Fungal Composition Research Articles

Sustainable Processes and Physico-Chemical Characterization of Artisanal Spontaneous Gluten Free Sourdough (Quinoa, Amaranth and Brown Rice) Compared to Wheat Sourdough

The industry predominantly depends on synthetic or artificial additives, occasionally permitting the inclusion of natural molecules sourced from plants or replicated from their original counterparts. The production of bakery products increasingly uses sourdough to improve the quality of bread or to obtain “clean label” products (free of artificial additives). The additive production sector contributes to this concern through the synthesis of potentially harmful compounds, the utilization of hazardous chemicals and solvents, the management of resulting by-products, and reliance on non-renewable resources for manufacturing. One percent of the world’s population suffers from celiac disease. Celiac disease is treated by excluding gluten from the diet. Most gluten-free bakery products have low nutritional and sensory quality. Therefore, sourdough is being used to replace chemical yeast to improve the sensory and nutritional quality and increase the shelf life of gluten-free bakery products. Three gluten-free sourdoughs were prepared with different flours: brown rice, quinoa and amaranth, in order to compare them with traditional sourdough (wheat) and optimize the most suitable temperature for the conservation of sourdoughs. Physicochemical analysis (pH, titratable acidity and color), antioxidant activity (FRAP, ORAC and ABTS), total phenolic compound content (Folin–Ciocalteu), total aflatoxin content, lactic and acetic acid content and microbiological analysis (mold and yeast content and bacterial and fungal composition (microbiota composition)) were carried out during the elaboration process and at different storage temperatures. A higher microbiological quantity of molds and yeasts (7.97 log CFU/mL), non-Saccharomyces yeasts (7.78 log CFU/mL) and lactic acid bacteria (8.10 log CFU/mL) and fungal composition were observed in the amaranth sourdough. The wheat sourdough obtained a higher total content of phenolic compounds (33.03 mg GAE g−1) and antioxidant capacity in ABTS and FRAP, but the quinoa sourdough had the highest ORAC content. In addition, it was observed that the adequate temperature for the conservation of the doughs is 25 °C, due to the predominance of Lactobacillus spp. and Pediococcus spp. bacteria in the sourdough. Therefore, pseudocereal sourdoughs (quinoa and amaranth) could be an alternative to incorporate into the preparation of gluten-free bread, since their microbial composition, physicochemical composition, antioxidant activity and total phenolic compounds would contribute to gluten-free bread and thus produce health benefits for people with celiac disease.

Effects of yeast culture on in vitro ruminal fermentation and microbial community of high concentrate diet in sheep.

This research aimed to investigate effects of different yeast culture (YC) levels on in vitro fermentation characteristics and bacterial and fungal community under high concentrate diet. A total of 5 groups were included in the experiment: control group without YC (CON), YC1 (0.5% YC proportion of substrate dry matter), YC2 (1%), YC3 (1.5%) and YC4 (2%). After 48h of fermentation, the incubation fluids and residues were collected to analyze the ruminal fermentation parameters and bacterial and fungal community. Results showed that the ruminal fluid pH of YC2 and YC4 groups was higher (P < 0.05) than that of CON group. Compared with CON group, the microbial protein, propionate and butyrate concentrations and cumulative gas production at 48h of YC2 group were significantly increased (P < 0.05), whereas an opposite trend of ammonia nitrogen and lactate was observed between two groups. Microbial analysis showed that the Chao1 and Shannon indexes of YC2 group were higher (P < 0.05) than those of CON group. Additionally, YC supplementation significantly decreased (P < 0.05) Succinivibrionaceae_UCG-001, Streptococcus bovis and Neosetophoma relative abundances. An opposite tendency of Aspergillus abundance was found between CON and YC treatments. Compared with CON group, the relative abundances of Prevotella, Succiniclasticum, Butyrivibrio and Megasphaera elsdenii were significantly increased (P < 0.05) in YC2 group, while Apiotrichum and unclassified Clostridiales relative abundances were decreased (P < 0.05). In conclusion, high concentrate substrate supplemented with appropriate YC (1%) can improve ruminal fermentation and regulate bacterial and fungal composition.

Sunken Riches: Ascomycete Diversity in the Western Mediterranean Coast through Direct Plating and Flocculation, and Description of Four New Taxa.

The Mediterranean Sea stands out as a hotspot of biodiversity, whose fungal composition remains underexplored. Marine sediments represent the most diverse substrate; however, the challenge of recovering fungi in culture hinders the precise identification of this diversity. Concentration techniques like skimmed milk flocculation (SMF) could represent a suitable solution. Here, we compare the effectiveness in recovering filamentous ascomycetes of direct plating and SMF in combination with three culture media and two incubation temperatures, and we describe the fungal diversity detected in marine sediments. Sediments were collected at different depths on two beaches (Miracle and Arrabassada) on the Spanish western Mediterranean coast between 2021 and 2022. We recovered 362 strains, and after a morphological selection, 188 were identified primarily with the LSU and ITS barcodes, representing 54 genera and 94 species. Aspergillus, Penicillium, and Scedosporium were the most common genera, with different percentages of abundance between both beaches. Arrabassada Beach was more heterogeneous, with 42 genera representing 60 species (Miracle Beach, 28 genera and 54 species). Although most species were recovered with direct plating (70 species), 20 species were exclusively obtained using SMF as a sample pre-treatment, improving our ability to detect fungi in culture. In addition, we propose three new species in the genera Exophiala, Nigrocephalum, and Queenslandipenidiella, and a fourth representing the novel genus Schizochlamydosporiella. We concluded that SMF is a useful technique that, in combination with direct plating, including different culture media and incubation temperatures, improves the chance of recovering marine fungal communities in culture-dependent studies.

Checklist of Macrofungi Associated with Nine Different Habitats of Taburno-Camposauro Massif in Campania, Southern Italy.

The checklist serves as an informative method for evaluating the diversity, geography, and ecology of established and reproducing macrofungi. Additionally, considering macrofungi as bioindicator species, their census should be incorporated into efforts to monitor the state of health of ecosystems and directly applied to conservation policies. Between 2019 and 2023, a census of macrofungal species was conducted in Taburno-Camposauro Regional Park (Campania, Italy) across nine distinct habitats. A total of 453 fungal taxa were identified, including several new records for the Campania region. The fungal diversity exhibited significant variations based on the dominant plant species in each habitat. Fagacean tree species and Carpinus spp. shared similar fungal communities. Equally, coniferous tree species displayed a comparable fungal composition. In Abies alba and mixed broad-leaved forests, low levels of ectomycorrhizal taxa were observed alongside a concurrent increase in saprotrophs, indicating a disturbed habitat and a reduction in the Gadgil effect. Notably, lower fungal diversity was documented in the grassland habitat, suggesting the potential implications of wildlife imbalance and excessive grazing. The provided checklist constitutes a valuable resource for local management authorities, providing insights to formulate specific management policies.

The disparate effects of omega-3 PUFAs on intestinal microbial homeostasis in experimental rodents under physiological condition

The health benefits of omega-3 polyunsaturated fatty acids (omega-3 PUFAs), primarily eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA), are linked to their regulatory effects on the composition of the gut microbiota. However, there is a lack of direct evidence on whether omega-3 PUFAs regulate the gut microbial homeostasis under physiological conditions. This study investigated the impact of equivalent doses of EPA, DHA, and fish oil (FO) with a DHA to EPA ratio of approximately 1:1 on the bacterial and fungal composition of normal young mice. This study also analyzed changes in key components of the gut microenvironment, including the colonic mucus barrier and short-chain fatty acids, to address the prebiotic potential of omega-3 PUFAs. The results showed that all three omega-3 PUFAs interventions induced significant fluctuations in the gut bacteria and fungi, leading to an increase in the abundance of some probiotics. Notably, DHA, EPA, and FO interventions significantly increased the abundance of the probiotic Lactobacillus, Bifidobacterium, and Akkermansia, respectively. Both DHA and fish oil interventions also significantly reduced the abundance of potentially pathogenic fungi, such as Aspergillus and Penicillium. Association analysis of the top 19 differential fungal and bacterial genera in abundance revealed a much more bacteria-bacteria and bacteria-fungi connections, but fewer fungi-fungi connections. This highlights the importance of bacteria in the gut microecological network. Furthermore, the levels of butyric acid and valeric acid in the colonic contents of DHA intervention group were significantly increased, and the colonic mucus layer thickness was increased in three treatment groups. In summary, DHA, EPA and FO interventions showed targeted enhancement of different probiotics and enhanced colon defense barrier (mucus barrier), showing potential prebiotic effects.

Stem decomposition of temperate tree species is determined by stem traits and fungal community composition during early stem decay

Abstract Dead trees are vital structural elements in forests playing key roles in the carbon and nutrient cycle. Stem traits and fungal community composition are both important drivers of stem decay, and thereby affect ecosystem functioning, but their relative importance for stem decomposition over time remains unclear. To address this issue, we used a common garden decomposition experiment in a Dutch larch forest hosting fresh logs from 13 common temperate tree species. In total, 25 fresh wood and bark traits were measured as indicators of wood accessibility for decomposers, nutritional quality and chemical or physical defence mechanisms. After 1 and 4 years of decay, we assessed the richness and composition of wood‐inhabiting fungi using amplicon sequencing and determined the proportional wood density loss. Average proportional wood density loss for the first year was 18.5%, with further decomposition occurring at a rate of 4.3% year−1 for the subsequent 3 years across tree species. Proportional wood density loss varied widely across tree species in the first year (8.7–24.8% year−1) and subsequent years (0–11.3% year−1). The variation was directly driven by initial wood traits during the first decay year, then later directly driven by bark traits and fungal community composition. Moreover, bark traits affected the composition of wood‐inhabiting fungi and thereby indirectly affected decomposition rates. Specifically, traits promoting resource acquisition of the living tree, such as wide conduits that increase accessibility and high nutrient concentration, increased initial wood decomposition rates. Fungal community composition, but not fungal richness explained differences in wood decomposition after 4 years of exposure in the field, where fungal communities dominated by brown‐rot and white‐rot Basidiomycetes were linked to higher wood decomposition rate. Synthesis: Understanding what drives deadwood decomposition through time is important to understand the dynamics of carbon stocks. Here, using a tailor‐made experimental design in a temperate forest setting, we have shown that stem trait variation is key to understanding the roles of these drivers; initially, wood traits explained decomposition rates while subsequently, bark traits and fungal decomposer composition drove decomposition rates. These findings inform forest management with a view to selecting tree species to promote carbon storage.

Soil fungal composition under decomposing deadwood is largely affected by tree bark density rather than soil properties

Deadwood is an important structural and biological component of forest ecosystems habitating for a variety of soil fungal communities. However, it is unknown how decomposition of deadwood impacts fungal communities in the soil underneath functionally different tree species in forests. This study compared the effects of the barks of seven tree species, differing in physicochemical characteristics, on soil fungal communities during the early stages of deadwood decomposition in a subtropical forest. A field experiment consisting of 3 evergreen broadleaf, 3 deciduous broadleaf and 1 coniferous tree species, was conducted for 18 months to examine the impact of deadwood decomposition on soil fungal community using real-time PCR and high-throughput sequencing. Our results demonstrated that wood decomposition led to significant declines in soil pH. Functionally distinct tree species significantly shaped the distinct soil fungal composition and abundances underneath the deadwood of both broadleaf and coniferous trees after 18 months of decomposition. The fungal ecological guilds underneath the deadwood were altered, with symbiotrophs being more prominent, and a higher proportion of pathogens were observed under certain broadleaf tree species. Out of the soil fungal ASVs detected, only 51 (3 %) were generalists, while 1053 ASVs (52 %) exhibited traits indicating potential fungal specialists. There were stronger coniferous tree species preferences in soil fungal composition, compared to broadleaf trees. The initial bark density from broadleaf and coniferous species illustrated the most obvious difference. Interestingly, tree bark density, rather than soil chemistry, was the key driver causing the fluctuations in fungal composition during deadwood decomposition. Tree species traits notably affected soil fungal community during early wood decomposition. These findings highlight the importance of considering the bark traits in understanding the dynamics of soil fungal communities and its implications for forest health and ecosystem management.

Drought and vegetation restoration lead to shifts in soil microbial diversity and co-occurrence networks in California coastal prairie

Abstract Background and aims Both drought and vegetation restoration can have dramatic effects on plant community composition, but how they influence soil microbial community diversity, structure, and co-occurrence networks remain less well known. Methods To better understand the regulatory mechanisms of drought and vegetation restoration on soil microorganisms, we planted 12 native species in precipitation manipulation experimental plots in an invaded coastal grassland in California, USA. We measured soil bacterial and fungal community composition by amplicon sequencing, and quantified plant species richness and coverage in the third experimental year. Results Our results showed that drought significantly altered soil bacterial diversity and composition; however, neither drought nor vegetation restoration had significant effects on fungal diversity and composition. The control plots had the most cooperative interactions (greatest number of correlations) among bacterial and/or fungal species, while drought plots yielded the most complex co-occurrence network with the highest modularity and clustering coefficient. Structural equation modeling revealed that plant species richness, net gains, and soil moisture played dominant roles in shaping bacterial community structure. Drought and bacterial community structure directly affected fungal community structure. Plant dominant species cover, common species cover, and bacterial diversity were the key drivers in regulating the microbial co-occurrence network complex. Conclusion We conclude that soil bacterial and fungal communities differ in their responses to abiotic and biotic environmental changes, which may weaken the interspecies interactions among soil microorganisms.

Fungal community composition predicts forest carbon storage at a continental scale.

Forest soils harbor hyper-diverse microbial communities which fundamentally regulate carbon and nutrient cycling across the globe. Directly testing hypotheses on how microbiome diversity is linked to forest carbon storage has been difficult, due to a lack of paired data on microbiome diversity and in situ observations of forest carbon accumulation and storage. Here, we investigated the relationship between soil microbiomes and forest carbon across 238 forest inventory plots spanning 15 European countries. We show that the composition and diversity of fungal, but not bacterial, species is tightly coupled to both forest biotic conditions and a seven-fold variation in tree growth rates and biomass carbon stocks when controlling for the effects of dominant tree type, climate, and other environmental factors. This linkage is particularly strong for symbiotic endophytic and ectomycorrhizal fungi known to directly facilitate tree growth. Since tree growth rates in this system are closely and positively correlated with belowground soil carbon stocks, we conclude that fungal composition is a strong predictor of overall forest carbon storage across the European continent.

High-throughput sequencing reveals differences in microbial community structure and diversity in the conjunctival tissue of healthy and type 2 diabetic mice

BackgroundTo investigate the differences in bacterial and fungal community structure and diversity in conjunctival tissue of healthy and diabetic mice.MethodsRNA-seq assays and high-throughput sequencing of bacterial 16 S rDNA and fungal internal transcribed spacer (ITS) gene sequences were used to identify differentially expressed host genes and fungal composition profiles in conjunctival tissues of diabetic BKS-db/db mice and BKS (control) mice. Functional enrichment analysis of differentially expressed genes and the correlation between the relative abundance of bacterial and fungal taxa in the intestinal mucosa were also performed.ResultsTotally, 449 differential up-regulated genes and 1,006 down-regulated genes were identified in the conjunctival tissues of diabetic mice. The differentially expressed genes were mainly enriched in metabolism-related functions and pathways. A decrease in conjunctival bacterial species diversity and abundance in diabetic mice compared to control mice. In contrast, fungal species richness and diversity were not affected by diabetes. The microbial colonies were mainly associated with cellular process pathways regulating carbohydrate and lipid metabolism, as well as cell growth and death. Additionally, some interactions between bacteria and fungi at different taxonomic levels were also observed.ConclusionThe present study revealed significant differences in the abundance and composition of bacterial and fungal communities in the conjunctival tissue of diabetic mice compared to control mice. The study also highlighted interactions between bacteria and fungi at different taxonomic levels. These findings may have implications for the diagnosis and treatment of diabetes.

Research Note: Analysis of microbial diversity on the shell surface of eggs collected from geographically distinct farms in China

Micro-organisms on the eggshell surface of affect the quality of the egg. Sometimes, these microbes even pose a serious threat to the health of the egg's consumer. Bacterial 16S rDNA and fungal internal transcribed spacer region were sequenced to analyze the microbial diversity on the shell surface of the eggs collected from 4 distinct regions of China: Guyuan (GY; 1.5 million hens), Langfang (LF; 0.1 million hens), Beihai (BH; 1.2 million hens), and Dongguan (DG; 0.2 million hens). The results showed a higher bacterial and fungal abundance on the eggs collected from the northern and southern China farms, respectively. The dominant bacterial phylum detected across all egg samples was Firmicutes. In addition, the shell surfaces of the DG and LF samples harbored abundant levels of Proteobacteria. The dominant fungal phyla detected across all egg samples were Ascomycota and Basidiomycota. The bacterial compositions on eggshell surfaces differed significantly across all geographic regions, and the fungal composition differed significantly between samples collected from the southern and northern farms (P < 0.05). The abundance and composition of microbial colonies on the eggshell surface varied based on their geographical location (climate and environment) and farming scale (management). Our findings provide an important reference for optimizing the cleaning and disinfection methods for fresh eggs collected from different sources.

Short impact on soil microbiome of a Bacillus amyloliquefaciens QST713 based product that correlates with higher potato yield across USA.

Potato (Solanum tuberosum L.) is considered one of the most widely consumed crops worldwide, due to its high yield and nutritional profile, climate change-related environmental threats and increasing food demand. This scenario highlights the need of sustainable agricultural practices to enhance potato productivity, while preserving and maintaining soil health. Plant growth-promoting bacteria (PGPB) stimulate crop production through biofertilization mechanisms with low environmental impact. For instance, PGPB promote biological nitrogen fixation, phosphate solubilization, production of phytohormones, and biocontrol processes. Hence, these microbes provide a promising solution for more productive and sustainable agriculture. In this study, the effects of Bacillus amyloliquefaciens QST713 based-product (MINUET™, Bayer) were assessed in terms of yield, soil microbiome, potato peel and petiole nutrient profile as a promising PGPB in a wide range of potato cultivars across the United States of America. Depending on the location, potato yield and boron petiole content increased after biostimulant inoculation to maximum of 24% and 14%, respectively. Similarly, nutrient profile in potato peel was greatly improved depending on the location with a maximum of 73%, 62% and 36% for manganese, zinc and phosphorus. Notably, fungal composition was shifted in the treated group. Yield showed strong associations with specific microbial taxa, such as Pseudoarthrobacter, Ammoniphilus, Ideonella, Candidatus Berkiella, Dongia. Moreover, local networks strongly associated with yield, highlighting the important role of the native soil microbiome structure in indirectly maintaining soil health. Our results showed that treatment with B. amyloliquefaciens based product correlated with enhanced yield, with minor impacts on the soil microbiome diversity. Further studies are suggested to disentangle the underlying mechanisms of identified patterns and associations.

Consecutive Fertilization-Promoted Soil Nutrient Availability and Altered Rhizosphere Bacterial and Bulk Fungal Community Composition

Fertilization is an important measure to quickly supplement the soil nutrients required for plantation productivity. However, the response patterns of the microbial community and functional taxa in Larix plantation root, rhizosphere, and bulk soil to short-term and consecutive fertilization have rarely been reported. In this study, we assessed Larix root, rhizosphere, and bulk soil microbial community on days 0, 5, 15, and 30 after the first inorganic fertilization and after three consecutive years of fertilization. The bacterial 16S and fungal ITS high-throughput sequencing technology were used to monitor changes in microbial community composition and potential functional groups, as well as changes in soil nutrient content and enzyme activity to evaluate the status of plantation soil productivity. Consecutive fertilization treatment significantly increased the available nitrogen, phosphorus, and potassium (NPK) content and soil enzyme activity. The nonmetric multidimensional scaling (NMDS) and analysis of similarities (ANOSIM) results showed that there were significant differences in microbial community composition in root samples, rhizosphere soil, and bulk soil samples. The dominant microbial taxa were different between root and soil microbial community composition. Consecutive fertilization treatment had little effect on endophytic microbial community but significantly increased the abundance of Gaiellales in rhizosphere soil and Mortierella in bulk soil. The redundancy analysis (RDA) and co-occurrence network analyses showed that Gaiellales and Mortierellales had significant positive correlations with soil nutrient content and enzyme activity. The fungal functional group compositions were significantly affected by consecutive fertilization treatment and the proportions of ectomycorrhizal and saprotroph significantly decreased, but the proportion of endophyte significantly increased in bulk soil samples. Our results suggested that consecutive fertilization may promote soil nutrient availability by increasing the abundance of Gaiellales and Mortierella. Consecutive fertilization maintained the balance of the soil microbiota under Larix plantation and had a positive effect on promoting soil nutrient availability. This study provided a theoretical basis for consecutive fertilization to promote soil nutrient availability through specific microbial groups.

Dictyophora indusiata and Bacillus aryabhattai improve sugarcane yield by endogenously associating with the root and regulating flavonoid metabolism.

Endophytes play a significant role in regulating plant root development and facilitating nutrient solubilization and transportation. This association could improve plant growth. The present study has uncovered a distinct phenotype, which we refer to as "white root", arising from the intricate interactions between endophytic fungi and bacteria with the roots in a sugarcane and bamboo fungus (Dictyophora indusiata) intercropping system. We investigated the mechanisms underlying the formation of this "white root" phenotype and its impact on sugarcane yield and metabolism by metabarcoding and metabolome analysis. Initial analysis revealed that intercropping with D. indusiata increased sugarcane yield by enhancing the number of viable tillers compared with bagasse and no input control. Metabarcoding based on second-generation and third-generation sequencing indicated that D. indusiate and Bacillus aryabhattai dominates the fungal and bacterial composition in the "white root" phenotype of sugarcane root. The coexistence of D. indusiata and B. aryabhattai as endophytes induced plant growth-promoting metabolites in the sugarcane root system, such as lysoPC 18:1 and dihydrobenzofuran, probably contributing to increased sugarcane yield. Furthermore, the association also enhanced the metabolism of compounds, such as naringenin-7-O-glucoside (Prunin), naringenin-7-O-neohesperidoside (Naringin)*, hesperetin-7-O-neohesperidoside (Neohesperidin), epicatechin, and aromadendrin (Dihydrokaempferol), involved in flavonoid metabolism during the formation of the endophytic phenotype in the sugarcane root system. These observations suggest that the "white root" phenotype promotes sugarcane growth by activating flavonoid metabolism. This study reports an interesting phenomenon where D. indusiata, coordinate with the specific bacteria invade, forms a "white root" phenotype with sugarcane root. The study also provides new insights into using D. indusiata as a soil inoculant for promoting sugarcane growth and proposes a new approach for improve sugarcane cultivation.

Ant identity determines the fungi richness and composition of a myrmecochorous seed.

Myrmecochory-seed dispersal by ants-is a mutualistic interaction in which ants attracted by seed appendices take them away from the parental plant location, where seeds usually have better development odds. Not all ant species benefit plants, and the mechanisms of those divergent outcomes are still unclear, especially from the perspective of microbial third parties. Here, we explore the effects of seed manipulation on fungi communities promoted by two ant species with contrasting effects on seed germination and antimicrobial cleaning strategies. We hypothesize that: i) fungi richness is higher in seeds manipulated by Acromyrmex subterraneus (species that negatively affect seed germination), followed by unmanipulated seeds and seeds manipulated by Atta sexdens (ant species that increase seed germination) and ii) seeds manipulated by A. sexdens, Ac. subterraneus and unmanipulated seeds present dissimilar fungi compositions. We identified fungal morphotypes in three groups of seeds: i) manipulated by A. sexdens; ii) manipulated by Ac. subterraneus; iii) unmanipulated. Seeds manipulated by Ac. subterraneus exhibited higher fungal richness than those manipulated by A. sexdens and unmanipulated seeds, indicating that the ant species known to impair germination increases the fungal load on seeds. Additionally, we found that A. sexdens ants were unable to reduce fungal richness compared to unmanipulated seeds. Furthermore, fungal composition differed among all three treatments. Our results underscore the significance of ant species identity in shaping the fungal communities associated with myrmecochorous seeds. Given the potential influence of microbial infection on seed fate, we suggest considering manipulation strategies when evaluating the overall quality of an ant as a seed disperser.

Signatures of disease outcome severity in the intestinal fungal and bacterial microbiome of COVID-19 patients.

COVID-19, whose causative pathogen is the Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2), was declared a pandemic in March 2020. The gastrointestinal tract is one of the targets of this virus, and mounting evidence suggests that gastrointestinal symptoms may contribute to disease severity. The gut-lung axis is involved in the immune response to SARS-CoV-2; therefore, we investigated whether COVID-19 patients' bacterial and fungal gut microbiome composition was linked to disease clinical outcome. In May 2020, we collected stool samples and patient records from 24 hospitalized patients with laboratory-confirmed SARS-CoV-2 infection. Fungal and bacterial gut microbiome was characterized by amplicon sequencing on the MiSeq, Illumina's integrated next generation sequencing instrument. A cohort of 201 age- and sex-matched healthy volunteers from the project PRJNA661289 was used as a control group for the bacterial gut microbiota analysis. We observed that female COVID-19 patients had a lower gut bacterial microbiota richness than male patients, which was consistent with a different latency in hospital admittance time between the two groups. Both sexes in the COVID-19 patient study group displayed multiple positive associations with opportunistic bacterial pathogens such as Enterococcus, Streptococcus, and Actinomyces. Of note, the Candida genus dominated the gut mycobiota of COVID-19 patients, and adult patients showed a higher intestinal fungal diversity than elderly patients. We found that Saccharomycetales unassigned fungal genera were positively associated with bacterial short-chain fatty acid (SCFA) producers and negatively associated with the proinflammatory genus Bilophila in COVID-19 patients, and we observed that none of the patients who harbored it were admitted to the high-intensity unit. COVID-19 was associated with opportunistic bacterial pathogens, and Candida was the dominant fungal taxon in the intestine. Together, we found an association between commensal SCFA-producers and a fungal genus that was present in the intestines of patients who did not experience the most severe outcome of the disease. We believe that this taxon could have played a role in the disease outcome, and that further studies should be conducted to understand the role of fungi in gastrointestinal and health protection.

Diversity and Distribution Patterns of Culturable Airborne Fungi in Jiroft City

Background and Aims: Fungal spores constitute a significant portion of primary biological aerosol particles, and large amounts have been identified in the air. They are present in the atmosphere throughout the year, and their concentration varies due to meteorological factors such as temperature, relative humidity, location, construction conditions, and vegetation. Exposure to airborne fungi has been linked with diseases such as allergic respiratory symptoms, rhinitis, asthma, and various infections. This study investigates the diversity and distribution of airborne fungal spores in Jiroft City, located in the southern region of Iran. Materials and Methods: Airborne fungal composition was sampled from indoor, outdoor, and hospital air using the sedimentation plate method. Grown fungi were identified using standard mycological techniques, including determining macroscopic and microscopic characteristics. Results: A total of 230 colonies belonging to 11 genera of fungi were isolated from all culture media. Fungi were isolated from 53 (80.3%) samples. The highest and lowest percent of positive samples were found in outdoor (100%) and hospital (64.3%) air samples, respectively. Cladosporium (43.9%) and Aspergillus (36.4%) were the most common fungi isolated from the samples. Rhodotorula, Syncephalastrum, Paecilomyces, Mucor, and Acremonium were the least isolated fungi (1.5%). Conclusion: This study showed the difference in the diversity and distribution of fungi in different environments. Cladosporium and Aspergillus were the most common fungi isolated, which need to be considered due to their ability to cause various diseases.

The microbiota-gut-brain axisin Huntington's disease: pathogenic mechanisms and therapeutic targets.

Huntington's disease (HD) is a currently incurable neurogenerative disorder and is typically characterized by progressive movement disorder (including chorea), cognitive deficits (culminating in dementia), psychiatric abnormalities (the most common of which is depression), and peripheral symptoms (including gastrointestinal dysfunction). There are currently no approved disease-modifying therapies available for HD, with death usually occurring approximately 10-25 years after onset, but some therapies hold promising potential. HD subjects are often burdened by chronic diarrhea, constipation, esophageal and gastric inflammation, and a susceptibility to diabetes. Our understanding of the microbiota-gut-brain axis in HD is in its infancy and growing evidence from preclinical and clinical studies suggests a role of gut microbial population imbalance (gut dysbiosis) in HD pathophysiology. The gut and the brain can communicate through the enteric nervous system, immune system, vagus nerve, and microbiota-derived-metabolites including short-chain fatty acids, bile acids, and branched-chain amino acids. This review summarizes supporting evidence demonstrating the alterations in bacterial and fungal composition that may be associated with HD. We focus on mechanisms through which gut dysbiosis may compromise brain and gut health, thus triggering neuroinflammatory responses, and further highlight outcomes of attempts to modulate the gut microbiota as promising therapeutic strategies for HD. Ultimately, we discuss the dearth of data and the need for more longitudinal and translational studies in this nascent field. We suggest future directions to improve our understanding of the association between gut microbes and the pathogenesis of HD, and other 'brain and body disorders'.

Microbial characterization of raw biomasses of Alaria esculenta, Chlorella vulgaris, Lemna minor

This study aimed to identify the types of microorganisms present in Alaria esculenta, Chlorella vulgaris, and Lemna minor as well as to characterize the microbial communities in their raw biomasses. The different raw biomass samples were assigned to a total of 35 and 32 classes, respectively, representing different bacterial and fungal phyla. The most common bacterial genera in all raw biomasses were Acinetobacter (11.68%) and Sphingobacterium (5.72%). Cyanobacteria was found to be the most abundant phylum (59.66%) in Chlorella vulgaris, followed by Lemna minor (type 2) (42.08%), Lemna minor (type 1) (35.97%), and Alaria esculenta (type 1) (26.07%). The most prevalent fungal genera in all raw biomasses were Mycosphaerella (31.64%), Cladosporium (5.08%) and Alternaria (3.63%), while Ascomycota was the most abundant phylum (89.04%) in Lemna minor (type 2), followed by Alaria esculenta (type 1) (80.0%), Lemna minor (type 1) (78.84%) and Chlorella vulgaris (67.14%). In addition, a taxonomic comparison was carried out to assess the variations in the microbiota across all samples. Chl. vulgaris and L. minor (type 2) exhibit a high prokaryotic and fungal composition according to the analyses in comparison to the others. Seven and six genera (>1%) dominated the bacterial and fungal communities, respectively, in all the samples according to the next generation sequencing (NGS) analysis. The development of effective measures to ensure the quality and safety of these aquaculture plants for consumption, as well as the improvement of their cultivation, processing, and storage will be greatly aided by these findings.

Highlighting the Microbial Community of Kuflu Cheese, an Artisanal Turkish Mold-Ripened Variety, by High-Throughput Sequencing.

Kuflu cheese, a popular variety of traditional Turkish mold-ripened cheeses, is characterized by its semi-hard texture and blue-green color. It is important to elucidate the microbiota of Kuflu cheese produced from raw milk to standardize and sustain its sensory properties. This study aimed to examine the bacteria, yeasts, and filamentous mold communities in Kuflu cheese using high-throughput amplicon sequencing based on 16S and ITS2 regions. Lactococcus, Streptococcus, and Staphylococcus were the most dominant bacterial genera while Bifidobacterium genus was found to be remarkably high in some Kuflu cheese samples. Penicillium genus dominated the filamentous mold biota while the yeasts with the highest relative abundances were detected as Debaryomyces, Pichia, and Candida. The genera Virgibacillus and Paraliobacillus, which were not previously reported for mold-ripened cheeses, were detected at high relative abundances in some Kuflu cheese samples. None of the genera that include important food pathogens like Salmonella, Campylobacter, Listeria were detected in the samples. This is the first experiment in which the microbiota of Kuflu cheeses were evaluated with a metagenomic approach. This study provided an opportunity to evaluate Kuflu cheese, which was previously examined for fungal composition, in terms of both pathogenic and beneficial bacteria.