Characterization of Altered Oropharyngeal Microbiota in Hospitalized Patients With Mild SARS-CoV-2 Infection.

Coronavirus disease 2019 (COVID-19) remains a serious emerging global health problem, and little is known about the role of oropharynx commensal microbes in infection susceptibility and severity. Here, we present the oropharyngeal microbiota characteristics identified by full-length 16S rRNA gene sequencing through the NANOPORE platform of oropharynx swab specimens from 10 mild COVID-19 patients and 10 healthy controls. Our results revealed a distinct oropharyngeal microbiota composition in mild COVID-19 patients, characterized by enrichment of opportunistic pathogens such as Peptostreptococcus anaerobius and Pseudomonas stutzeri and depletion of Sphingomonas yabuuchiae, Agrobacterium sullae, and Pseudomonas veronii. Based on the relative abundance of the oropharyngeal microbiota at the species level, we built a microbial classifier to distinguish COVID-19 patients from healthy controls, in which P. veronii, Pseudomonas fragi, and S. yabuuchiae were identified as the most prominent signatures for their depletion in the COVID-19 group. Several members of the genus Campylobacter, especially Campylobacter fetus and Campylobacter rectus, which were highly enriched in COVID-19 patients with higher severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral load and showed a significant correlation with disease status and several routine clinical blood indicators, indicate that several bacteria may transform into opportunistic pathogen in COVID-19 patients when facing the challenges of viral infection. We also found the diver taxa Streptococcus anginosus and Streptococcus alactolyticus in the network of disease patients, suggesting that these oropharynx microbiota alterations may impact COVID-19 severity by influencing the microbial association patterns. In conclusion, the low sample size of SARS-CoV-2 infection patients (n = 10) here makes these results tentative; however, we have provided the overall characterization that oropharyngeal microbiota alterations and microbial correlation patterns were associated with COVID-19 severity in Anhui Province.

Studies on the function and catalytic mechanism of O-methyltransferases SviOMT02, SviOMT03 and SviOMT06 from Streptomyces virginiae IBL14.

To identify the fuctions of the nine putative O-methyltransferase genes in Streptomyces virginiae IBL14, the evolutionary and functional relationship of these genes in its 8.0 Mb linear chromosome was set up via sequence comparison with those of other Streptomyces species. Further, the functions and catalytic mechanism of the three genes sviOMT02, sviOMT03 and sviOMT06 from this strain were studied through experimental and computational approaches. As a result, the nine putative O-methyltransferases belong to methyltransf_2 superfamily, amdomet-MTases superfamily, and leucine carboxyl methyltransferase superfamily, and are phylogenetically close to those of Streptomyces sp. C. The products of genes sviOMT03 and sviOMT06 could catalyze O-methylation of caffeic acid to form ferulic acid. Computational analysis indicated that the O-methylation mechanism of SviOMT03 and SviOMT06 proceeds from a direct transfer of the SAM-methyl group to caffeic acid with inversion of symmetry aided by a divalent metal ion in a SN2-like mechanism. Particularly, the conservative polar amino acid residues in SviOMT03 and SviOMT06, including Lys143 that reacts with caffeic acid, Ser74, Asp140 and Tyr149 that react with S-adenosyl methionine, and His142 (SviOMT03) or His171 (SviOMT06) that transfers the 3-hydroxyl proton of substrate caffeic acid, probably be essential in their O-methylation.