scholarly journals Characterization of the vaginal DNA virome in health and dysbiosis: an opening study in patients with non-female factor infertility

2019 ◽  
Author(s):  
Rasmus R. Jakobsen ◽  
Thor Haahr ◽  
Peter Humaidan ◽  
Jørgen Skov Jensen ◽  
Witold Kot ◽  
...  
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Bacterial Community Structure ◽  
Bacterial Species ◽  
Gardnerella Vaginalis ◽  
Metagenomic Sequencing ◽  
Double Stranded Dna ◽  
Viral Community ◽  
Atopobium Vaginae

AbstractBackgroundBacterial vaginosis (BV) is characterised by a reduction in Lactobacillus spp. abundance and increased abundance of facultative anaerobes, like Gardnerella vaginalis. BV aetiology is not fully understood, but bacteriophages could play a pivotal role causing perturbation of the vaginal bacterial community. Here we investigate the vaginal viral community, including bacteriophages, and its association to the bacterial community and BV-status.MethodsVaginal samples from 48 patients undergoing IVF treatment for non-female factor infertility were subjected to metagenomic sequencing of purified virus-like particles. The vaginal viral community was characterized and correlated with BV-status, bacterial community structure and presence of key vaginal bacterial species.ResultsThe majority of identified vaginal viruses belonged to the class of double-stranded DNA bacteriophages, with eukaryotic viruses constituting 4% of total reads. Clear links between viral community composition and BV (q = 0.006, R = 0.26) as well as presence of L. crispatus (q = 0.001, R = 0.43), L. iners, Gardnerella vaginalis and Atopobium vaginae were found (q < 0.002, R > 0.15). Interestingly, also the eukaryotic viral community was correlated with BV-status (q = 0.018, R = 0.20).ConclusionsThe vaginal virome is clearly linked with bacterial community structure and BV-status.Clinical Trials RegistrationNCT02042352.

scholarly journals Characterization of the Vaginal DNA Virome in Health and Dysbiosis

Viruses ◽  
2020 ◽  
Vol 12 (10) ◽  
pp. 1143 ◽  
Author(s):  
Rasmus Riemer Jakobsen ◽  
Thor Haahr ◽  
Peter Humaidan ◽  
Jørgen Skov Jensen ◽  
Witold Piotr Kot ◽  
...  
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Bacterial Community Structure ◽  
Bacterial Species ◽  
Metagenomic Sequencing ◽  
Nugent Score ◽  
Double Stranded Dna ◽  
Viral Community ◽  
Atopobium Vaginae

Bacterial vaginosis (BV) is characterized by a reduction in Lactobacillus (L.) spp. abundance and increased abundance of facultative anaerobes, such as Gardnerella spp. BV aetiology is not fully understood; however, bacteriophages could play a pivotal role in the perturbation of the vaginal bacterial community. We investigated the vaginal viral community, including bacteriophages and the association to the bacterial community and BV-status. Vaginal samples from 48 patients undergoing IVF treatment for non-female factor infertility were subjected to metagenomic sequencing of purified virus-like particles. The vaginal viral community was characterized and correlated with the BV-status by Nugent score, bacterial community, structure, and the presence of key vaginal bacterial species. The majority of identified vaginal viruses belonged to the class of double-stranded DNA bacteriophages, with eukaryotic viruses constituting 4% of the total reads. Clear links between the viral community composition and BV (q = 0.006, R = 0.26) as well as the presence of L. crispatus (q = 0.001, R = 0.43), L. iners, Gardnerella spp., and Atopobium vaginae were found (q < 0.002, R > 0.15). The eukaryotic viral community also correlated with BV-status (q = 0.018, R = 0.20). In conclusion, the vaginal virome was clearly linked with bacterial community structure and BV-status.

Characterization of bacterial community structure dynamics in a rat burn wound model using 16S rRNA gene sequencing

2022 ◽  
Author(s):  
Chen Zheng-li ◽  
Peng Yu ◽  
Wu Guo-sheng ◽  
Hong Xu-Dong ◽  
Fan Hao ◽  
...  
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Bacterial Community Structure ◽  
Bacterial Species ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Sprague Dawley ◽  
Rrna Gene Sequencing

Abstract Burns destroy the skin barrier and alter the resident bacterial community, thereby facilitating bacterial infection. To treat a wound infection, it is necessary to understand the changes in the wound bacterial community structure. However, traditional bacterial cultures allow the identification of only readily growing or purposely cultured bacterial species and lack the capacity to detect changes in the bacterial community. In this study, 16S rRNA gene sequencing was used to detect alterations in the bacterial community structure in deep partial-thickness burn wounds on the back of Sprague-Dawley rats. These results were then compared with those obtained from the bacterial culture. Bacterial samples were collected prior to wounding and 1, 7, 14, and 21 days after wounding. The 16S rRNA gene sequence analysis showed that the number of resident bacterial species decreased after the burn. Both resident bacterial richness and diversity, which were significantly reduced after the burn, recovered following wound healing. The dominant resident strains also changed, but the inhibition of bacterial community structure was in a non-volatile equilibrium state, even in the early stage after healing. Furthermore, the correlation between wound and environmental bacteria increased with the occurrence of burns. Hence, the 16S rRNA gene sequence analysis reflected the bacterial condition of the wounds better than the bacterial culture. 16S rRNA sequencing in the Sprague-Dawley rat burn model can provide more information for the prevention and treatment of burn infections in clinical settings and promote further development in this field.

Characterization of Bacterial Community Structure in Rhizosphere Soil of Grain Legumes

2005 ◽  
Vol 49 (3) ◽  
pp. 407-415 ◽  
Author(s):  
S. Sharma ◽  
M.K. Aneja ◽  
J. Mayer ◽  
J.C. Munch ◽  
M. Schloter
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Bacterial Community Structure ◽  
Rhizosphere Soil ◽  
Grain Legumes

Assessment and characterization of the bacterial community structure in advanced activated sludge systems

2019 ◽  
Vol 282 ◽  
pp. 254-261 ◽  
Author(s):  
Paolo Cinà ◽  
Giovanni Bacci ◽  
Walter Arancio ◽  
Giuseppe Gallo ◽  
Renato Fani ◽  
...  
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Activated Sludge ◽  
Bacterial Community Structure ◽  
Activated Sludge Systems

Evaluation of water sampling methodologies for amplicon-based characterization of bacterial community structure

2015 ◽  
Vol 114 ◽  
pp. 43-50 ◽  
Author(s):  
Christopher Staley ◽  
Trevor J. Gould ◽  
Ping Wang ◽  
Jane Phillips ◽  
James B. Cotner ◽  
...  
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Bacterial Community Structure ◽  
Water Sampling

scholarly journals Long-Term Combined Effects of Crude Oil and Dispersant on Sediment Bacterial Community

2020 ◽  
Vol 9 (1) ◽  
pp. 259-263
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Crude Oil ◽  
Bacterial Community Structure ◽  
Oil Spills ◽  
Bacterial Species ◽  
Combined Effects ◽  
Set Up ◽  
Sediment Bacterial Community

To better understand long-term combined effects of crude oil and dispersant on bacterial community, sediments microcosms were set up in triplicates and treated with dispersant (Corexit 9500A), crude oil, and Corexit 9500A plus crude oil. After 60 days exposure, there was a significant change in the bacterial community structure in all treatments. The shift in the bacterial community structure in Corexit 9500A plus crude oil treatment was considerably different from those by either Corexit 9500A or crude oil. DNA sequence analysis showed that Hydrocarboniphaga effuse, Parvibaculum lavamentivorans,and Alicyclobacillus ferrooxydans were the major bacterial species in crude oil treatment. Pandoraea thiooxydans, Janthinobacterium sp. and Hyphomicrobium nitrativorans were the most dominant species in Corexit 9500A treatment. The species Janthinobacterium sp., Parvibaculum lavamentivorans, and Dyella sp. were enriched in Corexit 9500A plus crude oil treatment. The majority of the detected species were hydrocarbons degraders. The study showed that Corexit 9500A addition enhanced the biodegradation rate by increasing the diversity and richness of hydrocarbons degrading species. Corexit A9500 application should be considered during crude oil spills to evaluate environmental impacts.

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