Human fungal diseases are infections caused by any fungus that invades human tissues, causing superficial, subcutaneous, or systemic diseases. Fungal infections that enter various human tissues and organs pose a significant threat to millions of individuals with weakened immune systems globally. Over recent decades, the reported cases of invasive fungal infections have increased substantially and research progress in this field has also been rapidly boosted. This review provides a comprehensive list of human fungal pathogens extracted from over 850 recent case reports, and a summary of the relevant disease conditions and their origins. Details of 281 human fungal pathogens belonging to 12 classes and 104 genera in the divisions ascomycota, basidiomycota, entomophthoromycota, and mucoromycota are listed. Among these, Aspergillus stands out as the genus with the greatest potential of infecting humans, comprising 16 species known to infect humans. Additionally, three other genera, Curvularia, Exophiala, and Trichophyton, are recognized as significant genera, each comprising 10 or more known human pathogenic species. A phylogenetic analysis based on partial sequences of the 28S nrRNA gene (LSU) of human fungal pathogens was performed to show their phylogenetic relationships and clarify their taxonomies. In addition, this review summarizes the recent advancements in fungal disease diagnosis and therapeutics.

The advantages and disadvantages of giving a valid name to a sequence of DNA detected from environmental specimens is presently a hot debate amongst the mycological community. The idea of using intracellular DNA (“mgDNA”) from environmental samples as holotypes seems at face value, to be a good idea, considering the expansion of knowledge among these ‘dark taxa’ or ‘dark matter fungi’ that it could provide (i.e. sequence based taxa without physical specimens and formal nomenclature). However, the limitations of using mgDNA as holotypes needs careful thought, i.e. can we use a short mgDNA fragment, which may contain a small amount of genetic information, to allow discrimination between species? What is the point and are the potential problems of giving valid scientific names to mgDNA? Numerous mycologists and taxonomists, who have many years of experience working on the taxonomy and phylogeny of different groups of fungi, are concerned about the consequences of providing valid names to mgDNA. There has been much debate, through several publications on the considerable problems of using mgDNA as holotypes. The proponents have tried to debate the virtues of using mgDNA as holotypes. Those against have shown that identification to species using mgDNA does not work in many fungal groups, while those for have shown cases where species can be identified with mgDNA. Different disciplines have different reasons and opinions for using mgDNA as holotypes, however even groups of the same disciplines have dissimilar ideas. In this paper we explore the use of mgDNA as holotypes. We provide evidences and opinions as to the use of mgDNA as holotypes from our own experiences. In no way do we attempt to degrade the study of DNA from environmental samples and the expansion of knowledge in to the dark taxa, but relate the issues to fungal taxonomy. In fact we show the value of using sequence data from these approaches, in dealing with the discovery of already named taxa, taxa numbers and ecological roles. We discuss the advantages and the pitfalls of using mgDNA from environmental samples as holotypes. The impacts of expanding the nomenclatural concept to allow using mgDNA from environmental samples as holotypes are also discussed. We provide evidence from case studies on Botryosphaeria, Colletotrichum, Penicillium and Xylaria. The case studies show that we cannot use mgDNA due to their short fragments and the fact that most ITS sequence data presently result from environmental sequencing. We conclude from the evidence that it is highly undesirable to use mgDNA as holotypes in naming fungal species. If this approach adopted, it would result in numerous problems where species identification cannot be confirmed due to limited sequence data available for the holotypes. We also propose an alternative DNA-based system for naming DNA based species which would provide considerably less problems and should be adopted.

Komagataeibacter hansenii HDM1-3 (K. hansenii HDM1-3) has been widely applied for producing bacterial cellulose (BC). The yield of BC has been frequently limited by the acidification during sugar metabolism, due to the generation of organic acids such as acetic acid. In this study, the acid resistance mechanism of K. hansenii HDM1-3 has been investigated from the aspect of metabolic adaptability of cell membrane fatty acids. Firstly, we observed that the survival rate of K. hansenii HDM1-3 was decreased with lowered pH values (adjusted with acetic acids), accompanied by increased leakage rate. Secondly, the cell membrane adaptability in response to acid stress was evaluated, including the variations of cell membrane fluidity and fatty acid composition. The proportion of unsaturated fatty acids was increased (especially, C18-1w9c and C19-Cyc), unsaturation degree and chain length of fatty acids were also increased. Thirdly, the potential molecular regulation mechanism was further elucidated. Under acid stress, the fatty acid synthesis pathway was involved in the structure and composition variations of fatty acids, which was proved by the activation of both fatty acid dehydrogenase (des) and cyclopropane fatty acid synthase (cfa) genes, as well as the addition of exogenous fatty acids. The fatty acid synthesis of K. hansenii HDM1-3 may be mediated by the activation of two-component sensor signaling pathways in response to the acid stress. The acid resistance mechanism of K. hansenii HDM1-3 adds to our knowledge of the acid stress adaptation, which may facilitate the development of new strategies for improving the industrial performance of this species under acid stress.

This article presents the results of an ongoing inventory of Ascomycota in Yunnan, China, carried out as part of the research project series “Exploring ascomycete diversity in Yunnan”. From over 100 samples collected from diverse host substrates, microfungi have been isolated, identified and are currently being documented. The primary objective of this research is to promote the discovery of novel taxa and explore the ascomycete diversity in the region, utilising a morphology-phylogeny approach. This article represents the second series of species descriptions for the project and introduces three undocumented species found in the families Bambusicolaceae, Dictyosporiaceae and Periconiaceae, belonging to the suborder Massarineae (Pleosporales, Dothideomycetes). These novel taxa exhibit typical morphological characteristics of Bambusicola, Periconia and Trichobotrys, leading to their designation as Bambusicola hongheensis, Periconia kunmingensis and Trichobotrys sinensis. Comprehensive multigene phylogenetic analyses were conducted to validate the novelty of these species. The results revealed well-defined clades that are clearly distinct from other related species, providing robust support for their placement within their respective families. Notably, this study unveils the phylogenetic affinity of Trichobotrys within Dictyosporiaceae for the first time. Additionally, the synanamorphism for the genus Trichobotrys is also reported for the first time. Detailed descriptions, illustrations and updated phylogenies of the novel species are provided, and thus presenting a valuable resource for researchers and mycologists interested in the diversity of ascomycetes in Yunnan. By enhancing our understanding of the Ascomycota diversity in this region, this research contributes to the broader field of fungal taxonomy and their phylogenetic understanding.

Parabambusicolaceae is a well-studied family in Massarineae, Pleosporales, comprising nine genera and approximately 16 species. The family was introduced to accommodate saprobic bambusicola-like species in both freshwater and terrestrial environments that mostly occur on bamboos and grasses but are also found on different host substrates. In the present study, we surveyed and collected ascomycetes from bamboo and submerged grass across Yunnan Province, China. A biphasic approach based on morphological characteristics and multigene phylogeny demonstrated five new taxa in Parabambusicolaceae. A novel genus Scolecohyalosporium is introduced as a monotypic genus to accommodate S. submersum sp. nov., collected from dead culms of grass submerged in a freshwater stream. The genus is unique in forming filiform ascospores, which differ from other known genera in Parabambusicolaceae. Multigene phylogeny showed that the genus has a close relationship with Multiseptospora. Moreover, the novel monotypic genus Neomultiseptospora, isolated from bamboo, was introduced to accommodate N. yunnanensis sp. nov. Neomultiseptospora yunnanensis formed a separated branch basal to Scolecohyalosporium submersum and Multiseptospora thailandica with high support (100% ML, 1.00 PP). Furthermore, the newly introduced species, Parabambusicola hongheensis sp. nov. was also isolated from bamboo in terrestrial habitats. Parabambusicola hongheensis clustered with the other three described Parabambusicola species and has a close relationship with P. bambusina with significant support (88% ML, 1.00 PP). Parabambusicola hongheensis was reported as the fourth species in this genus. Detailed description, illustration, and updated phylogeny of Parabambusicolaceae were provided.