Complete genome sequence of the sand-sediment actinobacterium Nocardioides dokdonensis FR1436T

Characterization of microbial diversity and eosinophilic otitis media biomarkers using next-generation sequencing

OBJECTIVE

Eosinophilic otitis media (EOM) is a chronic eosinophilic inflammatory disease linked to bronchial asthma and nasal polyps. EOM is often accompanied by tympanic membrane perforation. Although the primary treatment, steroid therapy, is generally effective, its efficacy may be limited in advanced cases, particularly those involving significant thickening of the middle ear mucosa. Despite its clinical importance, details regarding the pathogenesis of EOM have not been elucidated. Our study aimed to characterize the microbiome associated with EOM and explore changes with and without tympanic membrane perforation.

METHODS

We enrolled 27 patients clinically diagnosed with EOM, 25 controls without middle ear infections, and 10 patients with chronic suppurative otitis media (CSOM) [1] [2]. Specimens were collected by swabbing the middle ear, nasopharynx, and external auditory canal (EAC) of subjects in the EOM and control groups, whereas CSOM specimens were collected only from the middle ear. The V3-V4 regions of the 16S ribosomal RNA genes were amplified and subjected to high-throughput sequencing. We evaluated alpha and beta diversity indices between the EOM and control subjects, followed by Linear discriminant analysis Effect Size (LEfSe) analysis to identify potential biomarkers. Additionally, co-occurrence patterns were analyzed to explore the associated microbial interactions. To assess whether similar biomarkers were identified between the EOM and CSOM subjects, LEfSe analysis was conducted for these two groups.

RESULTS

Compared with controls, EOM patients were significantly enriched in Nocardioides in the middle ear, nasopharynx, and EAC, highlighting a distinct microbiological feature. Both alpha and beta diversity were significantly reduced in EOM patients with tympanic membrane perforation. When comparing the EOM and CSOM groups, Nocardioides was consistently identified as a significant biomarker for EOM, confirming its distinct association with EOM. In co-occurrence analysis, Nocardioides showed notable positive co-occurrence with several other genera.

CONCLUSION

This study reports the first detailed exploration of the EOM microbiome and identified Nocardioides as a new biomarker. The significant shift in microbial co-occurrence associated with tympanic membrane perforation may contribute to the disease's refractory nature, suggesting new avenues for understanding and managing EOM.

Different genome-wide transcriptome responses of Nocardioides simplex VKM Ac-2033D to phytosterol and cortisone 21-acetate

BACKGROUND

Bacterial degradation/transformation of steroids is widely investigated to create biotechnologically relevant strains for industrial application. The strain of Nocardioides simplex VKM Ac-2033D is well known mainly for its superior 3-ketosteroid Δ1-dehydrogenase activity towards various 3-oxosteroids and other important reactions of sterol degradation. However, its biocatalytic capacities and the molecular fundamentals of its activity towards natural sterols and synthetic steroids were not fully understood. In this study, a comparative investigation of the genome-wide transcriptome profiling of the N. simplex VKM Ac-2033D grown on phytosterol, or in the presence of cortisone 21-acetate was performed with RNA-seq.

RESULTS

Although the gene patterns induced by phytosterol generally resemble the gene sets involved in phytosterol degradation pathways in mycolic acid rich actinobacteria such as Mycolicibacterium, Mycobacterium and Rhodococcus species, the differences in gene organization and previously unreported genes with high expression level were revealed. Transcription of the genes related to KstR- and KstR2-regulons was mainly enhanced in response to phytosterol, and the role in steroid catabolism is predicted for some dozens of the genes in N. simplex. New transcription factors binding motifs and new candidate transcription regulators of steroid catabolism were predicted in N. simplex. Unlike phytosterol, cortisone 21-acetate does not provide induction of the genes with predicted KstR and KstR2 sites. Superior 3-ketosteroid-Δ1-dehydrogenase activity of N. simplex VKM Ac-2033D is due to the kstDs redundancy in the genome, with the highest expression level of the gene KR76_27125 orthologous to kstD2, in response to cortisone 21-acetate. The substrate spectrum of N. simplex 3-ketosteroid-Δ1-dehydrogenase was expanded in this study with progesterone and its 17α-hydroxylated and 11α,17α-dihydroxylated derivatives, that effectively were 1(2)-dehydrogenated in vivo by the whole cells of the N. simplex VKM Ac-2033D.

CONCLUSION

The results contribute to the knowledge of biocatalytic features and diversity of steroid modification capabilities of actinobacteria, defining targets for further bioengineering manipulations with the purpose of expansion of their biotechnological applications.

Characterization of the Rifamycin-Degrading Monooxygenase From Rifamycin Producers Implicating Its Involvement in Saliniketal Biosynthesis

Rifamycin derivatives, such as rifampicin, have potent antibiotic activity and have long been used in the clinic as mainstay components for the treatment of tuberculosis, leprosy, and AIDS-associated mycobacterial infections. However, the extensive usage of these antibiotics has resulted in the rapid development of bacterial resistance. The resistance mechanisms mainly include mutations of the rifamycin target RNA polymerase of bacteria and enzymatic modifications of rifamycin antibiotics. One modification is the recently characterized rifamycin degradation catalyzed by Rox enzymes, which belong to the widely occurring flavin monooxygenases. Intriguingly, our recent sequence analysis revealed the rifamycin producers also encode Rox homologs that are not yet characterized. In this work, we expanded the study of the Rox-catalyzed rifamycin degradation. We first showed that the Rox proteins from rifamycin producers have the enzymatic rifamycin SV-degrading activity. Then we used the structurally diverse rifamycin compounds rifampicin and 16-demethylrifamycin W to probe the substrate scope and found that they each have a slightly different substrate scope. Finally, we demonstrated that Rox proteins can also catalyze the transformation of 16-demethylsalinisporamycin to 16-demethylsaliniketal A. Since 16-demethylsalinisporamycin and 16-demethylsaliniketal A are the counterpart analogs of salinisporamycin and saliniketal A, our biochemical findings not only uncover a previously uncharacterized self-resistance mechanism in the rifamycin producers, but also bridge the gap between the biosynthesis of the potential antitumor compound saliniketal A.