Contamination in Low Microbial Biomass Microbiome Studies: Issues and Recommendations

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Items 501–600 of 1,000

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2. Next-Generation Sequencing for Bloodstream Infections: Shaping the Future of Rapid Diagnostics and Precision Medicine
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3. Gut microbiome in type 2 diabetes: insights from metagenomics, multi-omics, and diet–microbe interactions
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4. Biodiversity and biogeography of the multi-kingdom cancer microbiome
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5. Unexpected associations between respiratory viruses and bacteria with Pulmonary Function Testing in children suffering from Cystic Fibrosis (MUCOVIB study)
   Valentin Scherz, Giorgia Caruana, Patrick Taffé, René Brouillet, Claire Bertelli, Katia Jaton, Yves Fougère, Klara Maria Posfay-Barbe, Anne Mornand, Isabelle Rochat et al. · 2021 · Journal of Cystic Fibrosis
6. Uromycobiome in infants and toddlers with and without urinary tract infections
   Catherine S. Forster, Hui Liu, Marcia Kurs‐Lasky, Wendy Ullmer, Janina A. Krumbeck, Nader Shaikh · 2022 · Pediatric Nephrology
7. Application of beta and gamma carbonic anhydrase sequences as tools for identification of bacterial contamination in the whole genome sequence of inbred Wuzhishan minipig (Sus scrofa) annotated in databases
   Reza Zolfaghari Emameh, Seyed Nezamedin Hosseini, Seppo Parkkila · 2021 · Database
8. Formalin-Fixed Paraffin-Embedded (FFPE) samples are not a beneficial replacement for frozen tissues in fetal membrane microbiota research
   Rochelle Hockney, Caroline Hayley Orr, Gareth Waring, Inge Christiaens, Gillian Taylor, Stephen P. Cummings, Stephen Courtenay Robson, Andrew Nelson · 2022 · PLoS ONE
9. Tardigrade Community Microbiomes in North American Orchards Include Putative Endosymbionts and Plant Pathogens
   Laura E. Tibbs‐Cortes, Bienvenido W. Tibbs‐Cortes, Stephan Schmitz‐Esser · 2022 · Frontiers in Microbiology
10. Prospect of bacteria for tumor diagnosis and treatment
    Yuyao Xu, Chenhao Zhao, Xin Ma, Haifang Zhang · 2022 · Life Sciences
11. Metagenome sequencing and 982 microbial genomes from Kermadec and Diamantina Trenches sediments
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12. The road not taken: host genetics in shaping intergenerational microbiomes
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13. Comparison of two methods for bioaerosol sampling and characterization in a low-biomass chamber environment
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14. Microbial genomics: a potential toolkit for forensic investigations
    Pooja Tripathi, Riya Render, Sweta Nidhi, Vijay Shankar Tripathi · 2024 · Forensic Science Medicine and Pathology
15. Seminal plasma microbiomes, sperm parameters, and cryopreservation in a healthy fertile population
    Longlong Fu, Yuanlei Lou, Ying Lan Guo, Fang Zhou, Jing Ma, Shusong Wang, Yiqun Gu, Bin Fu, Wenhong Lu · 2024 · Frontiers in Microbiology
16. Persistent tissue‐specific resident microbiota in oysters across a broad geographical range
    Andrea Unzueta‐Martínez, Jennifer L. Bowen · 2024 · Environmental Microbiology Reports
17. Ancient environmental microbiomes and the cryosphere
    Alexander D. Williams, Vivian W. Leung, Julian Wei-Tze Tang, Nishimura Hidekazu, Nobuhiro Suzuki, Andrew C. Clarke, David A. Pearce, Tommy Tsan‐Yuk Lam · 2024 · Trends in Microbiology
18. Circulating microbiome DNA features and its effect on predicting clinicopathological characteristics of patients with colorectal cancer
    Liang Ma, Mingliang Shi, Xue Zhang, Yan Liu, Hui Zi Jin, Dan Xiao Li, Hui Zhang, Feng Li, Jing Zuo, Yudong Wang et al. · 2025 · Journal of Translational Medicine
19. Bioinformatic approaches to blood and tissue microbiome analyses: challenges and perspectives
    Jammi Prasanthi Sirasani, Cory Gardner, Gihwan Jung, Hyunju Lee, Tae-Hyuk Ahn · 2025 · Briefings in Bioinformatics
20. Dupilumab treatment has no effect on the nasal microbiome in patients with NSAID-exacerbated respiratory disease: a longitudinal pilot study
    Tina Josefin Bartosik, Petra Pjevac, Joana Séneca, Christina Morgenstern, Tamara Arnoldner, Katharina Gangl, Christoph Sinz, Nicholas James Campion, Aldine Tu, Victoria Stanek et al. · 2025 · Frontiers in Immunology
21. Evaluating urine volume and host depletion methods to enable genome-resolved metagenomics of the urobiome
    Zachary J. Lewis, Angela Scott, Christopher C. Madden, Dean R. Vik, Ahmed A. Zayed, Garrett J. Smith, Sheryl S. Justice, Adam Joseph Rudinsky, Jessica Anne Hokamp, Vanessa L. Hale · 2025 · Microbiome
22. Integrated profiling of semen microbiota and metabolome reveals dysregulation in primary idiopathic male infertility
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23. Multi-omics analysis reveals the association between intratumoral bacteria and somatic mutational signatures in oral squamous cell carcinoma
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24. Micromanagement: how the male reproductive microbiome shapes male fertility
    Sohei Kuribayashi, Noopur C. Naik, Aaron W. Miller, Scott D. Lundy · 2026 · Fertility and Sterility
25. The microbiome of the ice-capped Cayambe Volcanic Complex in Ecuador
    Magdalena Díaz, Pablo Monfort‐Lanzas, Cristian Daniel Quiroz-Moreno, Erika Rivadeneira, Pablo Castillejo, Vicente Arnau, Wladimiro Dı́az-Villanueva, Spiros Nicolas Agathos, Félix Javier Sangari, Pablo Jarrín–V et al. · 2023 · Frontiers in Microbiology
26. Quality Control in Metagenomics Data
    Abraham Gihawi, Ryan P Cardenas, Rachel Hurst, Daniel S. Brewer · 2023 · Methods in molecular biology
27. An efficient method for high molecular weight bacterial DNA extraction suitable for shotgun metagenomics from skin swabs
    Iliana R. Serghiou, Dave Baker, Rhiannon Evans, Matthew J. Dalby, Raymond Kiu, Eleftheria Trampari, Sarah Phillips, Rachel Watt, Thomas Atkinson, Barry Murphy et al. · 2023 · Microbial Genomics
28. Context matters: environmental microbiota from ice cream processing facilities affected the inhibitory performance of two lactic acid bacteria strains against Listeria monocytogenes
    M. Laura Rolon, Tyler Chandross-Cohen, Kerry E. Kaylegian, Robert F. Roberts, Jasna Kovač · 2023 · Microbiology Spectrum
29. Altitude-associated trends in bacterial communities in ultrahigh-altitude residences
    Yiran Lu, Mengjie Duan, Yifan Li, Shengyu Zhang, Xiaomin Hu, Li Liu · 2024 · Environment International
30. Comparison of DNA Extraction Methods for Optimal Recovery of Metagenomic DNA from Human and Environmental Samples
    Mohita Gaur, Aarushi Vasudeva, Anoop Singh, Vishal Sharma, Himani Khurana, Ram Krishan Negi, Jung-Kul Lee, Vipin Chandra Kalia, Richa Misra, Yogendra Prakash Singh · 2019 · Indian Journal of Microbiology
31. Mapping Microbial Abundance and Prevalence to Changing Oxygen Concentration in Deep-Sea Sediments Using Machine Learning and Differential Abundance
    Tor Einar Møller, Sven Le Moine Bauer, Bjarte Hannisdal, Rui Zhao, Tamara Baumberger, Desiree L. Roerdink, Amandine Dupuis, Ingunn H. Thorseth, Rolf B. Pedersen, Steffen L. Jørgensen · 2022 · Frontiers in Microbiology
32. Ear mite infection restructures otic microbial networks in conservation–reliant Santa Catalina Island foxes (Urocyon littoralis catalinae)
    Jasmine Lu, Emily E. Hamblen, Lara J. Brenner, Julie L. King, Bridgett M. vonHoldt, Alexandra L. DeCandia · 2022 · Molecular Ecology
33. Profiling the Urobiota in a Pediatric Population with Neurogenic Bladder Secondary to Spinal Dysraphism
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34. The making of the oral microbiome in Agta hunter–gatherers
    Begoña Dobón, Federico Musciotto, Álex Mira, Michael John Greenacre, Rodolph Schlaepfer, Gabriela Aguileta, Leonora H. Astete, Marilyn L Ngales, Vito Latora, Federico Battiston et al. · 2023 · Evolutionary Human Sciences
35. Effects of exogenous elevation of corticosterone on immunity and the skin microbiome of eastern newts ( Notophthalmus viridescens )
    Kenzie E. Pereira, Molly C. Bletz, Julia A. McCartney, Douglas C. Woodhams, Sarah K. Woodley · 2023 · Philosophical Transactions of the Royal Society B Biological Sciences
36. Applying high-throughput rRNA gene sequencing to assess microbial contamination of a 40-year old exposed archaeological profile
    Daniel S. Jones, Gilliane Monnier, Aspen Cooper, Mile Baković, Goran Pajović, Nikola Borovinić, Gilbert B. Tostevin · 2020 · Journal of Archaeological Science
37. Approaching the sterile womb theory in dogs and cats: A multi-technique investigation
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38. Emerging roles of intratumoral microbiota: a key to novel cancer therapies
    Pengzhong Fang, H. J. Yang, Huiyun Zhang, Diankui Shuai, Min Li, Lin Chen, Liping Liu · 2025 · Frontiers in Oncology
39. Revisiting cattle respiratory health: key roles of the gut-lung axis in the dynamics of respiratory tract pathobiome
    Yue Wang, Nilusha Malmuthuge, Junhu Yao, Le Luo Guan · 2025 · Microbiology and Molecular Biology Reviews
40. Intratumoral microbiome in breast cancer: A hidden player in tumor development, progression and treatment response
    Jacopo Canzian, Flavia Jacobs, Anna Floreani, Chiara Miggiano, Paola Tiberio, Chiara Pozzi, Armando Santoro, Alberto Zambelli, María Rescigno, Rita De Sanctis · 2025 · Critical Reviews in Oncology/Hematology
41. Setting higher standards for reports of microbial species in human cancers
    Steven L. Salzberg, Minghao Chia, Chin Yen Tay, Noel F.C.C. de Miranda, Vincent T.H.B.M. Smit, Jelle Wesseling, Rafael A. Irizarry, Barry James Marshall, Eske Willerslev, Jacques Neefjes et al. · 2026 · Nature Cancer
42. Endometrial Microbiome and Implantation: From Basic Knowledge to Clinical Medicine
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43. Microbial communities and lipid records of the Linxia Basin, NE Tibetan Plateau: Implications for enhanced aridity in the Late Miocene
    Wei He, Gen Wang, Yongli Wang, Zhifu Wei, Zhiyong Huang, Ting Zhang, Xueyun Ma, He Ma, Xiaoli Yu · 2020 · Journal of Asian Earth Sciences
44. Impact of DNA extraction methods on 16S rRNA-based profiling of bacterial communities in cheese
    Barbora Markusková, Jana Minarovičová, Adriana Véghová, Hana Drahovská, Eva Kaclı́ková · 2021 · Journal of Microbiological Methods
45. Association Between Human Gut Microbiome and N-Glycan Composition of Total Plasma Proteome
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46. The effects of antibiotics and illness on gut microbial composition in the fawn-footed mosaic-tailed rat (Melomys cervinipes)
    Tasmin Lee Rymer, Neville Pillay · 2023 · PLoS ONE
47. Metagenomic Methods for Addressing NASA's Planetary Protection Policy Requirements on Future Missions: A Workshop Report
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48. Current Trends and Challenges of Microbiome Research in Prostate Cancer
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49. Origin and modern microbial ecology of secondary mineral deposits in Lehman Caves, Great Basin National Park, NV , USA
    Zoë E. Havlena, Louise D. Hose, Harvey R. DuChene, Gretchen Baker, J. Douglas Powell, Amanda L. Labrado, Benjamin Brunner, Daniel S. Jones · 2024 · Geobiology
50. Technical pitfalls that bias comparative microbial community analyses of aquatic disease Ian Hewson*
    Ian Hewson · 2019 · Diseases of Aquatic Organisms
51. Different Non-Structural Carbohydrates/Crude Proteins (NCS/CP) Ratios in Diet Shape the Gastrointestinal Microbiota of Water Buffalo
    Rubina Paradiso, Giorgia Borriello, Sergio Bolletti Censi, Angela Salzano, Roberta Cimmino, Giorgio Galiero, Giovanna Fusco, Esterina De Carlo, Giuseppe Campanile · 2021 · Veterinary Sciences
52. A Standardized Approach for Shotgun Metagenomic Analysis of Ancient Dental Calculus
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53. Effects of perioperative managements on ocular surface microbiota in intravitreal injection patients
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54. Exploring the patient-microbiome interaction patterns for pan-cancer
    Lan Zhao, William Chi Shing Cho, Jun‐Li Luo · 2022 · Computational and Structural Biotechnology Journal
55. Sarcoptic mange changes bacterial and fungal microbiota of bare-nosed wombats (Vombatus ursinus)
    Christina Næsborg‐Nielsen, Raphael Eisenhofer, Tamieka A. Fraser, Vicky Wilkinson, Christopher Paul Burridge, Scott Carver · 2022 · Parasites & Vectors
56. Skin microbiota analysis in patients with anorexia nervosa and healthy-weight controls reveals microbial indicators of healthy weight and associations with the antimicrobial peptide psoriasin
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57. Optimization of DNA extraction and sampling methods for successful forensic microbiome analyses of the skin and saliva
    Kyeong-Min Yu, A-mi Lee, Hye-Seon Cho, Ji-Woo Lee, Si‐Keun Lim · 2022 · International Journal of Legal Medicine
58. aKmerBroom: Ancient oral DNA decontamination using Bloom filters on k-mer sets
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59. The Use of Whole Genome and Next-Generation Sequencing in the Diagnosis of Invasive Fungal Disease
    Sam El-Kamand, Alexie Papanicolaou, Charles Oliver Morton · 2019 · Current Fungal Infection Reports
60. Nasal bacterial microbiota during an outbreak of equine herpesvirus 1 at a farm in southern Ontario.
    Diego E Gomez, Luis Guillermo Arroyo, Brandon N. Lillie, J. Scott Weese · 2021 · PubMed Central
61. Parallel Sequencing Reveals Campylobacter spp. in Commercial Meat Chickens Less than 8 Days Old
    F. M. Colles, S. J. Hedges, R. Dixon, Stephen G. Preston, P. Thornhill, Kenneth Klingenberg Barfod, S. G. Gebhardt-Henrich, P. Créach, Martin C. J. Maiden, M. S. Dawkins et al. · 2021 · Applied and Environmental Microbiology
62. Injection site microflora in persons with diabetes: why needle reuse is not associated with increased infections?
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63. Gut Bacterial Communities in the Ground Beetle Carabus convexus
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64. Next-Generation Sequencing in Periprosthetic Joint Infections
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65. Blood microbiome signatures in systemic diseases: current insights, methodological pitfalls, and future horizons
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66. Deciphering the impact of contaminating microbiota in DNA extraction reagents on metagenomic next-generation sequencing workflows
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67. Association of Enterotoxigenic Bacteroides fragilis with Immune Modulation in Colorectal Cancer Liver Metastasis
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68. Integrating multi-omics in bile for biomarker discovery in cholangiocarcinoma
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69. Gut feelings–the gut microbiome as a regulator of mental health in polycystic ovary syndrome
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70. Multifaceted effects of the microbiome in pancreatic cancer: from association to modulation
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71. The respiratory tract virome: unravelling the role of viral dark matter in respiratory health and disease
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72. Intratumoral Microbiome: Impact on Cancer Progression and Cellular Immunotherapy
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73. The impact of maternal microbial transfer on the infant gut microbiome after cesarean delivery: a systematic review
    Jan Jurgiel, Tomasz Gromowski, Joanna Weronika Król, Dorota Agata Bomba-Opon, Tomasz Kościółek, Mirosław Wielgoś · 2026 · American Journal of Obstetrics and Gynecology
74. Translational Implications of Microbiome Testing Methodologies in Lung Cancer: A Systematic Review of 16S rRNA Sequencing, Shotgun Metagenomics, and Short-Chain Fatty Acid Profiling
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75. Multi-omics biomarkers in female fertility: from oocyte quality to endometrial receptivity and clinical translation
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76. Getting off tract: contributions of intraorgan microbiota to cancer in extraintestinal organs
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77. The lower airway microbiome in paediatric health and chronic disease
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78. Blood Microbiota and Its Products: Mechanisms of Interference with Host Cells and Clinical Outcomes
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79. Assessment of the fecal microbiome of healthy rabbits (Oryctolagus cuniculus domesticus) compared with rabbits with gastrointestinal disease using next-generation DNA sequencing
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80. Identifying background microbiomes in an evidence recovery laboratory: A preliminary study
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81. Chronic rejection as a persisting phantom menace in organ transplantation: a new hope in the microbiota?
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82. Developing Inside a Layer of Germs—A Potential Role for Multiciliated Surface Cells in Vertebrate Embryos
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83. Detecting Redox Potentials Using Porous Boron Nitride/ATP-DNA Aptamer/Methylene Blue Biosensor to Monitor Microbial Activities
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84. Evaluation of potentiality of traditional hygienic practices for the mitigation of the 2019–2020 Corona Pandemic
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85. Rare genera differentiate urban green space soil bacterial communities in three cities across the world
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86. The prevalence of controls in phyllosphere microbiome research: a methodological review
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87. Releasing the microbes from old bones: the effect of different DNA extraction protocols on microbial community profiling
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88. Nasal microbiome research in ANCA-associated vasculitis: Strengths, limitations, and future directions
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89. Patterns of Structural and Functional Bacterioplankton Metacommunity along a River under Anthropogenic Pressure
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90. Antarctic Bacteria as Astrobiological Models
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91. Diverse recruitment to a globally structured atmospheric microbiome
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92. Cross-laboratory replication of pseudomyxoma peritonei tumor microbiome reveals reproducible microbial signatures
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93. Gut Microecology of Four Sympatric Desert Rodents Varies by Diet
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94. The Association Between Maternal Diet and the Human Milk Microbiome: A Review of Evidence and Methodological Challenges
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95. The association between the adenoid microbiome and chronic otitis media with effusion in children differs according to age
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96. Ten questions concerning indoor dust
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97. Intratumoral microbiota and metabolites: dual roles in cancer progression and therapeutic opportunities
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98. Peripheral blood biomarkers in PD-1/PD-L1 immunotherapy: distinguishing predictive from prognostic biomarkers
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99. Touching the (almost) untouchable: a minimally invasive workflow for microbiological and biomolecular analyses of cultural heritage objects
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100. The telencephalon is a neuronal substrate for systemic inflammatory responses in teleosts via polyamine metabolism
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