Volume 5 Number 2 2022
Host DNA Depletion in Clinical Metagenomic Sequencing: Emerging Strategies, Ecological Insights, and the Hidden Challenge of Microbial Signal Recovery
An Duy Duong 1*
Microbial Bioactives 5 (2) 1-8 https://doi.org/10.25163/microbbioacts.5210708
Submitted: 20 January 2022 Revised: 12 March 2022 Accepted: 21 March 2022 Published: 23 March 2022
Metagenomic next-generation sequencing (mNGS) has increasingly positioned itself as one of the more promising approaches for broad-spectrum infectious disease diagnostics. Yet the field continues to encounter a surprisingly persistent obstacle: the overwhelming dominance of host-derived nucleic acids within clinical samples. In many specimen types, particularly blood, cerebrospinal fluid, and respiratory aspirates, human DNA can comprise more than 99% of total extracted genetic material, leaving diagnostically relevant microbial reads buried within an immense genomic background. This review explores how the challenge of host DNA depletion intersects with concepts long recognized in environmental microbiology, microbial ecology, and natural-product discovery. Drawing from studies involving Streptomyces bioprospecting, marine microbial symbioses, biosynthetic gene cluster mining, and computational dereplication, the review examines how selective enrichment, sequence-guided discovery, and bioinformatic filtering collectively shape modern metagenomic workflows. Emerging depletion strategies—including differential lysis, enzymatic digestion, density-based separation, and computational host-read removal—are discussed alongside their limitations, particularly regarding viral nucleic acid preservation and interpretative ambiguity. The review further argues that host-associated material may not simply represent analytical contamination but instead reflects biologically dynamic ecological systems that influence microbial adaptation and pathogenicity. Overall, the findings suggest that the future of clinical metagenomics may depend less on sequencing depth alone and more on integrated ecological, computational, and molecular strategies capable of selectively recovering meaningful microbial signals from overwhelmingly complex genomic environments.
Keywords: Clinical metagenomics; Host DNA depletion; Metagenomic next-generation sequencing; Streptomyces; Biosynthetic gene clusters; Bioinformatic dereplication; Microbial dark matter
Almeida, J. F., Marques, M., Oliveira, V., Egas, C., Mil-Homens, D., Viana, R., Cleary, D. F. R., Huang, Y. M., Fialho, A. M., Teixeira, M. C., Gomes, N. C. M., Costa, R., & Keller-Costa, T. (2023). Marine sponge- and octocoral-associated bacteria exhibit versatile potential for secondary metabolite biosynthesis and antimicrobial activity against human pathogens. Marine Drugs, 21(1), 34. https://doi.org/10.3390/md21010034
Aminov, R. I. (2010). A brief history of the antibiotic era: Lessons learned and challenges for the future. Frontiers in Microbiology, 1, 134. https://doi.org/10.3389/fmicb.2010.00134
Bentley, S. D., Chater, K. F., Cerdeño-Tárraga, A.-M., Challis, G. L., Thomson, N. R., James, K. D., Harris, D. E., Quail, M. A., Kieser, H., Harper, D., et al. (2002). Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2). Nature, 417(6885), 141–147. https://doi.org/10.1038/417141a
Chen, R., Wong, H. L., & Burns, B. P. (2019). New approaches to detect biosynthetic gene clusters in the environment. Medicines, 6(1), 32. https://doi.org/10.3390/medicines6010032
Donald, L., Pipite, A., Subramani, R., Owen, J., Keyzers, R. A., & Taufa, T. (2022). Streptomyces: Still the biggest producer of new natural secondary metabolites, a current perspective. Microbiological Research, 13(3), 418–465. https://doi.org/10.3390/microbiolres13030031
Edgcomb, V. P., & Bernhard, J. M. (2013). Heterotrophic protists in hypersaline microbial mats and deep hypersaline basin water columns. Life, 3(2), 346–362. https://doi.org/10.3390/life3020346
Genilloud, O., Gonzalez, I., Salazar, O., Martin, J., Tormo, J. R., & Vicente, F. (2011). Current approaches to exploit actinomycetes as a source of novel natural products. Journal of Industrial Microbiology & Biotechnology, 38(3), 375–389. https://doi.org/10.1007/s10295-010-0882-7
Guo, X., Chang, J., & Lin, K. (2020). Topographical properties of scaffolds for MSC differentiation. Nanomaterials, 10(9), 2070. https://doi.org/10.3390/nano10092070
Hug, J. J., Bader, C. D., Remškar, M., Cirnski, K., & Müller, R. (2018). Concepts and methods to access novel antibiotics from actinomycetes. Antibiotics, 7(2), 44. https://doi.org/10.3390/antibiotics7020044
Macintyre, L., Zhang, T., Viegelmann, C., Martinez, I. J., Dowdells, C., Cheng, C., Ramadan, U., Gernert, C., Hentschel, U., & Edrada-Ebel, R. (2014). Metabolomic tools for secondary metabolite discovery from marine microbial symbionts. Marine Drugs, 12(6), 3416–3448. https://doi.org/10.3390/md12063416
Mohimani, H., Gurevich, A., Mikheenko, A., Garg, N., Nothias, L.-F., Ninomiya, A., Takada, K., Dorrestein, P. C., & Pevzner, P. A. (2018). Metagenomics for natural product discovery. Antibiotics, 7(2), 44. https://doi.org/10.3390/antibiotics7020044
Mohr, K. I. (2018). Diversity of myxobacteria—We only see the tip of the iceberg. Microorganisms, 6(3), 84. https://doi.org/10.3390/microorganisms6030084
Montiel, D., Kang, H.-S., Chang, F.-Y., Charlop-Powers, Z., & Brady, S. F. (2015). Yeast homologous recombination-based promoter engineering for the activation of silent natural product biosynthetic gene clusters. Proceedings of the National Academy of Sciences of the United States of America, 112(29), 8953–8958. https://doi.org/10.1073/pnas.1507600112
Moore, J. M., Bradshaw, E., Seipke, R. F., Hutchings, M. I., & McArthur, M. (2012). Use and discovery of chemical elicitors that stimulate biosynthetic gene clusters in Streptomyces bacteria. Methods in Enzymology, 517, 367–385. https://doi.org/10.1016/B978-0-12-404634-4.00018-8
Okoro, C. K., Brown, R., Jones, A. L., Andrews, B. A., Asenjo, J. A., Goodfellow, M., & Bull, A. T. (2009). Diversity of culturable actinomycetes in hyper-arid soils of the Atacama Desert, Chile. Antonie van Leeuwenhoek, 95(2), 121–133. https://doi.org/10.1007/s10482-008-9295-2
Ramganesh, S., Maredza, A., & Tekere, M. (2017). Bacterial secondary metabolites in salt pans. Molecules, 22(4), 657. https://doi.org/10.3390/molecules22040657
Stewart, E. J. (2012). Growing unculturable bacteria. Journal of Bacteriology, 194(16), 4151–4160. https://doi.org/10.1128/JB.00345-12
Subramani, R., & Aalbersberg, W. (2013). Culturable rare actinomycetes: Diversity, isolation and marine natural product discovery. Applied Microbiology and Biotechnology, 97(21), 9291–9321. https://doi.org/10.1007/s00253-013-5229-7
Utermann, C., Echelmeyer, V. A., Oppong-Danquah, E., Blümel, M., & Tasdemir, D. (2020). Gut microbiota of Ciona intestinalis: Biodiversity, bioactive compounds, and secondary metabolite potential. Marine Drugs, 19(1), 6. https://doi.org/10.3390/md19010006
Vartoukian, S. R., Palmer, R. M., & Wade, W. G. (2010). Strategies for culture of “unculturable” bacteria. FEMS Microbiology Letters, 309(1), 1–7. https://doi.org/10.1111/j.1574-6968.2010.02000.x
Zvi-Kedem, T., Lalzar, M., Sun, J., Li, J., Tchernov, D., & Meron, D. (2022). Exploring the microbial mosaic: Insights into composition, diversity, and environmental drivers in the Pearl River Estuary sediments. Microorganisms, 12(7), 1273. https://doi.org/10.3390/microorganisms12071273
Microbial Frontiers in Extreme Environments: Rethinking Bioactive Potential Across Marine and Pristine Ecosystems
Illuminating Biological Dark Matter: Integrating Metagenomics, Synthetic Biology, and AI to Unlock Microbial and Genomic Potential for Therapeutics and Biotechnology
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