scholarly journals Analysis of bacterial community structure in Saba-Narezushi (Narezushi of Mackerel) by 16S rRNA gene clone library

2011 ◽  
Vol 50 (4) ◽  
pp. 791-796 ◽  
Author(s):  
Hiroki Matsui ◽  
Rie Tsuchiya ◽  
Yuka Isobe ◽  
Miyo Narita
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Clone Library ◽  
Bacterial Community Structure ◽  
Gene Clone ◽  
Rrna Gene

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.

Insights into Bacterial Community Structure of a Commercial Copper Bioheapleaching Plant: Growth of Heterotrophic Bacteria in the System

2013 ◽  
Vol 825 ◽  
pp. 50-53 ◽  
Author(s):  
Xing Yu Liu ◽  
Bo Wei Chen ◽  
Jian Kang Wen
Keyword(s):  
Bacterial Community ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Clone Library ◽  
Heterotrophic Bacteria ◽  
Outer Part ◽  
Gene Clone ◽  
Rrna Gene ◽  
Liquid Samples ◽  
Lower Depth

The distribution and diversity of bacterial community in Zijinshan commercial non-aeration copper bioheapleaching system operated at pH 0.8 for three years were investigated. The 24 meters high heap was cut off by mechanical digger. On the trapezoidal cross-section of the heap, 9 ore samples were taken from different vertical and horizontal locations and investigated by 16S rRNA gene clone library. Another 3 liquid samples from raffinate solution pond, spray solution pond and pregnant solution pond were also applied to 16S rRNA gene clone library analysis. The retrieved 1166 clone sequences from 12 samples were mainly related to genus Acidithiobacillus (42.36%), genus Leptospirillum (37.73%) and genus Sulfobacillus (6.52%). Relative high amount of heterotrophic bacteria were distributed at the ore surface in the internal part of the heap and in the liquid samples respectively. The retrieved heterotrophic bacterial sequences were mainly related to genus Acidiphilium (accounting 11.11% to 32.00% percent in the liquid samples), genus Acidovorax (accounting 12.37% in A1 sample), genus Pelomonas (accounting 4.17% to 10.31% in several ore samples) and genus Aquabacterium (accounting 10.31% in C2 sample). Bacterial diversity in the heap was increased from the surfcae layer to the interior of the heap. The proportion of genus Leptospirillum horizontally increased from the inner to the outer part while vertically decreased from lower depth (2-3 years leaching time) to higher depth(3-6 month leaching time), and reverse correlation of genus Acidithiobacillus was found in the heap. Our finding indicated that heterotrophic bacteria may play very important roles in the commercial bioheapleaching system, and revealed high distribution of genus Leptospirillum in the outer part of this non-aerated heap.

scholarly journals Restructuring of the Aquatic Bacterial Community by Hydric Dynamics Associated with Superstorm Sandy

2016 ◽  
Vol 82 (12) ◽  
pp. 3525-3536 ◽  
Author(s):  
Nikea Ulrich ◽  
Abigail Rosenberger ◽  
Colin Brislawn ◽  
Justin Wright ◽  
Collin Kessler ◽  
...  
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
High Throughput ◽  
Bacterial Community Structure ◽  
High Throughput Sequencing ◽  
Storm Event ◽  
Rrna Gene ◽  
Content Type

ABSTRACTBacterial community composition and longitudinal fluctuations were monitored in a riverine system during and after Superstorm Sandy to better characterize inter- and intracommunity responses associated with the disturbance associated with a 100-year storm event. High-throughput sequencing of the 16S rRNA gene was used to assess microbial community structure within water samples from Muddy Creek Run, a second-order stream in Huntingdon, PA, at 12 different time points during the storm event (29 October to 3 November 2012) and under seasonally matched baseline conditions. High-throughput sequencing of the 16S rRNA gene was used to track changes in bacterial community structure and divergence during and after Superstorm Sandy. Bacterial community dynamics were correlated to measured physicochemical parameters and fecal indicator bacteria (FIB) concentrations. Bioinformatics analyses of 2.1 million 16S rRNA gene sequences revealed a significant increase in bacterial diversity in samples taken during peak discharge of the storm. Beta-diversity analyses revealed longitudinal shifts in the bacterial community structure. Successional changes were observed, in whichBetaproteobacteriaandGammaproteobacteriadecreased in 16S rRNA gene relative abundance, while the relative abundance of members of theFirmicutesincreased. Furthermore, 16S rRNA gene sequences matching pathogenic bacteria, including strains ofLegionella,Campylobacter,Arcobacter, andHelicobacter, as well as bacteria of fecal origin (e.g.,Bacteroides), exhibited an increase in abundance after peak discharge of the storm. This study revealed a significant restructuring of in-stream bacterial community structure associated with hydric dynamics of a storm event.IMPORTANCEIn order to better understand the microbial risks associated with freshwater environments during a storm event, a more comprehensive understanding of the variations in aquatic bacterial diversity is warranted. This study investigated the bacterial communities during and after Superstorm Sandy to provide fine time point resolution of dynamic changes in bacterial composition. This study adds to the current literature by revealing the variation in bacterial community structure during the course of a storm. This study employed high-throughput DNA sequencing, which generated a deep analysis of inter- and intracommunity responses during a significant storm event. This study has highlighted the utility of applying high-throughput sequencing for water quality monitoring purposes, as this approach enabled a more comprehensive investigation of the bacterial community structure. Altogether, these data suggest a drastic restructuring of the stream bacterial community during a storm event and highlight the potential of high-throughput sequencing approaches for assessing the microbiological quality of our environment.

scholarly journals Characteristics of bacterial community in cloud water at Mt Tai: similarity and disparity under polluted and non-polluted cloud episodes

2017 ◽  
Vol 17 (8) ◽  
pp. 5253-5270 ◽  
Author(s):  
Min Wei ◽  
Caihong Xu ◽  
Jianmin Chen ◽  
Chao Zhu ◽  
Jiarong Li ◽  
...  
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Bacterial Community Structure ◽  
Major Ions ◽  
Cloud Water ◽  
Rrna Gene ◽  
Bacterial Gene ◽  
Wide Range

Abstract. Bacteria are widely distributed in atmospheric aerosols and are indispensable components of clouds, playing an important role in the atmospheric hydrological cycle. However, limited information is available about the bacterial community structure and function, especially for the increasing air pollution in the North China Plain. Here, we present a comprehensive characterization of bacterial community composition, function, variation, and environmental influence for cloud water collected at Mt Tai from 24 July to 23 August 2014. Using Miseq 16S rRNA gene sequencing, the highly diverse bacterial community in cloud water and the predominant phyla of Proteobacteria, Bacteroidetes, Cyanobacteria, and Firmicutes were investigated. Bacteria that survive at low temperature, radiation, and poor nutrient conditions were found in cloud water, suggesting adaption to an extreme environment. The bacterial gene functions predicted from the 16S rRNA gene using the Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) suggested that the pathways related to metabolism and disease infections were significantly correlated with the predominant genera. The abundant genera Acinetobacter, Stenotrophomonas, Pseudomonas, and Empedobacter originated from a wide range of habitats including cloud condensation nuclei and ice nuclei active species, opportunistic pathogens, and functional species, demonstrating the importance of ecology and health in cloud water. Cluster analysis including hierarchical cluster (Hcluster) and principal coordinate analysis (PCoA) indicated a significant disparity between polluted and non-polluted samples. Linear discriminant analysis effect size (LEfSe) demonstrated that potential pathogens were enriched in the polluted cloud samples, whereas the diverse ecological function groups were significant in the non-polluted samples. Discrepant community structure determined by redundancy analysis (RDA) indicated that the major ions in cloud water and PM2. 5 in the atmosphere have a negative impact on bacteria, playing a vital role in shaping microbial community structure. The major ions might provide nutrition to bacteria and directly influence the bacterial community, whereas PM2. 5 in air has an indirect impact on bacterial community structure. During wet deposition, soluble particulate matter was dissolved in water droplets resulting in elevated concentration in cloud water. PM2. 5 was possibly associated with different origins and pathways of air mass as determined using source tracking by the backward trajectory, mainly related to long-range transport. This work enhanced our understanding of the characteristics of bacterial ecology in the atmospheric aqueous phase, highlighting the potential influence of environmental variables on the bacterial community in cloud processes. It may provide fundamental information of the bacterial community response in cloud water under increasing pollution. However, due to the limited sample size (13 samples) collected at the summit of Mt Tai, these issues need in-depth discussion. Further studies based on an annual series of field observation experiments and laboratory simulations will continue to track these issues.

scholarly journals Effect of Dietary Supplementation with a Saccharomyces cerevisiae Mannan Oligosaccharide on the Bacterial Community Structure of Broiler Cecal Contents

2011 ◽  
Vol 77 (18) ◽  
pp. 6653-6662 ◽  
Author(s):  
A. Corrigan ◽  
K. Horgan ◽  
N. Clipson ◽  
R. A. Murphy
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Bacterial Community Structure ◽  
Dietary Supplementation ◽  
Control Group ◽  
Rrna Gene ◽  
Content Type ◽  
Mannan Oligosaccharide

ABSTRACTThis study investigated the effects of dietary supplementation with a prebiotic mannan oligosaccharide (MOS) on broiler performance, bacterial community structure, and phylogenetic populations of cecal contents. Bird performance data were collected, and cecal samples were extracted from randomly caught poults from each treatment group every 7 days from hatching to the age of 42 days. Weight gain, feed consumption, and feed efficiency ratios did not differ significantly between groups. Automated ribosomal intergenic spacer analysis (ARISA) of the bacterial communities in birds receiving MOS-supplemented diets indicated that dietary supplementation with MOS at either of 2 levels significantly altered the bacterial community structure from that of the control group on all sample days. The phylogenetic identities of bacteria contained within the cecum were determined by constructing a 16S rRNA gene clone library. A total of 594 partial 16S rRNA gene sequences from the cecal contents were analyzed and compared for the three dietary treatments. The dominant bacteria of the cecum belonged to three phyla,Firmicutes,Bacteroidetes, andProteobacteria; of these,Firmicuteswere the most dominant in all treatment groups. Statistical analysis of the bacterial 16S rRNA gene clone libraries showed that the compositions of the clone libraries from broilers receiving MOS-supplemented diets were, in most cases, significantly different from that of the control group. It can be concluded that in this trial MOS supplementation significantly altered the cecal bacterial community structure.

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