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Virulence Apr 2017Many species of fungi have been detected in the healthy human gut; however, nearly half of all taxa reported have only been found in one sample or one study. Fungi... (Review)
Review
Many species of fungi have been detected in the healthy human gut; however, nearly half of all taxa reported have only been found in one sample or one study. Fungi capable of growing in and colonizing the gut are limited to a small number of species, mostly Candida yeasts and yeasts in the family Dipodascaceae (Galactomyces, Geotrichum, Saprochaete). Malassezia and the filamentous fungus Cladosporium are potential colonizers; more work is needed to clarify their role. Other commonly-detected fungi come from the diet or environment but either cannot or do not colonize (Penicillium and Debaryomyces species, which are common on fermented foods but cannot grow at human body temperature), while still others have dietary or environmental sources (Saccharomyces cerevisiae, a fermentation agent and sometime probiotic; Aspergillus species, ubiquitous molds) yet are likely to impact gut ecology. The gut mycobiome appears less stable than the bacterial microbiome, and is likely subject to environmental factors.
Topics: Diet; Environmental Exposure; Fungi; Gastrointestinal Microbiome; Gastrointestinal Tract; Humans; Microbiota; Mycobiome
PubMed: 27736307
DOI: 10.1080/21505594.2016.1247140 -
Science (New York, N.Y.) Mar 2021Alterations of the mycobiota composition associated with Crohn's disease (CD) are challenging to link to defining elements of pathophysiology, such as poor injury...
Alterations of the mycobiota composition associated with Crohn's disease (CD) are challenging to link to defining elements of pathophysiology, such as poor injury repair. Using culture-dependent and -independent methods, we discovered that preferentially localized to and was abundant within incompletely healed intestinal wounds of mice and inflamed mucosal tissues of CD human subjects. cultures from injured mice and inflamed CD tissues impaired colonic healing when introduced into injured conventionally raised or gnotobiotic mice. We reisolated from injured areas of these mice, fulfilling Koch's postulates. Mechanistically, impaired mucosal healing through the myeloid cell-specific type 1 interferon-CCL5 axis. Taken together, we have identified a fungus that inhabits inflamed CD tissue and can lead to dysregulated mucosal healing.
Topics: Amphotericin B; Animals; Anti-Bacterial Agents; Antifungal Agents; Chemokine CCL5; Colon; Crohn Disease; Debaryomyces; Female; Gastrointestinal Microbiome; Germ-Free Life; Humans; Ileum; Inflammation; Interferon Type I; Intestinal Mucosa; Macrophages; Male; Mice; Mice, Inbred C57BL
PubMed: 33707263
DOI: 10.1126/science.abd0919 -
Microbiology Spectrum Dec 2022In recent decades, the incidence of infections has increased in immunocompromised patients. This multicenter study aimed to evaluate antifungal activities of 8...
In recent decades, the incidence of infections has increased in immunocompromised patients. This multicenter study aimed to evaluate antifungal activities of 8 antifungal agents against the species isolated from 10 university hospitals in Iran. During the period from Dec 2019 to Dec 2021, species were collected from clinical samples of patients. The isolates were identified by PCR restriction fragment length polymorphism and sequencing methods. The antifungal susceptibility tests of each isolate to eight antifungal agents were performed according to the microdilution CLSI M27, M59, and M60 standard methods. A total of 598 strains were isolated from clinical samples. The most commonly isolated species was C. albicans, followed by C. glabrata, C. parapsilosis, Debaryomyces hansenii (Candida famata), C. tropicalis, (Candida krusei), C. orthopsilosis, Meyerozyma guilliermondii (Candida guilliermondii), Kluyveromyces marxianus (Candida kefyr), and Clavispora lusitaniae (Candida lusitaniae). MIC values in all species were as follows: 0.25 μg/mL for caspofungin and voriconazole; 0.5 μg/mL for amphotericin B and isavuconazole; 2 μg/mL for itraconazole, luliconazole, and posaconazole; and 16 μg/mL for fluconazole. Although 30/285 C. albicans, 15/31 3/12 , 67/125 C. glabrata, 5/15 , 6/60 C. parapsilosis, and 5/23 C. tropicalis isolates were multiazole resistant with resistance to 2 to 4 azoles, pan-azole resistance was not observed. According to our data, Candida albicans and C. glabrata were the most frequent species isolated from clinical samples in Iran. Caspofungin and voriconazole, with lower MIC values, are the most effective than other antifungal agents for the treatment of infections in this region. species cause severe invasive infections of the heart, brain, eyes, bones, and other parts of the body. Knowledge of regional distributions of causative agents and their antifungal susceptibility patterns can help to monitor resistance to antifungal agents of various species and support local and national surveillance programs. In the present study, C. albicans and C. glabrata were the most frequently isolated species from clinical samples in Iran. Increasing rates of non- isolates from the Iranian population should be looked at as alarming due to various levels of intrinsic MIC values or resistance to various antifungal drugs. Caspofungin and voriconazole are recommended over fluconazole for the treatment of infections in the study region. However, amphotericin B and isavuconazole are also active against the most common species isolated from patients. Pan azole-resistant species were not observed in the present study.
Topics: Humans; Amphotericin B; Antifungal Agents; Azoles; Candida; Candida albicans; Candida glabrata; Candidiasis; Caspofungin; Drug Resistance, Fungal; Fluconazole; Iran; Microbial Sensitivity Tests; Tertiary Care Centers; Voriconazole
PubMed: 36445122
DOI: 10.1128/spectrum.02453-22 -
Gastroenterology Jan 2024The gut microbiota plays a significant role in the pathogenesis of both forms of inflammatory bowel disease (IBD), namely, Crohn's disease (CD) and ulcerative colitis... (Review)
Review
The gut microbiota plays a significant role in the pathogenesis of both forms of inflammatory bowel disease (IBD), namely, Crohn's disease (CD) and ulcerative colitis (UC). Although evidence suggests dysbiosis and loss of beneficial microbial species can exacerbate IBD, many new studies have identified microbes with pathogenic qualities, termed "pathobionts," within the intestines of patients with IBD. The concept of pathobionts initiating or driving the chronicity of IBD has largely focused on the putative aggravating role that adherent invasive Escherichia coli may play in CD. However, recent studies have identified additional bacterial and fungal pathobionts in patients with CD and UC. This review will highlight the characteristics of these pathobionts and their implications for IBD treatment. Beyond exploring the origins of pathobionts, we discuss those associated with specific clinical features and the potential mechanisms involved, such as creeping fat (Clostridium innocuum) and impaired wound healing (Debaryomyces hansenii) in patients with CD as well as the increased fecal proteolytic activity (Bacteroides vulgatus) seen as a biomarker for UC severity. Finally, we examine the potential impact of pathobionts on current IBD therapies, and several new approaches to target pathobionts currently in the early stages of development. Despite recognizing that pathobionts likely contribute to the pathogenesis of IBD, more work is needed to define their modes of action. Determining whether causal relationships exist between pathobionts and specific disease characteristics could pave the way for improved care for patients, particularly for those not responding to current IBD therapies.
Topics: Humans; Inflammatory Bowel Diseases; Colitis, Ulcerative; Crohn Disease; Intestines; Feces
PubMed: 37734419
DOI: 10.1053/j.gastro.2023.09.019 -
Animal : An International Journal of... Aug 2021This study was undertaken to determine the effect of a yeast (Candida famata) and a bacterium (Lactobacillus plantarum), administered alone or in combination in the...
The effect of Candida famata and Lactobacillus plantarum on the number of coliforms and the antibiotic resistance and virulence of Escherichia coli in the gut of broilers.
This study was undertaken to determine the effect of a yeast (Candida famata) and a bacterium (Lactobacillus plantarum), administered alone or in combination in the drinking water, on the population of yeast, Lactobacillus sp. and coliforms, and the prevalence of antimicrobial resistance (AMR) and virulence genes in Escherichia coli (E. coli) isolated from digesta samples taken throughout the life of broiler chickens. Male (Ross 308) day-old chicks (220) were used. C. famata (isolated from a chicken) and L. plantarum (isolated from a pig) were administered via the drinking water. Water was provided either untreated or with C. famata (CF; 10/ml), L. plantarum (LP; 10-10/ml), or a combination of CF and LP (10-10/ml) in water hoppers on 2 days each week for 35 days. Administering probiotics did not affect the growth performance in broiler chickens. No significant interactions were observed between main effects, and neither CF nor LP had any effect on the population size of Lactobacillus sp. or coliforms. The administration of C. famata increased the population density of yeasts in the small intestine at these ages. The population density of coliforms, Lactobacillus sp. and yeast decreased with age (P < 0.001). There was no significant effect of probiotics on the prevalence of phenotypic AMR and virulence genes in these studies. The prevalence of E. coli that was resistant to ampicillin and tetracycline, as well as carrying ≥3 virulence-associated genes, was greatest at the end of the starter phase (around 8 days old), before declining through the grower and finisher phases. There was only limited evidence that administering either CF or LP affected either the AMR or the virulence of E. coli in the bird. However, tetracycline resistance in E. coli was associated (P < 0.001, P < 0.01, P < 0.05, and P < 0.05) with the carriage of the iron uptake systems of E. coli D, iron-repressible protein, increased serum survival and temperature-sensitive haemagglutinin genes respectively, suggesting that the accumulation of iron and the genetic element conferring tetracycline resistance may be intertwined.
Topics: Animals; Anti-Bacterial Agents; Candida; Chickens; Drug Resistance, Microbial; Escherichia coli; Escherichia coli Infections; Lactobacillus plantarum; Male; Swine; Swine Diseases; Virulence
PubMed: 34311191
DOI: 10.1016/j.animal.2021.100310 -
Pathogens (Basel, Switzerland) Aug 2022Atypical spp. infections are rising, mostly due to the increasing numbers of immunocompromised patients. The most common spp. is still ; however, in the last decades,... (Review)
Review
Atypical spp. infections are rising, mostly due to the increasing numbers of immunocompromised patients. The most common spp. is still ; however, in the last decades, there has been an increase in non- species infections (e.g., , , and ). Furthermore, in the last 10 years, the reports on uncommon yeasts, such as , or , have also worryingly increased. This review summarizes the information, mostly related to the last decade, regarding the infections, diagnosis, treatment, and resistance of these uncommon species. In general, there has been an increase in the number of articles associated with the incidence of these species. Additionally, in several cases, there was a suggestive antifungal resistance, particularly with azoles, which is troublesome for therapeutic success.
PubMed: 36145394
DOI: 10.3390/pathogens11090963 -
AIMS Microbiology 2021Yeasts constitute an important part of cheeses, and especially the artisanal ones. The current study reviews the occurrence of yeasts in different cheese varieties and... (Review)
Review
Yeasts constitute an important part of cheeses, and especially the artisanal ones. The current study reviews the occurrence of yeasts in different cheese varieties and the role of yeasts in cheesemaking process. The use of molecular methods for identification and strain typing has extended the knowledge for yeast diversity in cheeses. For the study of the occurrence of yeasts in different cheese types, seven categories are used, that is: 1) hard, 2) semi-hard, 3) soft, which includes soft pasta-filata and whey cheeses, 4) white brined cheeses, 5) mould surface ripened, 6) bacterial surface ripened cheeses, and 7) blue cheeses. For some cheese types, yeasts are the main microbial group, at least for some part of their ripening process, while for some other types, yeasts are absent. Differences between industrially manufactured cheeses and artisanal cheeses have specified. Artisanal cheeses possess a diverse assortment of yeast species, mainly belonging to the genera , , , , , , , , , , , , , , , and . The role of the yeasts for selected cheeses from the seven cheese categories is discussed.
PubMed: 35071942
DOI: 10.3934/microbiol.2021027 -
Microorganisms Sep 2022The use of yeasts as starter cultures was boosted with the emergence of large-scale fermentations in the 20th century. Since then, has been the most common and widely... (Review)
Review
The use of yeasts as starter cultures was boosted with the emergence of large-scale fermentations in the 20th century. Since then, has been the most common and widely used microorganism in the food industry. However, species have also been used as an adjuvant in cheese production or as starters for coffee, cocoa, vegetable, meat, beer, and wine fermentations. A thorough screening of candidate is sometimes performed to obtain the best performing strains to enhance specific features. Some commonly selected species include (teleomorph ) (wine), (teleomorph ) (coffee), (teleomorph ) (cheese), and (teleomorph ) and (teleomorph ) (cocoa). These species are associated with the production of key metabolites (food aroma formation) and different enzymes. However, safety-associated selection criteria are often neglected. It is widely known that some species are opportunistic human pathogens, with important clinical relevance. Here, the physiology and metabolism of species are addressed, initially emphasizing their clinical aspects and potential pathogenicity. Then, species used in food fermentations and their functional roles are reported. We recommended that not be used as food cultures if safety assessments are not performed. Some safety features are highlighted to help researchers choose methods and selection criteria.
PubMed: 36144457
DOI: 10.3390/microorganisms10091855 -
Antimicrobial Agents and Chemotherapy Jun 2018A total of 46 clinical isolates of and were reidentified genetically, resulting in 27 and 12 strains. The majority of strains, but not strains, were isolated from...
A total of 46 clinical isolates of and were reidentified genetically, resulting in 27 and 12 strains. The majority of strains, but not strains, were isolated from blood cultures. was more sensitive to antifungals, hydrogen peroxide, and killing by murine macrophages than was The isolates were echinocandin susceptible but resistant to micafungin in a murine model of invasive candidiasis.
Topics: Aged; Aged, 80 and over; Animals; Antifungal Agents; Candida; Candidiasis; Echinocandins; Female; Humans; Hydrogen Peroxide; Male; Micafungin; Mice; Microbial Sensitivity Tests; Middle Aged
PubMed: 29581115
DOI: 10.1128/AAC.02528-17 -
Biotechnology Reports (Amsterdam,... Jun 2022Probiotics are vital and beneficial organisms which offers the health benefits to the host organisms. The fungal probiotic field is one of the developing fields... (Review)
Review
Probiotics are vital and beneficial organisms which offers the health benefits to the host organisms. The fungal probiotic field is one of the developing fields nowadays. Yeast has an enormous and diverse group of microorganisms that is attracting and expanding the attention from researchers and industries. , the only patented strain belonging to yeast genera for the human use, has been broadly evaluated for its probiotic effect. Yeasts belonging to the genera etc.., have attained more interest because of their beneficial and probable probiotic features. These yeast probiotics produce VOCs (Volatile organic compounds), mycocins and antimicrobials which shows the antagonistic effect against pathogenic fungi and bacteria. Additionally, those yeasts have been recorded as good plant growth promoting microorganisms. Yeast has an important role in environmental applications such as bioremediation and removal of metals like chromium, mercury, lead etc., from waste water. Probiotic yeasts with their promising antimicrobial, antioxidant, anticancer properties, cholesterol assimilation and immunomodulatory effects can also be utilized as biotherapeutics. In this review article we have made an attempt to address important yeast probiotic attributes.
PubMed: 35257004
DOI: 10.1016/j.btre.2022.e00716