Abstract:
:The skin microbiota is characterized by high intra- and inter-variability among individuals, due to a multitude of intrinsic and extrinsic parameters such as genetics, lifestyles or pollution. This variability may be heightened due to sampling method as the skin is a multilayer organ and its outermost layer consists of dead cells. In order to investigate this biological variability in a reproducible way, we studied how sampling procedure and DNA extraction methods influence the qualitative and quantitative gathering of bacterial communities. Here, we tested a new sampling procedure that consists in exerting a slight abrasion (scrubbing) on the skin prior to swabbing and extracting DNA in order to remove squames and access deeper ecological niches. Scrubbed and non-scrubbed samples were collected from a panel of six volunteers, and four DNA extraction methods were performed on the samples. The abundance, diversity and structure of the bacterial communities were measured using qPCR technics and 16S rDNA gene-metabarcoding. Bacterial community abundance was significantly impacted by the DNA extraction method (in favor of a method designed for tissues) but not by sampling procedure, as scrubbing does not increase bacterial biomass gathered. Bacterial α- and β-diversities were both affected by DNA extraction methods and sampling procedure. Scrubbing reveals different microbial composition by gathering bacteria living in deeper skin layer, resulting in a lower intra-personal variability. The taxonomic analysis showed that more bacteria belonging to anaerobes groups were present in scrubbed samples. We conclude that DNA extraction methods designed for tissue are not necessarily associated with high qualitative efficiency and slight scrubbing prior DNA extraction reduces intrapersonal variability and give access to a new microbial diversity.
journal_name
J Microbiol Methodsjournal_title
Journal of microbiological methodsauthors
Boulesnane Y,Leloup J,Lerch TZ,Roynette A,Pensé-Lhéritier AM,Mielcarek C,Changey Fdoi
10.1016/j.mimet.2020.105880subject
Has Abstractpub_date
2020-04-01 00:00:00pages
105880eissn
0167-7012issn
1872-8359pii
S0167-7012(19)31108-Xjournal_volume
171pub_type
杂志文章abstract::Many methods are developed to assess antimicrobial action of ZnO nanoparticles (NPs). A large number of methods associated with the use of fluorescent probes are developed, including Spectrofluorometry, fluorescence microscopy, and cytometry. In this study, flowcytometry, Spectrofluorometry and fluorescent microscopy ...
journal_title:Journal of microbiological methods
pub_type: 杂志文章
doi:10.1016/j.mimet.2020.105920
更新日期:2020-06-01 00:00:00
abstract::Quantification of the biosurfactants produced by a variety of microorganisms is a time taking and difficult task due to the lack of rapid, efficient and accurate methods. This work presents a simple turbidometric method for quantification of crude biosurfactants based on their property to become insoluble at low pH va...
journal_title:Journal of microbiological methods
pub_type: 杂志文章
doi:10.1016/j.mimet.2008.09.010
更新日期:2009-01-01 00:00:00
abstract::In Europe, alternative methods for the detection of food-borne pathogens can be used instead of the standard ISO/CEN reference protocol, if validated according to the protocol outlined in ISO 16140, 2003. In this study, the performance of two novel methods for the detection of Salmonella sp. using real-time PCR techno...
journal_title:Journal of microbiological methods
pub_type: 杂志文章
doi:10.1016/j.mimet.2010.10.004
更新日期:2011-01-01 00:00:00
abstract::Mycoplasma synoviae, an important poultry pathogen, belonging to the class Mollicutes, causes airsacculitis, synovitis, decreased egg production and produces significant economic losses. Efforts to determine M. synoviae virulence factors and their role in pathogenicity require suitable tools for genetic manipulation o...
journal_title:Journal of microbiological methods
pub_type: 杂志文章
doi:10.1016/j.mimet.2014.05.014
更新日期:2014-08-01 00:00:00
abstract::Several outbreaks of foodborne yersiniosis have been documented and this disease continues to be source of infections transmitted through foods. The selective agars most commonly used to isolate Yersinia enterocolitica in clinical, food and environmental samples, cefsulodin-irgasan-novobiocin (CIN) and MacConkey (MAC)...
journal_title:Journal of microbiological methods
pub_type: 杂志文章
doi:10.1016/j.mimet.2007.11.019
更新日期:2008-02-01 00:00:00
abstract::Strains of Bacillus subtilis are plant growth-promoting bacteria (PGPB) of many crops and are used as inoculants. PGPB colonization is an important trait for success of a PGPB on plants. A specific probe, based on the 16 s rRNA of Bacillus subtilis, was designed and evaluated to distinguishing, by fluorescence in situ...
journal_title:Journal of microbiological methods
pub_type: 杂志文章
doi:10.1016/j.mimet.2016.05.029
更新日期:2016-09-01 00:00:00
abstract::A rapid immunological method for trapping and selection of functionally regulated prokaryotic promoters is described. The method is based on application of a novel mini-Tn5 derived promoter probe (pUTTKZY-promoterless lacZY as a reporter and kanamycin resistance) to mutagenise a plant growth promoting fluorescent pseu...
journal_title:Journal of microbiological methods
pub_type: 杂志文章
doi:10.1016/s0167-7012(00)00139-1
更新日期:2000-06-01 00:00:00
abstract::Thermophilic strains of Geobacillus, Anoxybacillus and Bacillus that are able to grow at 55 degrees C and above are recognized as commonly occurring contaminants during the production of milk powders. In particular, Anoxybacillus flavithermus strain C and Bacillus licheniformis strain F are often the most prevalent. W...
journal_title:Journal of microbiological methods
pub_type: 杂志文章
doi:10.1016/j.mimet.2004.09.008
更新日期:2005-02-01 00:00:00
abstract::A novel method for directly increasing the recovery of Escherichia coli O157:H7 and efficiently eliminating PCR inhibitors in oyster tissue without preenrichment was developed with the use of activated carbon coated with bentonite. The recovery of E. coli O157:H7 was significantly affected by the amount of bentonite u...
journal_title:Journal of microbiological methods
pub_type: 杂志文章
doi:10.1016/j.mimet.2007.10.010
更新日期:2008-01-01 00:00:00
abstract::Although recent technological advances in DNA sequencing and computational biology now allow scientists to compare entire microbial genomes, comparisons of closely related bacterial species and individual isolates by whole-genome sequencing approaches remains prohibitively expensive for most laboratories. Here we repo...
journal_title:Journal of microbiological methods
pub_type: 杂志文章
doi:10.1016/j.mimet.2005.12.006
更新日期:2006-08-01 00:00:00
abstract::Analysis of microbial communities is of broad interest in biology and high throughput sequencing is now the preferred method. However, some studies may not need the level of detail high throughput sequencing provides and its cost may limit the number of samples that can be sequenced. High resolution melting analysis (...
journal_title:Journal of microbiological methods
pub_type: 杂志文章
doi:10.1016/j.mimet.2017.07.006
更新日期:2017-09-01 00:00:00
abstract::Industrial antimicrobials have been extensively used to control unwanted microbial growth by incorporation into a variety of products such as plastics and paints, reducing biodeterioration and biofouling and extending the lifespan of the product. Industrial antimicrobials generally have broad sites of action affecting...
journal_title:Journal of microbiological methods
pub_type: 杂志文章
doi:10.1016/j.mimet.2017.08.005
更新日期:2017-10-01 00:00:00
abstract::We aimed to establish the role of MALDI-TOF MS on species discrimination of phenotypically indistinguishable A. baumannii, A. pittii and A. nosocomialis. Compared to multiplex PCR, the gold standard, MALDI-TOF MS yielded a high sensitivity for A. baumannii (97.9%) and specificity for A. pittii (98.9%) and A. nosocomia...
journal_title:Journal of microbiological methods
pub_type: 杂志文章
doi:10.1016/j.mimet.2017.06.019
更新日期:2017-09-01 00:00:00
abstract::Silver scurf caused by Helminthosporium solani causes significant economic losses in table stock, seed and processing potatoes. Specific polymerase chain reaction (PCR) primers, Hs1F1/Hs2R1, from H. solani were used for the amplification of a 447-bp product from 20 tissue samples and 54 single spore H. solani isolates...
journal_title:Journal of microbiological methods
pub_type: 杂志文章
doi:10.1016/s0167-7012(00)00240-2
更新日期:2001-02-01 00:00:00
abstract::Gene expression analysis provides significant insight to understand regulatory mechanisms of biology, yet acquisition and reproduction of quality data, as well as data confirmation and verification remain challenging due to a lack of proper quality controls across different assay platforms. We present a set of six uni...
journal_title:Journal of microbiological methods
pub_type: 杂志文章
doi:10.1016/j.mimet.2006.10.014
更新日期:2007-03-01 00:00:00
abstract::The use of DNA microarrays for detection and identification of bacteria and genes of interest from various environments (e.g. soil, sediment, water column...) is a major challenge for microbiologists working on functional diversity. So far, most of the genomic methods that have been described rely on the use of taxono...
journal_title:Journal of microbiological methods
pub_type: 杂志文章,评审
doi:10.1016/j.mimet.2006.11.007
更新日期:2007-05-01 00:00:00
abstract:OBJECTIVES:Galactomannan (GM) and Aspergillus DNA detection are useful tools for the diagnosis of invasive pulmonary aspergillosis (IPA), primarily in blood and bronchoscopy samples. This study aimed to evaluate the utility of both markers for detection of Aspergillus in sputum from patients with allergic bronchopulmon...
journal_title:Journal of microbiological methods
pub_type: 杂志文章
doi:10.1016/j.mimet.2017.06.016
更新日期:2017-09-01 00:00:00
abstract::Bacterial biofilms are populations of bacteria within a self-produced adherent extracellular matrix that are notoriously resistant to treatment. Existing methods for biofilm quantification are often limited in their dynamic range of detection (signal-to-background), throughput, and require modifications to the protoco...
journal_title:Journal of microbiological methods
pub_type: 杂志文章
doi:10.1016/j.mimet.2019.02.018
更新日期:2019-04-01 00:00:00
abstract::In order to reduce the risk of transmission of infectious diseases through transplantation of tissue allografts, one should examine tissues for the presence of microorganisms. However, there are no detailed tissue banking guidelines describing the culture method or incubation time to be used. Therefore, we compared tw...
journal_title:Journal of microbiological methods
pub_type: 杂志文章
doi:10.1016/j.mimet.2007.05.014
更新日期:2007-08-01 00:00:00
abstract::Recently developed 13CO2 pulse labelling and stable isotope probing (SIP) methods offer the potential to track 13C-labelled plant photosynthate into phylogenetic groups of microbial taxa in the rhizosphere, permitting an examination of the link between soil microbial diversity and carbon flow in situ. We tested the fe...
journal_title:Journal of microbiological methods
pub_type: 杂志文章
doi:10.1016/j.mimet.2004.03.011
更新日期:2004-07-01 00:00:00
abstract::Drinking water quality typically degrades after treatment during conveyance through the distribution system. Potential causes include biofilm growth in distribution pipes which may result in pathogen retention, inhibited disinfectant diffusion, and proliferation of bad tastes and odors. However, there is no standard m...
journal_title:Journal of microbiological methods
pub_type: 杂志文章
doi:10.1016/j.mimet.2017.10.013
更新日期:2018-01-01 00:00:00
abstract::A method for rapidly and selectively isolating Salmonellae from buffer solutions and concentrating the bacteria by a factor of approximately 500 was developed. Anti-Salmonellae antibody was covalently linked to 40 microm polyacrylamide beads to prepare a solid phase with affinity for the bacteria. The beads were packe...
journal_title:Journal of microbiological methods
pub_type: 杂志文章
doi:10.1016/s0167-7012(03)00163-5
更新日期:2003-10-01 00:00:00
abstract::Actinomyces naeslundii is an early colonizer with important roles in the development of the oral biofilm. The effects of butyric acid, one of short chain fatty acids in A. naeslundii biofilm formation was observed using a flow cell system with Tryptic soy broth without dextrose and with 0.25% sucrose (TSB sucrose). Si...
journal_title:Journal of microbiological methods
pub_type: 杂志文章
doi:10.1016/j.mimet.2014.12.021
更新日期:2015-02-01 00:00:00
abstract::Development of a high-throughput eukaryotic screening procedure is important to increase success in obtaining improved enzymes through directed enzyme evolution. This procedure was developed for the yeast Yarrowia lipolytica which becomes the second eukaryotic host for this purpose. The extracellular lipase Lip2 was u...
journal_title:Journal of microbiological methods
pub_type: 杂志文章
doi:10.1016/j.mimet.2007.06.008
更新日期:2007-09-01 00:00:00
abstract::Molecular tools for Gram-positive bacteria such as Mycobacterium are less well-developed than those for Gram-negatives such as Escherichiacoli. This has slowed the molecular-genetic characterisation of Mycobacterium spp, which is unfortunate, since this genus has high medical, environmental and industrial significance...
journal_title:Journal of microbiological methods
pub_type: 杂志文章
doi:10.1016/j.mimet.2011.06.005
更新日期:2011-09-01 00:00:00
abstract::Several studies have been conducted to develop rapid methods for quantification of lipid content in microalgae, as an alternative for time consuming gravimetric methods. Different studies showed that lipid staining with Nile Red in whole cell suspensions and subsequently quantification by the use of a spectrofluoromet...
journal_title:Journal of microbiological methods
pub_type: 杂志文章
doi:10.1016/j.mimet.2015.09.009
更新日期:2015-11-01 00:00:00
abstract::To date, no single reported DNA extraction method is suitable for the efficient extraction of DNA from all fungal species. The efficiency of extraction is of particular importance in PCR-based medical diagnostic applications where the quantity of fungus in a tissue biopsy may be limited. We subjected 16 medically rele...
journal_title:Journal of microbiological methods
pub_type: 杂志文章
doi:10.1016/j.mimet.2005.06.008
更新日期:2006-04-01 00:00:00
abstract::Toxoplasmosis is caused by the protozoan parasite Toxoplasma gondii, which belongs to the phylum Apicomplexa. Since this parasite causes severe clinical symptoms in immunocompromised patients, early diagnosis of toxoplasmosis is essential. PCR is currently used for early diagnosis, but there is no consensus regarding ...
journal_title:Journal of microbiological methods
pub_type: 杂志文章
doi:10.1016/j.mimet.2017.08.001
更新日期:2017-10-01 00:00:00
abstract::Site-directed mutagenesis is one of the most widely used techniques in life sciences. Here we describe an improved and simplified method for introducing mutations at desired sites. It consists of an inverse PCR using a plasmid template and two partially complementary primers. The synthesis step is followed by annealin...
journal_title:Journal of microbiological methods
pub_type: 杂志文章
doi:10.1016/j.mimet.2014.08.003
更新日期:2014-11-01 00:00:00
abstract::Flow cytometry was used to characterize bacterioplankton from two tropical environments in Brazil: the eutrophic Guanabara Bay and the oligotrophic southwest Atlantic Ocean. Bacterial abundance was evaluated by flow cytometry, and cells were stained with SYTO 13, allowing demonstration of differences in nucleic acid c...
journal_title:Journal of microbiological methods
pub_type: 杂志文章
doi:10.1016/j.mimet.2003.08.002
更新日期:2003-12-01 00:00:00