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Microbiome candida

Tonya L Ward, Maria Gloria Dominguez-Bello, Tim Heisel, Gabriel Al-Ghalith, Dan Knights, Cheryl A Gale
With the advent of next-generation sequencing and microbial community characterization, we are beginning to understand the key factors that shape early-life microbial colonization and associated health outcomes. Studies characterizing infant microbial colonization have focused mostly on bacteria in the microbiome and have largely neglected fungi (the mycobiome), despite their relevance to mucosal infections in healthy infants. In this pilot study, we characterized the skin, oral, and anal mycobiomes of infants over the first month of life ( n = 17) and the anal and vaginal mycobiomes of mothers ( n = 16) by internal transcribed spacer 2 (ITS2) amplicon sequencing...
May 2018: MSystems
Hong Wang, Xiao-Bin Ji, Bei Mao, Cheng-Wei Li, Hai-Wen Lu, Jin-Fu Xu
OBJECTIVES: Pseudomonas aeruginosa (P. aeruginosa) occupies an important niche in the pathogenic microbiome of bronchiectasis. The objective of this study is to evaluate the clinical characteristics and prognostic value of P. aeruginosa in Chinese adult patients with bronchiectasis. METHODS: This retrospective and follow-up study enrolled 1188 patients diagnosed with bronchiectasis at Shanghai Pulmonary Hospital between January 2011 and December 2012. The patients' clinical data including anthropometry, clinical symptoms, serum biomarkers, radiographic manifestations and lung function indices were reviewed...
March 14, 2018: BMJ Open
Jitendra Keshri, Yaira Chen, Riky Pinto, Yulia Kroupitski, Zwi G Weinberg, Shlomo Sela Saldinger
Microbial population dynamics associated with corn silage, with and without Lactobacillus plantarum treatment, was studied. Whole crop corn was ensiled using laboratory silos and sampled at different times, up to 3 months. The dominant bacteria, before ensiling, were Acinetobacter (38.5%) and Klebsiella (16.3%), while the dominant fungi were Meyerozyma (53.5%) and Candida (27.7%). During ensiling, the microbial population shifted considerably, and Lactobacillus (> 94%) and Candida (> 74%) became the most dominant microbial genera in both treated and untreated silages...
March 13, 2018: Applied Microbiology and Biotechnology
Lifeng Zhu, Qi Wu, Cao Deng, Mengjie Zhang, Chenglin Zhang, Hua Chen, Guoqing Lu, Fuwen Wei
Carnivorous members of the Carnivora reside at the apex of food chains and consume meat-only diets, rich in purine, fats and protein. Here, we aimed to identify potential adaptive evolutionary signatures compatible with high purine and fat metabolism based on analysis of host genomes and symbiotic gut microbial metagenomes. We found that the gut microbiomes of carnivorous Carnivora (e.g. Felidae, Canidae) clustered in the same clade, and other clades comprised omnivorous and herbivorous Carnivora (e.g. badgers, bears and pandas)...
March 12, 2018: Environmental Microbiology
Gilbert Gerard Ghislain Donders, G Bellen, Kateryna Ruban, Ben Van Bulck
BACKGROUND: Recurrent vulvovaginal infections are a frequent complaint in young women in need of contraception. However, the influence of the contraceptive method on the course of the disease is not well known. AIM: To investigate the influence of the levonorgestrel-releasing intrauterine-system (LNG-IUS) on the vaginal microflora. METHODS: Short-term (3 months) and long-term (1 to 5 years) changes of vaginal microbiota were compared with pre-insertion values in 252 women presenting for LNG-IUS insertion...
January 29, 2018: Journal of Medical Microbiology
Paul D Donovan, Gabriel Gonzalez, Desmond G Higgins, Geraldine Butler, Kimihito Ito
Metagenomics uses nucleic acid sequencing to characterize species diversity in different niches such as environmental biomes or the human microbiome. Most studies have used 16S rRNA amplicon sequencing to identify bacteria. However, the decreasing cost of sequencing has resulted in a gradual shift away from amplicon analyses and towards shotgun metagenomic sequencing. Shotgun metagenomic data can be used to identify a wide range of species, but have rarely been applied to fungal identification. Here, we develop a sequence classification pipeline, FindFungi, and use it to identify fungal sequences in public metagenome datasets...
2018: PloS One
Ibrahim Hamad, Rita Abou Abdallah, Isabelle Ravaux, Saadia Mokhtari, Hervé Tissot-Dupont, Caroline Michelle, Andreas Stein, Jean-Christophe Lagier, Didier Raoult, Fadi Bittar
Research on the relationship between changes in the gut microbiota and human disease, including AIDS, is a growing field. However, studies on the eukaryotic component of the intestinal microbiota have just begun and have not yet been conducted in HIV-infected patients. Moreover, eukaryotic community profiling is influenced by the use of different methodologies at each step of culture-independent techniques. Herein, initially, four DNA extraction protocols were compared to test the efficiency of each method in recovering eukaryotic DNA from fecal samples...
2018: PloS One
Dong Zhu, Xin-Li An, Qing-Lin Chen, Xiaoru Yang, Peter Christie, Xin Ke, Longhua Wu, Yong-Guan Zhu
Gut microbiota make an important contribution to host health but the effects of environmental pressures on the gut microbiota of soil fauna are largely uncharacterized. Here, we examine the effects of norfloxacin and oxytetracycline on the gut microbiome of the common soil collembolan Folsomia candida and concomitant changes in the incidence of antibiotic resistance genes (ARGs) in the gut and in growth of the collembolan. Exposure to 10 mg antibiotics kg-1 for two weeks significantly inhibited the growth of the collembolan with roughly a ten-fold decrease in 16S rRNA gene abundance...
January 29, 2018: Environmental Science & Technology
Linda Davidson, Mihai G Netea, Bart Jan Kullberg
Candida spp. are colonizing fungi of human skin and mucosae of the gastrointestinal and genitourinary tract, present in 30-50% of healthy individuals in a population at any given moment. The host defense mechanisms prevent this commensal fungus from invading and causing disease. Loss of skin or mucosal barrier function, microbiome imbalances, or defects of immune defense mechanisms can lead to an increased susceptibility to severe mucocutaneous or invasive candidiasis. A comprehensive understanding of the immune defense against Candida is essential for developing adjunctive immunotherapy...
January 9, 2018: Journal of Fungi (Basel, Switzerland)
Prem Krishnan Raghupathi, Jerneja Zupančič, Asker Daniel Brejnrod, Samuel Jacquiod, Kurt Houf, Mette Burmølle, Nina Gunde-Cimerman, Søren J Sørensen
Extreme habitats are not only limited to natural environments, but also apply to man-made systems, for instance household appliances such as dishwashers. Limiting factors, such as high temperatures, high and low pH, high NaCl concentrations, presence of detergents and shear force from water during washing cycles define the microbial survival in this extreme system. Fungal and bacterial diversity in biofilms isolated from rubber seals of 24 different household dishwashers were investigated using next generation sequencing...
January 12, 2018: Applied and Environmental Microbiology
Mikko T Nieminen, Mikko Salaspuro
The resident microbiome plays a key role in exposure of the upper gastrointestinal (GI) tract mucosa to acetaldehyde (ACH), a carcinogenic metabolite of ethanol. Poor oral health is a significant risk factor for oral and esophageal carcinogenesis and is characterized by a dysbiotic microbiome. Dysbiosis leads to increased growth of opportunistic pathogens (such as Candida yeasts) and may cause an up to 100% increase in the local ACH production, which is further modified by organ-specific expression and gene polymorphisms of ethanol-metabolizing and ACH-metabolizing enzymes...
January 5, 2018: Cancers
Abdrazak Amer, Sheila Galvin, Claire M Healy, Gary P Moran
Oral leukoplakia presents as a white patch on the oral mucosa and is recognized as having significant malignant potential. Although colonization of these patches with Candida albicans is common, little is known about the bacterial microbiota of these patches. In the current study we analyzed the microbiome of oral leukoplakia in 36 patients compared to healthy mucosal tissue from the same patients and healthy control subjects to determine if specific microbial enrichments could be identified early in the malignant process that could play a role in the progression of the disease...
2017: Frontiers in Microbiology
Mykhaylo Usyk, Christine P Zolnik, Hitesh Patel, Michael H Levi, Robert D Burk
Studies of the human microbiome frequently omit characterization of fungal communities (the mycobiome), which limits our ability to investigate how fungal communities influence human health. The internal transcribed spacer 1 (ITS1) region of the eukaryotic ribosomal cluster has features allowing for wide taxonomic coverage and has been recognized as a suitable barcode region for species-level identification of fungal organisms. We developed custom ITS1 primer sets using iterative alignment refinement. Primer performance was evaluated using in silico testing and experimental testing of fungal cultures and human samples...
November 2017: MSphere
Andrea K Nash, Thomas A Auchtung, Matthew C Wong, Daniel P Smith, Jonathan R Gesell, Matthew C Ross, Christopher J Stewart, Ginger A Metcalf, Donna M Muzny, Richard A Gibbs, Nadim J Ajami, Joseph F Petrosino
BACKGROUND: Most studies describing the human gut microbiome in healthy and diseased states have emphasized the bacterial component, but the fungal microbiome (i.e., the mycobiome) is beginning to gain recognition as a fundamental part of our microbiome. To date, human gut mycobiome studies have primarily been disease centric or in small cohorts of healthy individuals. To contribute to existing knowledge of the human mycobiome, we investigated the gut mycobiome of the Human Microbiome Project (HMP) cohort by sequencing the Internal Transcribed Spacer 2 (ITS2) region as well as the 18S rRNA gene...
November 25, 2017: Microbiome
Peter R Flanagan, Ning-Ning Liu, Darren J Fitzpatrick, Karsten Hokamp, Julia R Köhler, Gary P Moran
Target of rapamycin complex 1 (TORC1) is an essential regulator of metabolism in eukaryotic cells and in the fungal pathogen Candida albicans regulates morphogenesis and nitrogen acquisition. Gtr1 encodes a highly conserved GTPase that in Saccharomyces cerevisiae regulates nitrogen sensing and TORC1 activation. Here, we characterize the role of C. albicans GTR1 in TORC1 activation and compare it with the previously characterized GTPase Rhb1. A homozygous gtr1/gtr1 mutant exhibited impaired TORC1-mediated phosphorylation of ribosomal protein S6 and increased susceptibility to rapamycin...
November 2017: MSphere
M A O Lewis, D W Williams
Candida is a fungus (yeast) that is generally regarded as a normal and harmless member of the oral microbiome in humans. Should host defences against these commensals be compromised in any way then Candida can cause clinical signs and symptoms, which manifest as distinct forms of oral candidosis (candidiasis). Candida albicans is the most frequently isolated candidal species from the oral cavity, although a range of non-C. albicans Candida species are being increasingly encountered. The basic principle of the management of candidosis is to identify and eliminate any underlying host predisposing factor...
November 10, 2017: British Dental Journal
Jason Burch, Siavash Mashayekh, Dennis D Wykoff, Catherine Leimkuhler Grimes
The dimorphic yeast Candida albicans is the most common pathologic fungus found in humans. While this species is normally commensal, a morphological switch from budding yeast to filamentous hyphae allows the fungi to invade epithelial cells and cause infections. The phenotypic change is controlled by the adenylyl cyclase, Cyr1. Interestingly, this protein contains a leucine-rich repeat (LRR) domain, which is commonly found in innate immune receptors from plants and animals. A functional and pure LRR domain was obtained in high yields from E...
October 17, 2017: ACS Infectious Diseases
Kelley R Healey, Yoji Nagasaki, Matthew Zimmerman, Milena Kordalewska, Steven Park, Yanan Zhao, David S Perlin
Candida species are a part of the human microbiome and can cause systemic infection upon immune suppression. Candida glabrata infections are increasing and have greater rates of antifungal resistance than other species. Here, we present a C. glabrata gastrointestinal (GI) colonization model to explore whether colonized yeast exposed to caspofungin, an echinocandin antifungal, develop characteristic resistance mutations and, upon immunosuppression, breakthrough causing systemic infection. Daily therapeutic dosing (5 mg/kg of body weight) of caspofungin resulted in no reduction in fecal burdens, organ breakthrough rates similar to control groups, and resistance rates (0 to 10%) similar to those reported clinically...
December 2017: Antimicrobial Agents and Chemotherapy
Geethavani Babu, Balamuru Ganvelu Singaravelu, R Srikumar, Sreenivasalu V Reddy, Afraa Kokan
INTRODUCTION: The normal vaginal flora is highly complex, dominated by lactobacilli of doderlein that plays a vital role in maintaining the women's health and inhibits other pathogenic microorganisms. Fluctuation in local environment or exposure to any exogenous and endogenous sources changes the vaginal flora over a period of time. Disruption of the vaginal ecosystem changes the microflora of the healthy vagina, altering the pH and predisposing to lower reproductive tract infections...
August 2017: Journal of Clinical and Diagnostic Research: JCDR
Z Rafat, S J Hashemi, K Ahamdikia, R Daie Ghazvini, F Bazvandi
The skin is the body's largest organ that hosts heterogeneous inhabitants. Until now, the diversity of the cutaneous microbiome was mainly investigated for bacteria and there is a little information about the skin fungal flora. Also, among skin fungal flora, Candida is found as a main member whose distribution is affected by sex, age, climate. In this study, differences in Candida community structure associated with 9 different skin sites of 238 healthy people during 10 months from July to March 2016, are described...
December 2017: Journal de Mycologie Médicale
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