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Virulence Apr 2017The fungi that reside in the human lungs represent an understudied, but medically relevant comm-unity. From the few studies published on the lung mycobiome, we find that... (Review)
Review
The fungi that reside in the human lungs represent an understudied, but medically relevant comm-unity. From the few studies published on the lung mycobiome, we find that there are fungi in both the healthy and diseased respiratory tract, that these fungi vary widely between individuals, and that there is a trend toward lower fungal diversity among individuals with disease. This review discusses the few studies of the lung mycobiome and details the challenges that accompany lung mycobiome studies. These challenges include sample collection and processing, sequence amplification and processing, and a history of multiple names for species. Some challenges may never be solved, but others can be solved with more data and additional studies of the lung mycobiome.
Topics: Fungi; High-Throughput Nucleotide Sequencing; Humans; Lung; Microbiota; Mycobiome
PubMed: 27687858
DOI: 10.1080/21505594.2016.1235671 -
Microbiology Spectrum Feb 2023The gut microbiota plays an essential role in the regulation of the immune system and the etiology of human autoimmune diseases. However, a holistic understanding of the...
The gut microbiota plays an essential role in the regulation of the immune system and the etiology of human autoimmune diseases. However, a holistic understanding of the gut bacteriome, mycobiome, and virome in patients with osteoarthritis (OA) remains lacking. Here, we explored the gut microbiotas of 44 OA patients and 46 healthy volunteers via deep whole-metagenome shotgun sequencing of their fecal samples. The gut bacteriome and mycobiome were analyzed using a reference-based strategy. Gut viruses were identified from the metagenomic assembled contigs, and the gut virome was profiled based on 6,567 nonredundant viral operational taxonomic units (vOTUs). We revealed that the gut microbiome (including bacteriome, mycobiome, and virome) of OA patients is fundamentally altered, characterized by a panel of 279 differentially abundant bacterial species, 10 fungal species, and 627 vOTUs. The representative OA-enriched bacteria included Anaerostipes hadrus (GENOME147149), sp900313215 (GENOME08259), Eubacterium_E hallii (GENOME000299), and A (GENOME001004), while Bacteroides plebeius A (GENOME239725), Roseburia inulinivorans (GENOME 001770), sp900343095 (GENOME075103), Phascolarctobacterium faecium (GENOME233517), and several members of and were depleted in OA patients. Fungi such as Debaryomyces fabryi (GenBank accession no. GCA_003708665), Candida parapsilosis (GCA_000182765), and Apophysomyces trapeziformis (GCA_000696975) were enriched in the OA gut microbiota, and Malassezia restricta (GCA_003290485), Aspergillus fumigatus (GCA_003069565), Mucor circinelloides (GCA_010203745) were depleted. The OA-depleted viruses spanned (95 vOTUs), (70 vOTUs), and (5 vOTUs), while 30 vOTUs were enriched in OA patients. Functional analysis of the gut bacteriome and virome also uncovered their functional signatures in relation to OA. Moreover, we demonstrated that the OA-associated gut bacterial and viral signatures are tightly interconnected, suggesting that they may impact disease together. Finally, we showed that the multikingdom signatures are effective in discriminating the OA patients from healthy controls, suggesting the potential of gut microbiota for the prediction of OA and related diseases. Our results delineated the fecal bacteriome, mycobiome, and virome landscapes of the OA microbiota and provided biomarkers that will aid in future mechanistic and clinical intervention studies. The gut microbiome of OA patients was completely altered compared to that in healthy individuals, including 279 differentially abundant bacterial species, 10 fungal species and 627 viral operational taxonomic units (vOTUs). Functional analysis of the gut bacteriome and virome also revealed their functional signatures in relation to OA. We found that OA-associated gut bacterial and viral signatures were tightly interconnected, indicating that they may affect the disease together. The OA patients can be discriminated effectively from healthy controls using the multikingdom signatures, suggesting the potential of gut microbiota for the prediction of OA and related diseases.
Topics: Humans; Mycobiome; Virome; Microbiota; Gastrointestinal Microbiome; Viruses; Bacteria
PubMed: 36515546
DOI: 10.1128/spectrum.01711-22 -
Virulence Apr 2017Skin constantly encounters external elements, including microbes. Culture-based studies have identified fungi present on human skin and have linked some species with... (Review)
Review
Skin constantly encounters external elements, including microbes. Culture-based studies have identified fungi present on human skin and have linked some species with certain skin diseases. Moreover, modern medical treatments, especially immunosuppressants, have increased the population at risk for cutaneous and invasive fungal infections, emphasizing the need to understand skin fungal communities in health and disease. A major hurdle for studying fungal flora at a community level has been the heterogeneous culture conditions required by skin fungi. Recent advances in DNA sequencing technologies have dramatically expanded our knowledge of the skin microbiome through culture-free methods. This review discusses historical and recent research on skin fungal communities - the mycobiome - in health and disease, and challenges associated with sequencing-based mycobiome research.
Topics: Fungi; Health; Humans; Microbiota; Mycobiome; Mycoses; Skin
PubMed: 27754756
DOI: 10.1080/21505594.2016.1249093 -
Gut Microbes 2023In recent years, it has become clear that gut microbiota plays a major role in the human body, both in health and disease. Because of that, the gut microbiome and its... (Review)
Review
In recent years, it has become clear that gut microbiota plays a major role in the human body, both in health and disease. Because of that, the gut microbiome and its impact on human well-being are getting wider and wider attention. Studies focused on the liver are not an exception. However, the majority of the analyses are concentrated on the bacterial part of the gut microbiota, while the fungi living in the human intestines are often omitted or underappreciated. This review is focused on the gut mycobiome as an important factor that should be taken into consideration regarding liver homeostasis and its perturbations. We have collected the findings in this field and we discuss their importance. We aim to emphasize the fungal compositional changes related to liver diseases and, by that, provide novel insights into the directions of liver research and gut microbiota as a therapeutic target for liver diseases.
Topics: Humans; Mycobiome; Gastrointestinal Microbiome; Liver Diseases
PubMed: 37184158
DOI: 10.1080/19490976.2023.2211922 -
Cancer Letters Aug 2023A variety of bacteria, viruses, fungi, protists, archaea and protozoa coexists within the mammalian gastrointestinal (GI) tract such as that fungi are detectable in all... (Review)
Review
A variety of bacteria, viruses, fungi, protists, archaea and protozoa coexists within the mammalian gastrointestinal (GI) tract such as that fungi are detectable in all intestinal and colon segments in almost all healthy adults. Although fungi can cause infectious diseases, they are also related to gut and systemic homeostasis. Importantly, through transformation of different forms such as from yeast to hyphae, interaction among gut microbiota such as fungal and bacterial interaction, host factors such as immune and host derived factors, and fungus genetic and epigenetic factors, fungi can be transformed from commensal into pathogenic lifestyles. Recent studies have shown that fungi play a significant role in the occurrence and development of tumors such as colorectal cancer. Indeed, evidences have shown that multiple species of different fungi exist in different tumors. Studies have also demonstrated that fungi are related to the occurrence and development of tumors, and also survival of patients. Here we summarize recent advances in the transformation of fungi from commensal into pathogenic lifestyles, and the effects of gut pathogenic fungi on the occurrence and development of tumors such as colorectal and pancreatic cancers.
Topics: Adult; Animals; Humans; Mycobiome; Fungi; Gastrointestinal Tract; Gastrointestinal Microbiome; Bacteria; Neoplasms; Mammals
PubMed: 37451425
DOI: 10.1016/j.canlet.2023.216302 -
Frontiers in Cellular and Infection... 2023infection (CDI) is common in patients with inflammatory bowel disease (IBD) and has been reported as a risk factor for poor outcome. However, gut microbiome and...
BACKGROUND
infection (CDI) is common in patients with inflammatory bowel disease (IBD) and has been reported as a risk factor for poor outcome. However, gut microbiome and mycobiome of IBD patients with CDI have been barely investigated. This study aimed to assess the gut microbiome and mycobiome in IBD patients with CDI.
METHODS
We collected fecal samples from patients with active IBD and concomitant CDI (IBD-CDI group, n=25), patients with active IBD and no CDI (IBD-only group, n=51), and healthy subjects (HC, n=40). Patients' characteristics including demographic data, disease severity, and medication history were collected. Metagenomic sequencing, taxonomic and functional analysis were carried out in the samples.
RESULTS
We found that the bacterial alpha diversity of the IBD-CDI group was decreased. The bacterial and fungal beta diversity variations between IBD patients and HC were significant, regardless of CDI status. But the IBD-CDI group did not significantly cluster separately from the IBD-only group. Several bacterial taxa, including , , and were overrepresented in the IBD-CDI group. Furthermore, IBD patients with CDI were distinguished by several fungal taxa, including overrepresentation of . We also identified functional differences in IBD patients with CDI include enrichment of peptidoglycan biosynthesis. The network analysis indicated specific interactions between microbial markers in IBD-CDI patients.
CONCLUSION
IBD patients with CDI had pronounced microbial dysbiosis. Gut micro-ecological changes in IBD patients with CDI might provide insight into the pathological process and potential strategies for diagnosis and treatment in this subset of patients.
Topics: Humans; Gastrointestinal Microbiome; Mycobiome; Clostridioides difficile; Inflammatory Bowel Diseases; Bacteria; Clostridium Infections
PubMed: 36814443
DOI: 10.3389/fcimb.2023.1129043 -
Gut Dec 2023The gastrointestinal ecosystem has received the most attention when examining the contributions of the human microbiome to health and disease. This concentration of... (Review)
Review
The gastrointestinal ecosystem has received the most attention when examining the contributions of the human microbiome to health and disease. This concentration of effort is logical due to the overwhelming abundance of microbes in the gut coupled with the relative ease of sampling compared with other organs. However, the intestines are intimately connected to multiple extraintestinal organs, providing an opportunity for homeostatic microbial colonisation and pathogenesis in organs traditionally thought to be sterile or only transiently harbouring microbiota. These habitats are challenging to sample, and their low microbial biomass among large amounts of host tissue can make study challenging. Nevertheless, recent findings have shown that many extraintestinal organs that are intimately linked to the gut harbour stable microbiomes, which are colonised from the gut in selective manners and have highlighted not just the influence of the bacteriome but that of the mycobiome and virome on oncogenesis and health.
Topics: Humans; Microbiota; Gastrointestinal Microbiome; Mycobiome; Virome; Neoplasms
PubMed: 37918889
DOI: 10.1136/gutjnl-2022-328834 -
Virulence Apr 2017Research on oral fungi has centered on Candida. However, recent internal transcribed spacer (ITS)-based studies revealed a vast number of fungal taxa as potential oral... (Review)
Review
Research on oral fungi has centered on Candida. However, recent internal transcribed spacer (ITS)-based studies revealed a vast number of fungal taxa as potential oral residents. We review DNA-based studies of the oral mycobiome and contrast them with cultivation-based surveys, showing that most genera encountered by cultivation have also been detected molecularly. Some taxa such as Malassezia, however, appear in high prevalence and abundance in molecular studies but have not been cultivated. Important technical and bioinformatic challenges to ITS-based oral mycobiome studies are discussed. These include optimization of sample lysis, variability in length of ITS amplicons, high intra-species ITS sequence variability, high inter-species variability in ITS copy number and challenges in nomenclature and maintenance of curated reference databases. Molecular surveys are powerful first steps to characterize the oral mycobiome but further research is needed to unravel which fungi detected by DNA are true oral residents and what role they play in oral homeostasis.
Topics: Fungi; Metagenomics; Microbiological Techniques; Microbiota; Mouth; Mycobiome
PubMed: 27791473
DOI: 10.1080/21505594.2016.1252015 -
International Journal of Molecular... Feb 2017The advent of sequencing technology has endowed us with the capacity to study microbes constituting the human commensal community that were previously non-culturable.... (Review)
Review
The advent of sequencing technology has endowed us with the capacity to study microbes constituting the human commensal community that were previously non-culturable. Much of the initial works have concentrated on the bacterial flora constituting the gut microbiome, since specimens are readily accessible in health and disease. Less, however, is understood of the "silent population"-the fungal species, also known as the mycobiome. Living in symbiosis with bacteria as commensals in our body, it is perceivable that the mycobiome exerts an inadvertent influence on the microbiome. We review here the recent knowledge gained from study of the interaction between the mycobiome and microbiome in health and disease susceptibility, immunity, and consequences from antimicrobial treatment.
Topics: Animals; Antibiosis; Bacteria; Diet; Disease Susceptibility; Fungi; Gastrointestinal Microbiome; Host-Pathogen Interactions; Humans; Immunity; Microbial Interactions; Mycobiome; Obesity
PubMed: 28165395
DOI: 10.3390/ijms18020330 -
BMC Microbiology Nov 2023The gut microbial composition has been linked to metabolic and autoimmune diseases, including arthritis. However, there is a dearth of knowledge on the gut bacteriome,...
OBJECTIVE
The gut microbial composition has been linked to metabolic and autoimmune diseases, including arthritis. However, there is a dearth of knowledge on the gut bacteriome, mycobiome, and virome in patients with gouty arthritis (GA).
METHODS
We conducted a comprehensive analysis of the multi-kingdom gut microbiome of 26 GA patients and 28 healthy controls, using whole-metagenome shotgun sequencing of their stool samples.
RESULTS
Profound alterations were observed in the gut bacteriome, mycobiome, and virome of GA patients. We identified 1,117 differentially abundant bacterial species, 23 fungal species, and 4,115 viral operational taxonomic units (vOTUs). GA-enriched bacteria included Escherichia coli_D GENOME144544, Bifidobacterium infantis GENOME095938, Blautia_A wexlerae GENOME096067, and Klebsiella pneumoniae GENOME147598, while control-enriched bacteria comprised Faecalibacterium prausnitzii_G GENOME147678, Agathobacter rectalis GENOME143712, and Bacteroides_A plebeius_A GENOME239725. GA-enriched fungi included opportunistic pathogens like Cryptococcus neoformans GCA_011057565, Candida parapsilosis GCA_000182765, and Malassezia spp., while control-enriched fungi featured several Hortaea werneckii subclades and Aspergillus fumigatus GCA_000002655. GA-enriched vOTUs mainly attributed to Siphoviridae, Myoviridae, Podoviridae, and Microviridae, whereas control-enriched vOTUs spanned 13 families, including Siphoviridae, Myoviridae, Podoviridae, Quimbyviridae, Phycodnaviridae, and crAss-like. A co-abundance network revealed intricate interactions among these multi-kingdom signatures, signifying their collective influence on the disease. Furthermore, these microbial signatures demonstrated the potential to effectively discriminate between patients and controls, highlighting their diagnostic utility.
CONCLUSIONS
This study yields crucial insights into the characteristics of the GA microbiota that may inform future mechanistic and therapeutic investigations.
Topics: Humans; Gastrointestinal Microbiome; Arthritis, Gouty; East Asian People; Microbiota; Mycobiome; Bacteria
PubMed: 38001408
DOI: 10.1186/s12866-023-03097-0