BackgroundBacterial and viral infections are commonly implicated in the development of pneumonia. We aimed to compare the diversity and composition of lung bacteria among severe pneumonia patients who were influenza virus positive (IFVP) and influenza virus negative (IFVN).MethodsBronchoalveolar lavage fluid specimens were procured from patients diagnosed with severe pneumonia to investigate the microbiome utilizing 16S-rDNA sequencing. The alpha diversity of the microbiome was evaluated employing Chao1, Shannon, and Simpson indexes, while the beta diversity was assessed using principal component analysis and principal coordinate analysis. Linear discriminant analysis effect size (LEfSe) was employed to determine the taxonomic differences between the IFVP and IFVN groups.ResultsA total of 84 patients with 42 in the IFVP group and 42 in the IFVN group were enrolled. Slightly higher indexes of Shannon and Simpson were observed in the IFVP group without statistically significant difference. The dominant bacterial genera wereStreptococcus,Klebsiella,Escherichia-Shigellain the IFVN group andAcinetobacter,Streptococcus,Staphylococcusin the IFVP group.Streptococcus pneumoniaeandAcinetobacter baumanniiwere the most abundant species in the IFVN and IFVP groups, respectively. LEfSe analysis indicated a greater abundance ofKlebsiellain the IFVN group.ConclusionsIndividuals with severe pneumonia infected with IFV exhibit heightened susceptibility to certain bacteria, especiallyAcinetobacter baumannii, and the underlying mechanism of the interaction between IFV andAcinetobacter baumanniiin the progression of pneumonia needs further investigation.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12941-023-00590-2.