De novo assembly of Roseomonas mucosa isolated from patients with atopic dermatitis

Kent Barbian, Daniel Bruno, Lydia Sykora, Stacy Ricklefs, Prem Prashant Chaudhary, Paul A. Beare, Ian A. Myles, Craig M. Martens

ABSTRACT

Roseomonas mucosa is associated with the normal skin microflora. Here, we present de novo sequence assemblies from R. mucosa isolates obtained from the skin lesions of three atopic dermatitis patients.

ANNOUNCEMENT

Roseomonas mucosa is a Gram-negative coccobacillus found in aquatic environments and from various clinical samples (1 – 5). R. mucosa is commonly isolated from the microbiota of human skin (4, 6). Atopic dermatitis (AD), an inflammatory skin disease, causes susceptibility to Staphylococcus aureus infection, immune dysregulation function, and an impaired skin barrier. Improved AD clinical outcome was observed when R. mucosa was used to topically treat patients with AD (2, 4, 7). This treatment had an improved outcome in mouse models of AD. Interestingly, this mouse model treated with R. mucosa from AD patients, had no impact or a worse clinical outcome (2). We present the sequences from three AD-sourced R. mucosa isolates (2).

R. mucosa from lesions of three AD patients was isolated using a FloqSwab moistened in phosphate-buffered saline. Swabs were placed in Reasoner’s 2A (R2A) broth containing amphotericin B and vancomycin and incubated for 48–72 h at 32°C. Cultures were spread on R2A agar and incubated as above to form single colonies (4). Bacteria, stored at −80°C, were spread on R2A agar and a single colony used to inoculate 100 mls of R2A broth, and grown at 32°C for 20–25 h (8). Bacteria were washed, resuspended, and heated to 65°C, followed by separate incubations with proteinase k, lysozyme, and SDS. Each sample was incubated with RNaseI for 30 min at 37°C, then combined with a 3/4 vol of saturated phenol solution, mixed for 10 min and centrifugated at 12,800 × g for 10 min. The aqueous phase was removed and treated with phenol:chloroform:isoamyl alcohol (25:24:1) until the white precipitate interface was absent. A chloroform-only extraction was performed, and aqueous solution was collected. DNA was precipitated with 3 M sodium acetate, washed 2× with 70% EtOH, and resuspended in Qiagen’s EB buffer.

PacBio and Illumina sequencing libraries were generated from the same DNA using the 10 kb Template Preparation and Sequencing kit with Covaris g-tubes (sheared to >8,700 bp) and Illumina TruSeq Nano DNA kit using a Covaris M220 (sheared to ~550 bp), respectively (PacBio protocol 100-092-800-06 and TruSeq protocol 15041110 rev. D). Libraries were sequenced with PacBio Sequel and Illumina MiSeq (2 × 300 bp read length) platforms. Illumina reads were adapter trimmed using cutadapt (v.1.12) and trimmed and filtered for quality using FASTX-Toolkit (v.0.0.14). Bioinformatic analysis and construction of the genomes were performed using the following programs: CANU (v.1.0), Bowtie2 (v.2.2.4), pilon (v.1.16), and MIRA (v.4.0). All software was used with default parameters. The PacBio data were used to construct DNA scaffolds which were optimized using Illumina data. Igenbio Inc. annotated the genomes, while public annotation was compiled by the NCBI Prokaryotic Genome Annotation Pipeline (9).

The R. mucosa genomes consist of a single large circular chromosome (4.01–4.28 Mb) and five to six autonomously replicating plasmid sequences (8.9–506.3 kb) (Table 1). Genome properties and annotation statistics are listed in Table 1. These genomes may help determine the genes that are important for successful treatment of AD.

ACKNOWLEDGMENTS

We would like to thank Igenbio Inc. their sequencing services and data analysis.

This work was supported by funding from the Intramural Research Program of the NIH, NIAID 67 (Z01-147170). The content is solely the responsibility of the author and does not necessarily represent the official views of the National Institutes of Health.

Safety evaluation of Fy Protein™ (Nutritional Fungi Protein), a macroingredient for human consumption

Brian Furey, Kathleen Slingerland, Mark R. Bauter, Celeste Dunn, Richard E. Goodman, Sophia Koo

Abstract

Fy Protein™ (Nutritional Fungi Protein) is a macro-ingredient produced from the fermentation of the fungal microorganism Fusarium strain flavolapis, isolated from springs in Yellowstone National Park. Fy Protein contains all of the essential amino acids plus fiber, fat, carbohydrates, vitamins, and minerals and is developed as an alternative to animal-based protein foods such as meat and dairy.

Fy Protein's nutritional, digestibility, genotoxicity, allergenicity, toxicity, secondary metabolites, and pathogenicity were evaluated. Fy Protein did not show mutagenic or genotoxic potential in in vitro tests. In an allergenicity review, Fy Protein was found to be of low allergenic potential. In a 90-day sub chronic dietary study in rats, administration of Fy Protein did not produce any significant toxicologic manifestations, and the No Observed Adverse Effect Level (NOAEL) was the highest-level fed of 150,000 ppm (15% in the diet). Regulated secondary metabolites from fungi (termed mycotoxins) were non-detectable and below regulated levels using quantitative analytical techniques. A literature review was completed to identify the potential human pathogenicity of Fusarium sp., showing that Fusarium rarely infects humans, with infections seldom developing even in immunocompromised individuals.

The results of these studies confirm that Fy Protein from fermented F. str. flavolapis has low toxicological, genotoxic, pathogenic, and allergenic potential under the conditions tested and anticipated use.

New genomic resources and comparative analyses reveal differences in floral gene expression in selfing and outcrossing Collinsia sister species

Lauren J. Frazee, Joanna Rifkin 2 Dinusha C. Maheepala, Alannie-Grace Grant, Stephen Wright , Susan Kalisz, Amy Litt, and Rachel Spigler

The evolutionary transition from outcross- to self-fertilization is one of the most common in angiosperms and is often associated with a parallel shift in floral morphological and developmental traits, such as reduced flower size and pollen to ovule ratios, known as the “selfing syndrome.” How these convergent phenotypes arise, the extent to which they are shaped by selection, and the nature of their underlying genetic basis are unsettled questions in evolutionary biology. The genus Collinsia (Plantaginaceae) includes seven independent transitions from outcrossing or mixed mating to high selfing rates accompanied by selfing syndrome traits. Accordingly, Collinsia represents an ideal system for investigating this parallelism, but requires genomic resource development. We present a high quality de novo genome assembly for the highly selfing species Collinsia rattanii. To begin addressing the basis of selfing syndrome developmental shifts, we evaluate and contrast patterns of gene expression from floral transcriptomes across three stages of bud development for C. rattanii and its outcrossing sister species Collinsia linearis. Relative to C. linearis, total gene expression is less variable among individuals and bud stages in C. rattanii. In addition, there is a common pattern among differentially expressed genes: lower expression levels that are more constant across bud development in C. rattanii relative to C. linearis. Transcriptional regulation of enzymes involved in pollen formation specifically in early bud development may influence floral traits that distinguish selfing and outcrossing Collinsia species through pleiotropic functions. Future work will include additional Collinsia outcrossing-selfing species pairs to identify genomic signatures of parallel evolution. Keywords: Collinsia; RNA-seq; selfing syndrome; pollen; floral development; differential gene expression; DESeq2; dichogamy; evolutionary genomics; Hi-C scaffolding; parallel evolution

Evaluating potential risks of food allergy of novel food sources based on comparison of proteins predicted from genomes and compared to www.AllergenOnline.org

Mohamed Abdelmoteleb, Chi Zhang, Brian Furey, Mark Kozubal, Hywel Griffiths, Marion Champeaud, Richard E. Goodman

Potential proteins from three novel food sources (Chlorella variabilis, Galdieria sulphuraria, and Fusarium strain flavolapis) were predicted from genomic sequences and were evaluated for potential risks of allergic cross-reactivity by comparing the predicted amino acid sequences against the allergens in the www.AllergenOnline.org (AOL) database. The preliminary analysis used CODEX Alimentarius limits of >35% identity over 80 amino acids to evaluate the predicted proteins which include many evolutionarily conserved proteins. Regulators might expect clinical serum IgE tests based on identity matches above the criteria if the proteins were introduced in genetically engineered crops. Some regulators have the same expectations for proteins in novel foods. To address the inequality of extensively conserved sequences, we compared the predicted proteins from curated genomes of 23 highly diverse allergenic species from animals, plants and arthropods as well as humans to AOL sequences and compiled identities. Identity matches greater than CODEX limits (>35% ID over 80 AA) are common for many proteins that are conserved through extensive evolution but are not predictive of published allergy risks based on observed taxonomic cross-reactivity. Therefore, we recommend changes in the allergen databases or methods of identifying matches for risk evaluation of new food sources. Our results provide critical data for redefining allergens in AOL or for providing guidance on more predictive sequence identity matches for risk assessment of possible risks of food allergy.