BackgroundsThe respiratory microbiota and radiomics correlate with the disease severity and prognosis of chronic obstructive pulmonary disease (COPD). We aim to characterize the respiratory microbiota and radiomics features of COPD patients and explore the relationship between them.MethodsSputa from stable COPD patients were collected for bacterial 16 S rRNA gene sequencing and fungal Internal Transcribed Spacer (ITS) sequencing. Chest computed tomography (CT) and 3D-CT analysis were conducted for radiomics information, including the percentages of low attenuation area below − 950 Hounsfield Units (LAA%), wall thickness (WT), and intraluminal area (Ai). WT and Ai were adjusted by body surface area (BSA) to WT/\documentclass[12pt]{minimal}
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				\begin{document}$$\sqrt{\text{B}\text{S}\text{A}}$$\end{document}and Ai/BSA, respectively. Some key pulmonary function indicators were collected, which included forced expiratory volume in one second (FEV1), forced vital capacity (FVC), diffusion lung carbon monoxide (DLco). Differences and correlations of microbiomics with radiomics and clinical indicators between different patient subgroups were assessed.ResultsTwo bacterial clusters dominated byStreptococcusandRothiawere identified. Chao and Shannon indices were higher in theStreptococcuscluster than that in theRothiacluster. Principal Co-ordinates Analysis (PCoA) indicated significant differences between their community structures. Higher relative abundance ofActinobacteriawas detected in theRothiacluster. Some genera were more common in theStreptococcuscluster, mainly includingLeptotrichia,Oribacterium, Peptostreptococcus.Peptostreptococcuswas positively correlated with DLco per unit of alveolar volume as a percentage of predicted value (DLco/VA%pred). The patients with past-year exacerbations were more in theStreptococcuscluster. Fungal analysis revealed two clusters dominated byAspergillusandCandida. Chao and Shannon indices of theAspergilluscluster were higher than that in theCandidacluster. PCoA showed distinct community compositions between the two clusters. Greater abundance ofCladosporiumandPenicilliumwas found in theAspergilluscluster. The patients of theCandidacluster had upper FEV1 and FEV1/FVC levels. In radiomics, the patients of theRothiacluster had higher LAA% and WT/\documentclass[12pt]{minimal}
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				\begin{document}$$\sqrt{\text{B}\text{S}\text{A}}$$\end{document}than those of theStreptococcuscluster.Haemophilus, Neisseria and Cutaneotrichosporonpositively correlated with Ai/BSA, butCladosporiumnegatively correlated with Ai/BSA.ConclusionsAmong respiratory microbiota in stable COPD patients,Streptococcusdominance was associated with an increased risk of exacerbation,and Rothiadominance was relevant to worse emphysema and airway lesions.Peptostreptococcus,Haemophilus, Neisseria and Cutaneotrichosporonprobably affected COPD progression and potentially could be disease prediction biomarkers.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12931-023-02434-1.