Evaluation and optimization of lysis method for microbial DNA extraction from epiphytic phyllosphere samples

Analysis of microbial communities in the epiphytic phyllosphere can be challenging, especially when applying sequencing-based techniques, owing to the interference of plant-derived biomolecules such as nucleic acids. A review of recent studies on the epiphytic microbiome revealed that both mechanical and enzymatic lysis methods are widely used. Here, we evaluated the effects of the two lysis methods on DNA extraction yield, purity, integrity, and microbial 16S rRNA gene copy number per ng of template genomic DNA under different extraction conditions. Furthermore, the effect on bacterial community composition, diversity, and reproducibility was examined using 16S rRNA gene amplicon sequencing. The enzymatic lysis method yielded one to two orders of magnitude more DNA, but the DNA quality was suboptimal. Conversely, the samples prepared using the mechanical method showed high DNA purity albeit lower yield. Unexpectedly, mechanical lysis showed a higher DNA integrity number (DIN) than enzymatic lysis. The 16S rRNA amplicon sequencing results demonstrated that the samples prepared via mechanical disruption exhibited reproducibly similar microbial community compositions regardless of the extraction conditions. In contrast, the enzymatic lysis method resulted in inconsistent taxonomic compositions under different extraction conditions. This study demonstrates that mechanical DNA disruption is more suitable for epiphytic phyllosphere samples than enzymatic disruption.

Detection of Clostridium botulinum group III in environmental samples from farms by real-time PCR using four commercial DNA extraction kits

Objectives

Few studies have tested DNA extraction methods to optimize the detection of Clostridium botulinum in environmental samples that can be collected during animal botulism outbreaks. In this study, we evaluated four commercial DNA extraction kits for the detection of C. botulinum group III in 82 various environmental samples (9 manure, 53 swabs, 3 insects, 8 water, 1 silage and 8 soil samples) collected in a context of animal botulism outbreaks.

Results

The PowerSoil^® kit was the most efficient for almost all matrices (83.6% of the 73 tested samples), except manure for which the NucleoSpin^® Soil kit was the most efficient. The NucleoSpin^® Soil kit enabled detection in 75.3%, the QIAamp^® DNA Mini Kit in 68.5%, and the QIAamp^® Fast DNA Stool Mini Kit in 45.2%. However, the NucleoSpin^® Soil kit detected C. botulinum in 9 of the 9 manure samples tested, while the PowerSoil^® kit found C. botulinum in only two samples, and the other two kits in none of the samples. This study showed that PowerSoil^® can be recommended for DNA extraction from environmental samples except for manure, for which the NucleoSpin^® Soil kit appeared to be far more appropriate.

Intuitionistic fuzzy-based model for failure detection

In identifying to-be-improved product component(s), the customer/user requirements which are mainly considered, and achieved through customer surveys using the quality function deployment (QFD) tool, often fail to guarantee or cover aspects of the product reliability. Even when they do, there are always many misunderstandings. To improve the product reliability and quality during product redesigning phase and to create that novel product(s) for the customers, the failure information of the existing product, and its component(s) should ordinarily be analyzed and converted to appropriate design knowledge for the design engineer. In this paper, a new intuitionistic fuzzy multi-criteria decision-making method has been proposed. The new approach which is based on an intuitionistic fuzzy TOPSIS model uses an exponential-related function for the computation of the separation measures from the intuitionistic fuzzy positive ideal solution (IFPIS) and intuitionistic fuzzy negative ideal solution (IFNIS) of alternatives. The proposed method has been applied to two practical case studies, and the result from the different cases has been compared with some similar computational approaches in the literature.

Presence of Archaea in the Indoor Environment and Their Relationships with Housing Characteristics

Archaea are widespread and abundant in soils, oceans, or human and animal gastrointestinal (GI) tracts. However, very little is known about the presence of Archaea in indoor environments and factors that can regulate their abundances. Using a quantitative PCR approach, and targeting the archaeal and bacterial 16S rRNA genes in floor dust samples, we found that Archaea are a common part of the indoor microbiota, 5.01 ± 0.14 (log 16S rRNA gene copies/g dust, mean ± SE) in bedrooms and 5.58 ± 0.13 in common rooms, such as living rooms. Their abundance, however, was lower than bacteria: 9.20 ± 0.32 and 9.17 ± 0.32 in bedrooms and common rooms, respectively. In addition, by measuring a broad array of environmental factors, we obtained preliminary insights into how the abundance of total archaeal 16S rRNA gene copies in indoor environment would be associated with building characteristics and occupants' activities. Based on the results, Archaea are not equally distributed within houses, and the areas with greater input of outdoor microbiome and higher traffic and material heterogeneity tend to have a higher abundance of Archaea. Nevertheless, more research is needed to better understand causes and consequences of this microbial group in indoor environments.