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Profiling bacterial community in upper respiratory tracts.

ABSTRACT: BACKGROUND:Infection by pathogenic viruses results in rapid epithelial damage and significantly impacts on the condition of the upper respiratory tract, thus the effects of viral infection may induce changes in microbiota. Thus, we aimed to define the healthy microbiota and the viral pathogen-affected microbiota in the upper respiratory tract. In addition, any association between the type of viral agent and the resultant microbiota profile was assessed. METHODS:We analyzed the upper respiratory tract bacterial content of 57 healthy asymptomatic people (17 health-care workers and 40 community people) and 59 patients acutely infected with influenza, parainfluenza, rhino, respiratory syncytial, corona, adeno, or metapneumo viruses using culture-independent pyrosequencing. RESULTS:The healthy subjects harbored primarily Streptococcus, whereas the patients showed an enrichment of Haemophilus or Moraxella. Quantifying the similarities between bacterial populations by using Fast UniFrac analysis indicated that bacterial profiles were apparently divisible into 6 oropharyngeal types in the tested subjects. The oropharyngeal types were not associated with the type of viruses, but were rather linked to the age of the subjects. Moraxella nonliquefaciens exhibited unprecedentedly high abundance in young subjects aged <6 years. The genome of M. nonliquefaciens was found to encode various proteins that may play roles in pathogenesis. CONCLUSIONS:This study identified 6 oropharyngeal microbiome types. No virus-specific bacterial profile was discovered, but comparative analysis of healthy adults and patients identified a bacterium specific to young patients, M. nonliquefaciens.

SUBMITTER: Yi H

PROVIDER: S-EPMC4236460 | biostudies-literature | 2014 Nov

REPOSITORIES: biostudies-literature

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Profiling bacterial community in upper respiratory tracts.

Yi Hana H Yong Dongeun D Lee Kyungwon K Cho Yong-Joon YJ Chun Jongsik J

BMC infectious diseases 20141113

<h4>Background</h4>Infection by pathogenic viruses results in rapid epithelial damage and significantly impacts on the condition of the upper respiratory tract, thus the effects of viral infection may induce changes in microbiota. Thus, we aimed to define the healthy microbiota and the viral pathogen-affected microbiota in the upper respiratory tract. In addition, any association between the type of viral agent and the resultant microbiota profile was assessed.<h4>Methods</h4>We analyzed the upp ...[more]

PMID: 25391813

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Project description:Microbial communities play critical roles in the gastrointestinal tracts (GIT) of preruminant calves by influencing performance and health. However, little is known about the establishment of microbial communities in the calf GIT or their dynamics during development. In this study, next-generation sequencing was used to assess changes in the bacterial communities of the rumen, jejunum, cecum, and colon in 26 crossbred calves at four developmental stages (7, 28, 49, and 63 days old). Alpha diversity differed among GIT regions with the lowest diversity and evenness in the jejunum, whereas no changes in alpha diversity were observed across developmental stage. Beta diversity analysis showed both region and age effects, with low numbers of operational taxonomic units (OTUs) shared between regions within a given age group or between ages in a given region. Taxonomic analysis revealed that several taxa coexisted in the rumen, jejunum, cecum, and colon but that their abundances differed considerably by GIT region and age. As calves aged, we observed lower abundances of taxa such as Bacteroides, Parabacteroides, and Paraprevotella with higher abundances of Bulleidia and Succiniclasticum in the rumen. The jejunum also displayed taxonomic changes with increases in Clostridiaceae and Turicibacter taxa in older calves. In the lower gut, taxa such as Lactobacillus, Blautia, and Faecalibacterium decreased and S24-7, Paraprevotella, and Prevotella increased as calves aged. These data support a model whereby early and successive colonization by bacteria occurs across the GIT of calves and provides insights into the temporal dynamics of the GIT microbiota of dairy calves during preweaning development.IMPORTANCE The gastrointestinal tracts (GIT) of ruminants, such as dairy cows, house complex microbial communities that contribute to their overall health and support their ability to produce milk. For example, the rumen microbiota converts feed into usable nutrients, while the jejunal microbiota provides access to protein. Thus, establishing a properly functioning GIT microbiota in dairy calves is critical to their productivity as adult cows. However, little is known about the establishment, maintenance, and dynamics of the calf GIT microbiota in early life. In this study, we evaluated the bacterial communities in the rumen, jejunum, cecum, and colon in dairy calves across preweaning development and show that they are highly variable early on in life before transitioning to a stable community. Understanding the dairy calf GIT microbiota has implications for ensuring proper health during early life and will aid in efforts to develop strategies for improving downstream production.

Project description:Background Respiratory tract infection (RTI) is a common disease among children of all ages that causes high hospitalization and mortality rates. Infection with more than one pathogen has been reported in RTI; however, the association of the pathogen spectrum in upper and lower respiratory tract infections remains unclear. Methods A prospective study was conducted during February to October 2016. Fifty-five nasopharyngeal swabs (NPS) and 30 bronchoalveolar lavage fluid (BALF) samples from 55 hospitalized children aged less than 14 years (mean age 40 months) and diagnosed with an RTI were collected. All samples were detected for 18 respiratory pathogens using the Filmarray assay, real-time PCR, or nested PCR methods. Detection results and clinical characteristics of all cases were analyzed using chi-square and t tests. Results Forty-one of 55 (74.5%) NPS obtained from children were positive for at least one pathogen by the Filmarray assay. Of these cases, 53.7% (22/41) were co-infected. The most commonly detected pathogen was rhinovirus (RV), followed by Mycoplasma pneumoniae (MP) and respiratory syncytial virus (RSV). Infection by both RV and MP was the most frequently observed pattern of co-infection. Similar results were observed using real-time PCR. The pathogens in the NPS from 76.6% of cases detected by Filmarray and 80.0% of cases by real-time PCR included all the pathogens detected in the BALF sample from the same individual. The Filmarray assay showed an 80% concordance rate with real-time PCR and had a turnaround time of less than 1.2 h. No significant differences were observed between the association of single-infection and co-infection with clinical characteristics, neither by Filmarray nor real-time PCR. Conclusion The spectrum of pathogens is mostly concordant in the upper and lower respiratory tract. Collecting NPS for detection can be a non-invasive and more convenient option compared with BALF. Although co-infection is common in children with an RTI, the clinical significance of co-infection remains unclear and warrants further analysis.

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Profiling bacterial community in upper respiratory tracts.

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Profiling bacterial community in upper respiratory tracts.

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