-
International Microbiology : the... May 2024Abies pindrow, commonly known as the West-Himalayan Fir, holds great ecological importance as a native tree species in the Himalayas. Beyond its value as a fuel and...
Abies pindrow, commonly known as the West-Himalayan Fir, holds great ecological importance as a native tree species in the Himalayas. Beyond its value as a fuel and timber source, it serves as a keystone species within the ecosystem. However, over recent years, extensive degradation and deforestation have afflicted A. pindrow forests. Utilizing ectomycorrhizal fungal symbionts of A. pindrow could prove pivotal in restoring these deteriorated forests. This study aimed to evaluate the diversity and composition of the ectomycorrhizal fungal community associated with A. pindrow. We employed ectomycorrhizal root tip morphotyping, sporocarp sampling, and Illumina MiSeq metabarcoding of the ITS region of fungal nrDNA. The ectomycorrhizal root tips were categorized into 10 morphotypes based on their morphological characteristics, exhibiting an average colonization rate of 74%. Sporocarp sampling revealed 22 species across 10 genera, with Russula being the most prevalent. The metabarcoding yielded 285,148 raw sequences, identifying 326 operational taxonomic units (OTUs) belonging to 193 genera, 114 families, 45 orders, 22 classes, and 6 divisions. Of these, 36 OTUs across 20 genera were ectomycorrhizal, constituting 63.1% of the fungal community. Notably, Tuber was the most abundant, representing 37.42% of the fungal population, followed by Russula at 21.06%. This study provides a comprehensive understanding of mycorrhizal symbionts of A. pindrow. The findings hold significant implications for utilizing dominant ectomycorrhizal fungi in reforestation endeavors aimed at restoring this important Himalayan conifer.
PubMed: 38717563
DOI: 10.1007/s10123-024-00522-w -
Frontiers in Cellular and Infection... 2024Although the existence of species in the respiratory tract is often considered commensal, it is crucial to recognize the significance of colonization in...
INTRODUCTION
Although the existence of species in the respiratory tract is often considered commensal, it is crucial to recognize the significance of colonization in immunocompromised or COVID-19 patients. The emergence of as an emerging pathogen further emphasizes the importance of monitoring yeast infection/colonization, particularly in COVID-19 patients.
METHODS
In this study, respiratory samples mainly from COVID-19 patients, primarily those suspected of having a fungal infection, were cultured on Sabouraud dextrose agar plates and the yeast colonies were identified using a two-step multiplex PCR method. The samples suspected of underwent specific nested PCR followed by sequence analysis.
RESULTS
A total of 199 respiratory samples were collected from 73 women and 126 men, ranging in age from 1.6 to 88 years. Among the patients, 141 had COVID-19, 32 had cancer, 5 were hospitalized in ICU, 2 had chronic obstructive pulmonary disease)COPD(, and others were patients with combination diseases. From these samples, a total of 334 yeast strains were identified. (n=132, 39.52%) was the most common species, followed by (n=67, 20%), (n=56, 16.76%), (n=18, 5.4%), (n=17, 5.08%), (n=10, 3%), (n=9, 2.6%), (n=7, 2.1%), (n=5, 1.5%), (n=3, 0.9%), (n=2, 0.6%), (n=1, 0.3%), (n=1, 0.3%), and spp. (n=1, 0.3%). was detected in a patient in ICU and two COVID-19 patients. While its presence was confirmed through sequence analysis, our extensive efforts to isolate were unsuccessful.
CONCLUSION
While colonization remains prevalent, our study found no evidence of lung infection. Since the role of colonization in airway secretions remains ambiguous due to limited research, further studies are imperative to shed light on this matter.
Topics: Humans; COVID-19; Aged; Middle Aged; Female; Male; Aged, 80 and over; Adult; Child, Preschool; Candidiasis; Child; Adolescent; Young Adult; SARS-CoV-2; Infant; Candida auris; Candida; Respiratory System; Multiplex Polymerase Chain Reaction
PubMed: 38707510
DOI: 10.3389/fcimb.2024.1295841 -
Scientific Reports May 2024The Himalayas provide unique opportunities for the extension of shrubs beyond the upper limit of the tree. However, little is known about the limitation of the biotic...
The Himalayas provide unique opportunities for the extension of shrubs beyond the upper limit of the tree. However, little is known about the limitation of the biotic factors belowground of shrub growth at these cruising altitudes. To fill this gap, the present study deals with the documentation of root-associated microbiota with their predicted functional profiles and interactions in the host Rhododendron campanulatum, a krummholz species. While processing 12 root samples of R. campanulatum from the sites using Omics we could identify 134 root-associated fungal species belonging to 104 genera, 74 families, 39 orders, 17 classes, and 5 phyla. The root-associated microbiota members of Ascomycota were unambiguously dominant followed by Basidiomycota. Using FUNGuild, we reported that symbiotroph and pathotroph as abundant trophic modes. Furthermore, FUNGuild revealed the dominant prevalence of the saptroptroph guild followed by plant pathogens and wood saprotrophs. Alpha diversity was significantly different at the sites. The heatmap dendrogram showed the correlation between various soil nutrients and some fungal species. The study paves the way for a more in-depth exploration of unidentified root fungal symbionts, their interactions and their probable functional roles, which may serve as an important factor for the growth and conservation of these high-altitude ericaceous plants.
Topics: Rhododendron; Plant Roots; High-Throughput Nucleotide Sequencing; Fungi; Mycobiome; Soil Microbiology; Symbiosis; Phylogeny
PubMed: 38704448
DOI: 10.1038/s41598-024-61120-4 -
EBioMedicine May 2024Coronary artery disease (CAD) is a prevalent cardiovascular condition, and numerous studies have linked gut bacterial imbalance to CAD. However, the relationship of gut...
BACKGROUND
Coronary artery disease (CAD) is a prevalent cardiovascular condition, and numerous studies have linked gut bacterial imbalance to CAD. However, the relationship of gut fungi, another essential component of the intestinal microbiota, with CAD remains poorly understood.
METHODS
In this cross-sectional study, we analyzed fecal samples from 132 participants, split into 31 healthy controls and 101 CAD patients, further categorized into stable CAD (38), unstable angina (41), and acute myocardial infarction (22) groups. We conducted internal transcribed spacer 1 (ITS1) and 16S sequencing to examine gut fungal and bacterial communities.
FINDINGS
Based on ITS1 analyses, Ascomycota and Basidiomycota were the dominant fungal phyla in all the groups. The α diversity of gut mycobiome remained unaltered among the control group and CAD subgroups; however, the structure and composition of the mycobiota differed significantly with the progression of CAD. The abundances of 15 taxa gradually changed with the occurrence and progression of the disease and were significantly correlated with major CAD risk factor indicators. The mycobiome changes were closely linked to gut microbiome dysbiosis in patients with CAD. Furthermore, disease classifiers based on gut fungi effectively identified subgroups with different degrees of CAD. Finally, the FUNGuild analysis further categorized these fungi into distinct ecological guilds.
INTERPRETATION
In conclusion, the structure and composition of the gut fungal community differed from healthy controls to various subtypes of CAD, revealing key fungi taxa alterations linked to the onset and progression of CAD. Our study highlights the potential role of gut fungi in CAD and may facilitate the development of novel biomarkers and therapeutic targets for CAD.
FUNDING
This work was supported by the grants from the National Natural Science Foundation of China (No. 82170302, 92168117, 82370432), National clinical key specialty construction project- Cardiovascular Surgery, the Reform and Development Program of Beijing Institute of Respiratory Medicine (No. Ggyfz202417, Ggyfz202308), the Beijing Natural Science Foundation (No. 7222068); and the Clinical Research Incubation Program of Beijing Chaoyang Hospital Affiliated to Capital Medical University (No. CYFH202209).
Topics: Humans; Gastrointestinal Microbiome; Coronary Artery Disease; Male; Female; Middle Aged; Mycobiome; Aged; Cross-Sectional Studies; Feces; Metagenomics; Fungi; Severity of Illness Index; Dysbiosis; Case-Control Studies; RNA, Ribosomal, 16S; Adult
PubMed: 38703606
DOI: 10.1016/j.ebiom.2024.105137 -
Microbial Ecology May 2024Despite the importance of wood-inhabiting fungi on nutrient cycling and ecosystem functions, their ecology, especially related to their community assembly, is still...
Despite the importance of wood-inhabiting fungi on nutrient cycling and ecosystem functions, their ecology, especially related to their community assembly, is still highly unexplored. In this study, we analyzed the wood-inhabiting fungal richness, community composition, and phylogenetics using PacBio sequencing. Opposite to what has been expected that deterministic processes especially environmental filtering through wood-physicochemical properties controls the community assembly of wood-inhabiting fungal communities, here we showed that both deterministic and stochastic processes can highly contribute to the community assembly processes of wood-inhabiting fungi in this tropical forest. We demonstrated that the dynamics of stochastic and deterministic processes varied with wood decomposition stages. The initial stage was mainly governed by a deterministic process (homogenous selection), whereas the early and later decomposition stages were governed by the stochastic processes (ecological drift). Deterministic processes were highly contributed by wood physicochemical properties (especially macronutrients and hemicellulose) rather than soil physicochemical factors. We elucidated that fine-scale fungal-fungal interactions, especially the network topology, modularity, and keystone taxa of wood-inhabiting fungal communities, strongly differed in an initial and decomposing deadwood. This current study contributes to a better understanding of the ecological processes of wood-inhabiting fungi in tropical regions where the knowledge of wood-inhabiting fungi is highly limited.
Topics: Mycobiome; Wood; Fungi; Forests; Tropical Climate; Phylogeny; High-Throughput Nucleotide Sequencing; Biodiversity
PubMed: 38700528
DOI: 10.1007/s00248-024-02372-5 -
Mycorrhiza Jun 2024In European forests, most tree species form symbioses with ectomycorrhizal (EM) and arbuscular mycorrhizal (AM) fungi. The EM fungi are classified into different...
In European forests, most tree species form symbioses with ectomycorrhizal (EM) and arbuscular mycorrhizal (AM) fungi. The EM fungi are classified into different morphological types based on the development and structure of their extraradical mycelium. These structures could be root extensions that help trees to acquire nutrients. However, the relationship between these morphological traits and functions involved in soil nutrient foraging is still under debate.We described the composition of mycorrhizal fungal communities under 23 tree species in a wide range of climates and humus forms in Europe and investigated the exploratory types of EM fungi. We assessed the response of this tree extended phenotype to humus forms, as an indicator of the functioning and quality of forest soils. We found a significant relationship between the relative proportion of the two broad categories of EM exploration types (short- or long-distance) and the humus form, showing a greater proportion of long-distance types in the least dynamic soils. As past land-use and host tree species are significant factors structuring fungal communities, we showed this relationship was modulated by host trait (gymnosperms versus angiosperms), soil depth and past land use (farmland or forest).We propose that this potential functional trait of EM fungi be used in future studies to improve predictive models of forest soil functioning and tree adaptation to environmental nutrient conditions.
Topics: Mycorrhizae; Forests; Symbiosis; Trees; Soil Microbiology; Soil; Europe; Mycobiome
PubMed: 38700516
DOI: 10.1007/s00572-024-01146-8 -
Future Microbiology May 2024Endogenous ethanol production emerges as a mechanism of nonalcoholic steatohepatitis, obesity, diabetes and auto-brewery syndrome. To identify ethanol-producing... (Review)
Review
Endogenous ethanol production emerges as a mechanism of nonalcoholic steatohepatitis, obesity, diabetes and auto-brewery syndrome. To identify ethanol-producing microbes in humans, we used the NCBI taxonomy browser and the PubMed database with an automatic query and manual verification. 85 ethanol-producing microbes in human were identified. , and were the most represented fungi. Enterobacteriaceae was the most represented bacterial family with mainly and . Species of the Lachnospiraceae and Clostridiaceae family, of the Lactobacillales order and of the genus were also identified. This catalog will help the study of ethanol-producing microbes in human in the pathophysiology, diagnosis, prevention and management of human diseases associated with endogenous ethanol production.
PubMed: 38700288
DOI: 10.2217/fmb-2023-0250 -
One Health (Amsterdam, Netherlands) Jun 2024Today, over 300 million individuals worldwide are afflicted by severe fungal infections, many of whom will perish. Fungi, as a result of their plastic genomes have the... (Review)
Review
Today, over 300 million individuals worldwide are afflicted by severe fungal infections, many of whom will perish. Fungi, as a result of their plastic genomes have the ability to adapt to new environments and extreme conditions as a consequence of globalization, including urbanization, agricultural intensification, and, notably, climate change. Soils and the impact of these anthropogenic environmental factors can be the source of pathogenic and non-pathogenic fungi and subsequent fungal threats to public health. This underscores the growing understanding that not only is fungal diversity in the soil mycobiome a critical component of a functioning ecosystem, but also that soil microbial communities can significantly contribute to plant, animal, and human health, as underscored by the One Health concept. Collectively, this stresses the importance of investigating the soil microbiome in order to gain a deeper understanding of soil fungal ecology and its interplay with the rhizosphere microbiome, which carries significant implications for human health, animal health and environmental health.
PubMed: 38699438
DOI: 10.1016/j.onehlt.2024.100720 -
Applied Microbiology and Biotechnology Apr 2024The plant microbes are an integral part of the host and play fundamental roles in plant growth and health. There is evidence indicating that plants have the ability to...
The plant microbes are an integral part of the host and play fundamental roles in plant growth and health. There is evidence indicating that plants have the ability to attract beneficial microorganisms through their roots in order to defend against pathogens. However, the mechanisms of plant microbial community assembly from below- to aboveground compartments under pathogen infection remain unclear. In this study, we investigated the bacterial and fungal communities in bulk soil, rhizosphere soil, root, stem, and leaf of both healthy and infected (Potato virus Y disease, PVY) plants. The results indicated that bacterial and fungal communities showed different recruitment strategies in plant organs. The number and abundance of shared bacterial ASVs between bulk and rhizosphere soils decreased with ascending migration from below- to aboveground compartments, while the number and abundance of fungal ASVs showed no obvious changes. Field type, plant compartments, and PVY infection all affected the diversity and structures of microbial community, with stronger effects observed in the bacterial community than the fungal community. Furthermore, PVY infection, rhizosphere soil pH, and water content (WC) contributed more to the assembly of the bacterial community than the fungal community. The analysis of microbial networks revealed that the bacterial communities were more sensitive to PVY infection than the fungal communities, as evidenced by the lower network stability of the bacterial community, which was characterized by a higher proportion of positive edges. PVY infection further increased the bacterial network stability and decreased the fungal network stability. These findings advance our understanding of how microbes respond to pathogen infections and provide a rationale and theoretical basis for biocontrol technology in promoting sustainable agriculture. KEY POINTS: • Different recruitment strategies between plant bacterial and fungal communities. • Bacterial community was more sensitive to PVY infection than fungal community. • pH and WC drove the microbial community assembly under PVY infection.
Topics: Fungi; Soil Microbiology; Bacteria; Rhizosphere; Plant Diseases; Plant Roots; Microbiota; Plant Leaves; Hydrogen-Ion Concentration; Mycobiome; Plants
PubMed: 38689185
DOI: 10.1007/s00253-024-13150-1 -
Microbiology Spectrum Jun 2024Bacterial communities are often concomitantly present with numerous microorganisms in the human body and other natural environments. Amplicon-based microbiome studies...
UNLABELLED
Bacterial communities are often concomitantly present with numerous microorganisms in the human body and other natural environments. Amplicon-based microbiome studies have generally paid skewed attention, that too at a rather shallow genus level resolution, to the highly abundant bacteriome, with interest now forking toward the other microorganisms, particularly fungi. Given the generally sparse abundance of other microbes in the total microbiome, simultaneous sequencing of amplicons targeting multiple microbial kingdoms could be possible even with full multiplexing. Guiding studies are currently needed for performing and monitoring multi-kingdom-amplicon sequencing and data capture at scale. Aiming to address these gaps, amplification of full-length bacterial 16S rRNA gene and entire fungal internal-transcribed spacer (ITS) region was performed for human saliva samples ( = 96, including negative and positive controls). Combined amplicon DNA libraries were prepared for nanopore sequencing using a major fraction of 16S molecules and a minor fraction of ITS amplicons. Sequencing was performed in a single run of an R10.4.1 flow cell employing the latest V14 chemistry. An approach for real-time monitoring of the species saturation using dynamic rarefaction was designed as a guiding determinant of optimal run time. Real-time saturation monitoring for both bacterial and fungal species enabled the completion of sequencing within 30 hours, utilizing less than 60% of the total nanopores. Approximately 5 million high quality (HQ) taxonomically assigned reads were generated (~4.2 million bacterial and 0.7 million fungal), providing a wider (beyond bacteriome) snapshot of human oral microbiota at species-level resolution. Among the more than 400 bacterial and 240 fungal species identified in the studied samples, the species of (e.g., and ) and (e.g., and ) were observed to be the dominating microbes in the oral cavity, respectively. This conformed well with the previous reports of the human oral microbiota. EnsembleSeq provides a proof-of-concept toward the identification of both fungal and bacterial species simultaneously in a single fully multiplexed nanopore sequencing run in a time- and resource-effective manner. Details of this workflow, along with the associated codebase, are provided to enable large-scale application for a holistic species-level microbiome study.
IMPORTANCE
Human microbiome is a sum total of a variety of microbial genomes (including bacteria, fungi, protists, viruses, etc.) present in and on the human body. Yet, a majority of amplicon-based microbiome studies have largely remained skewed toward bacteriome as an assumed proxy of the total microbiome, primarily at a shallow genus level. Cost, time, effort, data quality/management, and importantly lack of guiding studies often limit progress in the direction of moving beyond bacteriome. Here, EnsembleSeq presents a proof-of-concept toward concomitantly capturing multiple-kingdoms of microorganisms (bacteriome and mycobiome) in a fully multiplexed (96-sample) single run of long-read amplicon sequencing. In addition, the workflow captures dynamic tracking of species-level saturation in a time- and resource-effective manner.
Topics: Humans; RNA, Ribosomal, 16S; Microbiota; Bacteria; Saliva; Fungi; Workflow; DNA, Bacterial; High-Throughput Nucleotide Sequencing; Sequence Analysis, DNA; DNA, Fungal
PubMed: 38687072
DOI: 10.1128/spectrum.04150-23