17 June 2024

Analysing microbiomes in fluid from the lungs may help manage the risks faced by children who undergo bone marrow transplant, researchers have reported.

Researchers used metagenomic next generation sequencing (mNGS) to analyse the fluid, sequencing all the RNA present to detect every type of microorganism. The samples were grouped in four clusters, based upon the types of microorganisms present – and these clusters appeared to predict the risk that patients faced of fatal lung disease.

The greatest risk came when patients had the least number of microbial species, but also significant populations of viruses and of Staphylococcus bacteria, the researchers report.

Researcher Dr Matt Zinter, of the University of California San Francisco, said: “There’s a delicate balance between the microbiome blossoming so big that it represents infection or contracting to the point that it’s depleted and non-existent. It’s like the Goldilocks analogy — the middle ground seems to be just right.”

The research, reported in Nature Medicine, involved 229 patients in 32 hospitals across the USA, Canada, and Australia. The findings were validated in a separate cohort of patients in the Netherlands.

The tests also revealed some unexpected pathogens including a soil amoeba, a parasite found in cats, and several fungi. The researchers say that mNGS testing would mean doctors do not need to order tests for specific pathogens.

Dr Zinter summarised: “Our results, which we validated in an entirely separate cohort, indicate that lung microenvironments are predictive, or prognostic, for the risk of mortality. Our ultimate goal is to figure out how to modulate pulmonary biology for the benefit of our patients.”


Zinter MS, Dvorak CC, Mayday MY, Reyes G, Simon MR, Pearce EM, Kim H, Shaw PJ, Rowan CM, Auletta JJ, Martin PL, Godder K, Duncan CN, Lalefar NR, Kreml EM, Hume JR, Abdel-Azim H, Hurley C, Cuvelier GDE, Keating AK, Qayed M, Killinger JS, Fitzgerald JC, Hanna R, Mahadeo KM, Quigg TC, Satwani P, Castillo P, Gertz SJ, Moore TB, Hanisch B, Abdel-Mageed A, Phelan R, Davis DB, Hudspeth MP, Yanik GA, Pulsipher MA, Sulaiman I, Segal LN, Versluys BA, Lindemans CA, Boelens JJ, DeRisi JL, and the Pediatric Transplantation and Cell Therapy Consortium. (2024) “Pathobiological signatures of dysbiotic lung injury in pediatric patients undergoing stem cell transplantation.” Nature Medicine, 23 May 2024, doi: 10.1038/s41591-024-02999-4.

Link: https://www.nature.com/articles/s41591-024-02999-4

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