Table_2_Phylogeny Trumps Chemotaxonomy: A Case Study Involving Turicella otitidis.PDF

<p>The genus Turicella was proposed to harbor clinical strains isolated from middle-ear fluids of patients with otitis media. 16S rRNA phylogeny showed that it belonged to the mycolic acid-containing actinobacteria, currently classified in the order Corynebacteriales, and was closely related to the genus Corynebacterium. A new genus was proposed for the organisms as unlike corynebacteria they lacked mycolic acids and had different menaquinones. Here, we carried out large-scale comparative genomics on representative strains of the genera Corynebacterium and Turicella to check if this chemotaxonomic classification is justified. Three genes that are known to play an essential role in mycolic acid biosynthesis were absent in Turicella and two other mycolate-less Corynebacterium spp., explaining the lack of mycolic acids resulted from the deletion of genes and does not confer any phylogenetic context. Polyphasic phylogenetic analyses using 16S rRNA, bacterial core genes and genes responsible for synthesizing menaquinones unequivocally indicate that Turicella is a true member of the genus Corynebacterium. Here, we demonstrate that menaquinone and mycolic acid that have been used as critical taxonomic markers should be interpreted carefully, particularly when genome-based taxonomy is readily available. Based on the phylogenetic analysis, we propose to reclassify Turicella otitidis as Corynebacterium otitidis comb. nov.</p

Table_3_Phylogeny Trumps Chemotaxonomy: A Case Study Involving Turicella otitidis.PDF

<p>The genus Turicella was proposed to harbor clinical strains isolated from middle-ear fluids of patients with otitis media. 16S rRNA phylogeny showed that it belonged to the mycolic acid-containing actinobacteria, currently classified in the order Corynebacteriales, and was closely related to the genus Corynebacterium. A new genus was proposed for the organisms as unlike corynebacteria they lacked mycolic acids and had different menaquinones. Here, we carried out large-scale comparative genomics on representative strains of the genera Corynebacterium and Turicella to check if this chemotaxonomic classification is justified. Three genes that are known to play an essential role in mycolic acid biosynthesis were absent in Turicella and two other mycolate-less Corynebacterium spp., explaining the lack of mycolic acids resulted from the deletion of genes and does not confer any phylogenetic context. Polyphasic phylogenetic analyses using 16S rRNA, bacterial core genes and genes responsible for synthesizing menaquinones unequivocally indicate that Turicella is a true member of the genus Corynebacterium. Here, we demonstrate that menaquinone and mycolic acid that have been used as critical taxonomic markers should be interpreted carefully, particularly when genome-based taxonomy is readily available. Based on the phylogenetic analysis, we propose to reclassify Turicella otitidis as Corynebacterium otitidis comb. nov.</p

Presentation_1_Phylogeny Trumps Chemotaxonomy: A Case Study Involving Turicella otitidis.pdf

<p>The genus Turicella was proposed to harbor clinical strains isolated from middle-ear fluids of patients with otitis media. 16S rRNA phylogeny showed that it belonged to the mycolic acid-containing actinobacteria, currently classified in the order Corynebacteriales, and was closely related to the genus Corynebacterium. A new genus was proposed for the organisms as unlike corynebacteria they lacked mycolic acids and had different menaquinones. Here, we carried out large-scale comparative genomics on representative strains of the genera Corynebacterium and Turicella to check if this chemotaxonomic classification is justified. Three genes that are known to play an essential role in mycolic acid biosynthesis were absent in Turicella and two other mycolate-less Corynebacterium spp., explaining the lack of mycolic acids resulted from the deletion of genes and does not confer any phylogenetic context. Polyphasic phylogenetic analyses using 16S rRNA, bacterial core genes and genes responsible for synthesizing menaquinones unequivocally indicate that Turicella is a true member of the genus Corynebacterium. Here, we demonstrate that menaquinone and mycolic acid that have been used as critical taxonomic markers should be interpreted carefully, particularly when genome-based taxonomy is readily available. Based on the phylogenetic analysis, we propose to reclassify Turicella otitidis as Corynebacterium otitidis comb. nov.</p

Relative abundance of bacteria identified at the genus level in indoor and outdoor air.

<p>The sampling sites and replicates are indicated as letters and numbers, respectively, shown in columns. The taxonomic groups that had an average abundance >1.2% are shown.</p

Metagenomic Insights into the Bioaerosols in the Indoor and Outdoor Environments of Childcare Facilities

<div><p>Airborne microorganisms have significant effects on human health, and children are more vulnerable to pathogens and allergens than adults. However, little is known about the microbial communities in the air of childcare facilities. Here, we analyzed the bacterial and fungal communities in 50 air samples collected from five daycare centers and five elementary schools located in Seoul, Korea using culture-independent high-throughput pyrosequencing. The microbial communities contained a wide variety of taxa not previously identified in child daycare centers and schools. Moreover, the dominant species differed from those reported in previous studies using culture-dependent methods. The well-known fungi detected in previous culture-based studies (<i>Alternaria</i>, <i>Aspergillus</i>, <i>Penicillium</i>, and <i>Cladosporium</i>) represented less than 12% of the total sequence reads. The composition of the fungal and bacterial communities in the indoor air differed greatly with regard to the source of the microorganisms. The bacterial community in the indoor air appeared to contain diverse bacteria associated with both humans and the outside environment. In contrast, the fungal community was largely derived from the surrounding outdoor environment and not from human activity. The profile of the microorganisms in bioaerosols identified in this study provides the fundamental knowledge needed to develop public health policies regarding the monitoring and management of indoor air quality.</p></div

Relative abundance of four allergenic fungi in indoor and outdoor air samples.

<p>The solid black lines represent the medians, and the circles are outliers. Bars denote the minimum and maximum values excluding the outliers.</p

Principal coordinate analysis (PCoA) of the (A) bacterial and (B) fungal communities in childcare facilities.

<p>Fifty samples were collected from the indoor (blue symbols) and outdoor (red symbols) air of five daycare centers (sites A–E, circles) and five elementary schools (sites F–J, triangles). Differences in the composition of the microbial communities were quantified using the weighted UniFrac distance metric. The green dotted lines and circles indicate pairs of indoor and outdoor samples from the same sampling site. The distinctive bacterial community structures in the indoor and outdoor air were supported by the p-values determined by Wilcoxon <i>t</i>-test.</p

Fungi in indoor and outdoor air identified at the phylum and class levels.

<p>The inner circles indicate the composition of fungal reads at the phylum level, and the outer circles indicate the composition of the fungal community at the class level.</p

The <i>rpoB</i> gene-based neighbor-joining tree showing the relationships among 53 genome-sequenced <i>Mycobacterium abscessus</i> strains.

<p>Each node number represents the percentage of bootstrap support (>70%) from 1,000 resampled datasets. The bar represents 0.001 substitutions per site. </p

The genome tree based on 262 highly conserved orthologous genes of 81 annotated genomes of <i>Mycobacterium</i>.

<p>The evolutionary distance matrix was calculated using the Jukes & Cantor model, and the tree was constructed using the neighbor-joining method. Each node number represents the percentage of bootstrap support (>70%) from 1,000 resampled datasets. The bar represents 0.02 substitutions per site.</p