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PLoS Pathogens Jul 2020
Review
Topics: Animals; Fungi; Humans; Lung; Mycobiome; Sequence Analysis, DNA
PubMed: 32730326
DOI: 10.1371/journal.ppat.1008684 -
Nature Reviews. Microbiology Jul 2016Fungi represent a large proportion of the genetic diversity on Earth and fungal activity influences the structure of plant and animal communities, as well as rates of... (Review)
Review
Fungi represent a large proportion of the genetic diversity on Earth and fungal activity influences the structure of plant and animal communities, as well as rates of ecosystem processes. Large-scale DNA-sequencing datasets are beginning to reveal the dimensions of fungal biodiversity, which seem to be fundamentally different to bacteria, plants and animals. In this Review, we describe the patterns of fungal biodiversity that have been revealed by molecular-based studies. Furthermore, we consider the evidence that supports the roles of different candidate drivers of fungal diversity at a range of spatial scales, as well as the role of dispersal limitation in maintaining regional endemism and influencing local community assembly. Finally, we discuss the ecological mechanisms that are likely to be responsible for the high heterogeneity that is observed in fungal communities at local scales.
Topics: Animals; Biodiversity; Ecosystem; Fungi; High-Throughput Nucleotide Sequencing; Microbial Consortia; Mycobiome; Phylogeography; Plants; Soil Microbiology
PubMed: 27296482
DOI: 10.1038/nrmicro.2016.59 -
Cell Reports. Medicine Feb 2023Unlike the bacterial microbiome, the role of early-life gut fungi in host metabolism and childhood obesity development remains poorly characterized. To address this, we...
Unlike the bacterial microbiome, the role of early-life gut fungi in host metabolism and childhood obesity development remains poorly characterized. To address this, we investigate the relationship between the gut mycobiome of 100 infants from the Canadian Healthy Infant Longitudinal Development (CHILD) Cohort Study and body mass index Z scores (BMIz) in the first 5 years of life. An increase in fungal richness during the first year of life is linked to parental and infant BMI. The relationship between richness pattern and early-life BMIz is modified by maternal BMI, maternal diet, infant antibiotic exposure, and bacterial beta diversity. Further, the abundances of Saccharomyces, Rhodotorula, and Malassezia are differentially associated with early-life BMIz. Using structural equation modeling, we determine that the mycobiome's contribution to BMIz is likely mediated by the bacterial microbiome. This demonstrates that mycobiome maturation and infant growth trajectories are distinctly linked, advocating for inclusion of fungi in larger pediatric microbiome studies.
Topics: Humans; Infant; Child; Body Mass Index; Mycobiome; Cohort Studies; Pediatric Obesity; Gastrointestinal Microbiome; Canada
PubMed: 36736319
DOI: 10.1016/j.xcrm.2023.100928 -
PloS One 2022The current study compared the gut mycobiomes of diabetic rats generated by a streptozotocin chemical challenge, diabetic rats with retinal changes and normal control...
The current study compared the gut mycobiomes of diabetic rats generated by a streptozotocin chemical challenge, diabetic rats with retinal changes and normal control rats over a period of 4 months. Sustained increase in blood sugar levels (>150 mg/dL) confirmed the induction of diabetes. Histology and immunohistochemistry were used to identify changes in the retinal tissues in the diabetic rats indicative of the animals progressing into diabetic retinopathy. Gut mycobiomes generated using faecal DNA, indicated dysbiosis at the genus level in both diabetic (DM) and diabetic rats with retinal changes (DRC) when compared with the control rats. In Tables 3-6 the specific genera that were significantly increased/decreased in DM1 and DM2 and in DRC1 and DRC2 respectively compared to the respective controls CT1-CT4 rats are listed. Further, the mycobiomes of the DM and DRC rats separated into distinct clusters following heat-map analysis of the discriminating genera. In addition, β-diversity analysis separated the mycobiomes of DM and DRC rats from that of the control rats, but the mycobiomes of diabetic rats and diabetic rats with retinal changes showed an overlap. Based on the inferred functions of the discriminating genera in the mycobiomes, we speculated that increase in pathogenic fungi might contribute to the inflammatory status both in diabetic rats and rats showing retinal changes.
Topics: Animals; Diabetes Mellitus, Experimental; Diabetic Retinopathy; Dysbiosis; Feces; Mycobiome; Rats
PubMed: 35439275
DOI: 10.1371/journal.pone.0267080 -
Frontiers in Immunology 2021The first 1000 days of life, including the intrauterine period, are regarded as a fundamental stepping stone for the development of a human. Unequivocally, nutrition... (Review)
Review
The first 1000 days of life, including the intrauterine period, are regarded as a fundamental stepping stone for the development of a human. Unequivocally, nutrition during this period plays a key role on the proper development of a child, both directly through the intake of essential nutrients and indirectly by affecting the composition of the gut microbiota. The gut microbiota, including bacteria, viruses, fungi, protists and other microorganisms, is a highly modifiable and adaptive system that is influenced by diet, lifestyle, medicinal products and the environment. Reversely, it affects the immune system in multiple complex ways. Many noncommunicable diseases (NCDs) associated with dysbiosis are "programmed" during childhood. Nutrition is a potent determinant of the children's microbiota composition and maturation and, therefore, a strong determinant of the NCDs' programming. In this review we explore the interplay between nutrition during the first 1000 days of life, the gut microbiota, virome and mycobiome composition and the development of NCDs.
Topics: Child; Child Nutritional Physiological Phenomena; Gastrointestinal Microbiome; Humans; Immune System; Mycobiome; Noncommunicable Diseases; Virome
PubMed: 33815397
DOI: 10.3389/fimmu.2021.644269 -
Chest Feb 2021
Topics: Adult; Female; Fungi; Humans; Male; Middle Aged; Mycobiome; Respiratory System; Singapore
PubMed: 32926873
DOI: 10.1016/j.chest.2020.09.072 -
American Journal of Veterinary Research Sep 2023To report the density, and constituents, of the mycobiome on the skin surface of normal dogs.
OBJECTIVE
To report the density, and constituents, of the mycobiome on the skin surface of normal dogs.
ANIMALS
20 normal dogs were recruited for this study, with informed consent in all cases.
METHODS
Flocked swabs were used to sample the skin surface and to sample the skin surface after superficial scraping with a blunted scapula. Both samples were taken within a brass guide with an internal area of 3.5 cm-2. Next-generation DNA sequencing was used to identify and quantify components of the mycobiome.
RESULTS
The median density of the mycobiome was 1.1 X 105 cm-2 (IQR, 27,561, 409,572). Cladosporium spp and Vishniacozyma victoriae were found on all 20 dogs.
CLINICAL RELEVANCE
Knowledge of the density and the composition of the cutaneous mycobiome will increase our understanding of skin biology and may have relevance to future therapeutic trials.
Topics: Dogs; Animals; Mycobiome; Skin; Fungi
PubMed: 37536686
DOI: 10.2460/ajvr.23.04.0071 -
The Journal of Surgical Research Nov 2021Microbiome research has expanded to consider contributions of microbial kingdoms beyond bacteria, including fungi (i.e., the mycobiome). However, optimal specimen...
BACKGROUND
Microbiome research has expanded to consider contributions of microbial kingdoms beyond bacteria, including fungi (i.e., the mycobiome). However, optimal specimen handling protocols are varied, including uncertainty of how enzymes utilized to facilitate fungal DNA recovery may interfere with bacterial microbiome sequencing from the same samples.
METHODS
With Institutional Animal Care and Use Committee approval, fecal samples were obtained from 20 rhesus macaques (10 males, 10 females; Macaca mulatta). DNA was extracted using commercially available kits, with or without lyticase enzyme treatment. 16S ribosomal RNA (bacterial) and Internal Transcribed Spacer (ITS; fungal) sequencing was performed on the Illumina MiSeq platform. Bioinformatics analysis was performed using Qiime and Calypso.
RESULTS
Inclusion of lyticase in the sample preparation pipeline significantly increased usable fungal ITS reads, community alpha diversity, and enhanced detection of numerous fungal genera that were otherwise poorly or not detected in primate fecal samples. Bacterial 16S ribosomal RNA amplicons obtained from library preparation were statistically unchanged by the presence of lyticase.
CONCLUSIONS
We demonstrate inclusion of the enzyme lyticase for fungal cell wall digestion markedly enhances mycobiota detection while maintaining fidelity of microbiome identification and community features in non-human primates. In restricted sample volumes, as are common in limited human samples, use of single sample DNA isolation will facilitate increased rigor and controlled approaches in future work.
Topics: Animals; Female; Glucan Endo-1,3-beta-D-Glucosidase; Macaca mulatta; Male; Microbiota; Multienzyme Complexes; Mycobiome; Peptide Hydrolases; RNA, Ribosomal, 16S
PubMed: 34186310
DOI: 10.1016/j.jss.2021.06.023 -
Frontiers in Immunology 2022Human gut microbiome has gained great attention for its proposed roles in the development of hypertension. The fungal microbiome in the human gut (i.e. the mycobiome) is...
OBJECTIVES
Human gut microbiome has gained great attention for its proposed roles in the development of hypertension. The fungal microbiome in the human gut (i.e. the mycobiome) is beginning to gain recognition as a fundamental part of our microbiome. However, the existing knowledge of human mycobiome has never revealed the association between gut mycobiome and hypertension. It is known that inflammation and immunity contribute to human hypertension. Here, we sought to investigate whether gut mycobiome could predict the development of hypertension and its association with immunoglobulin light chains.
METHODS AND MATERIALS
Participants were classified into three cohorts: prehypertension (pre-HTN), hypertension (HTN), and normal-tension (NT) based on their blood pressure. Fresh samples were collected, and the ITS transcribed spacer ribosomal RNA gene sequence was performed. An immunoturbidimetric test was used to examine the serum levels of immunological light chains.
RESULTS
Subjects in both of the states of pre-HTN and HTN had different fungal microbiome community compared to the NT group (FDR<0.05). Slightly higher levels of fungal richness and diversity were observed in the groups of pre-HTN and HTN. The relative abundance of increased in the HTN group compared to that in the NT group, and the relative abundance of enriched in the NT group. For the pre-HTN group, the relative abundance of was positively associated with serum the concentration of light chain (LC) κ (r=0.510, P=0.044); for the HTN group, the relative abundance of was positively associated with the serum concentration of LC κ (P<0.05), the relative abundance of was positively associated with both the serum concentrations of LC κ and LC λ (r>0.30, P<0.05).
CONCLUSIONS
Our present study demonstrated that gut fungal dysbiosis occurred in the state of prehypertension, and fungal dysbiosis can predict the dysregulation of serum light chains in hypertension patients. Further study on modulating gut fungal community should be focused on balancing the immunological features in hypertension.
Topics: Humans; Mycobiome; Immunoglobulin Light Chains; Prehypertension; Dysbiosis; Hypertension
PubMed: 36643913
DOI: 10.3389/fimmu.2022.1089295 -
Virulence Apr 2017
Topics: Fungi; Gastrointestinal Microbiome; Gastrointestinal Tract; Humans; Mycobiome
PubMed: 28102762
DOI: 10.1080/21505594.2017.1279780