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  • Microbiota
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  • 1
    Language: English
    In: PLoS One, CA: Public Library of Science
    Description: This article explores the interrelationship between the urinary microbiota and host antimicrobial peptides as mechanisms for urinary tract infection risk.
    Keywords: Resident Bacterial Communities ; Host Antimicrobial Peptides ; Urinary Tract Infection
    ISSN: 19326203
    E-ISSN: 19326203
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  • 2
    Language: English
    In: PLoS One, San Francisco: Public Library of Science
    Description: Article discussing the bacterial composition of subgingival plaque among diabetic and non-diabetic subjects to determine the effect that diabetes mellitus has on dental health.
    Keywords: Periodontiitis ; Bacteria ; Diabetes ; Pyrosequencing
    ISSN: 19326203
    E-ISSN: 19326203
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  • 3
    Language: English
    In: PLoS One, San Francisco: Public Library of Science
    Description: Article discussing a study that was conducted to understand the basis of a bacterial infection that is common among dairy cows.
    Keywords: Dairy ; Cows ; Pyrosequencing ; Amplicons ; Bacteria ; Microbiology
    ISSN: 19326203
    E-ISSN: 19326203
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  • 4
    In: PLoS ONE, 2017, Vol.12(8)
    Description: Several ecological hypotheses ( e . g ., specific plaque, non-specific plaque and keystone pathogen) regarding the etiology of periodontitis have been proposed since the 1990s, most of which have been centered on the concept of dysbiosis associated with periodontitis. Nevertheless, none of the existing hypotheses have presented mechanistic interpretations on how and why dysbiosis actually occurs. Hubbell’s neutral theory of biodiversity offers a powerful null model to test hypothesis regarding the mechanism of community assembly and diversity maintenance from the metagenomic sequencing data, which can help to understand the forces that shape the community dynamics such as dysbiosis. Here we reanalyze the dataset from Abusleme et al .’s comparative study of the oral microbial communities from periodontitis patients and healthy individuals. Our study demonstrates that 14 out of 61 communities (23%) passed the neutrality test, a percentage significantly higher than the previous reported neutrality rate of 1% in human microbiome (Li & Ma 2016, Scientific Reports ). This suggests that, while the niche selection may play a predominant role in the assembly and diversity maintenance in oral microbiome, the effect of neutral dynamics may not be ignored. However, no statistically significant differences in the neutrality passing rates were detected between the periodontitis and healthy treatments with Fisher’s exact probability test and multiple testing corrections, suggesting that the mechanism of community assembly is robust against disturbances such as periodontitis. In addition, our study confirmed previous finding that periodontitis patients exhibited higher biodiversity. These findings suggest that while periodontitis may significantly change the community composition measured by diversity ( i . e ., the exhibition or ‘phenotype’ of community assembly), it does not seem to cause the ‘mutation’ of the ‘genotype” (mechanism) of community assembly. We argue that the ‘phenotypic’ changes explain the observed link (not necessarily causal) between periodontitis and community dysbiosis, which is certainly worthy of further investigation.
    Keywords: Research Article ; Medicine And Health Sciences ; Biology And Life Sciences ; Ecology And Environmental Sciences ; Biology And Life Sciences ; Ecology And Environmental Sciences ; Biology And Life Sciences ; Biology And Life Sciences ; Biology And Life Sciences ; Biology And Life Sciences ; Biology And Life Sciences ; Ecology And Environmental Sciences ; Biology And Life Sciences ; Biology And Life Sciences ; Biology And Life Sciences ; Biology And Life Sciences ; Ecology And Environmental Sciences ; Biology And Life Sciences ; Ecology And Environmental Sciences
    E-ISSN: 1932-6203
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  • 5
    Language: English
    In: PLOS ONE, 1/2/2018, Vol.13(1), p.e0190266
    Description: Synechococcus is an important photosynthetic picoplankton in the temperate to tropical oceans. As a photosynthetic bacterium, Synechococcus has an efficient mechanism to adapt to the changes in salinity and light intensity. The analysis of the distributions and functions of such microorganisms in the ever changing river mouth environment, where freshwater and seawater mix, should help better understand their roles in the ecosystem. Toward this objective, we have collected and sequenced the ocean microbiome in the river mouth of Kwangyang Bay, Korea, as a function of salinity and temperature. In conjunction with comparative genomics approaches using the sequenced genomes of a wide phylogeny of Synechococcus, the ocean microbiome was analyzed in terms of their composition and clade-specific functions. The results showed significant differences in the compositions of Synechococcus sampled in different seasons. The photosynthetic functions in such enhanced Synechococcus strains were also observed in the microbiomes in summer, which is significantly different from those in other seasons.
    Keywords: Sciences (General);
    ISSN: PLOS ONE
    E-ISSN: 1932-6203
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  • 6
    Language: English
    In: PLoS ONE, 2012, Vol.7(5), p.e36298
    Description: Lactobacillus- dominated vaginal microbiotas are associated with reproductive health and STI resistance in women, whereas altered microbiotas are associated with bacterial vaginosis (BV), STI risk and poor reproductive outcomes. Putative vaginal taxa have been observed in male first-catch urine, urethral swab and coronal sulcus (CS) specimens but the significance of these observations is unclear. We used 16 S rRNA sequencing to characterize the microbiota of the CS and urine collected from 18 adolescent men over three consecutive months. CS microbiotas of most participants were more stable than their urine microbiotas and the composition of CS microbiotas were strongly influenced by circumcision. BV-associated taxa, including Atopobium , Megasphaera , Mobiluncus , Prevotella and Gemella , were detected in CS specimens from sexually experienced and inexperienced participants. In contrast, urine primarily contained taxa that were not abundant in CS specimens. Lactobacilllus and Streptococcus were major urine taxa but their abundance was inversely correlated. In contrast, Sneathia , Mycoplasma and Ureaplasma were only found in urine from sexually active participants. Thus, the CS and urine support stable and distinct bacterial communities. Finally, our results suggest that the penis and the urethra can be colonized by a variety of BV-associated taxa and that some of these colonizations result from partnered sexual activity.
    Keywords: Research Article ; Biology ; Medicine ; Public Health And Epidemiology ; Infectious Diseases ; Microbiology ; Urology
    E-ISSN: 1932-6203
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  • 7
    In: Critical Care Medicine, 2017, Vol.45(6), pp.e543-e551
    Description: OBJECTIVES:: Characterization of urinary bacterial microbiome and antimicrobial peptides after burn injury to identify potential mechanisms leading to urinary tract infections and associated morbidities in burn patients. DESIGN:: Retrospective cohort study using human urine from control and burn subjects. SETTING:: University research laboratory. PATIENTS:: Burn patients. INTERVENTIONS:: None. MEASUREMENTS AND MAIN RESULTS:: Urine samples from catheterized burn patients were collected hourly for up to 40 hours. Control urine was collected from “healthy” volunteers. The urinary bacterial microbiome and antimicrobial peptide levels and activity were compared with patient outcomes. We observed a significant increase in urinary microbial diversity in burn patients versus controls, which positively correlated with a larger percent burn and with the development of urinary tract infection and sepsis postadmission, regardless of age or gender. Urinary psoriasin and β-defensin antimicrobial peptide levels were significantly reduced in burn patients at 1 and 40 hours postadmission. We observed a shift in antimicrobial peptide hydrophobicity and activity between control and burn patients when urinary fractions were tested against Escherichia coli and Enterococcus faecalis urinary tract infection isolates. Furthermore, the antimicrobial peptide activity in burn patients was more effective against E. coli than E. faecalis. Urinary tract infection–positive burn patients with altered urinary antimicrobial peptide activity developed either an E. faecalis or Pseudomonas aeruginosa urinary tract infection, suggesting a role for urinary antimicrobial peptides in susceptibility to select uropathogens. CONCLUSIONS:: Our data reveal potential links for urinary tract infection development and several morbidities in burn patients through alterations in the urinary microbiome and antimicrobial peptides. Overall, this study supports the concept that early assessment of urinary antimicrobial peptide responses and the bacterial microbiome may be used to predict susceptibility to urinary tract infections and sepsis in burn patients.
    Keywords: Medicine;
    ISSN: 0090-3493
    E-ISSN: 15300293
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  • 8
    Language: English
    In: mSphere, 01 December 2017, Vol.2(6), p.e00536-17
    Description: By incorporating prior information on disease prevalence, Bayes classifiers have the potential to estimate disease probability better than other common machine-learning methods. Thus, it is important to develop Bayes classifiers specifically tailored for microbiome data. Our method shows higher classification accuracy than the only existing Bayesian classifier and the popular random forest method, and thus provides an alternative option for using microbial compositions for disease diagnosis. ABSTRACT Dysbiosis of microbial communities is associated with various human diseases, raising the possibility of using microbial compositions as biomarkers for disease diagnosis. We have developed a Bayes classifier by modeling microbial compositions with Dirichlet-multinomial distributions, which are widely used to model multicategorical count data with extra variation. The parameters of the Dirichlet-multinomial distributions are estimated from training microbiome data sets based on maximum likelihood. The posterior probability of a microbiome sample belonging to a disease or healthy category is calculated based on Bayes’ theorem, using the likelihood values computed from the estimated Dirichlet-multinomial distribution, as well as a prior probability estimated from the training microbiome data set or previously published information on disease prevalence. When tested on real-world microbiome data sets, our method, called DMBC (for Dirichlet-multinomial Bayes classifier), shows better classification accuracy than the only existing Bayesian microbiome classifier based on a Dirichlet-multinomial mixture model and the popular random forest method. The advantage of DMBC is its built-in automatic feature selection, capable of identifying a subset of microbial taxa with the best classification accuracy between different classes of samples based on cross-validation. This unique ability enables DMBC to maintain and even improve its accuracy at modeling species-level taxa. The R package for DMBC is freely available at https://github.com/qunfengdong/DMBC . IMPORTANCE By incorporating prior information on disease prevalence, Bayes classifiers have the potential to estimate disease probability better than other common machine-learning methods. Thus, it is important to develop Bayes classifiers specifically tailored for microbiome data. Our method shows higher classification accuracy than the only existing Bayesian classifier and the popular random forest method, and thus provides an alternative option for using microbial compositions for disease diagnosis.
    Keywords: Biology
    E-ISSN: 2379-5042
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  • 9
    Language: English
    In: International urogynecology journal, December 2018, Vol.29(12), pp.1797-1805
    Description: Women have a 20% risk of developing a urinary tract infection (UTI) following urogynecologic surgery. This study assessed the association of postoperative UTI with bacteria in preoperative samples of catheterized urine. Immediately before surgery, vaginal swabs, perineal swabs, and catheterized urine samples were collected, and the V4 region of the 16S ribosomal RNA (rRNA) gene was sequenced. The cohort was dichotomized in two ways: (1) standard day-of-surgery urine culture result (positive/negative), and (2) occurrence of postoperative UTI (positive/negative). Characteristics of bladder, vaginal, and perineal microbiomes were assessed to identify factors associated with postoperative UTI. Eighty-seven percent of the 104 surgical patients with pelvic organ prolapse/urinary incontinence (POP/UI) were white; mean age was 57 years. The most common genus was Lactobacillus, with a mean relative abundance of 39.91% in catheterized urine, 53.88% in vaginal swabs, and 30.28% in perineal swabs. Two distinct clusters, based on dispersion of catheterized urine (i.e., bladder) microbiomes, had highly significant (p 〈 2.2-16) differences in age, microbes, and postoperative UTI risk. Postoperative UTI was most frequently associated with the bladder microbiome; microbes in adjacent pelvic floor niches also contributed to UTI risk. UTI risk was associated with depletion of Lactobacillus iners and enrichment of a diverse mixture of uropathogens. Postoperative UTI risk appears to be associated with preoperative bladder microbiome composition, where an abundance of L. iners appears to protect against postoperative UTI.
    Keywords: Postoperative Infection ; Surgical Infection ; Urinary Tract Infection ; Urobiome ; Gynecologic Surgical Procedures ; Microbiota ; Postoperative Complications -- Microbiology ; Urinary Tract Infections -- Microbiology
    ISSN: 09373462
    E-ISSN: 1433-3023
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  • 10
    Language: English
    In: American journal of respiratory and critical care medicine, 15 July 2016, Vol.194(2), pp.226-35
    Description: Previous work found the lung microbiome in healthy subjects infected with HIV was similar to that in uninfected subjects. We hypothesized the lung microbiome from subjects infected with HIV with more advanced disease would differ from that of an uninfected control population. To measure the lung microbiome in an HIV-infected population with advanced disease. 16s RNA gene sequencing was performed on acellular bronchoalveolar lavage (BAL) fluid from 30 subjects infected with HIV with advanced disease (baseline mean CD4 count, 262 cells/mm(3)) before and up to 3 years after starting highly active antiretroviral therapy (HAART) and compared with 22 uninfected control subjects. The lung microbiome in subjects infected with HIV with advanced disease demonstrated decreased alpha diversity (richness and diversity) and greater beta diversity compared with uninfected BAL. Differences improved with HAART, but still persisted up to 3 years after starting therapy. Population dispersion in the group infected with HIV was significantly greater than in the uninfected cohort and declined after treatment. There were differences in the relative abundance of some bacteria between the two groups at baseline and after 1 year of therapy. After 1 year on HAART, HIV BAL contained an increased abundance of Prevotella and Veillonella, bacteria previously associated with lung inflammation. The lung microbiome in subjects infected with HIV with advanced disease is altered compared with an uninfected population both in diversity and bacterial composition. Differences remain up to 3 years after starting HAART. We speculate an altered lung microbiome in HIV infection may contribute to chronic inflammation and lung complications seen in the HAART era.
    Keywords: HIV Infection ; Advanced Disease ; Lung Microbiome ; Microbial Diversity ; Microbiota ; HIV Infections -- Microbiology ; Lung -- Microbiology
    ISSN: 1073449X
    E-ISSN: 1535-4970
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