Matthew Anderson

Matthew Anderson
The Ohio State University | OSU · Department of Microbiology, Dept of Microbial Infection and Immunity

Ph.D.

About

110
Publications
6,070
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Introduction
My interests lie in understanding how human fungal pathogens cause disease and acquire resistance to antifungal drugs. My primary approaches use genomic and genetic variation to identify loci that contribute to pathogenic traits through analysis of .large datasets and quantitative genetics.
Additional affiliations
August 2016 - present
The Ohio State University
Position
  • Professor (Assistant)
August 2013 - August 2016
Brown University
Position
  • PostDoc Position
April 2010 - July 2013
University of Minnesota Twin Cities
Position
  • PostDoc Position
Education
September 2003 - December 2009
Stanford University
Field of study
  • Genetics
January 1999 - December 2002
University of Wisconsin–Madison
Field of study
  • Genetics

Publications

Publications (110)
Preprint
Full-text available
Subtelomeres are dynamic genomic regions shaped by elevated rates of recombination, mutation, and gene birth/death. These processes contribute to formation of lineage-specific gene family expansions that commonly occupy subtelomeres across eukaryotes. Investigating the evolution of subtelomeric gene families is complicated by the presence of repeti...
Article
Full-text available
Pseudomonas aeruginosa is a Gram-negative bacterium responsible for numerous human infections. Previously, novel antibiotic tolerant variants known as phoenix colonies as well as variants similar to viable but non-culturable (VBNC) colonies were identified in response to high concentrations of aminoglycosides. In this study, the mechanisms behind p...
Preprint
Pseudomonas aeruginosa is a Gram-negative bacterium responsible for numerous human infections. Previously, novel antibiotic tolerant variants known as phoenix colonies as well as variants similar to viable but non-culturable (VBNC) colonies were identified in response to high concentrations of aminoglycosides. In this study, the mechanisms behind p...
Article
Full-text available
The field of genomics has benefited greatly from its “openness” approach to data sharing. However, with the increasing volume of sequence information being created and stored and the growing number of international genomics efforts, the equity of openness is under question. The United Nations Convention of Biodiversity aims to develop and adopt a s...
Article
Full-text available
While most fungi have the ability to reproduce sexually, multiple independent lineages have lost meiosis and developed parasexual cycles in its place. Emergence of parasexual cycles is particularly prominent in medically relevant fungi from the CUG paraphyletic group of Candida species. Since the discovery of parasex in C. albicans roughly two deca...
Article
Full-text available
The human commensal and opportunistic fungal pathogen Candida albicans displays extensive genetic and phenotypic variation across clinical isolates. Here, we performed RNA sequencing on 21 well-characterized isolates to examine how genetic variation contributes to gene expression differences and to link these differences to phenotypic traits. C. al...
Preprint
Full-text available
The human commensal and opportunistic fungal pathogen Candida albicans displays extensive genetic and phenotypic variation across clinical isolates. Here, we performed RNA sequencing on 21 well-characterized isolates to examine how genetic variation contributes to gene expression differences, and to link these differences to phenotypic traits. C. a...
Article
Full-text available
Background Non-caloric artificial sweeteners (NCAS) are widely used as a substitute for dietary sugars to control body weight or glycemia. Paradoxically, some interventional studies in humans and rodents have shown unfavorable changes in glucose homeostasis in response to NCAS consumption. The causative mechanisms are largely unknown, but adverse c...
Article
Full-text available
Biofilms are organized communities of microbial cells that promote persistence among bacterial and fungal species. Biofilm formation by host-associated Candida species of fungi occurs on both tissue surfaces and implanted devices, contributing to host colonization and disease. In C. albicans, biofilms are built sequentially by adherence of yeast to...
Article
Pseudomonas aeruginosa is an opportunistic bacterial pathogen and is known to produce biofilms. We have previously shown the emergence of colony variants in the presence of tobramycin-loaded calcium sulfate beads. In this study, we characterized the variant colonies, which survived the antibiotic treatment and identified three distinct phenotypes -...
Article
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Butyrate is an abundant metabolite produced by gut microbiota. While butyrate is a known histone deacetylase inhibitor that activates expression of many genes involved in immune system pathways, its effects on virus infections and on the antiviral type I interferon (IFN) response have not been adequately investigated. We found that butyrate increas...
Article
Full-text available
Microbiome research has increased dramatically in recent years, driven by advances in technology and significant reductions in the cost of analysis. Such research has unlocked a wealth of data, which has yielded tremendous insight into the nature of the microbial communities, including their interactions and effects, both within a host and in an ex...
Preprint
Background : Non-caloric artificial sweeteners (NCAS) are widely used as a substitute for dietary sugars to control body weight or glycemia. Paradoxically, saccharin and other NCAS have been reported to induce glucose intolerance in mice fed a high-fat diet and in a subset of humans by directly inducing unfavorable changes in gut microbiota. These...
Preprint
Full-text available
Butyrate is an abundant metabolite produced by the gut microbiota and is known to modulate multiple immune system pathways and inflammatory diseases. However, studies of its effects on virus infection of cells are limited and enigmatic. We found that butyrate increases cellular infection and virus replication in influenza virus, reovirus, and human...
Article
Full-text available
Genome instability often leads to cell death but can also give rise to innovative genotypic and phenotypic variation through mutation and structural rearrangements. Repetitive sequences and chromatin architecture in particular are critical modulators of recombination and mutability. In Candida albicans, four major classes of repeats exist in the ge...
Article
Full-text available
Background: Increased serum levels of C-reactive protein (CRP), an important component of the innate immune response, are associated with increased risk of cardiovascular disease (CVD). Multiple single nucleotide polymorphisms (SNP) have been identified which are associated with CRP levels, and Mendelian randomization studies have shown a positive...
Article
Full-text available
Meiosis is a conserved tenet of sexual reproduction in eukaryotes, yet this program is seemingly absent from many extant species. In the human fungal pathogen Candida albicans, mating of diploid cells generates tetraploid products that return to the diploid state via a non-meiotic process of depolyploidization known as concerted chromosome loss (CC...
Article
Full-text available
Matt Anderson works in the field of genetics and infectious disease, with a focus on the human fungal pathogen Candida albicans . In this mSphere of Influence article, he reflects on how two papers, “Gene Flow Contributes to Diversification of the Major Fungal Pathogen Candida albicans ” (J. Ropars, C. Maufrais, D. Diogo, M. Marcet-Houben, A. Perin...
Article
The fungus Candida albicans exists as a prevalent commensal and an important opportunistic pathogen that can infect multiple niches of its human host. Recent studies have examined the diploid genome of C. albicans by performing both short-term microevolution studies and comparative genomics on collections of clinical isolates. Common mechanisms dri...
Article
Full-text available
Mediator complex has recently emerged as an important regulator of gene expression in pathogenic fungi. Mediator is a multi-subunit complex of polypeptides involved in transcriptional activation in eukaryotes, with roles including preinitiation complex (PIC) assembly and chromatin remodeling. Within the last decade, Mediator has been shown to play...
Article
Full-text available
Fungi are a diverse kingdom of organisms capable of thriving in various niches across the world including those in close association with multicellular eukaryotes. Fungal pathogens that contribute to human disease reside both within the host as commensal organisms of the microbiota and the environment. Their niche of origin dictates how infection i...
Article
Candida albicans is a commensal fungus of human gastrointestinal and reproductive tracts, but also causes life-threatening systemic infections. The balance between colonization and pathogenesis is associated with phenotypic plasticity, with alternative cell states producing different outcomes in a mammalian host. Here, we reveal that gene dosage of...
Article
Full-text available
Cardiovascular disease (CVD) is an important contributor to morbidity and mortality in American Indian communities. The Strong Heart Study (SHS) was initiated in response to the need for population based estimates of cardiovascular disease in American Indians. Previous studies within SHS have identified correlations between heart disease and defici...
Data
MBL2 allele frequencies in the SHS cohort conformed to the Hardy-Weinberg equilibrium. (TIF)
Data
MBL2 Exon 1 frequencies in the SHS cohort conformed to the Hardy-Weinberg equilibrium. (TIF)
Data
Association of promoter and coding allelic variants are associated in MBL2. The relationship between MBL2 genetic variants and Cp antibody titers was constructed using hierarchical clustering and Euclidean distances. (TIF)
Data
Nomenclature of studied MBL2 variant positions. (TIF)
Data
Correlation analysis of genotypic and phenotypic traits. Pairwise associations of traits were performed using a Spearman’s correlation analysis for all genetic polymorphisms assayed and a number of important covariates. Pink indicates p<0.05 and red indicates p<0.01. (TIF)
Data
C. pneumoniae antibody titers for SHS cohort genotypes. The C. pneumoniae antibody titer for IgG (A) or IgA (B) are plotted for all genotypes among the 553 individuals found within the SHS cohort. (TIF)
Article
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Integration of genomic technology into healthcare settings establishes new capabilities to predict disease susceptibility and optimize treatment regimes. Yet, Indigenous peoples remain starkly underrepresented in genetic and clinical health research and are unlikely to benefit from such efforts. To foster collaboration with Indigenous communities,...
Article
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Candida species are common fungal commensals of humans colonizing the skin, mucosal surfaces, and gastrointestinal tract. Under certainconditions, Candida can overgrow their natural niches resulting in debilitating mucosal infections as well as life-threatening systemic infections,which are a major focus of investigation due to their associated hig...
Article
Full-text available
The opportunistic fungal pathogen Candida albicans lacks a conventional sexual program and is thought to evolve, at least primarily, through the clonal acquisition of genetic changes. Here, we performed an analysis of heterozygous diploid genomes from 21 clinical isolates to determine the natural evolutionary processes acting on the C. albicans gen...
Article
Full-text available
Candida albicans surface-attached biofilms such as those formed on intravenous catheters with direct access to the bloodstream often serve as a nidus for continuous release of cells capable of initiating new infectious foci. We previously reported that cells dispersed from a biofilm are yeast cells that originate from the top-most hyphal layers of...
Preprint
Full-text available
The opportunistic fungal pathogen Candida albicans lacks a conventional sexual program and is thought to evolve, at least primarily, through the clonal acquisition of genetic changes. Here, we performed an analysis of heterozygous diploid genomes from 21 clinical isolates to determine the natural evolutionary processes acting on the C. albicans gen...
Article
Full-text available
Gene duplication facilitates functional diversification and provides greater phenotypic flexibility to an organism. Expanded gene families arise through repeated gene duplication but the extent of functional divergence that accompanies each paralogous gene is generally unexplored because of the difficulty in isolating the effects of single family m...
Data
Growth rates across a range of nutrient conditions are affected by induced TLO expression. Tet-regulated TLO strains were grown overnight in the presence or absence of 50 mg/ml Dox. Cells were diluted 1:2000 and grown in logarithmic phase for 16 hours at 30°C under sustained +/–Dox conditions. Growth on different minimal media, YP without added sug...
Data
TLOα3 alters HU resistance at high concentrations. A. Cells were grown overnight in the presence or absence of 50 μg/ml Dox and plated using ten-fold spot dilutions starting at an OD600 of 1.0 on SCD solid agar media containing 2mM HU in the absence of Dox. B. Cells were grown overnight in the presence or absence of 50 μg/ml Dox and diluted 1:2000...
Data
Induction of TLO expression has little effect on tolerance or rate of change in growth to fluconazole. Tet-induced TLO strains were grown overnight in the presence or absence of 50 μg/ml Dox. Cells were plated onto YPD and allowed to grow in the presence of a 25 μg fluconazole disc. Plates were photographed after 2 days. The tolerance as measured b...
Data
Mutations have accumulated in the chromosome internal TLO𝛂34 gene. A. Polymorphic sites identified between the Sanger sequenced TLOα34 sequence used in this study and Assembly 21 (A21) are plotted across the gene. SNPs are highlighted in yellow and indels are highlighted in red. B. The resulting protein sequences from A21, both homologs in A22, and...
Data
TLO transcript abundance in the absence or presence of Dox. Tet-regulated TLO strains were grown for 4 hours in the presence or absence of 50 μg/ml Dox and transcript abundance of each regulated TLO was determined by qRT-PCR using ACT1 as a reference gene. (TIF)
Data
TLOs do not influence response to a variety of stressors. Cells were grown overnight in the presence or absence of 50 μg/ml Dox and plated using ten-fold spot dilutions starting at an OD600 of 1.0 on SCD solid agar media in the absence of Dox. Growth at 30°C (A), 37°C (B), 6mM H2O2 (C), pH 4.0 (D), pH 8.0 (E), and 100 μg Calcofluor white (F) was un...
Data
Cell size was not affected by TLO induction. Strains were grown overnight in the presence or absence of 50 μg/ml Dox were diluted 1:2 and visualized by light microscopy. Bar = 30 μm. (TIF)
Data
Induced expression of most TLOs does not alter agar adhesion and invasion. Tet-regulated TLO strains were grown for 5 days on YPD and Spider solid agar plates following induction in the presence or absence of 50 mg/ml Dox. Prior to testing for adhesion, colony morphology was imaged (top). Water was then lightly run over the surface of the colonies...
Data
Correlation of phenotypic scores across induced TLOs. Pairwise correlations of the phenotypic consequences following TLO induction were calculated for all genes. A heat map denotes similarity where yellow-red indicates positive correlations and green-cyan indicates negative correlations. (TIF)
Data
C. albicans strains used in this study. (TIF)
Data
Polymorphisms among C. albicans TLO𝛂34 sequences. (TIF)
Data
TLO induction regulates condition-specific filamentation. Surface filamentation was imaged following 7 days of growth on YPD (A) and Spider (B) media at 30°C and quantified as in Fig 4B. A minimum of three replicates was performed for each data point. A legend indicates the representative TLO gene for each color where solid bars indicate +Dox and h...
Data
Regulation of TLO integration and induced expression impacts biofilm formation. Biofilm production was assayed as described in Fig 5A. (A) Integration of the pTET promoter significantly reduced biofilm formation of two TLOs, TLOα34 and TLOα9. (B). Induced expression of Tet-regulated TLOs significantly increased biofilm formation for two TLOs, TLOα3...
Data
TLOs have undergone extensive positive selection. A. Selection coefficients (Ka/Ks) were calculated for all branch points within the TLO phylogeny. Major branch points separating the TLO clades (circled) possess exceptionally high Ka/Ks values whereas intra-clade branch points have more neutral selection coefficients. B. Selection coefficients were...
Data
Transcript abundance of Tet-induced TLO strains. (TIF)
Preprint
Full-text available
Candida albicans surface-attached biofilms are sites of amplification of an infection through continuous discharge of cells capable of initiating new infectious foci. Yeast cells released from biofilms on intravenous catheters have direct access to the bloodstream. We previously reported that dispersed cells are largely lateral yeast cells that ori...
Article
Full-text available
Several pathogenic Candida species are capable of heritable and reversible switching between two epigenetic states, "white" and "opaque." In Candida albicans, white cells are essentially sterile, whereas opaque cells are mating-proficient. Here, we interrogate the mechanism by which the white-opaque switch regulates sexual fecundity and identify fo...