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PreprintCC BYbioRxiv

Benchmarking Microbiome Methods for Improved Metagenomic Sequencing of Lower Respiratory Tract Samples

  • J. T. Sumner
  • E. M. Hartmann1
  1. 1Northwestern University
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Abstract

Bronchoalveolar lavage is a common diagnostic strategy used to sample immune cells and microbiota of the lower respiratory tract. Metagenomic sequencing of raw bronchoalveolar lavage fluid reveals a low biomass microbial community often obscured by abundant host DNA. Here, we set out to determine an optimal strategy to robustly purify microbial DNA in excess of human DNA using a combinatorial lysis, host-depletion, DNA extraction approach. We identify strategies that improve metagenomic sequencing success that are commensurate with purification challenges that reduce signal from respiratory microbiota. Finally, we present a general framework to further improve microbial sequencing of lower respiratory tract samples in a robust and reproducible manner.

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Cite

BibTeXRIS
BibTeX
@misc{sumner2026benchmarking,
  title = {{Benchmarking Microbiome Methods for Improved Metagenomic Sequencing of Lower Respiratory Tract Samples}},
  author = {J. T. Sumner and E. M. Hartmann},
  howpublished = {bioRxiv},
  year = {2026},
  month = oct,
  doi = {10.64898/2026.10.16.759757},
  url = {https://www.biorxiv.org/content/10.64898/2026.10.16.759757v1},
  note = {CC BY},
}
RIS
TY  - UNPB
TI  - Benchmarking Microbiome Methods for Improved Metagenomic Sequencing of Lower Respiratory Tract Samples
AU  - J. T. Sumner
AU  - E. M. Hartmann
PY  - 2026
DA  - 2026/10/16
PB  - bioRxiv
DO  - 10.64898/2026.10.16.759757
UR  - https://www.biorxiv.org/content/10.64898/2026.10.16.759757v1
AB  - Bronchoalveolar lavage is a common diagnostic strategy used to sample immune cells and microbiota of the lower respiratory tract. Metagenomic sequencing of raw bronchoalveolar lavage fluid reveals a low biomass microbial community often obscured by abundant host DNA. Here, we set out to determine an optimal strategy to robustly purify microbial DNA in excess of human DNA using a combinatorial lysis, host-depletion, DNA extraction approach. We identify strategies that improve metagenomic sequencing success that are commensurate with purification challenges that reduce signal from respiratory microbiota. Finally, we present a general framework to further improve microbial sequencing of lower respiratory tract samples in a robust and reproducible manner.
ER  -