Royal College of Surgeons in Ireland
Pleural fluid microbiota as a biomarker for malignancy and prognosis.pdf (4.95 MB)

Pleural fluid microbiota as a biomarker for malignancy and prognosis

Download (4.95 MB)
journal contribution
posted on 2023-02-20, 17:20 authored by Benjamin Kwok, Benjamin G Wu, Ibrahim F Kocak, Imran SulaimanImran Sulaiman, Rosemary Schluger, Yonghua Li, Raheel Anwer, Chandra Goparaju, Daniel J Ryan, Marla Sagatelian, Matthew S Dreier, Vivek Murthy, Samaan Rafeq, Gaetane C Michaud, Daniel H Sterman, Jamie L Bessich, Harvey I Pass, Leopoldo N Segal, Jun-Chieh J Tsay

Malignant pleural effusions (MPE) complicate malignancies and portend worse outcomes. MPE is comprised of various components, including immune cells, cancer cells, and cell-free DNA/RNA. There have been investigations into using these components to diagnose and prognosticate MPE. We hypothesize that the microbiome of MPE is unique and may be associated with diagnosis and prognosis. We compared the microbiota of MPE against microbiota of pleural effusions from non-malignant and paramalignant states. We collected a total of 165 pleural fluid samples from 165 subjects; Benign (n = 16), Paramalignant (n = 21), MPE-Lung (n = 57), MPE-Other (n = 22), and Mesothelioma (n = 49). We performed high throughput 16S rRNA gene sequencing on pleural fluid samples and controls. We showed that there are compositional differences among pleural effusions related to non-malignant, paramalignant, and malignant disease. Furthermore, we showed differential enrichment of bacterial taxa within MPE depending on the site of primary malignancy. Pleural fluid of MPE-Lung and Mesothelioma were associated with enrichment with oral and gut bacteria that are commonly thought to be commensals, including Rickettsiella, Ruminococcus, Enterococcus, and Lactobacillales. Mortality in MPE-Lung is associated with enrichment in Methylobacterium, Blattabacterium, and Deinococcus. These observations lay the groundwork for future studies that explore host-microbiome interactions and their influence on carcinogenesis 


Stony Wold-Herbert, Inc Fellowship Grant

U01CA214195 (NCI/NIH)

R37CA244775 (NCI/NIH)

PACT grant (FNIH)

American Association for Cancer Research Grant

The Genome Technology Center is partially supported by the Cancer Center Support Grant P30CA016087 at the Laura and Isaac Perlmutter Cancer Center

FAMRI Young Clinical Scientist Award

National Center for Advancing Translational Sciences (NCATS)


National Institutes of Health, through Grant Award Number KL2TR001446


Associated research data files

Data from the 16S rRNA gene sequencing is available at BioProject ID PRJNA865295. R scripts used for analyses are available at


The original article is available at

Published Citation

Kwok B. et al. Pleural fluid microbiota as a biomarker for malignancy and prognosis. Sci Rep. 2023;13(1):2229

Publication Date

8 February 2023

PubMed ID



  • Beaumont Hospital
  • Medicine


Nature Publishing Group


  • Published Version (Version of Record)