Bacterial diversity of middle ear cholesteatoma by 16S rRNA gene sequencing in China

Abstract

In this study, the bacterial diversity of acquired middle ear cholesteatoma (MEC) was evaluated to reveal its pathogenesis and provides a guide for the use of antibiotics. Twenty-nine cases of acquired MEC and eight cases of healthy middle ears undergoing cochlear implantation (CI) were evaluated. Full-length 16S rRNA gene sequencing was performed to profile the bacterial communities in lesions and healthy tissues of the middle ear. ACE (P = 0.043) and Chao1 (P = 0.039) indices showed significant differences in alpha diversity (P < 0.05). Analysis of PERMANOVA/Anosim using the Bray–Curtis distance matrix results suggested that the between-group differences were greater than the within-group differences (R = 0.238, P < 0.05, R2 = 0.066, P < 0.05). Bacterial community analysis revealed that Alphaproteobacteria at the class level and Caulobacterales and Sphingomonadales at the order level were significantly different (P < 0.05). In the LefSe (Linear discriminant analysis effect size) analysis, Porphyromonas bennonis was elevated, and Bryum argenteum and unclassified Cyanobacteriales were reduced at the species level in MEC (P < 0.05). Fifteen metabolic pathways were found to be significantly different between the two groups by analysing the abundance of metabolic pathways in level 2 of the Kyoto Encyclopaedia of Genes and Genomes (KEGG). Seven and eight metabolic pathways were significantly elevated in the MEC and control groups, respectively (P < 0.05). The role of bacteria in the pathogenesis of acquired MEC was further refined through analysis of metabolic pathways. These findings indicate that the acquired MEC and healthy middle ear contain more diverse microbial communities than previously thought.

Characterization of Rhizosphere Microbial Diversity and Selection of Plant-Growth-Promoting Bacteria at the Flowering and Fruiting Stages of Rapeseed

“…Replicates within samples were more strongly clustered in the PCoA plot than in the unweighted plot ( Figure 4 ). An R-value closer to 1 in PERMANOVA/Anosim means that the difference between groups is significant and is greater than the difference within groups [ 33 ]. The p -value was less than 0.05, which means the reliability of the test was good.…”

“…The "vegan" package in R was used for PERMANOVA/Anosim. PERMANOVA/Anosim was used following the Liang's method [33]. Significant differences between different species were determined via a linear discriminant analysis (LDA) effect size (LEfSe) (https: //github.com/biobakery/lefse/, accessed on 22 June 2023) with two as the default filter value for the LDA score.…”

Microbiota Profiles of Hen Eggs from the Different Seasons and Different Sectors of Shanghai, China

“…The specific forward primer 27F (5 -AGRGTTTGATYNTGGCTCAG-3 ) and reverse primer 1492R (5 -TASGGHTACCTTGTTASGACTT-3 ) that targeted the full 16S rRNA gene of the bacteria were synthesized with the barcodes attached, followed by PCR amplification and then product purification, quantification, and normalization to form the single-molecule real-time (SMRT) Bell sequencing libraries. The libraries were then treated with high-throughput sequencing (HTS) using a PacBio Sequel system (PacBio) [12], which resulted in data in bam format. These data were exported as CCS files via the SMRTlink analysis software (SMRTLink V12.0, Pacific Biosciences of California, Inc., San Diego, CA, USA).…”