Singh, N. K., Hood, A. D., Minich, J. J., Knight, R. D., Rucker, M. A., & Venkateswaran, K. J. (2020) · mSystems · doi:10.1128/msystems.00367-20 · Cited by 13

Comparing different sample collection and storage methods for field‐based skin microbiome research

Manus, M. B., Kuthyar, S., Perroni‐Marañón, A. G., la Mora, A. N., & Amato, K. R. (2021) · American Journal of Human Biology · doi:10.1002/ajhb.23584 · Cited by 15

Reply to: Caution Regarding the Specificities of Pan-Cancer Microbial StructurePreprint

Sepich‐Poore, G. D., Kopylova, E., Zhu, Q., Carpenter, C. S., Fraraccio, S., Wandro, S., Kościółek, T., Janssen, S., Metcalf, J. L., Song, S. J., et al. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.02.10.528049 · Cited by 13

Unveiling microbial diversity in deep geothermal fluids, from current knowledge and analogous environments

Bregnard, D., Leins, A., Cailleau, G., Vieth‐Hillebrand, A., Eichinger, F., Iannotta, J., Hoffmann, R., Uhde, J., Bindschedler, S., Regenspurg, S., et al. (2023) · Geothermal Energy · doi:10.1186/s40517-023-00269-z · Cited by 21

Alterations in sea urchin (Mesocentrotus nudus) microbiota and their potential contributions to host according to barren severity

Park, J.-Y., Jo, J.-W., An, Y.-J., Lee, J.-J., & Kim, B. S. (2023) · npj Biofilms and Microbiomes · doi:10.1038/s41522-023-00450-z · Cited by 11

The Breast Microbiome in Breast Cancer Risk and Progression: A Narrative Review

Peters, B. A., Kelly, L., Wang, T., Loudig, O. D., & Rohan, T. E. (2023) · Cancer Epidemiology Biomarkers & Prevention · doi:10.1158/1055-9965.epi-23-0965 · Cited by 12

Association of Cutibacterium acnes with human thyroid cancer

Trivedi, V., Noronha, V., Sreekanthreddy, P., Desai, S., Poojary, D., Varghese, L., Gowda, P., Butle, A. B., Mishra, R., Bal, M. M., et al. (2023) · Frontiers in Endocrinology · doi:10.3389/fendo.2023.1152514 · Cited by 14

Urbanization reduces gut bacterial microbiome diversity in a specialist ground beetle, Carabus convexus

Magura, T., Mizser, S., Horváth, R., Tóth, M., Likó, I., & Löveï, G. L. (2024) · Molecular Ecology · doi:10.1111/mec.17265 · Cited by 12

Exploring the Role of Gut-Lung Interactions in COPD Pathogenesis: A Comprehensive Review on Microbiota Characteristics and Inflammation Modulation

Cheng, Z.-X., & Zhang, J. (2024) · Chronic Obstructive Pulmonary Diseases Journal of the COPD Foundation · doi:10.15326/jcopdf.2023.0442 · Cited by 15

The microbiome of the pregnant uterus in Holstein dairy heifers and cows assessed by bacterial culture and 16S ribosomal RNA gene sequencing

Moraes, J. G. N., Gull, T. B., Ericsson, A. C., Poock, S. E., Caldeira, M. O., & Lucy, M. C. (2024) · Frontiers in Microbiology · doi:10.3389/fmicb.2024.1385497 · Cited by 12

An Overview of the Skin Microbiome, the Potential for Pathogen Shift, and Dysbiosis in Common Skin Pathologies

Smith, A. J., Dumbrava, R., Ghori, N.-U.-H., Foster, R. S., Campbell, J., Duthie, A., Hoyne, G. F., Rademaker, M., & Bowen, A. C. (2025) · Microorganisms · doi:10.3390/microorganisms13010054 · Cited by 15

Within-population diversity of bacterial microbiomes in winter ticks (Dermacentor albipictus)

Sperling, J. L. H., MacDonald, Z. G., Normandeau, J., Merrill, E. H., Sperling, F. A. H., & Magor, K. E. (2020) · Ticks and Tick-borne Diseases · doi:10.1016/j.ttbdis.2020.101535 · Cited by 12

Inline index helped in cleaning up data contamination generated during library preparation and the subsequent steps

Wang, Y., Yuan, H., Huang, J., & Li, C. (2021) · Molecular Biology Reports · doi:10.1007/s11033-021-06884-y · Cited by 11

Maternal IgA2 Recognizes Similar Fractions of Colostrum and Fecal Neonatal Microbiota

Santos‐Argumedo, L., Sánchez-Salguero, E., Guzmán-Aquino, H. A., de la Borbolla-Cruz, M. F., Contreras-Vargas, V., Corona-Cervantes, K., Piña-Escobedo, A., & Garcı́a-Mena, J. (2021) · Frontiers in Immunology · doi:10.3389/fimmu.2021.712130 · Cited by 15

Changes of the Freshwater Microbial Community Structure and Assembly Processes during Different Sample Storage Conditions

Wang, Y., Li, X., Chi, Y., SONG, W. B., Yan, Q., & Huang, J. (2022) · Microorganisms · doi:10.3390/microorganisms10061176 · Cited by 12

A practical guide for restoration ecologists to manage microbial contamination risks before laboratory processes during microbiota restoration studies

Cando‐Dumancela, C., Davies, T. C., Hodgson, R. J., Liddicoat, C., Peddle, S. D., Watson, C. D., & Breed, M. F. (2022) · Restoration Ecology · doi:10.1111/rec.13687 · Cited by 12

Next Generation Sequencing Approaches to Characterize the Respiratory Tract Virome

Sandybayev, N. T., Beloussov, V., Strochkov, V. M., Solomadin, M., Granica, J., & Yegorov, S. (2022) · Microorganisms · doi:10.3390/microorganisms10122327 · Cited by 13

A CRISPR-enhanced metagenomic NGS test to improve pandemic preparedness

Chan, A. P.-Y., Siddique, A., Desplat, Y., Choi, Y., Ranganathan, S., Choudhary, K. S., Khalid, M. F., Diaz, J., Bezney, J., DeAscanis, D., et al. (2023) · Cell Reports Methods · doi:10.1016/j.crmeth.2023.100463 · Cited by 16

Pan-cancer analyses reveal the stratification of patient prognosis by viral composition in tumor tissues

Zhang, Y., Ji, L., Wen, H., Chu, Y., Xing, W., Tian, G., Yao, Y., & Yang, J. (2023) · Computers in Biology and Medicine · doi:10.1016/j.compbiomed.2023.107586 · Cited by 12

Complex Microbiome in Brain Abscess Revealed by Whole-Genome Culture-Independent and Culture-Based Sequencing

Lin, J.-H., Wu, Z., Gong, L., Wong, C., Chao, W., Yen, C.-M., Wang, C.-P., Wei, C., Huang, Y., & Liu, P. (2019) · Journal of Clinical Medicine · doi:10.3390/jcm8030351 · Cited by 12

Characterization of cerebrospinal fluid (CSF) microbiota from patients with CSF shunt infection and reinfection using high throughput sequencing of 16S ribosomal RNAgenes

Whitlock, K. B., Pope, C. E., Hodor, P. G., Hoffman, L. R., Limbrick, D. L., McDonald, P. J., Hauptman, J. S., Ojemann, J. G., Simon, T. D., & on behalf of the Cerebrospinal FLuId MicroBiota in Shunts Study (CLIMB) Group (2021) · PLoS ONE · doi:10.1371/journal.pone.0244643 · Cited by 12

Evaluation of the ocular surface mycobiota in clinically normal horses

Walsh, M. L., Meason‐Smith, C., Arnold, C. E., Suchodolski, J. S., & Scott, E. M. (2021) · PLoS ONE · doi:10.1371/journal.pone.0246537 · Cited by 12

Full-Length SSU rRNA Gene Sequencing Allows Species-Level Detection of Bacteria, Archaea, and Yeasts Present in Milk

Abellan-Schneyder, I., Siebert, A., Hofmann, K., Wenning, M., & Neuhaus, K. (2021) · Microorganisms · doi:10.3390/microorganisms9061251 · Cited by 12

Metagenomics Approaches to Investigate the Neonatal Gut Microbiome

Boudar, Z., Sehli, S., Janahi, S. E., Idrissi, N. A., Hamdi, S., Dini, N., Brim, H., Amzazi, S., Nejjari, C., Lloyd-Puryear, M. A., et al. (2022) · Frontiers in Pediatrics · doi:10.3389/fped.2022.886627 · Cited by 16

When to suspect contamination rather than colonization – lessons from a putative fetal sheep microbiome

Bihl, S., de Goffau, M. C., Podlesny, D., Segata, N., Shanahan, F., Walter, J., & Fricke, W. F. (2021) · Gut Microbes · doi:10.1080/19490976.2021.2005751 · Cited by 13

Global biogeography of atmospheric microorganisms reflects diverse recruitment and environmental filteringPreprint

Archer, S. D. J., Lee, K. C. Y., Caruso, T., Leung, M. H. Y., Tong, X., Salter, S. J., Hinchliffe, G., Maki, T., Šantl‐Temkiv, T., Warren‐Rhodes, K., et al. (2022) · Research Square · doi:10.21203/rs.3.rs-244923/v4 · Cited by 12

Challenges and Opportunities in Analyzing Cancer-Associated Microbiomes

Chia, M., Pop, M., Salzberg, S. L., & Nagarajan, N. (2025) · Cancer Research · doi:10.1158/0008-5472.can-24-3629 · Cited by 11

Structure and metabolic potential of the prokaryotic communities from the hydrothermal system of Paleochori Bay, Milos, Greece

Bauer, S. L. M., Lu, G.-S., Goulaouic, S., Puzenat, V., Schouw, A., Barreyre, T., Pawlowsky‐Glahn, V., Egozcue, J. J., Martelat, J., Escartin, J., et al. (2023) · Frontiers in Microbiology · doi:10.3389/fmicb.2022.1060168 · Cited by 11

Metatranscriptome analysis of blood in healthy individuals and irritable bowel syndrome patients

Jagare, L., Rozenberga, M., Silamiķelis, I., Ansone, L., Elbere, I., Brīvība, M., Megnis, K., Konrāde, I., Birka, I., Straume, Z., et al. (2023) · Journal of Medical Microbiology · doi:10.1099/jmm.0.001719 · Cited by 11

Metatranscriptomic characterization of six types of forensic samples and its potential application to body fluid/tissue identification: A pilot study

Liu, Z., Liu, J., Geng, J., Wu, E., Zhu, J., Cong, B., Wu, R., & Sun, H. (2023) · Forensic Science International Genetics · doi:10.1016/j.fsigen.2023.102978 · Cited by 12

Microbial interactions amongGardnerella,PrevotellaandFannyhesseaprior to incident bacterial vaginosis: protocol for a prospective, observational study

Muzny, C. A., Elnaggar, J. H., Sousa, L. G. V., Lima, Â., Aaron, K. J., Eastlund, I. C., Graves, K. J., Dong, C., Gerwen, O. T. V., Luo, M., et al. (2024) · BMJ Open · doi:10.1136/bmjopen-2023-083516 · Cited by 13

Neutrophils in the Focus: Impact on Neuroimmune Dynamics and the Gut–Brain Axis

Kršek, A., & Batičić, L. (2024) · Gastrointestinal Disorders · doi:10.3390/gidisord6030039 · Cited by 13

Challenges for pathologists in implementing clinical microbiome diagnostic testing

Gerasimova, Y., Ali, H., & Nadeem, U. (2024) · The Journal of Pathology Clinical Research · doi:10.1002/2056-4538.70002 · Cited by 13

Unveiling the intratumor microbiome in liver cancer: Current insights and prospective applications

Ke, X., Jiang, S., Wei, Q., Sun, M., Sun, H., Pang, M., Liu, M., Sun, L., Yang, H., & Mao, Y. (2025) · Clinical and Molecular Hepatology · doi:10.3350/cmh.2024.1039 · Cited by 13

The relationship between the gastric cancer microbiome and clinicopathological factors: a metagenomic investigation from the 100,000 genomes project and The Cancer Genome Atlas

Booth, M. E., Wood, H. M., Travis, M. A., Ambrose, J. C., Arumugam, P., Bevers, R. P. J., Bleda, M., Boardman-Pretty, F., Boustred, C. R., Brittain, H. K., et al. (2025) · Gastric Cancer · doi:10.1007/s10120-025-01588-9 · Cited by 11

The intratumoral microbiota heterogenicity is related to the prognosis and tumorigenesis of cervical cancer

Guo, Y., Xiao, Y., Zhang, C., Wang, Y., Cao, G., Tse, K. Y., Han, Z., Li, F., & Zhi, Y. (2025) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2025.1574511 · Cited by 16

The gut-tumor connection: the role of microbiota in cancer progression and treatment strategies

Wei, Z., Gao, G., He, Q., Kwok, L., & Sun, Z. (2025) · Journal of Advanced Research · doi:10.1016/j.jare.2025.08.038 · Cited by 12

Variation in bacterial composition, diversity, and activity across different subglacial basal ice types

Doyle, S. M., & Christner, B. C. (2022) · The Cryosphere · doi:10.5194/tc-16-4033-2022 · Cited by 11

Advanced approaches for the diagnosis and chemoprevention of canine vector-borne pathogens and parasites—Implications for the Asia-Pacific region and beyond

Huggins, L. G., Koehler, A. V. A., Gasser, R. B., & Traub, R. J. (2023) · Advances in Parasitology/Advances in parasitology · doi:10.1016/bs.apar.2022.12.001 · Cited by 11

Profiling bacterial communities in low biomass samples: pitfalls and considerations

Stinson, L. F., Keelan, J. A., & Payne, M. S. (2019) · Microbiology Australia · doi:10.1071/ma19053 · Cited by 11

Peripheral blood mononuclear cells (PBMC) microbiome is not affected by colon microbiota in healthy goats

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Characterizing Microbiomes via Sequencing of Marker Loci: Techniques To Improve Throughput, Account for Cross-Contamination, and Reduce Cost

Harrison, J. G., Randolph, G. D., & Buerkle, C. A. (2021) · mSystems · doi:10.1128/msystems.00294-21 · Cited by 12

Variable preterm oral microbiome stabilizes and reflects a full-term infant profile within three months

Selway, C. A., Collins, C. T., Makrides, M., Sullivan, T., Gibson, R. A., Penttila, I., McPhee, A. J., & Weyrich, L. S. (2023) · Pediatric Research · doi:10.1038/s41390-023-02517-1 · Cited by 11

N/S element transformation modulating lithospheric microbial communities by single-species manipulation

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Aging-dependent skin microbiome alterations across body sites in a United Kingdom cohort

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Fast‐tracking bespoke DNA reference database generation from museum collections for biomonitoring and conservation

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Feeding on a Bartonella henselae Infected Host Triggers Temporary Changes in the Ctenocephalides felis Microbiome

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Impact of testosterone use on the vaginal microbiota of transgender men, including susceptibility to bacterial vaginosis: study protocol for a prospective, observational study

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Lung microbiota composition, respiratory mechanics, and outcomes in COVID-19-related ARDS

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The Gut and the Translocated Microbiomes in HIV Infection: Current Concepts and Future Avenues

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Association of oral fungal profiles with health status and bacterial composition in elderly adults receiving community support and home care service

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Nationwide multicentre study of Nanopore long-read sequencing for 16S rRNA-species identification

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Impact of study design, contamination, and data characteristics on results and interpretation of microbiome studies

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Analysis of Porcine Model of Fecal-Induced Peritonitis Reveals the Tropism of Blood Microbiome

Hyun, H., Lee, M. S., Park, I., Ko, H. S., Yun, S., Jang, D., Kim, S., Kim, H., Kang, J. H., Lee, J. H., et al. (2021) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2021.676650 · Cited by 10

Intratumor microbiota: Occult participants in the microenvironment of multiple myeloma

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Pinpointing the microbiota of tardigrades: What is really there?

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Progressive Multifocal Leukoencephalopathy Diagnosed by Metagenomic Next-Generation Sequencing of Cerebrospinal Fluid in an HIV Patient

Xia, H., Guan, Y., Zaongo, S. D., Xia, H., Wang, Z., Yan, Z., & Ma, P. (2019) · Frontiers in Neurology · doi:10.3389/fneur.2019.01202 · Cited by 10

Milk microbiome in dairy cattle and the challenges of low microbial biomass and exogenous contamination

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The infant pharyngeal microbiomes: origin, impact and manipulation

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Functional Diversity within Gut Microbiomes: Implications for Conserving Biodiversity

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Assessing the performance of historical skins and bones for museomics using wolf specimens as a case study

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Paleometagenomics reveals environmental microbiome response to vegetation changes in northern Siberia over the millennia

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Nearly (?) sterile avian egg in a passerine bird

Těšičký, M., Schmiedová, L., Krajzingrová, T., Gómez-Samblás, M., Bauerová, P., Kreisinger, J., & Vinkler, M. (2023) · FEMS Microbiology Ecology · doi:10.1093/femsec/fiad164 · Cited by 9

A prospective evaluation of the prostate microbiome in malignant and benign tissue using transperineal biopsy

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A brain microbiome in salmonids at homeostasis

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Optimisation of the sampling method for skin microbiome studies in healthy children: a pilot cohort study

Smith, A. J., Ghori, N.-U.-H., Foster, R. S., Nicol, M. P., Barnett, T. C., Pickering, J. L., Whelan, A., Strunk, T., Wood, F. M., Raby, E., et al. (2024) · Frontiers in Microbiomes · doi:10.3389/frmbi.2024.1446394 · Cited by 12

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

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Scrubbing contaminated microbiomes

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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

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

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Tracking down the sources of experimental contamination in microbiome studies

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