ArticleCell host & microbe2025
Microbial contribution to metabolic niche formation varies across the respiratory tract.
Abstract read
In one paragraph
Article in Cell host & microbe, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers, 1 of them a synthesis that pooled it.
0numbers the graph read from it
0cells of the map it votes in
9citing papers in PubMed, 1 pooled it
–field-weighted citation impact
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
9 citing papers in PubMed, 1 synthesis or guideline pooled it.
- The respiratory microbiome in pulmonary tuberculosis: a meta-analysis reveals niche-specific microbial and functional signatures.mSystems · 2026Pooled it
- Review
- Myeloid cell reprogramming drives enhanced defense againstbioRxiv : the preprint server for biology · 2026Article
- The respiratory microbiome: dynamics from health to disease.FEMS microbiology ecology · 2026Review
- Respiratory microbiota transplantation: optimized framework and its impact on metabolic and immune characteristics.Chinese medical journal pulmonary and critical care medicine · 2026Article
- Review
- Innovative Systems Biology in Baijiu Fermentation: Unveiling Omics Landscapes and Microbial Synergy.Foods (Basel, Switzerland) · 2026Review
- Airway microbiota and immunity associated with chronic obstructive pulmonary disease severity.Journal of translational medicine · 2025Article
- Structural and Functional Alterations of Microbiome in Upper and Lower Respiratory Tract in Patients With NSCLC.Cancer control : journal of the Moffitt Cancer CenterArticle
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
37 authors.
Kendrew K WongDivision of Pulmonary and Critical Care Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA; Department of Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA.
Benjamin G WuDivision of Pulmonary and Critical Care Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA; Department of Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA; Division of Pulmonary and Critical Care Medicine, VA New York Harbor Healthcare System, New York, NY, USA.
Matthew ChungSystems Genomics Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
Qinsheng LiDivision of Pulmonary and Critical Care Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA.
Fares DarawshyDivision of Pulmonary and Critical Care Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA.
Jun-Chieh J TsayDivision of Pulmonary and Critical Care Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA; Department of Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA; Division of Pulmonary and Critical Care Medicine, VA New York Harbor Healthcare System, New York, NY, USA.
Meredith HolubDivision of Pulmonary and Critical Care Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA; Department of Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA; Division of Pulmonary and Critical Care Medicine, Hartford Health Care, Hartford, CT, USA.
Clea R BarnettDivision of Pulmonary and Critical Care Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA; Department of Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA.
Benjamin KwokDivision of Pulmonary and Critical Care Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA; Department of Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA.
Matthias C KuglerDivision of Pulmonary and Critical Care Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA; Department of Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA.
Cecilia ChungDivision of Pulmonary and Critical Care Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA.
Jake G NataliniDivision of Pulmonary and Critical Care Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA; Department of Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA.
Shivani SinghDivision of Pulmonary and Critical Care Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA; Department of Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA.
Yonghua LiDivision of Pulmonary and Critical Care Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA; Department of Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA.
Rosemary SchlugerDivision of Pulmonary and Critical Care Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA; Department of Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA.
Lia FicaroDepartment of Biochemistry and Molecular Pharmacology and Department of Radiation Oncology, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA.
Joseph CarpenitoDivision of Pulmonary and Critical Care Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA; Department of Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA.
Destiny CollazoDivision of Pulmonary and Critical Care Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA; Department of Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA.
Luisanny PerezDivision of Pulmonary and Critical Care Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA; Department of Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA.
Yaa KyerematengDivision of Pulmonary and Critical Care Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA; Department of Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA.
Miao ChangDivision of Pulmonary and Critical Care Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA; Department of Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA.
Anna CzachorDivision of Pulmonary and Critical Care Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA.
Raj SinghDivision of Pulmonary and Critical Care Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA.
Colin MccormickDivision of Pulmonary and Critical Care Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA.
Christina D CampbellDepartment of Respiratory Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland; Department of Respiratory Medicine, Beaumont Hospital, Dublin, Ireland.
Ruaidhri KeaneDepartment of Respiratory Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland; Department of Respiratory Medicine, Beaumont Hospital, Dublin, Ireland.
Manor AskenaziBiomedical Hosting LLC, Arlington, MA, USA.
Philip M HansbroCentre for Inflammation, Centenary Institute and University of Technology Sydney, School of Life Sciences, Faculty of Science, Sydney, NSW, Australia.
Michael D WeidenDivision of Pulmonary and Critical Care Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA; Department of Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA.
Yvonne J HuangDepartment of Clinical Pharmacy, College of Pharmacy, University of Michigan, Ann Arbor, MI, USA; Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA.
Kathleen A StringerDepartment of Clinical Pharmacy, College of Pharmacy, University of Michigan, Ann Arbor, MI, USA; Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA.
Jose C ClementeDepartment of Genetics and Genomic Sciences and Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
Huilin LiDepartment of Population Health, New York University School of Medicine, NYU Langone Health, New York, NY, USA.
Drew JonesDepartment of Biochemistry and Molecular Pharmacology and Department of Radiation Oncology, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA.
Elodie GhedinSystems Genomics Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
Leopoldo N SegalDivision of Pulmonary and Critical Care Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA; Department of Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA; Laura and Isaac Perlmutter Cancer Center, New York University School of Medicine, NYU Langone Health, New York, NY, USA.
Imran SulaimanDivision of Pulmonary and Critical Care Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA; Department of Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA; Department of Respiratory Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland; Department of Respiratory Medicine, Beaumont Hospital, Dublin, Ireland. Electronic address: sheikmohammadimran.sulaiman@nyumc.org.
Funding
Vaccine FacilityP30CA016087 · NCI · NEW YORK UNIVERSITY SCHOOL OF MEDICINE · PI MARK Reid PHILIPS · 1985 to 2026
$83.1MInstitutional Career DevelopmentKL2TR001446 · NCATS · NEW YORK UNIVERSITY SCHOOL OF MEDICINE · PI PILLINGER, MICHAEL · 2015 to 2025
$6.7MNRSA Training CoreTL1TR001447 · NCATS · NEW YORK UNIVERSITY SCHOOL OF MEDICINE · PI MICOLI, KEITH J. · 2015 to 2025
$5.9MMicrobial and host biomarker development for detection and prognosis of early stage non-small cell lung cancerU2CCA271890 · NCI · NEW YORK UNIVERSITY SCHOOL OF MEDICINE · PI HARVEY Ira PASS, Leopoldo Nicolas Segal · 2023 to 2026
$4.7MLocal microbiota signatures of pro-tumor immunity and checkpoint inhibition susceptibility in lung cancerR37CA244775 · NCI · NEW YORK UNIVERSITY SCHOOL OF MEDICINE · PI Leopoldo Nicolas Segal · 2020 to 2026
$4.7MTranslational Metabolomics in Critical CareR35GM136312 · NIGMS · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI KATHLEEN A STRINGER · 2020 to 2026
$2.8MAge related loss of immune resilience during response to severe respiratory viral infectionsU01AG088351 · NIA · NEW YORK UNIVERSITY SCHOOL OF MEDICINE · PI CHRISTIAN FORST, Leopoldo Nicolas Segal · 2024 to 2026
$1.5MBIOREPOSITORY OPTIMIZATION AND USE FOR ENDOTYPING CRITICALLY ILL SARS-COV-2 INFECTED PATIENTSR33GM147800 · NIGMS · NEW YORK UNIVERSITY SCHOOL OF MEDICINE · PI SEGAL, LEOPOLDO NICOLAS · 2024 to 2025
$1.5MHedgehog and Platelet-derived growth factor pathway crosstalk in the lungR56HL151700 · NHLBI · NEW YORK UNIVERSITY SCHOOL OF MEDICINE · PI KUGLER, MATTHIAS CHRISTIAN · 2020 to 2020
$554kBLRD VA IK2 BX005309NCATS NIH HHS KL2 TR001446NCATS NIH HHS TL1 TR001447NCI NIH HHS P30 CA016087NCI NIH HHS R37 CA244775NCI NIH HHS U2C CA271890NHLBI NIH HHS R56 HL151700NIA NIH HHS U01 AG088351NIGMS NIH HHS R33 GM147800NIGMS NIH HHS R35 GM136312
Abstract
Variations in the airway microbiome are associated with inflammatory responses in the lung and pulmonary disease outcomes. Regional changes in microbiome composition could have spatial effects on the metabolic environment, contributing to differences in the host response. Here, we profiled the respiratory microbiome (metagenome/metatranscriptome) and metabolome of a patient cohort, uncovering topographical differences in microbial function, which were further delineated using isotope probing in mice. In humans, the functional activity of taxa varied across the respiratory tract and correlated with immunomodulatory metabolites such as glutamic acid/glutamate and methionine. Common oral commensals, such as Prevotella, Streptococcus, and Veillonella, were more functionally active in the lower airways. Inoculating mice with these commensals led to regional increases in several metabolites, notably methionine and tyrosine. Isotope labeling validated the contribution of Prevotella melaninogenica in generating specific metabolites. This functional characterization of microbial communities reveals topographical changes in the lung metabolome and potential impacts on host responses.
Indexed as
BacteriaMicrobiotaRespiratory SystemAnimalsFemaleGlutamic AcidHumansLungMaleMetabolomeMetagenomeMethionineMiceMice, Inbred C57BLPrevotellaStreptococcusGlutamic AcidMethionineCOPDgenomicslower airway dysbiosislung dysbiosislung inflammationmetabolomicsmetatranscriptomicsmicrobiomeoral commensalstranscriptomics
Identifiers
What OpenQuestion holds
Textmetadata
LicenceTDM
Read underepoch 390
Registered trials
None linked
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.