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

Experimental depletion of gut microbiota diversity reduces host thermal tolerance and fitness under heat stress in a vertebrate ectothermPreprint

Fontaine, S. S., Mineo, P. M., & Kohl, K. D. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.06.04.447101 · Cited by 3

Considerations for mosquito microbiome research from the Mosquito Microbiome ConsortiumPreprint

Dada, N., Jupatanakul, N., Minard, G., Short, S. M., Akorli, J., & Villegas, L. E. M. (2020) · doi:10.31219/osf.io/2s8he · Cited by 3

Bacterial profiles of the human placenta from term and preterm deliveriesPreprint

Theis, K. R., Winters, A. D., Romero, R. J., Alhousseini, A., Greenberg, J. M., Panzer, J. J., Galaz, J., Pacora, P., Shaffer, Z. D., Jung, E., et al. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.06.21.497119 · Cited by 2

Rapid Nanopore cloud-based monitoring and analysis of commercial aquaculture microbiomesPreprint

Strutt, J. P. B., Bessarab, I. N., Min, J. G. Y., Marican, H., & Summers, S. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.08.07.607111 · Cited by 3

Characterising the Tasmanian devil (Sarcophilus harrisii) pouch microbiome in lactating and non-lactating females

Ockert, L. E., McLennan, E. A., Fox, S., Belov, K., & Hogg, C. J. (2024) · Scientific Reports · doi:10.1038/s41598-024-66097-8 · Cited by 2

Has the two decades of research on the gut microbiome resulted in making healthier choices?

Azcárate-Peril, M. A. (2024) · Gut Microbiome · doi:10.1017/gmb.2024.13 · Cited by 2

Bacteria in the brain: do they have a role in the pathogenesis of Alzheimer's disease?

Bhattacharya, A., Shepherd, C. E., El‐Assaad, F., & Mather, K. A. (2025) · Current Opinion in Psychiatry · doi:10.1097/yco.0000000000000989 · Cited by 2

Field expedient stool collection methods for gut microbiome analysis in deployed military environments

Kok, C. R., Thissen, J. B., Cerroni, M., Tribble, D. R., Cancio, A. T., Tran, S., Schofield, C. M., Colombo, R. E., Troth, T., Joya, C., et al. (2025) · mSphere · doi:10.1128/msphere.00818-24 · Cited by 2

Blood bacterial DNA signatures in a prospective cohort of patients with MASLD cirrhosis

Kwan, S., Dolapchiev, L. I., Sanchez, C. I., Calderone, T. L., Sanchez, J. I., Bhongade, M. B., Sabagh, A. E., Cleere, D. W., Gupta, N., Jalal, P. K., et al. (2025) · Hepatology Communications · doi:10.1097/hc9.0000000000000722 · Cited by 2

Identification of clinically relevant profiles in colorectal cancer through integrated analysis of bacterial DNA and metabolome in serum

Vicente-Valor, J., Tesolato, S. E., Gómez‐Garré, D., Paz-Cabezas, M., Ortega‐Hernández, A., Fernández-Hernández, C., la Serna, S. C. D., Domínguez-Serrano, I., Dziaková, J., Rivera, D., et al. (2025) · Frontiers in Immunology · doi:10.3389/fimmu.2025.1562416 · Cited by 2

Data mining of public genomic repositories: harnessing off-target reads to expand microbial pathogen genomic resources

Richard, D., & Poulicard, N. (2025) · Peer Community Journal · doi:10.24072/pcjournal.637 · Cited by 2

Honey wasps differ from other wasps in possessing large gut communities dominated by host-restricted bacteria

Holley, J.-A. C., Martin, A. N., Pham, A. T., Schlauch, J., & Moran, N. A. (2025) · mBio · doi:10.1128/mbio.02608-24 · Cited by 2

Streamlined extraction of nucleic acids and metabolites from low- and high-biomass samples using isopropanol and matrix tubes

Brennan, C., Shaffer, J. P., Belda‐Ferre, P., Mohanty, I., Weng, Y., Cantrell, K., Ackermann, G. L., Allaband, C., Bryant, M., Farmer, S., et al. (2025) · Microbiology Spectrum · doi:10.1128/spectrum.01912-25 · Cited by 2

Biological macromolecules in bioremediation: Exploring OMICs approaches for environmental cleanup

Duhan, P., Verma, K., Lata, C., Gupta, B., & Bansal, P. (2025) · Ecological Genetics and Genomics · doi:10.1016/j.egg.2025.100434 · Cited by 2

Characterization and comparative analysis of urinary bacterial microbiome profiling in healthy cats and cats with feline idiopathic cystitis

Thassakorn, P., Fungbun, N., Sukon, P., & Phuektes, P. (2026) · Scientific Reports · doi:10.1038/s41598-025-34196-9 · Cited by 2

Unveiling balanced prenatal microbial colonization in amniotic fluid through an integrated culture and sequencing approach

González-Rovira, M., Sainz-Bueno, J. A., García‐Díaz, L., Martínez-Pancorbo, C., Sánchez, J., Gutiérrez, G., Magoutas, K., Mesías-Pérez, A., Mellado, E., Payne, M., et al. (2026) · Journal of Translational Medicine · doi:10.1186/s12967-025-07601-0 · Cited by 2

Establishing hospital-specific background microbial libraries to reduce false positives in mNGS diagnosis of periprosthetic joint infection

Cao, Y., Wang, C., Yin, H., Xu, D., Li, W., Yuan, Z., Xu, W., Song, Z., Pang, F., & Wang, D. (2026) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2025.1668697 · Cited by 2

A multicentre evaluation of metagenomic sequencing for pathogen detection in central nervous system infections

Wang, J., Ma, Y., Shi, X., Han, Y., Zhang, Y., Diao, Z., Li, Z., Lai, H., Meng, S., Zhang, C., et al. (2026) · Clinical Microbiology and Infection · doi:10.1016/j.cmi.2026.01.015 · Cited by 3

SIMPLseq: a high-sensitivity Plasmodium falciparum genotyping and PCR contamination tracking tool

Schwabl, P., Amaya-Romero, J.-E., Kelley, K., Manrique, P., Murphy, S. C., Crompton, P. D., & Neafsey, D. E. (2026) · Malaria Journal · doi:10.1186/s12936-026-05796-1 · Cited by 2

The Ocular and Gut Microbiome Axis in Understanding Glaucoma: A Systematic Review

Songel-Sanchis, B., Morales‐Fernández, L., García-Bardera, J., Güemes-Villahoz, N., Martínez-de-la-Casa, J. M., & Garcia-Feijoo, J. (2026) · Journal of Clinical Medicine · doi:10.3390/jcm15031245 · Cited by 2

The gut and circulating virome: emerging players in aging and longevity

Pazmay, G. V. B., Fortunato, C., Cianfruglia, L., Novazzi, F., Spezia, P. G., Rosa, L., Limongi, D., Prezioso, C., D’Argenio, V., Scudiero, O., et al. (2026) · Frontiers in Aging · doi:10.3389/fragi.2025.1731621 · Cited by 4

The persistence of COVID-19 vaccine artifacts in bodily fluids and tissues: a systematic review

Selem, E., Raszek, M., Varón, J., & Halma, M. T. J. (2026) · Future Journal of Pharmaceutical Sciences · doi:10.1186/s43094-026-00939-2 · Cited by 3

Development of a multiplex ddPCR assay for simultaneous absolute quantification of bacterial, fungal, and human DNA

Huang, G., Gallagher, T. L., Tsongalis, G. J., & Lefferts, J. A. (2026) · PLoS ONE · doi:10.1371/journal.pone.0341560 · Cited by 2

Precision Microbial Therapeutics for Infertility: Next‐Generation Probiotics, Engineered Biologics and Translational Pathways

Li, L., Feng, L., Li, Q., Zhou, Y., Liu, S., Song, H., Kang, S., Chen, H., Cong, H., & Liu, S. (2026) · Microbial Biotechnology · doi:10.1111/1751-7915.70330 · Cited by 2

Potential role of the ocular surface microbiome in dry eye: microbial interactions and symptom alleviation

Park, J.-Y., Yoon, C. J., Lee, J.-J., Shin, Y. J., & Kim, B. S. (2026) · mSystems · doi:10.1128/msystems.00104-26 · Cited by 2

Possible association between the microbiota in subgingival and atherosclerotic plaque in a cohort of patients with carotid stenosis

Schulz, S., Börner, S., Bitter, K., Gheit, H., Partsakhashvili, J., Ukkat, J., Misiak, D., & Reichert, S. (2026) · Journal of Oral Microbiology · doi:10.1080/20002297.2026.2648325 · Cited by 2

Parasite-associated microbiomes: An unseen microenvironment

McCann, P., Megaw, J., & Gobert, G. N. (2026) · Advances in Parasitology/Advances in parasitology · doi:10.1016/bs.apar.2026.03.001 · Cited by 2

Cross-kingdom signals: microbial, metabolites, and immune cells on the gut-breast axis

Cheong, K., Li, J., Wang, M., Wang, D., & Zhong, S. (2026) · Critical Reviews in Food Science and Nutrition · doi:10.1080/10408398.2026.2681931 · Cited by 2

Mapping spoilage microbiota in complex food systems: organisms, mechanisms, and omics-based characterization

Asadi, A., Sarand, I., Spuul, P., Fanning, S., & Macori, G. (2026) · Food Research International · doi:10.1016/j.foodres.2026.119633 · Cited by 2

Fifty Years after Viking: The Promise of Solar System Microbiology and Microbial Ecology

Cockell, C. S. (2026) · Astrobiology · doi:10.1177/15311074261464013 · Cited by 3

Spatial Heterogeneity of Intratumoral Microbiota and Its Roles in Tumor–Microbiota Interactions and Therapeutic Implications

Li, L., Shi, X., Liu, M., Xu, T., Chen, Y., Wang, R., Zhang, Q., & Li, D. (2026) · Pathogens · doi:10.3390/pathogens15070687 · Cited by 2

Carbon Dynamics in Climate Smart Agriculture Precision Land Leveling Practices on Topsoil Microbial Community Changes and Soil Organic Carbon in Cereal Based Cropping Systems of Sub-Tropical India: A Review

Naresh, R. K., Chandra, M. S., Baliyan, A., Kumar, B., Kanaujiya, P. K., Pathak, S. O., Singh, P. K., & Kumar, N. (2021) · International Journal of Plant & Soil Science · doi:10.9734/ijpss/2021/v33i730450 · Cited by 2

UTERINE MICROBIOME IN HEALTHY FERTILE WOMEN AND IN CASE OF ENDOMETRIUM PATHOLOGY IN MULTIPLE FAILURES OF IN-VITRO-FERTILIZATION PROGRAMS

Barinova, B. V. V., Kuznetsova, N. B., Bushtyreva, I. O., OKSENYUK, O. S., & Shatalov, A. (2021) · PERIÓDICO TCHÊ QUÍMICA · doi:10.52571/ptq.v18.n37.2021.20_barinova_pgs_293_308.pdf · Cited by 2

Identification of intratumor bacteria-associated prognostic risk score in adrenocortical carcinoma

Tan, L., Zhang, D., Li, Y., Li, Y., Guo, T., Sun, Y., Li, N., & Feng, C. (2024) · Microbiology Spectrum · doi:10.1128/spectrum.03727-23 · Cited by 2

New avenues for potentially seeking microbial responses to climate change beneath Antarctic ice shelves

Vicedo, A. L., Gómez, M. L., Zeising, O., Kleiner, T., Freitag, J., Martinez‐Hernández, F., Wilhelms, F., & Martínez‐García, M. (2024) · mSphere · doi:10.1128/msphere.00073-24 · Cited by 2

Influence of diabetes on microbiome in prostate tissues of patients with prostate cancer

Lee, J.-J., Kim, J. K., Oh, B., Hong, S. K., & Kim, B. S. (2024) · Frontiers in Oncology · doi:10.3389/fonc.2024.1445375 · Cited by 2

Diversity, phylogeny and taxonomy of forest fungal communities

Salazar-Vidal, V. E., Dibán, M. J., Rugolo, M., González, G., Barroetaveña, C., Urrutia, E., & Urrutia, H. (2024) · Elsevier eBooks · doi:10.1016/b978-0-443-18870-1.00007-x · Cited by 2

Exploring the Link Between Infections and Primary Osteoarthritis: A Next-Generation Metagenomic Sequencing Approach

Niecwietajewa, I., Banasiewicz, J., Zaremba-Wróblewski, G. L., & Majewska, A. (2024) · International Journal of Molecular Sciences · doi:10.3390/ijms26010020 · Cited by 2

Gut microbiota, immune cells, and chronic sinusitis: A Mendelian randomization analysis

Huang, J., Zhu, X. F., Yao, J., Yang, W., & Zhu, Z. (2025) · Medicine · doi:10.1097/md.0000000000041093 · Cited by 2

Assessment of the Structure and Activity of Bacterial Communities as a Tandem Tool for Estimating the Ecological Condition of Lakes in Poland

Kubera, Ł., Kalwasińska, A., & Perliński, P. (2025) · Ecosystems · doi:10.1007/s10021-025-00979-4 · Cited by 2

Bruton tyrosine kinase modulates systemic immune activation to bacterial translocation in primary antibody deficiencies

Ho, H.-E., Radigan, L., Qi, J., Roudko, V., Storek, M., Lee, J. H., Fuleihan, R., Sullivan, K. E., Kim‐Schulze, S., & Cunningham‐Rundles, C. (2025) · Journal of Allergy and Clinical Immunology · doi:10.1016/j.jaci.2025.09.019 · Cited by 3

Beyond nocardioform: Transcriptionally active microbes and host responses in equine mucoid placentitis

van Heule, M., Verstraete, M., Norris, J. K., Graniczkowsa, K. B., Scoggin, K. E. S., Ali, H. E., Ball, B. A., Spiegelaere, W. D., Daels, P. F., Weimer, B. C., et al. (2025) · Equine Veterinary Journal · doi:10.1111/evj.70112 · Cited by 2

Microbial translocation into amniotic fluid of vervet monkeys is common and unrelated to adverse infant outcomes

Kendziorski, J. A., Sherrill, C., Davis, A., & Kavanagh, K. (2019) · Journal of Medical Primatology · doi:10.1111/jmp.12432 · Cited by 2

Genome-Resolved Metagenomic Analyses Reveal the Presence of a Putative Bacterial Endosymbiont in an Avian Nasal Mite (Rhinonyssidae; Mesostigmata)

Osuna‐Mascaró, C., Doña, J., Johnson, K. P., & de Rojas, M. (2021) · Microorganisms · doi:10.3390/microorganisms9081734 · Cited by 2

New Paradigms for Familiar Diseases: Lessons Learned on Circulatory Bacterial Signatures in Cardiometabolic Diseases

Chakaroun, R., Massier, L., Musat, N., & Kovacs, P. L. (2022) · Experimental and Clinical Endocrinology & Diabetes · doi:10.1055/a-1756-4509 · Cited by 2

Metatranscriptomics Analysis Reveals Diverse Viral RNA in Cutaneous Papillomatous Lesions of Cattle

Fernandes, A. D. O., Barros, G., & Batista, M. V. D. A. (2022) · Evolutionary Bioinformatics · doi:10.1177/11769343221083960 · Cited by 2

Studying the pre-implantation uterine microbiota in cattle using transabdominal laparoscopic low-volume lavage: Aiming for zero-contamination

Lietaer, L., Pascottini, O. B., Lacoere, T., Kerckhof, F., Martens, A., de Wiele, T. V., & OPSOMER, G. (2022) · Journal of Microbiological Methods · doi:10.1016/j.mimet.2022.106664 · Cited by 2

Overview of Soil Microbe Dynamics in Different Biosystems

Farooq, B., Anjum, S., Farooq, M., Nazir, A., Farooq, M. U., Yousuf, S., Shafi, N., & Parray, J. A. (2023) · Climate change management · doi:10.1007/978-3-031-21079-2_3 · Cited by 2

Anionic nanocellulose as competing agent in microbial DNA extraction from mine process samples

Bomberg, M., & Miettinen, H. (2023) · Journal of Microbiological Methods · doi:10.1016/j.mimet.2023.106850 · Cited by 2

Effect of target gene sequence evenness and dominance on real-time PCR quantification of artificial sulfate-reducing microbial communities

Du, Z., & Behrens, S. (2024) · PLoS ONE · doi:10.1371/journal.pone.0299930 · Cited by 2

Metagenomic Applications for Infectious Disease Testing in Clinical Laboratories

Filkins, L., & Schlaberg, R. (2021) · Springer eBooks · doi:10.1007/978-3-030-62155-1_7 · Cited by 2

Evidence for the existence of microbiota in the placenta and blood of pregnant mice exposed to various bacteria

Li, S., Gao, Y., Shang, Q., Guo, W., Liu, H., Wei, J., & Chen, T. (2021) · Medicine in Microecology · doi:10.1016/j.medmic.2021.100040 · Cited by 2

The making of the oral microbiome in Agta hunter-gatherersPreprint

Dobón, B., Musciotto, F., Mira, Á., Greenacre, M. J., Schlaepfer, R., Aguileta, G., Astete, L. H., Ngales, M. L., Latora, V., Battiston, F., et al. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.05.03.490437 · Cited by 2

Termite diet rather than geographical origin determines the microbiome composition and functional genetic structure of nests from South American and African representatives, as revealed by a multiomics approachPreprint

Plaza, J. J. G., Hradecký, J., & Šobotník, J. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.08.13.503768 · Cited by 2

Outbreak and Postnatal Antibiotic Exposures Drive the Development Trajectory of the Nasopharyngeal Microbiota in the First Year of LifePreprint

Rajar, P., Dhariwal, A., Salvadori, G., Åmdal, H. A., Berild, D., Dahle, U. R., Fugelseth, D., Greisen, G. O., Lausten‐Thomsen, U., Saugstad, O. D., et al. (2023) · medRxiv · doi:10.1101/2023.09.14.23295567 · Cited by 2

The genital tract microbiota of IVF patients and oocyte donors: a comparative analysisPreprint

Haahr, T., Humaidan, P., Bernabeu, A., Lledó, B., Plummer, E. L., Bradshaw, C. S., Ingham, A. C., & Jensen, J. S. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.10.18.619104 · Cited by 2

Broad‐Range Diagnostic Amplification and Detection

Kommedal, Ø., & Dyrhovden, R. (2025) · Wiley eBooks · doi:10.1002/9781683674597.ch6 · Cited by 1

Ancient metagenomics reveals subglacial microbiomes driven by oxygen availabilityPreprint

Sanctis, B. D., Dragone, N. B., Wanket, C., de Mesquita, C. P. B., Crump, S. E., Piccione, G. G., Nirula, B., Bender, H., Corbett-Detig, R. B., Rasbury, E. T., et al. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2025.12.03.692186 · Cited by 2

Impact of delivery mode in early life microbiome and risk of disease

Martineau, E., & Clemente, J. C. (2020) · Elsevier eBooks · doi:10.1016/b978-0-12-818097-6.00005-5 · Cited by 1

Larvae of Deep-Sea Invertebrates Harbor Low-Diversity Bacterial Communities

Carrier, T. J., Beaulieu, S. E., Mills, S. W., Mullineaux, L. S., & Reitzel, A. M. (2021) · Biological Bulletin · doi:10.1086/715669 · Cited by 1

Microbiomes of native Aotearoa New Zealand animals

Ayriss, N., & Taylor, M. W. (2023) · New Zealand Journal of Ecology · doi:10.20417/nzjecol.47.3518 · Cited by 1

Microbiome typing in uveal melanoma is associated with plaque radiotherapy

Chen, Y., Luo, J., Li, H., Fang, R., Zhang, R., Liu, Y., Xiu, J., Xu, J., Li, Y., & Wei, W. (2023) · Medicine in Microecology · doi:10.1016/j.medmic.2023.100079 · Cited by 1

Cell-Free Microbial DNA Analysis: Effects of Blood Plasma and Serum Quantity, Biobanking Protocols, and Isolation Kits

Nikitina, D., Lukoševičius, R., Tilinde, D., Muskieta, T., Hov, J. R., Melum, E., Kloviņš, J., Org, E., Kiudelis, G., Kupčinskas, J., et al. (2024) · Biopreservation and Biobanking · doi:10.1089/bio.2023.0048 · Cited by 1

Best practices for the experimental design of one health studies on companion animal and owner microbiomes – From data collection to analysis

Clougher, S. B., Niedziela, D. A., Versura, P., & Mulcahy, G. M. (2025) · One Health · doi:10.1016/j.onehlt.2025.100977 · Cited by 1

Microbiomes of frozen blood plasma samples reveal potential pathogens in wild birds and rodents

Erickson, C. E., Fair, J. M., & Bartlow, A. W. (2025) · One Health · doi:10.1016/j.onehlt.2025.101109 · Cited by 1

Contamination-controlled upper gastrointestinal microbiota profiling reveals salivary-duodenal community types linked to opportunistic pathogen carriage and inflammation

Schmidt, N. S., Dörner, E., Podlesny, D., Bohlhammer, E., Bubeck, A. M., Ruple, H. K., Tetzlaff-Lelleck, V., Sina, C., Schmidt, H., & Fricke, W. F. (2025) · Gut Microbes · doi:10.1080/19490976.2025.2539452 · Cited by 2

Grundlagen der Mikrobiomforschung

Eckl‐Dorna, J., & Pjevac, P. (2025) · HNO · doi:10.1007/s00106-025-01656-7 · Cited by 1

Blood Microbiome Analysis Reveals Biomarkers of Treatment Response in Drug-Naïve Patients with First-Episode Psychosis: A Pilot Study

Logotheti, M., Γκέκας, Θ., Agioutantis, P. C., Hatzimanolis, A., Foteli, S., Mamma, D., Stefanis, N. C., Kolisis, F. N., & Loutrari, H. V. (2025) · Microorganisms · doi:10.3390/microorganisms13081935 · Cited by 1

Intratumoral Microbe Correlated with Expression of DNA Methylation Genes in Hepatocellular Carcinoma

Kumar, A., Raj, A., Lal, K. C., & Puja, P. (2025) · Digestive Diseases and Sciences · doi:10.1007/s10620-025-09351-x · Cited by 1

Wet‐lab preparation and automated dataset decontamination procedure for bacterial single‐cell genomics

Mauger, S., Sévellec, Y., Carret, L., Robert, N., Monard, C., Thion, C., Jarassier, L., & Vandenkoornhuyse, P. (2025) · Methods in Ecology and Evolution · doi:10.1111/2041-210x.70170 · Cited by 1

External factors influencing reproductive tract microbiota in cattle

Poole, R. K. (2025) · Reproduction Fertility and Development · doi:10.1071/rd25165 · Cited by 1

Endometrial Microbial Profile in Infertile Women with Chronic Endometritis: Intensified Culturomics and 16S rDNA Gene Sequencing

Lara-del-Río, B., Sánchez-Ruiz, R., Bernal, M., Ruiz‐Cabello, F., Navarro‐Marí, J. M., & Fernández, J. G. (2025) · Genes · doi:10.3390/genes16121432 · Cited by 1

Exploring local and regional contribution to airborne bacterial communities in the Antarctic Peninsula

Galbán, S., Almela, P., Quesada, A., & Justel, A. (2025) · Scientific Reports · doi:10.1038/s41598-025-32162-z · Cited by 1

How to search for microbiomes: the example of bacteria in gallbladder bile

Quintero, G. A., & Clay, O. (2025) · Future Microbiology · doi:10.1080/17460913.2025.2601522 · Cited by 2

Exploratory evaluation of the bacterial load of uterine microbiota: Potential implications for implantation and treatment response in assisted reproductive technology

Kadogami, D., Nakaoka, Y., & Morimoto, Y. (2025) · Journal of Reproductive Immunology · doi:10.1016/j.jri.2025.104830 · Cited by 1

Advanced Sequencing Approaches for the Subgingival Microbiome: Technology Selection, Quality Control, and Best Practices in Periodontal Research

Akram, H. M., & Saliem, S. S. (2026) · Bacteria · doi:10.3390/bacteria5010011 · Cited by 1

Live tissue microbiota and bacterial translocation: mechanisms and translational perspectives in cardiometabolic diseases

Minty, M., Lê, S., Addi, M., Canceill, T., Thomas, C., Loubières, P., Burcelin, R., & Blasco‐Baqué, V. (2026) · Reviews in Endocrine and Metabolic Disorders · doi:10.1007/s11154-026-10017-w · Cited by 1

The esophageal microbiome: mechanisms and clinical implications

Ebigbo, N. (2026) · Current Opinion in Gastroenterology · doi:10.1097/mog.0000000000001170 · Cited by 1

Weather conditions structure the taxonomic and functional diversity of the aeolian dust microbiome

Freund, L., Topacio, T. M., Miao, Y., Porter, W. C., Swenson, M. P., Maltz, M. R., Botthoff, J. K., & Aronson, E. L. (2026) · Frontiers in Microbiology · doi:10.3389/fmicb.2026.1691133 · Cited by 1

Harnessing the lung microbiome for precision management of fibrotic lung disease

Leroy, S., Roméo, B., Belaïd, A., Brest, P., Marquette, C., Vouret‐Craviari, V., Hofman, V., Hofman, P. M., & Mograbi, B. (2026) · Trends in Molecular Medicine · doi:10.1016/j.molmed.2026.02.002 · Cited by 1

Bridging the gap: improving methodologies for future avian microbiome research

Davies, C. S., Capilla‐Lasheras, P., Catelan‐Carphio, E., Corregidor‐Castro, A., Diez‐Méndez, D., Drobniak, S. M., Drzewińska‐Chańko, J., Kohl, K. D., Martínez‐Renau, E., Ramellini, S., et al. (2026) · Journal of Avian Biology · doi:10.1002/jav.03594 · Cited by 3

Hybrid expert system for robust detection of rare sequence signals: a computational proof-of-concept in host-dominated backgrounds

Wang, S., Xie, L., Yan, Z., Ma, J., & Zhao, R. (2026) · Frontiers in Microbiology · doi:10.3389/fmicb.2026.1821073 · Cited by 1

An infant nasal microbial gene atlas uncovers intervention-driven microbiome shifts and salt-resistant pathogen expansion

Steinberg, R., Pust, M., Arias-Rojas, A., Pishchany, G., Ramsey, K. A., Kieninger, E., Moeller, A., Casaulta, C., Hilty, M., Latzin, P., et al. (2026) · Cell Host & Microbe · doi:10.1016/j.chom.2026.03.019 · Cited by 1

Thanatomicrobiome and postmortem microbial succession: ecological dynamics, molecular advances, and emerging forensic applications

Devi, M., Sarma, V., Bardoloi, A., Kumar, D., Choudhary, N., Kondaveeti, S. B., & Sarma, A. D. (2026) · Annals of Microbiology · doi:10.1186/s13213-026-01856-8 · Cited by 1

Role of microbiome in ocular surface disease: interpreting biology in a low-biomass environment

Yashar, M., Thigale, U. Y., & Karakus, S. (2026) · Current Opinion in Ophthalmology · doi:10.1097/icu.0000000000001228 · Cited by 1

A Scalable and Cost‐Effective In‐Line Barcoding Strategy for Standardized 16S rRNA Gene Amplicon Sequencing: Performance Evaluation and Bias Assessment

Jourdain, L., Rossi, P., Charpagne, A., Chevalier, E., Praz, V., Marquis, J., Weber, J., & Gu, W. (2026) · Molecular Ecology Resources · doi:10.1111/1755-0998.70138 · Cited by 3

The microbiome across the prostate disease continuum: from health and BPH to prostatitis/CPPS and cancer

Cheng, B., Gong, L., Xu, H., Wang, Z., Huang, H., Guan, X., & Wu, P. (2026) · Oncogene · doi:10.1038/s41388-026-03815-8 · Cited by 1

The elephant (bird) in the room: unknown mechanisms and unresolved impacts of low DNA yields in avian microbiome research

Kohl, K. D., Anderson, R., Andreadis, C., Baiz, M. D., Bodawatta, K. H., Campos-Cerda, F., Chaves, J. A., Clark, A. B., Costantini, M. S., Davidson, G. L., et al. (2026) · Animal Microbiome · doi:10.1186/s42523-026-00579-0 · Cited by 1

Host–Microbiota Metabolic Interactions in Atherosclerosis: Oral, gut, and Blood Perspectives

Khan, I., Irfan, M., Bacha, A. S., Khan, I., Ali, Y., & Zhiqiang, L. (2026) · Probiotics and Antimicrobial Proteins · doi:10.1007/s12602-026-11054-2 · Cited by 1

The dialogue between breast cancer and microorganisms

Zeng, Y., Jiang, Y., Huang, Y., Yin, S., Yang, Z., & Zhang, F. (2026) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2026.1738739 · Cited by 1

Mapping the multigenomic human system: structural asymmetry and interface gaps in host–exogenous biological interactions

Gaspary, J. F. P., Lopes, L. F. D., Gaspary, F. P., Lopes, E. G., Edgar, A. L., Camara, E. P., & Camara, A. G. (2026) · Frontiers in Microbiology · doi:10.3389/fmicb.2026.1834677 · Cited by 1

Microbiome–Driven Carcinogenesis and Circulating Microbial Signals in Genitourinary Cancers

Kawashima, A., Jingushi, K., Saito, T., Uemura, T., Yamamoto, A., Sassi, N., Horitani, H., Inoguchi, S., Horibe, Y., Ishizuya, Y., et al. (2026) · Cancer Science · doi:10.1111/cas.70448 · Cited by 1

Absolute quantitative metagenomic profiling reveals divergent antimicrobial resistance and pathogen hazards in urban and rural aging community wastewater

Du, X., Long, Y., Qiu, Z., Liu, Z. Y., Han, C., & Fu, S. (2026) · Journal of Hazardous Materials Advances · doi:10.1016/j.hazadv.2026.101344 · Cited by 1

Isolation of Bacteria and Fungi from Human Pancreatic Tumors and Duodenum

Awad, D., Attebury, H., Hong, R., Kim, K., Zhang, L., Bischoff, A., Achi, S. C., denDekker, A., Lesniak, N., The, S., et al. (2026) · Gut Microbes · doi:10.1080/19490976.2026.2695522 · Cited by 3

Species composition and functional characteristics of the human multi-organ microbiome: A metagenomic study

Su, K., Tian, S., Xia, Y., Zhao, X., Huang, J., Hu, S., & Ye, J. (2026) · Journal of Forensic and Legal Medicine · doi:10.1016/j.jflm.2026.103213 · Cited by 1

An endocrine microbe immunity framework for granulomatous mastitis toward phenotype-oriented interpretation

Jiang, Y., Yang, K., Xue, B., Wang, Y., & Jia, H. (2026) · iScience · doi:10.1016/j.isci.2026.116654 · Cited by 1

Skin microbiome and cutaneous aging mechanisms and clinical implications

Bautista, J., Iñiguez-Ramírez, A., Chávez, J. A. V., Larco, D. S. B., & López-Cortés, A. (2026) · Frontiers in Microbiology · doi:10.3389/fmicb.2026.1917816 · Cited by 1

Implantation Outcome-Specific Associations Between Stromal Senescence and the Endometrial Microbiota

Parvanov, D. A., Ruseva, M., Ganeva, R., Tihomirova, T., Handzhiyska, M., Chapanova, S., Safir, J., Koristashevskaya, S., Pavlov, I. A., Metodiev, D., et al. (2026) · Microorganisms · doi:10.3390/microorganisms14091868 · Cited by 1

Interpreting oral microbiome research in clinical dentistry: terminology, limitations and clinical implications

Guo, K., & Edwards, D. (2026) · BDJ · doi:10.1038/s41415-026-9896-z · Cited by 1

Gastrointestinal microbiome: Evaluation of testing technologies

Spivak, I., & Elinav, E. (2023) · Elsevier eBooks · doi:10.1016/b978-0-323-95070-1.00002-3 · Cited by 1

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 191

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

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

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 190