Microbial analyses of blood spot surfaces collected from a laboratory and the bathroom of a female single-person household under different environmental conditions

2021 ◽  
Vol 368 (5) ◽  
Author(s):  
Hee Sang You ◽  
Song Hee Lee ◽  
Young Ju Lee ◽  
Ho Joong Sung ◽  
Hee-Gyoo Kang ◽  
...  
Keyword(s):  
Microbial Community ◽  
Bacterial Community ◽  
Microbial Communities ◽  
Community Analysis ◽  
Personal Identification ◽  
Microbial Interactions ◽  
Microbial Community Analysis ◽  
Single Person ◽  
Blood Spot ◽  
Over Time

Abstract Many people spend most of their time indoors, thereby exposing themselves to indoor environmental microbial communities that might interact with the human microbiota. These potential interactions have only been considered for personal identification; however, accumulating evidence indicates that these microbial interactions are potentially implicated with the identification of human interactions and location-specific factors including time and seasonal variations in the microbial community. To augment the potential of metagenomics-based forensic tools, we compared the composition of microbial communities in blood spot surfaces from healthy adults placed in different environments, such as in the bathroom of a female single-person household and on a laboratory, which were sampled across seasons and time points. The laboratory samples showed more changes in the bacterial community over time owing to the higher number of individuals using the laboratory, whereas the microbial communities in the bathroom samples remained relatively stable over time. Moreover, the two locations could be distinguished according to their specific bacterial community compositions. Variations were also observed related to changes in temperature and humidity, allowing for prediction of season-based microbial community. These findings offer a new perspective regarding the use of microbial community analysis in forensic science.

scholarly journals Impact of Substratum Surface on Microbial Community Structure and Treatment Performance in Biological Aerated Filters

2013 ◽  
Vol 80 (1) ◽  
pp. 177-183 ◽  
Author(s):  
Lavane Kim ◽  
Eulyn Pagaling ◽  
Yi Y. Zuo ◽  
Tao Yan
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Bacterial Species ◽  
Community Analysis ◽  
Microbial Community Analysis ◽  
Rrna Gene ◽  
Content Type ◽  
Property Change ◽  
And Control ◽  
Start Ups

ABSTRACTThe impact of substratum surface property change on biofilm community structure was investigated using laboratory biological aerated filter (BAF) reactors and molecular microbial community analysis. Two substratum surfaces that differed in surface properties were created via surface coating and used to develop biofilms in test (modified surface) and control (original surface) BAF reactors. Microbial community analysis by 16S rRNA gene-based PCR-denaturing gradient gel electrophoresis (DGGE) showed that the surface property change consistently resulted in distinct profiles of microbial populations during replicate reactor start-ups. Pyrosequencing of the bar-coded 16S rRNA gene amplicons surveyed more than 90% of the microbial diversity in the microbial communities and identified 72 unique bacterial species within 19 bacterial orders. Among the 19 orders of bacteria detected,BurkholderialesandRhodocyclalesof theBetaproteobacteriaclass were numerically dominant and accounted for 90.5 to 97.4% of the sequence reads, and their relative abundances in the test and control BAF reactors were different in consistent patterns during the two reactor start-ups. Three of the five dominant bacterial species also showed consistent relative abundance changes between the test and control BAF reactors. The different biofilm microbial communities led to different treatment efficiencies, with consistently higher total organic carbon (TOC) removal in the test reactor than in the control reactor. Further understanding of how surface properties affect biofilm microbial communities and functional performance would enable the rational design of new generations of substrata for the improvement of biofilm-based biological treatment processes.

Bacterial Community Analysis of Mine Contaminated Soils in Hechi City

2020 ◽  
Vol 14 (4) ◽  
pp. 476-486
Author(s):  
Tingting Liu ◽  
Caoping Pang ◽  
Fengcai Ye ◽  
Dafei Gong ◽  
Jieling Luo ◽  
...  
Keyword(s):  
Microbial Community ◽  
Genetic Engineering ◽  
Bacterial Community ◽  
Contaminated Soils ◽  
High Throughput Sequencing ◽  
Community Analysis ◽  
Microbial Community Analysis ◽  
Mine Soils ◽  
Sequencing Technology ◽  
Autonomous Region

Four mine contaminated soils located in northwest of Guangxi autonomous region were selected for microbial community analysis. These mine soils were contaminated by chromium (Cr) and cadmium (Cd). Microbial communities were described by high-throughput sequencing technology, which showed 39 different phyla in four samples. Among these phyla, Proteobacteria was the most abundant phylum in all samples. Acidobacteria, Actinobacteria, Planctomycetes, Firmicutes, Gemmatimonadetes, Bacteroidetes and Chloroflexi showed higher relative abundances than other phyla. In addition, a wide diversity of bacteria with the potential of bioremediation, such as Sphingomonas, Lysobacter and Gemmatimonas were detected in the tested mine contaminated soils. The results of microbial community analysis will provide a new target for isolation of microorganisms with the potential of bioremediation and lay the foundation for a great enhancement of bioremediation ability through the genetic engineering modification of indigenous microorganisms in future.

scholarly journals Evaluation of DESS as a storage medium for microbial community analysis

2018 ◽  
Author(s):  
Kevin M Lee ◽  
Madison Adams ◽  
Jonathan L Klassen
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Microbial Communities ◽  
Microbial Ecology ◽  
Microbial Community Structure ◽  
Community Analysis ◽  
Microbial Community Analysis ◽  
Ant Colonies ◽  
And Storage ◽  
Phosphate Buffered Saline

Microbial ecology research requires sampling strategies that accurately represent the microbial community under study. These communities must typically be transported from the collection location to the laboratory and then stored until they can be processed. However, there is a lack of consensus on how best to preserve microbial communities during transport and storage. Here, we evaluated DESS (Dimethyl sulfoxide, Ethylenediamine tetraacetic acid, Saturated Salt) solution as a broadly applicable preservative for microbial ecology experiments. We stored fungus gardens grown by the ant Trachymyrmex septentrionalis in DESS, 15% glycerol, and phosphate buffered saline (PBS) to test the ability of these preservatives to maintain the structure of fungus garden microbial communities. Variation in microbial community structure due to differences in preservative type was minimal when compared to variation between ant colonies. Additionally, DESS preserved the structure of a defined mock community more faithfully than either 15% glycerol or PBS. DESS is inexpensive, easy to transport, and effective in preserving microbial community structure. We therefore conclude that DESS is a valuable preservative for use in microbial ecology research.

scholarly journals Evaluation of DESS as a storage medium for microbial community analysis

2018 ◽  
Author(s):  
Kevin M Lee ◽  
Madison Adams ◽  
Jonathan L Klassen
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Microbial Communities ◽  
Microbial Ecology ◽  
Microbial Community Structure ◽  
Community Analysis ◽  
Microbial Community Analysis ◽  
Ant Colonies ◽  
And Storage ◽  
Phosphate Buffered Saline

Microbial ecology research requires sampling strategies that accurately represent the microbial community under study. These communities must typically be transported from the collection location to the laboratory and then stored until they can be processed. However, there is a lack of consensus on how best to preserve microbial communities during transport and storage. Here, we evaluated DESS (Dimethyl sulfoxide, Ethylenediamine tetraacetic acid, Saturated Salt) solution as a broadly applicable preservative for microbial ecology experiments. We stored fungus gardens grown by the ant Trachymyrmex septentrionalis in DESS, 15% glycerol, and phosphate buffered saline (PBS) to test the ability of these preservatives to maintain the structure of fungus garden microbial communities. Variation in microbial community structure due to differences in preservative type was minimal when compared to variation between ant colonies. Additionally, DESS preserved the structure of a defined mock community more faithfully than either 15% glycerol or PBS. DESS is inexpensive, easy to transport, and effective in preserving microbial community structure. We therefore conclude that DESS is a valuable preservative for use in microbial ecology research.

scholarly journals PCR Amplification-Independent Methods for Detection of Microbial Communities by the High-Density Microarray PhyloChip

2011 ◽  
Vol 77 (18) ◽  
pp. 6313-6322 ◽  
Author(s):  
Kristen M. DeAngelis ◽  
Cindy H. Wu ◽  
Harry R. Beller ◽  
Eoin L. Brodie ◽  
Romy Chakraborty ◽  
...  
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Pcr Amplification ◽  
Community Analysis ◽  
High Density ◽  
Microbial Community Analysis ◽  
Taxon Richness ◽  
Tropical Forest Soil ◽  
Global Biogeochemical Cycles ◽  
Direct Hybridization

ABSTRACTEnvironmental microbial community analysis typically involves amplification by PCR, despite well-documented biases. We have developed two methods of PCR-independent microbial community analysis using the high-density microarray PhyloChip: direct hybridization of 16S rRNA (dirRNA) or rRNA converted to double-stranded cDNA (dscDNA). We compared dirRNA and dscDNA communities to PCR-amplified DNA communities using a mock community of eight taxa, as well as experiments derived from three environmental sample types: chromium-contaminated aquifer groundwater, tropical forest soil, and secondary sewage in seawater. Community profiles by both direct hybridization methods showed differences that were expected based on accompanying data but that were missing in PCR-amplified communities. Taxon richness decreased in RNA compared to that in DNA communities, suggesting a subset of 20% in soil and 60% in groundwater that is active; secondary sewage showed no difference between active and inactive populations. Direct hybridization of dscDNA and RNA is thus a viable alternative to PCR-amplified microbial community analysis, providing identification of the active populations within microbial communities that attenuate pollutants, drive global biogeochemical cycles, or proliferate disease states.

scholarly journals Microbial Community Analysis of Field-Grown Soybeans with Different Nodulation Phenotypes

2008 ◽  
Vol 74 (18) ◽  
pp. 5704-5709 ◽  
Author(s):  
Seishi Ikeda ◽  
Lynn Esther E. Rallos ◽  
Takashi Okubo ◽  
Shima Eda ◽  
Shoko Inaba ◽  
...  
Keyword(s):  
Principal Component Analysis ◽  
Community Structure ◽  
Microbial Community ◽  
Bacterial Community ◽  
Bacterial Community Structure ◽  
Phylogenetic Analyses ◽  
Principal Component ◽  
Community Analysis ◽  
Component Analysis ◽  
Microbial Community Analysis

ABSTRACT Microorganisms associated with the stems and roots of nonnodulated (Nod−), wild-type nodulated (Nod+), and hypernodulated (Nod++) soybeans [Glycine max (L.) Merril] were analyzed by ribosomal intergenic transcribed spacer analysis (RISA) and automated RISA (ARISA). RISA of stem samples detected no bands specific to the nodulation phenotype, whereas RISA of root samples revealed differential bands for the nodulation phenotypes. Pseudomonas fluorescens was exclusively associated with Nod+ soybean roots. Fusarium solani was stably associated with nodulated (Nod+ and Nod++) roots and less abundant in Nod− soybeans, whereas the abundance of basidiomycetes was just the opposite. The phylogenetic analyses suggested that these basidiomycetous fungi might represent a root-associated group in the Auriculariales. Principal-component analysis of the ARISA results showed that there was no clear relationship between nodulation phenotype and bacterial community structure in the stem. In contrast, both the bacterial and fungal community structures in the roots were related to nodulation phenotype. The principal-component analysis further suggested that bacterial community structure in roots could be classified into three groups according to the nodulation phenotype (Nod−, Nod+, or Nod++). The analysis of root samples indicated that the microbial community in Nod− soybeans was more similar to that in Nod++ soybeans than to that in Nod+ soybeans.

scholarly journals Effect of fermentation stillage of food waste on bioelectricity production and microbial community structure in microbial fuel cells

2018 ◽  
Vol 5 (9) ◽  
pp. 180457 ◽  
Author(s):  
Hongzhi Ma ◽  
Cheng Peng ◽  
Yan Jia ◽  
Qunhui Wang ◽  
Maobing Tu ◽  
...  
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Food Waste ◽  
Microbial Fuel Cells ◽  
Fluorescence Spectra ◽  
Oxygen Demand ◽  
Community Analysis ◽  
Microbial Community Analysis ◽  
Chemical Oxygen Demand Removal ◽  
External Resistance

A single-chamber microbial fuel cell (MFC) was used in this study to treat recycled stillage obtained from food waste ethanol fermentation. Corresponding substrates inside the system were evaluated by fluorescence spectra, and microbial communities were also investigated. Results demonstrated that output voltage and current, respectively, reached 0.29 V and 1.4 mA with an external resistance of 200 Ω. Corresponding total organic carbon and chemical oxygen demand removal efficiency reached more than 50% and 70%, respectively. Results of fluorescence spectra demonstrated that tryptophan-like aromatic, soluble microbial by-product-like and humic acid-like substances accumulated and were not easily degraded. Microbial community analysis by high-throughput sequence indicated that Advenella and Moheibacter occupied the highest proportion among all genera at the anode instead of Geobacter . These results may be due to complicated accumulated stillage, and potential tetracyclines possibly influenced microbial communities. Details on how stillage affects MFC operation should be further studied, and a solution on relieving effects should be established.

scholarly journals Quantitative Microbial Community Analysis of Three Different Sulfidic Mine Tailing Dumps Generating Acid Mine Drainage

2008 ◽  
Vol 74 (16) ◽  
pp. 5211-5219 ◽  
Author(s):  
Dagmar Kock ◽  
Axel Schippers
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Community Analysis ◽  
Sybr Green ◽  
Microbial Community Analysis ◽  
Probable Number ◽  
Cell Numbers ◽  
Tailing Dumps ◽  
Sulfur Oxidizing ◽  
Card Fish

ABSTRACT The microbial communities of three different sulfidic and acidic mine waste tailing dumps located in Botswana, Germany, and Sweden were quantitatively analyzed using quantitative real-time PCR (Q-PCR), fluorescence in situ hybridization (FISH), catalyzed reporter deposition-FISH (CARD-FISH), Sybr green II direct counting, and the most probable number (MPN) cultivation technique. Depth profiles of cell numbers showed that the compositions of the microbial communities are greatly different at the three sites and also strongly varied between zones of oxidized and unoxidized tailings. Maximum cell numbers of up to 109 cells g−1 dry weight were determined in the pyrite or pyrrhotite oxidation zones, whereas cell numbers in unoxidized tailings were significantly lower. Bacteria dominated over Archaea and Eukarya at all tailing sites. The acidophilic Fe(II)- and/or sulfur-oxidizing Acidithiobacillus spp. dominated over the acidophilic Fe(II)-oxidizing Leptospirillum spp. among the Bacteria at two sites. The two genera were equally abundant at the third site. The acidophilic Fe(II)- and sulfur-oxidizing Sulfobacillus spp. were generally less abundant. The acidophilic Fe(III)-reducing Acidiphilium spp. could be found at only one site. The neutrophilic Fe(III)-reducing Geobacteraceae as well as the dsrA gene of sulfate reducers were quantifiable at all three sites. FISH analysis provided reliable data only for tailing zones with high microbial activity, whereas CARD-FISH, Q-PCR, Sybr green II staining, and MPN were suitable methods for a quantitative microbial community analysis of tailings in general.

A peek in the micro-sized world: a review of design principles, engineering tools, and applications of engineered microbial community

2020 ◽  
Vol 48 (2) ◽  
pp. 399-409
Author(s):  
Baizhen Gao ◽  
Rushant Sabnis ◽  
Tommaso Costantini ◽  
Robert Jinkerson ◽  
Qing Sun
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Environmental Remediation ◽  
Real Life ◽  
Design Principles ◽  
Microbial Interactions ◽  
Potential Applications ◽  
New Gene ◽  
Global Biogeochemical Cycles ◽  
Synthetic Microbial Communities

Microbial communities drive diverse processes that impact nearly everything on this planet, from global biogeochemical cycles to human health. Harnessing the power of these microorganisms could provide solutions to many of the challenges that face society. However, naturally occurring microbial communities are not optimized for anthropogenic use. An emerging area of research is focusing on engineering synthetic microbial communities to carry out predefined functions. Microbial community engineers are applying design principles like top-down and bottom-up approaches to create synthetic microbial communities having a myriad of real-life applications in health care, disease prevention, and environmental remediation. Multiple genetic engineering tools and delivery approaches can be used to ‘knock-in' new gene functions into microbial communities. A systematic study of the microbial interactions, community assembling principles, and engineering tools are necessary for us to understand the microbial community and to better utilize them. Continued analysis and effort are required to further the current and potential applications of synthetic microbial communities.

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