About

Marco Dias Coelho is an Assistant Research Professor in the Department of Molecular Genetics and Microbiology at Duke University. He is affiliated with the Heitman Lab and is based at the Box 3546, 321 CARL Building in Durham, NC. His research focuses on molecular genetics and microbiology, contributing to the understanding of host-microbial interactions, virology, and microbiome science. As part of Duke's research community, he is involved in advancing knowledge in these areas through his academic and scientific activities.

Research topics

• Biology
• Genetics
• Computer Science
• Immunology
• Programming language
• Microbiology
• Ecology
• Bioinformatics

Selected publications

• <i>Aimea</i> gen. nov. defines a novel plant-associated yeast genus in <i>Microbotryomycetes</i> with three novel species

  bioRxiv (Cold Spring Harbor Laboratory) · 2026-04-10

  articleOpen access

  Abstract Plant tissues and surfaces are among the largest microbial habitats on Earth, and commensal yeasts are common members of these communities, where they can contribute to plant-microbe interactions including the biological control of plant diseases. Here, we describe a novel genus, Aimea , of unpigmented, plant-associated basidiomycete yeasts, in the class Microbotryomycetes, and name three new species ( A. erigeronia , A. cardamina , and A. sorghi ) represented by four isolates from leaves and roots of multiple hosts. We characterize these taxa through analyses of metabolic requirements, tolerance to differences in osmolarity, pH, and temperature, and enzymatic activities. In parallel, we generate near-chromosome-scale hybrid genomes annotated with transcriptome data. We employ whole-genome and multilocus phylogenetic approaches to infer the placement of these species within a monophyletic clade. We use comparative genomics to examine how the gene content of these yeasts differs from that of other members of the Microbotryomycetes, including an apparent proliferation of retrotransposons. We further demonstrate the genetic transformability of these taxa using Agrobacterium tumefaciens -mediated transformation. The description of these new species, together with high-quality genome resources and a genetic transformation protocol, establishes a foundation for experimental studies of these novel plant-associated yeasts and their interactions with hosts and other microbes.

  PublisherDOI

• Fourier transform infrared spectroscopy reveals high intraspecies diversity of <i>Malassezia pachydermatis</i> in dogs with atopic dermatitis

  bioRxiv (Cold Spring Harbor Laboratory) · 2026-04-06

  articleOpen access

  1 ABSTRACT Canine atopic dermatitis (CAD) is a chronic inflammatory skin condition sometimes associated with microbial dysbiosis, including alterations in colonization by the lipophilic yeast Malassezia pachydermatis . This study investigated the population diversity of M. pachydermatis in the ear canals of healthy and CAD-affected dogs using Fourier-transform infrared (FTIR) spectroscopy and whole genome sequencing (WGS). Among 60 dogs, M. pachydermatis prevalence was significantly higher in CAD cases than in healthy controls. FTIR spectroscopy revealed greater strain heterogeneity in CAD-affected dogs, often with distinct genotypes in each ear, while healthy dogs exhibited more homogeneous populations. Using a previously developed FTIR-based artificial neural network classifier, we assigned strains to three phylogroups. Strains from phylogroups I and III were significantly enriched in CAD-affected dogs, while phylogroup II was most prevalent overall and the dominant phylogroup in healthy controls. This suggests that CAD-associated inflammation may favor specific M. pachydermatis phylogroups and sub-clusters within phylogroups, shaping colonization dynamics. FTIR-based typing showed full concordance with WGS across 35 sequenced isolates, recapitulating relationships among phylogenetically related isolates and their similar phenotypic profiles. Overall, our findings reveal strain-level shifts in M. pachydermatis populations associated with CAD and establish FTIR spectroscopy as a rapid, cost-effective tool for large-scale epidemiological studies.

  PublisherOA PDFDOI

• Genomic rearrangements at the MAT locus suggest reproductive shifts in Rhodotorula yeasts

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-09-12 · 1 citations

  preprintOpen access

  Rhodotorula, a red yeast genus inhabiting diverse environmental and clinical niches, is a promising microbial source for carotenoid and lipid production. Despite the coexistence of sexual and asexual species, the evolutionary mechanisms underlying their reproductive diversity remain poorly understood. Here, we present a global genomic survey of 249 Rhodotorula strains using Oxford Nanopore, PacBio, and Illumina sequencing. Phylogenomic analysis resolved a robust species tree, delineating three major clades with substantial cryptic species diversity. Chromosome-level assemblies revealed a constrained tetrapolar mating system characterized by unlinked pheromone/receptor (P/R) and homeodomain (HD) mating-type (MAT) loci but displaying infrequent recombination. This genomic architecture is widely conserved, even in species lacking observed sexual cycles, suggesting widespread sexual potential. The P/R locus functions as a supergene, exhibiting conserved gene content and order within mating types but variable configurations between compatible types. Clade-specific biases in mating-type allele distributions indicates asymmetric evolutionary pressures. Structural rearrangements and trans-specific polymorphism of mating-specific allele at the P/R locus, may drive sequence divergence, potentially generating novel mating compatibility within the same mating type. The intermediate P/R genomic states retaining pheromone genes from the opposite mating type may preserve residual functions or facilitate transitions in mating-type architecture. Together with the presence of homozygous hybrid strains, these genomic signatures suggest a potential shift toward same-sex-like mating. Our findings elucidate how mating-type architecture and allele dynamics underpin the evolution of reproductive strategies in fungi and suggest that innovations in MAT system may be a key evolutionary lever in fungal adaptation across environments.

  PublisherOA PDFDOI

• Fourier transform infrared spectroscopy enables rapid species discrimination across <i>Malassezia</i> and strain-level typing in <i>M. pachydermatis</i>

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-09-29 · 1 citations

  preprintOpen access

  1 Abstract Malassezia pachydermatis is a zoophilic yeast found on the skin and in the outer ear canal of many mammals. It normally maintains a commensal lifestyle but can cause dermatitis and otitis in predisposed hosts, particularly in atopic dogs. M. pachydermatis is genetically diverse, with strains clustering into at least three phylogroups based on molecular typing, a pattern we now confirm through whole-genome sequencing (WGS). Accurate species and strain-level identification is essential for understanding its epidemiology, pathogenic potential, and response to treatment. In this study, we established Fourier Transform Infrared (FTIR) spectroscopy as a rapid, cost-effective method for distinguishing M. pachydermatis from other Malassezia species, including M. globosa, M. furfur, M. restricta , and M. sympodialis . Within M. pachydermatis , FTIR spectroscopy resolved even closely related strains with high accuracy producing clusters congruent with WGS-based phylogeny. The incorporation of an Artificial Neural Network classifier further enhanced the discriminatory power, enabling robust and automated strain assignment. These findings demonstrate the potential of FTIR spectroscopy as a practical tool for large-scale epidemiological surveillance of M. pachydermatis and for clinical and veterinary applications where strain-level identification could inform treatment and management of Malassezia -associated diseases. Importance Malassezia pachydermatis is a yeast that commonly inhabits the skin and ear canals of mammals but can cause dermatitis and otitis in predisposed hosts, especially dogs with allergies. This species displays substantial genetic diversity, with strains falling into distinct phylogroups that may differ in their biology and clinical significance. Determining these differences has typically required advanced molecular or genomic methods, which can be costly and time-consuming. In this study, we demonstrate that Fourier transform infrared spectroscopy can rapidly and accurately distinguish M. pachydermatis from other Malassezia species and resolve genetic groups within the species in a way that reflects whole-genome relationships. This capability offers a practical tool for investigating the epidemiology and inter-/intraspecies diversity of M. pachydermatis and for guiding targeted management of Malassezia -associated diseases in both veterinary and, potentially, human medicine.

  PublisherOA PDFDOI

• Exploring biological properties of sulfa-based copper(II) complexes: in vitro genotoxicity, cytotoxicity (2D and 3D) and mechanistic insights

  BioMetals · 2025-07-13

  article1st authorCorresponding
  PublisherDOI

• Long transposon-rich centromeres in an oomycete reveal divergence of centromere features in Stramenopila-Alveolata-Rhizaria lineages

  UNC Libraries · 2025-11-06

  articleOpen access

  Centromeres are chromosomal regions that serve as platforms for kinetochore assembly and spindle attachments, ensuring accurate chromosome segregation during cell division. Despite functional conservation, centromere DNA sequences are diverse and often repetitive, making them challenging to assemble and identify. Here, we describe centromeres in an oomycete Phytophthora sojae by combining long-read sequencing-based genome assembly and chromatin immunoprecipitation for the centromeric histone CENP-A followed by high-throughput sequencing (ChIP-seq). P. sojae centromeres cluster at a single focus at different life stages and during nuclear division. We report an improved genome assembly of the P. sojae reference strain, which enabled identification of 15 enriched CENP-A binding regions as putative centromeres. By focusing on a subset of these regions, we demonstrate that centromeres in P. sojae are regional, spanning 211 to 356 kb. Most of these regions are transposon-rich, poorly transcribed, and lack the histone modification H3K4me2 but are embedded within regions with the heterochromatin marks H3K9me3 and H3K27me3. Strikingly, we discovered a Copia-like transposon (CoLT) that is highly enriched in the CENP-A chromatin. Similar clustered elements are also found in oomycete relatives of P. sojae, and may be applied as a criterion for prediction of oomycete centromeres. This work reveals a divergence of centromere features in oomycetes as compared to other organisms in the Stramenopila-Alveolata-Rhizaria (SAR) supergroup including diatoms and Plasmodium falciparum that have relatively short and simple regional centromeres. Identification of P. sojae centromeres in turn also advances the genome assembly.

  PublisherDOI

• Ten Pressing Questions (and Answers) About Marine Fungi and Opportunities for Collaborations in the Ocean Sciences

  Oceanography · 2025-01-01

  articleOpen access

  Nearly 200 years have passed since the first marine fungus, collected from the shores of North Africa, was described. In that time, marine mycologists have continued to observe, describe, and study fungi in every marine ecosystem examined. Nevertheless, fungi remain functionally “dark matter” of the ocean, presenting a grand opportunity to unravel their roles in ecosystem processes. This report outlines the discussion among participants of the second occasional meeting of marine mycologists at Asilomar, California, in March 2024, in which a diverse and interdisciplinary consortium of researchers enumerated the most pressing, and often basic, unanswered questions in marine fungi. We report on the questions facing the field of marine mycology, identify challenges in addressing those questions, and propose concrete and practical solutions for obtaining their answers. A common thread is the need for increasing cross talk and collaboration between mycologists and oceanographers that would present opportunities for readers to participate in a rapidly growing field.

  PublisherOA PDFDOI

• The complex evolution and genomic dynamics of mating-type loci in Cryptococcus and Kwoniella

  PLoS Biology · 2025-10-03 · 6 citations

  articleOpen access1st authorCorresponding

  Sexual reproduction in basidiomycete fungi is governed by MAT loci (P/R and HD), which exhibit remarkable evolutionary plasticity, characterized by expansions, rearrangements, and gene losses often associated with mating system transitions. The sister genera Cryptococcus and Kwoniella provide a powerful framework for studying MAT loci evolution owing to their diverse reproductive strategies and distinct architectures, spanning bipolar and tetrapolar systems with either linked or unlinked MAT loci. Building on recent comparative genomic analyses, we generated additional chromosome-level assemblies, uncovering distinct trajectories shaping MAT loci organization. Contrasting with the small-scale expansions and gene acquisitions observed in Kwoniella, our analyses revealed independent expansions of the P/R locus in tetrapolar Cryptococcus, possibly driven by pheromone gene duplications. Notably, these expansions coincided with a pronounced GC-content reduction best explained by reduced GC-biased gene conversion following recombination suppression, rather than relaxed codon usage selection. Diverse modes of MAT locus linkage were also identified, including three previously unrecognized transitions: one resulting in a pseudobipolar arrangement and two leading to bipolarity. All three transitions involved translocations. In the pseudobipolar configuration, the P/R and HD loci remained on the same chromosome but genetically unlinked, whereas the bipolar transitions additionally featured rearrangements that fused the two loci into a nonrecombining region. Mating assays confirmed a sexual cycle in Cryptococcus decagattii, demonstrating its ability to undergo mating and sporulation. Progeny analysis in Kwoniella mangrovensis revealed substantial ploidy variation and aneuploidy, likely stemming from haploid-diploid mating, yet evidence of recombination and loss of heterozygosity indicates that meiotic exchange occurs despite irregular chromosome segregation. Our findings underscore the importance of continued diversity sampling and provide further evidence for convergent evolution of fused MAT loci in basidiomycetes, offering new insights into the genetic and chromosomal changes driving reproductive transitions.

  PublisherDOI

• Genomic and phenotypic insights into the expanding phylogenetic landscape of the Cryptococcus genus

  PLoS Genetics · 2025-11-10

  articleOpen access1st authorCorresponding

  The fungal genus Cryptococcus includes several life-threatening human pathogens as well as diverse saprobic species whose genome architecture, ecology, and evolutionary history remain less well characterized. Understanding how some lineages evolved into major pathogens remains a central challenge and may be advanced by comparisons with their nonpathogenic counterparts. Integrative approaches have become essential for delimiting species and reconstructing evolutionary relationships, particularly in lineages with cryptic diversity or extensive chromosomal rearrangements. Here, we formally characterize six Cryptococcus species representing distinct evolutionary lineages, comprising both newly discovered and previously recognized but unnamed taxa, through a combination of phylogenomic analyses, divergence metrics, chromosomal comparisons, mating assays, and phenotypic profiling. Among pathogenic taxa, we formally name Cryptococcus hyracis sp. nov., corresponding to the previously characterized VGV lineage within the C. gattii complex. In parallel, we describe five saprobic, nonpathogenic species isolated from fruit, soil, and bark beetle galleries, spanning four phylogenetic clades. We identify a strong ecological association with bark beetles for Cryptococcus porticicola sp. nov., the only newly described nonpathogenic species with multiple sequenced strains from diverse sites. In this species, we detect strain-level chromosomal variation and evidence of sexual reproduction, along with population-level signatures of recombination. Across the genus, chromosome-level comparisons reveal extensive structural variation, including species- and strain-specific rearrangements that may restrict gene flow. We also identify multiple instances of chromosome number reduction, often accompanied by genomic signatures consistent with centromere inactivation or loss of centromeric identity. Comparative metabolic profiling with Biolog phenotype microarrays reveals clade-level differentiation and distinct substrate preferences, which may reflect metabolic divergence and habitat-specific diversification. Notably, we confirm that thermotolerance is restricted to clinically relevant taxa. These findings refine the species-level taxonomy of Cryptococcus, broaden its known genomic and ecological diversity, and strengthen the framework for investigating speciation, adaptation, and the emergence of pathogenicity within the genus.

  PublisherDOI

• Fungal sexual reproduction and mating-type loci

  Current Biology · 2025-06-01 · 10 citations

  reviewOpen access
  PublisherOA PDFDOI

Frequent coauthors

• Joseph Heitman

  Duke University Hospital

  150 shared

• Sheng Sun

  Duke Medical Center

  105 shared

• Márcia David‐Palma

  Duke University

  67 shared

• Tatiana Giraud

  Université Paris-Saclay

  41 shared

• Shelly Applen Clancey

  Duke University

  36 shared

• Paula Gonçalves

  Universidade Nova de Lisboa

  36 shared

• Anna Floyd Averette

  31 shared

• Andrew Ryan Passer

  Duke University

  31 shared

Education

• PhD in Biology (Molecular Genetics)

  Universidade Nova de Lisboa

  2011

• Degree (Licenciatura) in Biology

  Universidade do Porto

  2003