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Brazilian Journal of Microbiology :... May 2024Plant-fungus symbioses have functional relevance during plant growth and development. However, it is still unknown whether the endosphere fungi in mature plants...
Plant-fungus symbioses have functional relevance during plant growth and development. However, it is still unknown whether the endosphere fungi in mature plants originated from soils or seeds. To elucidate the origination of endosphere fungi in mature rice roots, the fungal communities in surface sterilized roots and shoots of mature rice plants germinated in soils, rhizosphere soils and seedlings germinated under sterile conditions were analyzed by Illumina-based sequencing and compared. Total 62 fungal OTUs shared in the seedlings, shoots and roots, 126 OTUs shared in the rhizosphere soils, shoots and roots. Fungal OTUs coexisted in the four types of samples belonged to genera of Rhizophagus, Trichoderma, Fusarium, Atractiella, Myrmecridium, Sporothrix, Microdochium, Massariosphaeria, and Phialemonium. The principle component analysis (PCA) and NMDS plot suggested that the fungal community structure in rhizosphere soils was different from that in seedlings significantly. Rhizosphere soil, shoot and root contained more similar fungal community. The fungal community in seedling was similar to that in shoot and root of mature plants. The results suggested that endophytic fungal communities in mature rice plants originated from both seedlings and rhizosphere soils, and more fungal taxa originated from rhizosphere soils. Mature rice plants contain mycobiome transmitted vertically from seeds, which suggests that inoculation of endophytic fungi isolated from seedlings might be an effective way to introduce beneficial fungal inoculants into rice plants successfully.
PubMed: 38802686
DOI: 10.1007/s42770-024-01384-0 -
Microorganisms May 2024Because data on the fungal gut community structure of African children are scarce, we aimed to describe it by reanalysing rRNA ITS1 and ITS2 metabarcoding data from a...
Because data on the fungal gut community structure of African children are scarce, we aimed to describe it by reanalysing rRNA ITS1 and ITS2 metabarcoding data from a study designed to assess the influence of microbiota in malaria susceptibility in Malian children from the Dogon country. More specifically, we aimed to establish the core gut mycobiome and compare the gut fungal community structure of breastfed children, aged 0-2 years, with other age groups. Briefly, DNA was extracted from 296 children's stool samples. Both rRNA ITS1 and ITS2 genomic barcodes were amplified and subjected to Illumina MiSeq sequencing. The ITS2 barcode generated 1,975,320 reads and 532 operational taxonomic units (OTUs), while the ITS1 barcode generated 647,816 reads and 532 OTUs. The alpha diversity was significantly higher by using the ITS1 compared to the ITS2 barcode ( < 0.05); but, regardless of the ITS barcode, we found no significant difference between breastfed children, aged 0-2 years, compared to the other age groups. The core gut mycobiome of the Malian children included , , , , and section , which were present in at least 50% of the 296 children. Further studies in other African countries are warranted to reach a global view of African children's core gut mycobiome.
PubMed: 38792756
DOI: 10.3390/microorganisms12050926 -
Microorganisms Apr 2024Multiple sclerosis (MS) arises from a complex interplay between host genetic factors and environmental components, with the gut microbiota emerging as a key area of...
Multiple sclerosis (MS) arises from a complex interplay between host genetic factors and environmental components, with the gut microbiota emerging as a key area of investigation. In the current study, we used ion torrent sequencing to delve into the bacteriome (bacterial microbiota) and mycobiome (fungal microbiota) of people with MS (pwMS), and compared them to healthy controls (HC). Through principal coordinate, diversity, and abundance analyses, as well as clustering and cross-kingdom microbial correlation assessments, we uncovered significant differences in the microbial profiles between pwMS and HC. Elevated levels of the fungus and the bacterial family were observed in pwMS, whereas beneficial bacterial taxa, such as and , were reduced. Notably, clustering analysis revealed overlapping patterns in the bacteriome and mycobiome data for 74% of the participants, with weakened cross-kingdom interactions evident in the altered microbiota of pwMS. Our findings highlight the dysbiosis of both bacterial and fungal microbiota in MS, characterized by shifts in biodiversity and composition. Furthermore, the distinct disease-associated pattern of fungi-bacteria interactions suggests that fungi, in addition to bacteria, contribute to the pathogenesis of MS. Overall, our study sheds light on the intricate microbial dynamics underlying MS, paving the way for further investigation into the potential therapeutic targeting of the gut microbiota in MS management.
PubMed: 38792701
DOI: 10.3390/microorganisms12050872 -
Journal of Fungi (Basel, Switzerland) May 2024Two ancient wooden vessels, specifically a monoxyle (1st century BCE to 1st century CE) and shipwreck (15th to 17th century CE), were excavated in a well-preserved state...
Two ancient wooden vessels, specifically a monoxyle (1st century BCE to 1st century CE) and shipwreck (15th to 17th century CE), were excavated in a well-preserved state east of the confluence of the old Mlava and the Danube rivers (Serbia). The vessels were found in the ground that used to be river sediment and were temporarily stored within the semi-underground exhibition space of Mammoth Park. As part of the pre-conservation investigations, the primary aim of the research presented was to characterize the culturable mycobiomes of two excavated wooden artifacts so that appropriate conservation procedures for alleviating post-excavation fungal infestation could be formulated. Utilizing culture-based methods, a total of 32 fungi from 15 genera were identified, mainly and to a lesser extent . Soft-rot of genus , followed by and species, were the most diverse of the isolated fungi. Out of a total of 38 isolates, screened on 7 biodegradation plate assays, 32 (84.21%) demonstrated at least one degradative property. had the highest deterioration potential, with a positive reaction in 5 separate plate assays. The obtained results further broaden the limited knowledge on the peculiarities of post-excavation soft-rot decay of archaeological wood and indicate the biochemical mechanisms at the root of post-excavation fungal deterioration.
PubMed: 38786698
DOI: 10.3390/jof10050343 -
Journal of Fungi (Basel, Switzerland) May 2024Nectarines can be affected by many diseases, resulting in significant production losses. Natural products, such as essential oils (EOs), are promising alternatives to...
Nectarines can be affected by many diseases, resulting in significant production losses. Natural products, such as essential oils (EOs), are promising alternatives to pesticides to control storage rots. This work aimed to test the efficacy of biofumigation with EOs in the control of nectarine postharvest diseases while also evaluating the effect on the quality parameters (firmness, total soluble solids, and titratable acidity) and on the fruit fungal microbiome. Basil, fennel, lemon, oregano, and thyme EOs were first tested at 0.1, 0.5, and 1.0% concentrations to evaluate their inhibition activity against . Subsequently, an screening trial was performed by treating nectarines inoculated with , with the five EOs at 2.0% concentration by biofumigation, performed using slow-release diffusers placed inside the storage cabinets. Fennel, lemon, and basil EOs were the most effective after storage and were selected to be tested in efficacy trials using naturally infected nectarines. After 28 days of storage, all treatments showed a significant rot reduction compared to the untreated control. Additionally, no evident phytotoxic effects were observed on the treated fruits. EO vapors did not affect the overall quality of the fruits but showed a positive effect in reducing firmness loss. Metabarcoding analysis showed a significant impact of tissue, treatment, and sampling time on the fruit microbiome composition. Treatments were able to reduce the abundance of spp., but basil EO favored a significant increase in spp. Moreover, the abundance of other fungal genera was found to be modified.
PubMed: 38786695
DOI: 10.3390/jof10050341 -
Journal of Fungi (Basel, Switzerland) May 2024Gut bacterial alterations have been previously linked to several non-communicable diseases in adults, while the association of mycobiome is not well understood in these...
Gut bacterial alterations have been previously linked to several non-communicable diseases in adults, while the association of mycobiome is not well understood in these diseases, especially in infants and children. Few studies have been conducted on the association between gut mycobiome and non-communicable diseases in children. We investigated gut mycobiome composition using 194 faecal samples collected at birth, 6 months after birth, and 18 months after birth in relation to atopic dermatitis (AD) and overweight diagnoses at the age of 18 or 36 months. The mycobiome exhibited distinct patterns, with prevalent in the meconium samples of both overweight and non-overweight groups. took precedence in overweight cases at 6 and 18 months, while dominated non-overweight samples at 6 months. emerged as a consistent high-abundance taxon across groups that had dermatitis and were overweight. We found a weak association between gut mycobiome and AD at birth and overweight at 18 months when using machine learning (ML) analyses. In ML, unidentified fungi, , and , were important for classifying AD, while , and were important for classifying overweight. Gut mycobiome might be associated with the development of AD and overweight in children.
PubMed: 38786688
DOI: 10.3390/jof10050333 -
Frontiers in Cellular and Infection... 2024Ulcerative colitis (UC) is a multifactorial chronic inflammatory bowel disease (IBD) that affects the large intestine with superficial mucosal inflammation. A dysbiotic...
BACKGROUND
Ulcerative colitis (UC) is a multifactorial chronic inflammatory bowel disease (IBD) that affects the large intestine with superficial mucosal inflammation. A dysbiotic gut microbial profile has been associated with UC. Our study aimed to characterize the UC gut bacterial, fungal, and metabolic fingerprints by omic approaches.
METHODS
The 16S rRNA- and ITS2-based metataxonomics and gas chromatography-mass spectrometry/solid phase microextraction (GC-MS/SPME) metabolomic analysis were performed on stool samples of 53 UC patients and 37 healthy subjects (CTRL). Univariate and multivariate approaches were applied to separated and integrated omic data, to define microbiota, mycobiota, and metabolic signatures in UC. The interaction between gut bacteria and fungi was investigated by network analysis.
RESULTS
In the UC cohort, we reported the increase of , , Enterobacteriaceae, TM7-3, , , , , , , Gemellaceae, and phenylethyl alcohol; and we also reported the decrease of ; Ruminococcaceae; ; ; ; ; ; ; ; ; ; hexadecane; cyclopentadecane; 5-hepten-2-ol, 6 methyl; 3-carene; caryophyllene; p-Cresol; 2-butenal; indole, 3-methyl-; 6-methyl-3,5-heptadiene-2-one; 5-octadecene; and 5-hepten-2-one, 6 methyl. The integration of the multi-omic data confirmed the presence of a distinctive bacterial, fungal, and metabolic fingerprint in UC gut microbiota. Moreover, the network analysis highlighted bacterial and fungal synergistic and/or divergent interkingdom interactions.
CONCLUSION
In this study, we identified intestinal bacterial, fungal, and metabolic UC-associated biomarkers. Furthermore, evidence on the relationships between bacterial and fungal ecosystems provides a comprehensive perspective on intestinal dysbiosis and ecological interactions between microorganisms in the framework of UC.
Topics: Humans; Colitis, Ulcerative; Gastrointestinal Microbiome; Male; Adult; Female; Bacteria; Middle Aged; Metabolomics; RNA, Ribosomal, 16S; Gas Chromatography-Mass Spectrometry; Feces; Fungi; Dysbiosis; Metabolome; Aged; Young Adult; Solid Phase Microextraction; Mycobiome; Multiomics
PubMed: 38779566
DOI: 10.3389/fcimb.2024.1366192 -
Cell Jun 2024The gut fungal community represents an essential element of human health, yet its functional and metabolic potential remains insufficiently elucidated, largely due to...
The gut fungal community represents an essential element of human health, yet its functional and metabolic potential remains insufficiently elucidated, largely due to the limited availability of reference genomes. To address this gap, we presented the cultivated gut fungi (CGF) catalog, encompassing 760 fungal genomes derived from the feces of healthy individuals. This catalog comprises 206 species spanning 48 families, including 69 species previously unidentified. We explored the functional and metabolic attributes of the CGF species and utilized this catalog to construct a phylogenetic representation of the gut mycobiome by analyzing over 11,000 fecal metagenomes from Chinese and non-Chinese populations. Moreover, we identified significant common disease-related variations in gut mycobiome composition and corroborated the associations between fungal signatures and inflammatory bowel disease (IBD) through animal experimentation. These resources and findings substantially enrich our understanding of the biological diversity and disease relevance of the human gut mycobiome.
Topics: Animals; Humans; Male; Mice; Feces; Fungi; Gastrointestinal Microbiome; Genome, Fungal; Genomics; Inflammatory Bowel Diseases; Metagenome; Mycobiome; Phylogeny; Female; Adult; Middle Aged
PubMed: 38776919
DOI: 10.1016/j.cell.2024.04.043 -
Applied and Environmental Microbiology Jun 2024Beech leaf disease (BLD) is a newly emerging disease in North America that affects American beech (). It is increasingly recognized that BLD is caused by a subspecies of...
UNLABELLED
Beech leaf disease (BLD) is a newly emerging disease in North America that affects American beech (). It is increasingly recognized that BLD is caused by a subspecies of the anguinid nematode subsp. (hereafter ) which is likely native to East Asia. How nematode infestation of leaves affects the leaf microbiome and whether changes in the microbiome could contribute to BLD symptoms remain uncertain. In this study, we examined bacterial and fungal communities associated with the leaves of across nine sites in Ohio and Pennsylvania that were either symptomatic or asymptomatic for BLD and used qPCR to measure relative nematode infestation levels. We found significantly higher levels of infestation at sites visibly symptomatic for BLD. Low levels of nematode infestation were also observed at asymptomatic sites, which suggests that nematodes can be present without visible symptoms evident. Bacterial and fungal communities were significantly affected by sampling site and symptomology, but only fungal communities were affected by nematode presence alone. We found many significant indicators of both bacteria and fungi related to symptoms of BLD, with taxa generally occurring in both asymptomatic and symptomatic leaves, suggesting that microbes are not responsible for BLD but could act as opportunistic pathogens. Of particular interest was the fungal genus which is common in the and is reported to overwinter in buds-a strategy consistent with . The specific role microbes play in opportunistic infection of leaves affected by will require additional study.
IMPORTANCE
Beech leaf disease (BLD) is an emerging threat to American beech () and has spread quickly throughout the northeastern United States and into southern Canada. This disease leads to disfigurement of leaves and is marked by characteristic dark, interveinal banding, followed by leaf curling and drop in more advanced stages. BLD tends to especially affect understory leaves, which can lead to substantial thinning of the forest understory where is a dominant tree species. Understanding the cause of BLD is necessary to employ management strategies that protect and the forests where it is a foundation tree species. Current research has confirmed that the foliar nematode subsp. is required for BLD, but whether other organisms are involved is currently unknown. Here, we present a study that investigated leaf-associated fungi and bacteria of to understand more about how microorganisms may contribute to BLD.
Topics: Fagus; Animals; Plant Leaves; Plant Diseases; Fungi; Bacteria; Mycobiome; Pennsylvania; Ohio; Microbiota; Nematoda
PubMed: 38775476
DOI: 10.1128/aem.00142-24 -
Frontiers in Microbiology 2024The cultivation of short-rotation tree species on non-forest land is increasing due to the growing demand for woody biomass for the future bioeconomy and to mitigate...
Soil mycobiomes in native European aspen forests and hybrid aspen plantations have a similar fungal richness but different compositions, mainly driven by edaphic and floristic factors.
BACKGROUND
The cultivation of short-rotation tree species on non-forest land is increasing due to the growing demand for woody biomass for the future bioeconomy and to mitigate climate change impacts. However, forest plantations are often seen as a trade-off between climate benefits and low biodiversity. The diversity and composition of soil fungal biota in plantations of hybrid aspen, one of the most planted tree species for short-rotation forestry in Northern Europe, are poorly studied.
METHODS
The goal of this study was to obtain baseline knowledge about the soil fungal biota and the edaphic, floristic and management factors that drive fungal richness and communities in 18-year-old hybrid aspen plantations on former agricultural soils and compare the fungal biota with those of European aspen stands on native forest land in a 130-year chronosequence. Sites were categorized as hybrid aspen (17-18-year-old plantations) and native aspen stands of three age classes (8-29, 30-55, and 65-131-year-old stands). High-throughput sequencing was applied to soil samples to investigate fungal diversity and assemblages.
RESULTS
Native aspen forests showed a higher ectomycorrhizal (EcM) fungal OTU richness than plantations, regardless of forest age. Short-distance type EcM genera dominated in both plantations and forests. The richness of saprotrophic fungi was similar between native forest and plantation sites and was highest in the middle-aged class (30-55-year-old stands) in the native aspen stands. The fungal communities of native forests and plantations were significantly different. Community composition varied more, and the natural forest sites were more diverse than the relatively homogeneous plantations. Soil pH was the best explanatory variable to describe soil fungal communities in hybrid aspen stands. Soil fungal community composition did not show any clear patterns between the age classes of native aspen stands.
CONCLUSION
We conclude that edaphic factors are more important in describing fungal communities in both native aspen forest sites and hybrid aspen plantation sites than forest thinning, age, or former land use for plantations. Although first-generation hybrid aspen plantations and native forests are similar in overall fungal diversity, their taxonomic and functional composition is strikingly different. Therefore, hybrid aspen plantations can be used to reduce felling pressure on native forests; however, our knowledge is still insufficient to conclude that plantations could replace native aspen forests from the soil biodiversity perspective.
PubMed: 38774505
DOI: 10.3389/fmicb.2024.1372938