Metabolic modelling uncovers the complex interplay between fungal probiotics, poultry microbiomes, and diet.

Background: The search for alternatives to antibiotic growth promoters in poultry production has increased interest in probiotics. However, the complexity of the interactions between probiotics, gut microbiome, and the host hinders the development of effective probiotic interventions. This study explores metabolic modelling to examine the possibility of designing informed probiotic interventions within poultry production.

The Oleaginous Yeast Displays Killer Activity against Avian-Derived Pathogenic Bacteria.

is a non-conventional yeast with potential to be used in biotechnological processes, especially those involving low-cost feedstock exploitation and biocontrol applications. The combination of traits that supports these industrial applications in also makes it an attractive option to study in the context of livestock health. In this study, we examined the specific interactions between and multiple avian pathogenic bacteria.

Variation among Isolates for Genetic Modification and Homologous Recombination.

is a non-conventional yeast with the potential to be used in biotechnological processes, especially involving low-cost feedstock exploitation. However, there are a lack of tools for researching it at a molecular level and for producing genetically modified strains. We tested the amenability to genetic modification of ten different strains, establishing a transformation protocol based on LiAc/PEG that allows us to introduce heterologous DNA.

Semi-continuous pilot-scale microbial oil production with on starch hydrolysate.

Background: Heterotrophic microbial oils are potentially a more sustainable alternative to vegetable or fossil oils for food and fuel applications. However, as almost all work in the area is conducted on the laboratory scale, such studies carry limited industrial relevance and do not give a clear indication of what is required to produce an actual industrial process. is a non-pathogenic industrially promising oleaginous yeast which exhibits numerous advantages for cost-effective lipid production, including a wide substrate uptake, antimicrobial activity and fermentation inhibitor tolerance.

Snf2 controls pulcherriminic acid biosynthesis and antifungal activity of the biocontrol yeast Metschnikowia pulcherrima.

Metschnikowia pulcherrima synthesises the pigment pulcherrimin, from cyclodileucine (cyclo(Leu-Leu)) as a precursor, and exhibits strong antifungal activity against notorious plant pathogenic fungi. This yeast therefore has great potential for biocontrol applications against fungal diseases; particularly in the phyllosphere where this species is frequently found. To elucidate the molecular basis of the antifungal activity of M.

Elevated production of the aromatic fragrance molecule, 2-phenylethanol, using Metschnikowia pulcherrima through both de novo and ex novo conversion in batch and continuous modes.

Background: 2-phenylethanol (2PE) is a fragrance molecule predominantly used in perfumes and the food industry. It can be made from petrochemicals inexpensively, however, this is unsuitable for most food applications. Currently, the main method of production for the bio-derived compound is to extract the trace amounts found in rose petals, which is extremely costly.

Microevolutionary traits and comparative population genomics of the emerging pathogenic fungus Cryptococcus gattii.

Emerging fungal pathogens cause an expanding burden of disease across the animal kingdom, including a rise in morbidity and mortality in humans. Yet, we currently have only a limited repertoire of available therapeutic interventions. A greater understanding of the mechanisms of fungal virulence and of the emergence of hypervirulence within species is therefore needed for new treatments and mitigation efforts.

Species-specific PCR to describe local-scale distributions of four cryptic species in the complex.

is a ubiquitous airborne fungus detected in every sampled region of the Earth. Owing to its role in Alexander Fleming's serendipitous discovery of Penicillin in 1928, the fungus has generated widespread scientific interest; however its natural history is not well understood. Research has demonstrated speciation within .

Transmission of Hypervirulence traits via sexual reproduction within and between lineages of the human fungal pathogen cryptococcus gattii.

Since 1999 a lineage of the pathogen Cryptococcus gattii has been infecting humans and other animals in Canada and the Pacific Northwest of the USA. It is now the largest outbreak of a life-threatening fungal infection in a healthy population in recorded history. The high virulence of outbreak strains is closely linked to the ability of the pathogen to undergo rapid mitochondrial tubularisation and proliferation following engulfment by host phagocytes.

Chromosomal copy number variation, selection and uneven rates of recombination reveal cryptic genome diversity linked to pathogenicity.

Pathogenic fungi constitute a growing threat to both plant and animal species on a global scale. Despite a clonal mode of reproduction dominating the population genetic structure of many fungi, putatively asexual species are known to adapt rapidly when confronted by efforts to control their growth and transmission. However, the mechanisms by which adaptive diversity is generated across a clonal background are often poorly understood.

Using false discovery rates to benchmark SNP-callers in next-generation sequencing projects.

Sequence alignments form the basis for many comparative and population genomic studies. Alignment tools provide a range of accuracies dependent on the divergence between the sequences and the alignment methods. Despite widespread use, there is no standard method for assessing the accuracy of a dataset and alignment strategy after resequencing.

Clonality despite sex: the evolution of host-associated sexual neighborhoods in the pathogenic fungus Penicillium marneffei.

Molecular genetic approaches typically detect recombination in microbes regardless of assumed asexuality. However, genetic data have shown the AIDS-associated pathogen Penicillium marneffei to have extensive spatial genetic structure at local and regional scales, and although there has been some genetic evidence that a sexual cycle is possible, this haploid fungus is thought to be genetically, as well as morphologically, asexual in nature because of its highly clonal population structure. Here we use comparative genomics, experimental mixed-genotype infections, and population genetic data to elucidate the role of recombination in natural populations of P.

Emerging fungal threats to animal, plant and ecosystem health.

The past two decades have seen an increasing number of virulent infectious diseases in natural populations and managed landscapes. In both animals and plants, an unprecedented number of fungal and fungal-like diseases have recently caused some of the most severe die-offs and extinctions ever witnessed in wild species, and are jeopardizing food security. Human activity is intensifying fungal disease dispersal by modifying natural environments and thus creating new opportunities for evolution.

Sex, drugs and recombination: the wild life of Aspergillus.

Throughout the eukaryotes, sexual reproduction is an almost universal phenomenon. However, within the Kingdom Fungi, this relationship is not so clear-cut. Fungi exhibit a spectrum of reproductive modes and life-cycles; amongst the better known species, sexual reproduction is often facultative, can be rare, and in over half of the known Ascomycota (the moulds) is unknown (Taylor et al.

The gut fungus Basidiobolus ranarum has a large genome and different copy numbers of putatively functionally redundant elongation factor genes.

Fungal genomes range in size from 2.3 Mb for the microsporidian Encephalitozoon intestinalis up to 8000 Mb for Entomophaga aulicae, with a mean genome size of 37 Mb. Basidiobolus, a common inhabitant of vertebrate guts, is distantly related to all other fungi, and is unique in possessing both EF-1α and EFL genes.

Multiple emergences of genetically diverse amphibian-infecting chytrids include a globalized hypervirulent recombinant lineage.

Batrachochytrium dendrobatidis (Bd) is a globally ubiquitous fungal infection that has emerged to become a primary driver of amphibian biodiversity loss. Despite widespread effort to understand the emergence of this panzootic, the origins of the infection, its patterns of global spread, and principle mode of evolution remain largely unknown. Using comparative population genomics, we discovered three deeply diverged lineages of Bd associated with amphibians.

Genetic diversity, recombination, and divergence in animal associated Penicillium dipodomyis.

Penicillium dipodomyis is thought to be an exclusively asexual fungus associated with Kangaroo Rats, Dipodomys species, and is unique among Penicillium species in growing at 37°C but producing no known toxins. Lack of recombination within P. dipodomyis would result in limited adaptive flexibility but possibly enhance local adaptation and host selection via maintenance of favourable genotypes.

Population genetic structure of clinical and environmental isolates of Blastomyces dermatitidis, based on 27 polymorphic microsatellite markers.

Blastomyces dermatitidis, a thermally dimorphic fungus, is the etiologic agent of North American blastomycosis. Clinical presentation is varied, ranging from silent infections to fulminant respiratory disease and dissemination to skin and other sites. Exploration of the population genetic structure of B.

Low diversity Cryptococcus neoformans variety grubii multilocus sequence types from Thailand are consistent with an ancestral African origin.

The global burden of HIV-associated cryptococcal meningitis is estimated at nearly one million cases per year, causing up to a third of all AIDS-related deaths. Molecular epidemiology constitutes the main methodology for understanding the factors underpinning the emergence of this understudied, yet increasingly important, group of pathogenic fungi. Cryptococcus species are notable in the degree that virulence differs amongst lineages, and highly-virulent emerging lineages are changing patterns of human disease both temporally and spatially.

Common reservoirs for Penicillium marneffei infection in humans and rodents, China.

Human penicilliosis marneffei is an emerging infectious disease caused by the fungus Penicillium marneffei. High prevalence of infection among bamboo rats of the genera Rhizomys and Cannomys suggest that these rodents are a key facet of the P. marneffei life cycle.

Factors driving pathogenicity vs. prevalence of amphibian panzootic chytridiomycosis in Iberia.

Amphibian chytridiomycosis is a disease caused by the fungus Batrachochytrium dendrobatidis (Bd). Whether Bd is a new emerging pathogen (the novel pathogen hypothesis; NPH) or whether environmental changes are exacerbating the host-pathogen dynamic (the endemic pathogen hypothesis; EPH) is debated. To disentangle these hypotheses we map the distribution of Bd and chytridiomycosis across the Iberian Peninsula centred on the first European outbreak site.

Molecular phylogeny suggests a single origin of insect symbiosis in the Pucciniomycetes with support for some relationships within the genus Septobasidium.

In the Pucciniomycetes, a class of fungi that includes the plant pathogenic rust fungi, insect parasitism is restricted to a single family, the Septobasidiaceae. The Septobasidiaceae form a variety of symbioses with scale insects and have remained largely unstudied since the 1930s. Transitions between plant and animal parasitism and between mutualism and parasitism cannot be fully addressed in the Basidiomycota without a clear phylogenetic hypothesis for the Septobasidiales.

Diversity and phylogenetic affinities of foliar fungal endophytes in loblolly pine inferred by culturing and environmental PCR.

We examined endophytic fungi in asymptomatic foliage of loblolly pine (Pinus taeda) in North Carolina, U.S.A.

An overview of the higher level classification of Pucciniomycotina based on combined analyses of nuclear large and small subunit rDNA sequences.

In this study we provide a phylogenetically based introduction to the classes and orders of Pucciniomycotina (= Urediniomycetes), one of three subphyla of Basidiomycota. More than 8000 species of Pucciniomycotina have been described including putative saprotrophs and parasites of plants, animals and fungi. The overwhelming majority of these (approximately 90%) belong to a single order of obligate plant pathogens, the Pucciniales (= Uredinales), or rust fungi.

New species of Septobasidium from southern Costa Rica and the southeastern United States.

New species are described in Septobasidium, a genus of urediniomycete parasites on scale insects. One new species, S. gomezii, is described from Costa Rica, and another, S.