{"doi":"10.1111/all.15438","title":"The nasopharyngeal and salivary microbiomes in COVID‐19 patients with and without asthma","abstract":"So far, our understanding of the associations between respiratory infections and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in the context of asthma is limited. Although our previous study and others did not find a correlation between preexisting asthma and increased risks of severe coronavirus disease 2019 (COVID-19) outcomes,1-3 people with asthma usually have an increased vulnerability to conventional respiratory viral infections. Thus, continuous investigation on SARS-CoV-2 infection in people with asthma is important. People with asthma harbor altered airway microbiota, which has been suggested to mediate an increased susceptibility to severe illnesses upon viral respiratory infections.4 However, the microbiomes of patients with asthma during SARS-CoV-2 infection have not yet been characterized. To this end, we performed a microbiome study using nasopharyngeal samples and saliva samples from COVID-19 patients with and without preexisting asthma. This study was approved by the Institutional Review Board of Washington University in St. Louis (IRB number 202003085), and all patients who were enrolled in the study provided informed consent. A total of 105 samples were collected from patients with COVID-19 within 14 days from the onset of any relevant symptoms between March and September of 2020. For the nasopharyngeal samples, seven were from patients with asthma and 41 were from patients with no asthma diagnosis. For the salivary samples, 16 were from patients with asthma and 41 were from patients with no asthma diagnosis. Demographics and clinical characteristics of the COVID-19 patients are shown in Table S1. Study participants were enrolled in both outpatient and inpatient settings. Nine patients (n = 3 asthma, and n = 6 non-asthma) provided both saliva and nasopharyngeal samples. The detailed methods and sequencing analysis procedures are presented in the Appendix S1. The read number of each sample and rarefaction curves are plotted in Figure S1A, B. The microbial communities of the nasopharyngeal and saliva samples were significantly different in alpha diversity represented by the Shannon Index (p-value <0.001, Figure 1A) and beta diversity based on weighted UniFrac distances (p-value = 0.001, Figure 1B). For the 48 nasopharyngeal samples, seven were from COVID-19 patients with asthma and 41 were from those who did not have an asthma diagnosis. There were no marked differences in relative abundance for any of the top five abundant phyla in nasopharyngeal samples between the asthma and non-asthma groups (Figure 1C). For the 57 saliva samples, the relative abundance of phylum Actinobacteria was significantly decreased in COVID-19 patients with asthma compared with those without preexisting asthma (adjusted p-value = 0.02, Figure 1D). The top ten abundant genera in the nasopharyngeal samples and saliva samples are displayed in Figure 1E, F, respectively. Differences at the genus-level, but not at the community level (Figure S2), were observed in the nasopharyngeal and salivary microbiomes between patients with and without preexisting asthma. In differential abundance tests using DESeq2 for nasal samples, seven genera were significantly different between the two groups, with all being less abundant (including Porphyromonas, Haemophilus, Alloprevotella, Moraxella, Facklamia, Campylobacter, and Janibacter) in those with preexisting asthma compared with those without asthma (Figure 2A). In the saliva samples, seven genera were significantly different between the two groups (Figure 2B), with three being less abundant (including Centipeda, Staphylococcus, and Actinomyces) and four being more abundant (including Porphyromonas, Capnocytophaga, Bergeyella, and Neisseria) in those with preexisting asthma compared with those without asthma. The normalized counts of each identified genus were displayed by asthma status, as shown in Figure 2C, D. We then compared the relative abundance of these identified genera based","journal":"Allergy","year":2022,"id":289403,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":5,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9557,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2022-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":970923,"name":"Ai Zhang","orcid":"0000-0002-9545-1300","position":1,"is_corresponding":false},{"id":246250,"name":"Adriana M. Rauseo","orcid":"0000-0001-9555-2550","position":2,"is_corresponding":false},{"id":615625,"name":"Charles W. Goss","orcid":"0000-0003-2682-7316","position":3,"is_corresponding":false},{"id":233402,"name":"Philip A. Mudd","orcid":"0000-0002-3860-5473","position":4,"is_corresponding":false},{"id":259653,"name":"Jane A. O’Halloran","orcid":"0000-0001-8265-9471","position":5,"is_corresponding":false},{"id":970998,"name":"Leyao Wang","orcid":"0000-0002-2396-9020","position":6,"is_corresponding":false},{"id":867153,"name":"Josh G. Kim","orcid":"0000-0003-2501-9149","position":0,"is_corresponding":true}],"reference_count":10,"raw_metadata":null,"created_at":"2026-07-19T00:30:22.686776Z","pmid":"35837881","pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}