Physiological Responses of Aspergillus niger Challenged with Itraconazole

cyp51A mutations, protein modeling, and efflux pump gene expression reveals multifactorial complexity towards understanding Aspergillus section Nigri azole resistance mechanism

Black Aspergillus species are the most common etiological agents of otomycosis, and pulmonary aspergillosis. However, limited data is available on their antifungal susceptibility profiles and associated resistance mechanisms. Here, we determined the azole susceptibility profiles of black Aspergillus species isolated from the Indian environment and explored the potential resistance mechanisms through cyp51A gene sequencing, protein homology modeling, and expression analysis of selected genes cyp51A, cyp51B, mdr1, and mfs based on their role in imparting resistance against antifungal drugs. In this study, we have isolated a total of 161 black aspergilli isolates from 174 agricultural soil samples. Isolates had variable resistance towards medical azoles; approximately 11.80%, 3.10%, and 1.24% of isolates were resistant to itraconazole (ITC), posaconazole (POS), and voriconazole (VRC), respectively. Further, cyp51A sequence analysis showed that non-synonymous mutations were present in 20 azole-resistant Aspergillus section Nigri and 10 susceptible isolates. However, Cyp51A homology modeling indicated insignificant protein structural variations because of these mutations. Most of the isolates showed the overexpression of mdr1, and mfs genes. Hence, the study concluded that azole-resistance in section Nigri cannot be attributed exclusively to the cyp51A gene mutation or its overexpression. However, overexpression of mdr1 and mfs genes may have a potential role in drug resistance.

Energetically exploiting lignocellulose-rich residues in anaerobic digestion technologies: from bioreactors to proteogenomics

The biogas produced through anaerobic digestion (AD) of renewable feedstocks is one of the promising alternatives to replace fossil-derived energy. Even though lignocellulosic biomass is the most abundant biomass on earth, only a small fraction is being used towards resources recovery, leaving a great potential unexploited. In this study, the combination of state-of-art genomic techniques and engineered systems were used to further advance the knowledge on biogas production from lignocellulosic-rich residues and the microbiome involved in the anaerobic digestion hereof. A long-term adapted anaerobic microbiome capable of degrading wheat straw as the sole substrate was investigated using protein stable isotope probing (protein-SIP). The results indicated that a diverse microbial community, primarily composed of Firmicutes and Methanogens, played crucial roles in cellulose degradation and methane production. Notably, Defluviitoga tunisiensis, Syntrophothermus lipocalidus, and Pelobacter carbinolicus were identified as direct metabolizers of cellulose, while Dehalobacterium assimilated labelled carbon through cross-feeding. This study provides direct evidence of primary cellulose degraders and sheds light on their genomic composition. By harnessing the potential of lignocellulosic biomass and understanding the microbial communities involved, we can promote sustainable biogas production, contributing to energy security and environmental preservation.

Proteomic Changes in Methicillin-Resistant Staphylococcus aureus Exposed to Cannabinoids

Methicillin-resistant Staphylococcus aureus (MRSA) is a major human pathogen that causes a wide range of infections. Its resistance to β-lactam antibiotics complicates treatment due to the limited number of antibiotics with activity against MRSA. To investigate development of alternative therapeutics, the mechanisms that mediate antibiotic resistance in MRSA need to be fully understood. In this study, MRSA cells were subjected to antibiotic stress from methicillin in combination with three cannabinoid compounds and analyzed using proteomics to assess the changes in physiology. Subjecting MRSA to nonlethal levels of methicillin resulted in an increased production of penicillin-binding protein 2 (PBP2). Exposure to cannabinoids showed antibiotic activity against MRSA, and differential proteomics revealed reduced levels of proteins involved in the energy production as well as PBP2 when used in combination with methicillin.

Assessing labelled carbon assimilation from poly butylene adipate-co-terephthalate (PBAT) monomers during thermophilic anaerobic digestion

PBAT (poly butylene adipate-co-terephthalate) is a widely used biodegradable plastic, but the knowledge about its metabolization in anaerobic environments is very limited. In this study, the anaerobic digester sludge from a municipal wastewater treatment plant was used as inoculum to investigate the biodegradability of PBAT monomers in thermophilic conditions. The research employs a combination of ¹³C-labelled monomers and proteogenomics to track the labelled carbon and identify the microorganisms involved. A total of 122 labelled peptides of interest were identified for adipic acid (AA) and 1,4-butanedio (BD). Through the time-dependent isotopic enrichment and isotopic profile distributions, Bacteroides, Ichthyobacterium, and Methanosarcina were proven to be directly involved in the metabolization of at least one monomer. This study provides a first insight into the identity and genomic potential of microorganisms responsible for biodegradability of PBAT monomers during anaerobic digestion under thermophilic conditions.

Antagonism of the Azoles to Olorofim and Cross-Resistance Are Governed by Linked Transcriptional Networks in Aspergillus fumigatus

Aspergillosis, in its various manifestations, is a major cause of morbidity and mortality. Very few classes of antifungal drugs have been approved for clinical use to treat these diseases and resistance to the first-line therapeutic class, the triazoles are increasing. A new class of antifungals that target pyrimidine biosynthesis, the orotomides, are currently in development with the first compound in this class, olorofim in late-stage clinical trials. In this study, we identified an antagonistic action of the triazoles on the action of olorofim. We showed that this antagonism was the result of an azole-induced upregulation of the pyrimidine biosynthesis pathway. Intriguingly, we showed that loss of function in the higher order transcription factor, HapB a member of the heterotrimeric HapB/C/E (CBC) complex or the regulator of nitrogen metabolic genes AreA, led to cross-resistance to both the azoles and olorofim, indicating that factors that govern resistance were under common regulatory control. However, the loss of azole-induced antagonism required decoupling of the pyrimidine biosynthetic pathway in a manner independent of the action of a single transcription factor. Our study provided evidence for complex transcriptional crosstalk between the pyrimidine and ergosterol biosynthetic pathways. IMPORTANCE Aspergillosis is a spectrum of diseases and a major cause of morbidity and mortality. To treat these diseases, there are a few classes of antifungal drugs approved for clinical use. Resistance to the first line treatment, the azoles, is increasing. The first antifungal, olorofim, which is in the novel class of orotomides, is currently in development. Here, we showed an antagonistic effect between the azoles and olorofim, which was a result of dysregulation of the pyrimidine pathway, the target of olorofim, and the ergosterol biosynthesis pathway, the target of the azoles.

Unravelling gradient layers of microbial communities, proteins, and chemical structure in aerobic granules

Most bacteria live in microbial assemblages like biofilms and granules, and each layer of these assemblages provides a niche for certain bacteria with specific metabolic functions. In this study, a gentle (non-destructive) extraction approach based on a cation exchange resin and defined shear was employed to gradually disintegrate biomass and collect single layers of aerobic granules from a full-scale municipal wastewater treatment plant. The microbial community composition of granule layers was characterized using next-generation sequencing (NGS) targeting the 16S rRNA gene, and protein composition was investigated using metaproteomics. The chemical composition of eroded layers was explored using Fourier Transformed Infrared Spectroscopy. On the surface of the granules, the microbial structure (flocculation-supporting Nannocystis sp.) as well as composition of extracellular polymers (extracellular DNA) and proteome (chaperonins and binding proteins) favored microbial aggregation. Extracellular polymeric substances in the granules were composed of mostly proteins and EPS-producers, such as Tetrasphaera sp. and Zoogloea sp., were evenly distributed throughout the granule structure. The interior of the granules harbored several denitrifiers (e.g., Thauera sp.), phosphate-accumulating denitrifiers (Candidatus Accumulibacter, Dechloromonas sp.) and nitrifiers (Candidatus Nitrotoga). Proteins associated with glycolytic activity were identified in the outer and middle granule layers, and proteins associated with phosphorus conversions, in the deeper layers. In conclusion, the use of an existing cation-exchange resin for gradual biomass disintegration, combined with NGS and metaproteomic analysis was demonstrated as a promising approach for simultaneously investigating the identity and functions of microbes in multilayered biofilm structures.

Characterisation of cellulose-degrading organisms in an anaerobic digester

The recalcitrant nature of lignocellulosic biomass hinders efficient exploitation of this fraction for energy production. A better understanding of the microorganisms able to convert plant-based feedstocks is needed to improve anaerobic digestion of lignocellulosic biomass. In this study, active thermophilic cellulose-degrading microorganisms were identified from a full-scale anaerobic digester fed with maize by using metagenome-resolved protein stable isotope probing (protein-SIP). ¹³C-cellulose was converted into ¹³C-methane with a ^13/12C isotope ratio of 0.127 after two days of incubation. Metagenomic analysis revealed 238 different genes coding for carbohydrate-active enzymes (CAZymes), six of which were directly associated with cellulose degradation. The protein-SIP analysis identified twenty heavily labelled peptides deriving from microorganisms actively assimilating labelled carbon from the degradation of ¹³C-cellulose, highlighting several members of the order Clostridiales. Corynebacterium was identified through CAZyme screening, amplicon analysis, and in the metagenome giving a strong identification of being a cellulose degrader.

Induced Cell Cycle Arrest in Triple-Negative Breast Cancer by Combined Treatment of Itraconazole and Rapamycin

Triple-negative breast cancer (TNBC) is the aggressive molecular type of breast carcinoma, with a high metastasis/relapse incidence and cancer-related death rate, due to lack of specific therapeutic targets in the clinic. Exploring potential therapeutic targets or developing novel therapeutic strategies are the focus of intense research to improve the survival and life quality of patients with TNBC. The current study focused on drugs targeting the mTOR signaling pathway by investigating the potential utilization of itraconazole (ITZ) combined with rapamycin in the treatment of TNBC. CCK-8, colony formation and transwell assays were conducted to evaluate the effect of ITZ with rapamycin in combination on MDA-MB-231 and BT-549 TNBC cells. Synergistic inhibition was found in terms of proliferation and motility of TNBC cells. However, apoptosis was not enhanced by the combined treatment of ITZ and rapamycin. Flow cytometry analysis showed that ITZ and/or rapamycin arrested cells in G0/G1 phase and prevented G1/S phase transition. Reduced cyclin D1 protein levels were consistent with G0/G1 phase arrest, especially when resulting from the combination of ITZ with rapamycin. In conclusion, the combination of ITZ with rapamycin is a promising therapeutic strategy for patients with TNBC through synergistically arresting cells in the G0/G1 phase of the cell cycle, rather than inducing apoptosis.

Occupational exposure to fungi on recyclable paper pots and growing media and associated health effects - A review of the literature

Different types of pots and growing and casing media, including biodegradable materials, are used for plant and mushroom production. The fungus Peziza ostracoderma has gained attention for its visible growth on growing media for plants and casing media for mushrooms. Through a review of the literature we aim to evaluate whether exposure to fungi from recyclable pots and different growing and casing media occurs and causes occupational health effects. Based on the published papers, specific fungal species were not related to a specific medium. Thus P. ostracoderma has been found on paper pots, peat, sterilized soil, vermiculite, and rockwool with plants, and on peat, pumice, and paper casing for mushrooms. It has been found in high concentrations in the air in mushroom farms. Also Acremonium spp., Aspergillus niger, A. fumigatus, Athelia turficola, Aureobasidium pullulans, Chaetomium globosum, Chrysonilia sitophila, Cladosporium spp., Cryptostroma corticale, Lecanicillium aphanocladii, Sporothrix schenckii, Stachybotrys chartarum, and Trichoderma spp. have been found on different types of growing or casing media. Most of the fungi have also been found in the air in greenhouses, but the knowledge about airborne fungal species in mushroom farms is very limited. Eight publications describe cases of health effects associated directly with exposure to fungi from pots or growing or casing media. These include cases of hypersensitivity pneumonitis caused by exposure to: A. fumigatus, A. niger, Au. pullulans, Cr. corticale, P. ostracoderma, and a mixture of fungi growing on different media. Different approaches have been used to avoid growth of saprophytes including: chemical fungicides, the formulation of biodegradable pots and growing media and types of peat. To increase the sustainability of growing media different types of media are tested for their use and with the present study we highlight the importance of also considering the occupational health of the growers who may be exposed to fungi from the media and pots.