Prognostic Insights from Longitudinal Multicompartment Study of Host-Microbiota Interactions in Critically Ill Patients

Critical illness can disrupt the composition and function of the microbiome, yet comprehensive longitudinal studies are lacking. We conducted a longitudinal analysis of oral, lung, and gut microbiota in a large cohort of 479 mechanically ventilated patients with acute respiratory failure. Progressive dysbiosis emerged in all three body compartments, characterized by reduced alpha diversity, depletion of obligate anaerobe bacteria, and pathogen enrichment. Clinical variables, including chronic obstructive pulmonary disease, immunosuppression, and antibiotic exposure, shaped dysbiosis. Notably, of the three body compartments, unsupervised clusters of lung microbiota diversity and composition independently predicted survival, transcending clinical predictors, organ dysfunction severity, and host-response sub-phenotypes. These independent associations of lung microbiota may serve as valuable biomarkers for prognostication and treatment decisions in critically ill patients. Insights into the dynamics of the microbiome during critical illness highlight the potential for microbiota-targeted interventions in precision medicine. ### Competing Interest Statement Dr. Kitsios has received research funding from Karius, Inc and Pfizer, Inc, both unrelated to this project. Dr. Morris has received research funding from Pfizer, Inc, unrelated to this project. Dr McVerry has received consulting fees from Boehringer Ingelheim, BioAegis, and Synairgen Research, Ltd. unrelated to this work. All other authors disclosed no conflict of interest. ### Funding Statement Funding information: Dr. Kitsios: University of Pittsburgh Clinical and Translational Science Institute, COVID-19 Pilot Award; NIH (R03 HL162655); Dr. Benos: NIH (R01 HL157879; R01 HL127349, R01DK130294); Dr. McVerry: NIH (P01 HL114453); Dr. Bain: Veterans Affairs (IK2BX004886); Dr. Lai: Massachusetts General Hospital Translational and Clinical Research Center, supported by Grant 1UL1TR002541 ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: Ethics approval and consent to participate: The University of Pittsburgh Institutional Review Board (IRB) approved the protocol for the UPMC-ARF and UPMC-COVID cohorts (STUDY19050099). We obtained written or electronic informed consent by all participants or their surrogates in accordance with the Declaration of Helsinki. For the MGH-COVID cohort, the Study protocol #2020P000804 was approved by the Mass General Brigham IRB. For the healthy controls, the University of Pittsburgh IRB approved the study protocols (STUDY19060243 for respiratory biospecimens and STUDY20060312 for stool biospecimens). All participants or their healthcare proxy provided written informed consent to participate. I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes Data and code availability: Sequencing data collected for the study have been deposited to the Sequencing Resource Archive, through the following Accession numbers: -PRJNA595346 for 16S data of UPMC-ARF and UPMC-COVID cohorts, -PRJNA726955 for ITS data of UPMC-ARF cohort, -PRJNA554461 for Nanopore data of UPMC-ARF cohort, -PRJNA940725 for 16S data of the Healthy Controls, -PRJNA976404 for Metagenomic data of the MGH-COVID cohort. Primary code and de-identified data for replication of analyses will be available on the github repository (https://github.com/MicrobiomeALIR/MultiCompartmentMicrobiome) upon acceptable of the manuscript for publication. Any additional information required to reanalyze the data reported in this paper is available from the lead contact upon request.