A correlative study of the genomic underpinning of virulence traits and drug tolerance of Candida auris

Authors: Bo Yang, Benjamin Vaisvil, Daniel Schmitt, Joseph Collins, Eric Young, Vinayak Kapatral, Reeta Rao

Candida auris is an opportunistic fungal pathogen with high mortality rates which presents a clear threat to public health. The risk of C. auris infection is high because it can colonize the body, resist antifungal treatment, and evade the immune system. The genetic mechanisms for these traits are not well known. Identifying them could lead to new targets for new treatments. To this end, we present an analysis of the genetics and gene expression patterns of C. auris carbon metabolism, drug resistance, and macrophage interaction. We chose to study two C. auris isolates simultaneously, one drug sensitive (B11220 from Clade II) and one drug resistant (B11221 from Clade III). Comparing the genomes, we confirm the previously reported finding that B11220 was missing a 12.8 kb region on chromosome VI. This region contains a gene cluster encoding proteins related to alternative sugar utilization. We show that B11221, which has the gene cluster, readily assimilates and utilizes D-galactose and L-rhamnose as compared to B11220, which harbors the deletion. B11221 exhibits increased adherence and drug resistance compared to B11220 when grown in these sugars. Transcriptomic analysis of both isolates grown on glucose or galactose showed that the gene cluster was upregulated when grown on D-galactose. These findings reinforce growing evidence of a link between metabolism and drug tolerance. B11221 resists phagocytosis by macrophages and exhibits decreased β-1,3-glucan exposure, a key determinant that allows Candida to evade the host immune system, as compared to B11220. In a transcriptomic analysis of both isolates co-cultured with macrophages, we find upregulation of genes associated with transport and transcription factors in B11221. Our studies show a positive correlation between membrane composition and immune evasion, alternate sugar utilization, and drug tolerance in C. auris.

Organic farming practices utilizing spent microbial biomass from an industrial fermentation facility promote transition to copiotrophic soil communities

Mathew Halter, Benjamin Vaisvil, Vinayak Kapatral & James Zahn

Organic farming has become more prevalent in recent years as consumer demand for organic food and fiber has rapidly grown. Until recently, organic fertilizers and soil amendments have largely been based on the practices of returning crop residues, manures and related agricultural wastes back to crop production areas. One rapidly growing segment in commercial organic fertilizer development is the use of spent microbial biomass (SMB) from industrial fermentation processes. While SMB is widely accepted in many organic farming systems (OFS), little is known concerning the effectiveness, environmental impact, and influence on prokaryotic communities in soils receiving this treatment. In this study, a comparative analysis of bacterial communities associated with OFS and conventional farming systems was performed over a growing season for a field containing yellow dent corn (Zea mays). A statistically significant increase in microbial population α-diversity, along with a strong recruitment of Proteobacteria and Actinobacteria populations, was observed in soils treated with SMB when compared to areas in the field that utilized conventional farmer practices. These phyla are members of the copiotrophic subgroup, and considered a signature for the use of traditional organic fertilizers. These results provide valuable new information that SMB functions similarly to traditional organic fertilizers in promoting a high level of functional prokaryotic diversity and plant growth-promoting bacteria, but in contrast do not contribute directly to viable microorganisms in the soil due to the sterilization of SMB prior to land application.

Fermentation Optimization by Understanding the Yeast Gene Transcriptomics in Cellulosic Ethanol Production in Bench-top Bioreactors

Joseph Bridges, Ananda Nanjundaswamy, Lydia Batey, Keerthi Mandyam, Vinayak Kapatral, Benjamin Vaisvil, and Daniel Schmitt

Poster presentation at SIMB Annual Meeting 2019.

SIMB 2019

Poster presentation

Yeast Transcriptomics During Bioprocessing: A Powerful Tool in Cellulosic Ethanol Production and Process Optimization

Ananda Nanjundaswamy, Alcorn State University Co-Author(s): Keerthi Mandyam, Department of Agriculture, Alcorn State University; Vinayak Kapatral and Benjamin, Vaisvil, and Daniel Schmitt, Igenbio, Inc

Yeast, saccharomyces cerevisiae, is very critical for ethanol production and its performance determines whether a process is economical or not. At first glance, ethanol production appears simple with dosing of yeast to a sugar rich medium where yeast produces ethanol through a fermentation process. But a closer look reveals a much complex biochemical processes involved in ethanol production. During fermentation, yeast will be growing in a high solid medium in presence of inhibitors such as ethanol and furfurals. Also there will be mass transfer limitations such as depletion of oxygen which creates stress for the yeast. In order to optimize the ideal conditions for the yeast growth and ethanol production, it is critical to understand the yeast behavior at transcriptional level. The present study employed leading cellulosic feedstock miscanthus for ethanol production in a benchtop bioreactor. Samples were collected at 24, 48 and 72h and analyzed for yeast behavior during fermentation. Transcriptional analysis of yeast indicated that yeast behaves differently in different me points. Transcriptional information of important biochemical pathways as influenced by the fermentation conditions will be discussed.

Genomic Comparisons of Endophytic Periconia from North American and European Grasslands

Keerthi Mandyam, Alcorn State University Co-Author(s): Anna Kazarina and Ananda Nanjundaswamy, Dept of Agriculture, Alcorn State University; Benjamin Vaisvil, Daniel Schmitt, and Vinayak Kapatral, Igenbio Inc

Plants are associated with a suite of microbial symbioses, with roots offering a unique niche for fungal endophytes. Among root fungal symbionts, dark septate endophytic (DSE) fungi are common, sometimes abundant but enigmatic with poor clarity on their functional roles. Biogeographical distinctions likely exist in DSE communities from forests and grasslands, with North American and European grasslands predominantly represented by Periconia macrospinosa. To understand their endophyc roles, the genome of dark septate P. macrospinosa and Cadophora isolated from Festuca vaginata from semi-arid European grassland were sequenced. To further comprehend DSE funconal roles, the objecve of this study was to compare the North American P. macrospinosa genome with that of the European P. macrospinosa. Periconia was isolated from a stand of Freedom Giant Miscanthus culvated in Lorman, MS and was confirmed to be a DSE. We hypothesized that despite the geographical disncons and diverse grass hosts, P. macrospinosa associated with grasses would have similar funconal roles. Periconia genome was sequenced using Illumina and PacBio plaorms. Our Periconia genome was determined to be ~ 53.5 MB in size with 45% GC content. At least 12,059 ORFs with 9,086 ORFs with introns were idenfied and nearly 35% of the ORFs were assigned funcons. As expected, several plant cell wall degrading enzymes (PCWDEs) like cellulases (12 ORFs), amylases (2 ORFs), pecn esterase (1 ORF), tannase (2 ORFs), laccase (6 ORFs) were idenfied along with several sugar transport systems such as maltose, lactate, sucrose, maltose, xylose isomaltose, palanose, etc. However, ORFs for lignin peroxidase, manganese peroxidase, glyoxal oxidase were not observed. As hypothesized, the Periconia genomes were comparable. Periconia macrospinosa genomics data will be discussed to draw big picture inferences regarding DSE symbiosis.