Altered Nasal Microbiome in Atrophic Rhinitis: A Novel Theory of Etiopathogenesis and Therapy

Background: Atrophic rhinitis (AtR) is a chronic nasal condition with polygenic and polybacterial etiology. We investigated the clinical outcomes of honey therapy and the associated nasal microbiome in AtR. Methods: For eight weeks, a nonrandomized control trial using a nasal spray of 10% manuka honey and saline on the right and left sides of the nose was conducted on 19 primary AtR patients. A nasal endoscopy was performed and a mucosal biopsy were taken before and after the intervention. Five of the nineteen patients were selected for microbiome and GPR43 expression studies. Results: We used manuka honey to describe an effective prebiotic treatment for atrophic rhinitis. There were nine males and ten females with an average (±SD) age of 33.8 (±10.7) years. Endoscopic scores and clinical symptoms improved in honey-treated nasal cavities (p < 0.003). There was a significant decrease in inflammation, restoration of mucus glands, and increased expression of GPR43 in the nasal cavities with honey therapy. The nasal microbiome composition before and after treatment was documented. Particularly, short chain fatty acid (SCFA) producers were positively enriched after honey therapy and correlated with improved clinical outcomes like nasal crusting, congestion, and discharge. Conclusion: Our approach to treating AtR patients with manuka honey illustrated effective clinical outcomes such as (1) decreased fetid smell, (2) thickening of the mucosa, (3) decreased inflammation with healed mucosal ulcers, (4) increased concentration of the mucosal glands, (5) altered nasal microbiome, and (6) increased expression of SCFA receptors. These changes are consequent to resetting the nasal microbiome due to honey therapy

VibrioBase: A Model for Next-Generation Genome and Annotation Database Development

To facilitate the ongoing research of Vibrio spp., a dedicated platform for the Vibrio research community is needed to host the fast-growing amount of genomic data and facilitate the analysis of these data. We present VibrioBase, a useful resource platform, providing all basic features of a sequence database with the addition of unique analysis tools which could be valuable for the Vibrio research community. VibrioBase currently houses a total of 252 Vibrio genomes developed in a user-friendly manner and useful to enable the analysis of these genomic data, particularly in the field of comparative genomics. Besides general data browsing features, VibrioBase offers analysis tools such as BLAST interfaces and JBrowse genome browser. Other important features of this platform include our newly developed in-house tools, the pairwise genome comparison (PGC) tool, and pathogenomics profiling tool (PathoProT). The PGC tool is useful in the identification and comparative analysis of two genomes, whereas PathoProT is designed for comparative pathogenomics analysis of Vibrio strains. Both of these tools will enable researchers with little experience in bioinformatics to get meaningful information from Vibrio genomes with ease. We have tested the validity and suitability of these tools and features for use in the next-generation database development

The isolation details of 27 <i>Streptococcus</i> strains includes isolation source, geographical area and strain author.

<p>The isolation details of 27 <i>Streptococcus</i> strains includes isolation source, geographical area and strain author.</p

Genome Assembly and Analysis of the Flavonoid and Phenylpropanoid Biosynthetic Pathways in Fingerroot Ginger (<i>Boesenbergia rotunda</i>)

Boesenbergia rotunda (Zingiberaceae), is a high-value culinary and ethno-medicinal plant of Southeast Asia. The rhizomes of this herb have a high flavanone and chalcone content. Here we report the genome analysis of B. rotunda together with a complete genome sequence as a hybrid assembly. B. rotunda has an estimated genome size of 2.4 Gb which is assembled as 27,491 contigs with an N50 size of 12.386 Mb. The highly heterozygous genome encodes 71,072 protein-coding genes and has a 72% repeat content, with class I TEs occupying ~67% of the assembled genome. Fluorescence in situ hybridization of the 18 chromosome pairs at the metaphase showed six sites of 45S rDNA and two sites of 5S rDNA. An SSR analysis identified 238,441 gSSRs and 4604 EST-SSRs with 49 SSR markers common among related species. Genome-wide methylation percentages ranged from 73% CpG, 36% CHG and 34% CHH in the leaf to 53% CpG, 18% CHG and 25% CHH in the embryogenic callus. Panduratin A biosynthetic unigenes were most highly expressed in the watery callus. B rotunda has a relatively large genome with a high heterozygosity and TE content. This assembly and data (PRJNA71294) comprise a source for further research on the functional genomics of B. rotunda, the evolution of the ginger plant family and the potential genetic selection or improvement of gingers

Pairwise genome comparison between <i>S</i>. <i>mitis</i> B6 <i>and S</i>. <i>mitis</i> 17/34 using PGC tool incorporated in StreptoBase.

<p>50% sequence identity and 50% sequence coverage were used to compare strains using the PGC tool. A and B highlight the indels of the pairwise genome comparison between <i>S</i>. <i>mitis</i> B6 <i>and S</i>. <i>mitis</i> 17/34.</p

StreptoBase structure and composition.

<p>(A) Flowchart of functional annotation of <i>Streptococcus</i> genomes. (B) Diagram of the StreptoBase web server. (C) Web interface of the StreptoBase sitemap.</p

The isolation details of 27 <i>Streptococcus</i> strains includes isolation source, geographical area and strain author.

<p>The isolation details of 27 <i>Streptococcus</i> strains includes isolation source, geographical area and strain author.</p

Intact prophage detected in <i>S</i>. <i>mitis</i> B6. This prophage has 85 predicted genes.

<p>Intact prophage detected in <i>S</i>. <i>mitis</i> B6. This prophage has 85 predicted genes.</p

StreptoBase: An Oral <i>Streptococcus mitis</i> Group Genomic Resource and Analysis Platform

<div><p>The oral streptococci are spherical Gram-positive bacteria categorized under the phylum <i>Firmicutes</i> which are among the most common causative agents of bacterial infective endocarditis (IE) and are also important agents in septicaemia in neutropenic patients. The <i>Streptococcus mitis</i> group is comprised of 13 species including some of the most common human oral colonizers such as <i>S</i>. <i>mitis</i>, <i>S</i>. <i>oralis</i>, <i>S</i>. <i>sanguinis</i> and <i>S</i>. <i>gordonii</i> as well as species such as <i>S</i>. <i>tigurinus</i>, <i>S</i>. <i>oligofermentans</i> and <i>S</i>. <i>australis</i> that have only recently been classified and are poorly understood at present. We present StreptoBase, which provides a specialized free resource focusing on the genomic analyses of oral species from the mitis group. It currently hosts 104 <i>S</i>. <i>mitis</i> group genomes including 27 novel mitis group strains that we sequenced using the high throughput Illumina HiSeq technology platform, and provides a comprehensive set of genome sequences for analyses, particularly comparative analyses and visualization of both cross-species and cross-strain characteristics of <i>S</i>. <i>mitis</i> group bacteria. StreptoBase incorporates sophisticated in-house designed bioinformatics web tools such as Pairwise Genome Comparison (PGC) tool and Pathogenomic Profiling Tool (PathoProT), which facilitate comparative pathogenomics analysis of <i>Streptococcus</i> strains. Examples are provided to demonstrate how StreptoBase can be employed to compare genome structure of different <i>S</i>. <i>mitis</i> group bacteria and putative virulence genes profile across multiple streptococcal strains. In conclusion, StreptoBase offers access to a range of streptococci genomic resources as well as analysis tools and will be an invaluable platform to accelerate research in streptococci. <b>Database URL</b>: <a href="http://streptococcus.um.edu.my" target="_blank">http://streptococcus.um.edu.my</a>.</p></div

The ATP synthases within the <i>atp</i> operon of <i>S</i>. <i>mitis</i> B6.

<p>The ATP synthases within the <i>atp</i> operon of <i>S</i>. <i>mitis</i> B6.</p