scholarly journals Impact of DNA extraction and sampling methods on bacterial communities monitored by 16S rDNA metabarcoding in cold-smoked salmon and processing plant surfaces

2021 ◽  
Vol 95 ◽  
pp. 103705
Author(s):  
Aurélien Maillet ◽  
Agnès Bouju-Albert ◽  
Steven Roblin ◽  
Pauline Vaissié ◽  
Sébastien Leuillet ◽  
...  
Keyword(s):  
16S Rdna ◽  
Dna Extraction ◽  
Bacterial Communities ◽  
Sampling Methods ◽  
Processing Plant ◽  
Smoked Salmon ◽  
Plant Surfaces

scholarly journals Characterization of Bacterial Communities of Cold-Smoked Salmon during Storage

Foods ◽  
2021 ◽  
Vol 10 (2) ◽  
pp. 362
Author(s):  
Aurélien Maillet ◽  
Pauline Denojean ◽  
Agnès Bouju-Albert ◽  
Erwann Scaon ◽  
Sébastien Leuillet ◽  
...  
Keyword(s):  
Shelf Life ◽  
Microbial Ecology ◽  
Bacterial Communities ◽  
Polyphasic Approach ◽  
Rrna Gene ◽  
Processing Plant ◽  
Operational Taxonomic Units ◽  
Smoked Salmon ◽  
Negative Effect ◽  
Seafood Products

Cold-smoked salmon is a widely consumed ready-to-eat seafood product that is a fragile commodity with a long shelf-life. The microbial ecology of cold-smoked salmon during its shelf-life is well known. However, to our knowledge, no study on the microbial ecology of cold-smoked salmon using next-generation sequencing has yet been undertaken. In this study, cold-smoked salmon microbiotas were investigated using a polyphasic approach composed of cultivable methods, V3—V4 16S rRNA gene metabarcoding and chemical analyses. Forty-five cold-smoked salmon products processed in three different factories were analyzed. The metabarcoding approach highlighted 12 dominant genera previously reported as fish spoilers: Firmicutes Staphylococcus, Carnobacterium, Lactobacillus, β-Proteobacteria Photobacterium, Vibrio, Aliivibrio, Salinivibrio, Enterobacteriaceae Serratia,Pantoea, γ-Proteobacteria Psychrobacter, Shewanella and Pseudomonas. Specific operational taxonomic units were identified during the 28-day storage study period. Operational taxonomic units specific to the processing environment were also identified. Although the 45 cold-smoked salmon products shared a core microbiota, a processing plant signature was found. This suggest that the bacterial communities of cold-smoked salmon products are impacted by the processing environment, and this environment could have a negative effect on product quality. The use of a polyphasic approach for seafood products and food processing environments could provide better insights into residential bacteria dynamics and their impact on food safety and quality.

Method for rapid DNA extraction from bacterial communities of different soils

Microbiology ◽  
2006 ◽  
Vol 75 (1) ◽  
pp. 105-111 ◽  
Author(s):  
E. V. Zaporozhenko ◽  
N. V. Slobodova ◽  
E. S. Boulygina ◽  
I. K. Kravchenko ◽  
B. B. Kuznetsov
Keyword(s):  
Dna Extraction ◽  
Bacterial Communities ◽  
Different Soils

scholarly journals DNA Extraction and Host Depletion Methods Significantly Impact and Potentially Bias Bacterial Detection in a Biological Fluid

mSystems ◽  
2021 ◽  
Author(s):  
Erika Ganda ◽  
Kristen L. Beck ◽  
Niina Haiminen ◽  
Justin D. Silverman ◽  
Ban Kawas ◽  
...  
Keyword(s):  
Food Safety ◽  
Dna Extraction ◽  
Bacterial Communities ◽  
Biological Fluid ◽  
Genetic Material ◽  
Next Generation ◽  
Microbial Composition ◽  
Chemical Methods ◽  
Bacterial Detection ◽  
Do So

Tracking the bacterial communities present in our food has the potential to inform food safety and product origin. To do so, the entire genetic material present in a sample is extracted using chemical methods or commercially available kits and sequenced using next-generation platforms to provide a snapshot of the microbial composition.

scholarly journals Comparison of two commercial DNA extraction kits for the analysis of nasopharyngeal bacterial communities

2016 ◽  
Vol 2 (2) ◽  
pp. 108-119 ◽  
Author(s):  
Marcos Pérez-Losada ◽  
◽  
Keith A. Crandall ◽  
Robert J. Freishtat
Keyword(s):  
Dna Extraction ◽  
Bacterial Communities

scholarly journals Comparison of different conditions for DNA extraction in sputum - a pilot study

2019 ◽  
Vol 14 ◽  
Author(s):  
Martina Oriano ◽  
Leonardo Terranova ◽  
Antonio Teri ◽  
Samantha Sottotetti ◽  
Luca Ruggiero ◽  
...  
Keyword(s):  
Real Time ◽  
16S Rdna ◽  
Dna Extraction ◽  
Real Time Pcr ◽  
Alpha Diversity ◽  
Diversity Indices ◽  
Extraction Yield ◽  
Chronic Respiratory Diseases ◽  
Dna Yield ◽  
Selection Of

Background: The analysis of microbiome in respiratory samples is a topic of great interest in chronic respiratory diseases. The method used to prepare sputum samples for microbiome analysis is very heterogeneous. The selection of the most suitable methodology for DNA extraction is fundamental to have the most representative data. The objective of this study was to compare different conditions for DNA extraction from sputum in adult patients with bronchiectasis. Methods: Five sputum samples from bronchiectasis patients were collected at the Policlinico Hospital in Milan, Italy. Eighteen conditions for DNA extraction were compared, including two enzyme-based (Roche and Zymo) and one beads-based (Mobio) technique. These techniques were tested with/without Dithiothreitol (DTT) and with/without lysostaphin (0.18 and 0.36 mg/mL) step. DNA was quantified, tested using Real-time PCR for 16S rDNA and S. aureus and, then, microbiome was evaluated. Results: Although 16S rDNA was similarly detected across all the different techniques, Roche kit gave the highest DNA yield. The lowest Ct values for Real-time PCR for S. aureus was identified when lysostaphin was added. Considering genera from microbiome, alpha diversity indices did not show any significant differences between techniques, while relative abundances were more similar in presence of DTT. Conclusions: None of the conditions emerged to be superior to the others even if enzyme-based kits seem to be needed in order to have a higher extraction yield.

Analysis of bacterial communities on aging flue-cured tobacco leaves by 16S rDNA PCR–DGGE technology

2007 ◽  
Vol 73 (6) ◽  
pp. 1435-1440 ◽  
Author(s):  
Mingqin Zhao ◽  
Baoxiang Wang ◽  
Fuxin Li ◽  
Liyou Qiu ◽  
Fangfang Li ◽  
...  
Keyword(s):  
16S Rdna ◽  
Bacterial Communities ◽  
Tobacco Leaves ◽  
16S Rdna Pcr

scholarly journals Oropharyngeal HPV infection: prevalence and sampling methods among HIV-infected men in South Africa

2018 ◽  
Vol 29 (8) ◽  
pp. 776-780 ◽  
Author(s):  
Admire Chikandiwa ◽  
Pedro T Pisa ◽  
Matthew F Chersich ◽  
Etienne E Muller ◽  
Philippe Mayaud ◽  
...  
Keyword(s):  
Dna Extraction ◽  
Sampling Methods ◽  
Kappa Statistic ◽  
Hpv Infection ◽  
Infection Prevalence ◽  
Hpv Dna ◽  
Oral Rinse ◽  
Roche Linear Array ◽  
Cellular Dna ◽  
Array Performance

Worldwide, 96,000 cases of oropharyngeal cancer (OPC) occurred in 2012. Human papillomavirus (HPV) is a risk factor for OPC. Data on oropharyngeal HPV infection are limited. There is no consensus on the best sampling method for detecting the infection. We describe the prevalence of oropharyngeal HPV infection among HIV-infected men and compare the performance of oral rinses and swabs in detecting oropharyngeal HPV infection. Paired oral rinses and swabs for 181 men were tested for HPV DNA using the Roche Linear Array. Performance was determined by the number of infections detected and the percentage of samples with adequate DNA extraction. Agreement between sampling methods was assessed by the kappa statistic. Prevalence of oropharyngeal HPV infection with rinse samples was 1.8% (three infections) and 0.6% (one infection) with swabs (p = 0.06). Adequate cellular DNA extraction was more likely with rinse (93.4%) than swab samples (89.0%, p = 0.05). There was moderate agreement between the methods (kappa = 0.49). The prevalence of oropharyngeal HPV DNA infection among this predominantly heterosexual sample of men living with HIV was low and consistent with the infrequent oral sex practices. Oral rinse performed better than oral swab in detecting oropharyngeal HPV DNA infection and might contribute to screening for OPCs.

scholarly journals Assessment of Spoilage Bacterial Communities in Food Wrap and Modified Atmospheres-Packed Minced Pork Meat Samples by 16S rDNA Metagenetic Analysis

2020 ◽  
Vol 10 ◽  
Author(s):  
Emilie Cauchie ◽  
Laurent Delhalle ◽  
Bernard Taminiau ◽  
Assia Tahiri ◽  
Nicolas Korsak ◽  
...  
Keyword(s):  
16S Rdna ◽  
Bacterial Communities ◽  
Pork Meat ◽  
Modified Atmospheres ◽  
Meat Samples

Molecular bacterial diversity and distribution in waste from a steel plant

2008 ◽  
Vol 54 (12) ◽  
pp. 996-1005 ◽  
Author(s):  
Dulcecleide B. Freitas ◽  
Mariana P. Reis ◽  
Leandro M. Freitas ◽  
Paulo S. Assis ◽  
Edmar Chartone-Souza ◽  
...  
Keyword(s):  
Bacterial Diversity ◽  
16S Rdna ◽  
Bacterial Communities ◽  
Sequence Similarity ◽  
Diversity Indices ◽  
Operational Taxonomic Units ◽  
Rdna Sequences ◽  
Partial Length ◽  
16S Rdna Sequences ◽  
Novel Taxa

We characterized the bacterial diversity of newly produced steelmaking wastes (NPSW) and steelmaking wastes deposited (SWD) in a restricted land area, generated by the siderurgic industry, using the 16S rDNA clone library approach. A total of 212 partial-length sequences were analyzed, revealing 123 distinct operational taxonomic units (OTUs) determined by the DOTUR program to 97% sequence similarity. Phylogenetic analysis of bacterial 16S rDNA sequences from the NPSW and SWD libraries demonstrated that Gammaproteobacteria, Betaproteobacteria, Alphaproteobacteria, Actinobacteria, Planctomycetes, Firmicutes, and Bacteroidetes were represented in both libraries. Deltaproteobacteria, Acidobacteria, Chloroflexi, Deinococcus-thermus, Gemmatimonadetes, and candidate divisions OP10 and OD1 were only present in the SWD library, and Nitrospira was only present in the NPSW library. The abundance of sequences affiliated with Gammaproteobacteria was high in both libraries. Six previously unclassified OTUs may represent novel taxa. Based on diversity indices (Simpson, Shannon–Weaver, Chao1, and ACE), the SWD library had a higher diversity. LIBSHUFF comparisons of the composition of the 2 libraries showed that they were significantly different. These results indicate that the bacterial communities in steelmaking wastes present high phylogenetic diversity and complexity. A possible association between the functional diversity and the bacterial communities’ complexity requires further phenotypic investigation.

scholarly journals Molecular Monitoring of Succession of Bacterial Communities in Human Neonates

2002 ◽  
Vol 68 (1) ◽  
pp. 219-226 ◽  
Author(s):  
Christine F. Favier ◽  
Elaine E. Vaughan ◽  
Willem M. De Vos ◽  
Antoon D. L. Akkermans
Keyword(s):  
Sequence Analysis ◽  
16S Rdna ◽  
Bacterial Communities ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Bacterial Colonization ◽  
Molecular Monitoring ◽  
Fecal Samples ◽  
16S Rdna Sequence Analysis ◽  
Rdna Sequences ◽  
Gradient Gel Electrophoresis

ABSTRACT The establishment of bacterial communities in two healthy babies was examined for more than the first 10 months of life by monitoring 16S ribosomal DNA (rDNA) diversity in fecal samples by PCR and denaturing gradient gel electrophoresis (DGGE) and by analyzing the sequences of the major ribotypes. DGGE profiles of the dominant populations in the intestines of the infants were obtained by analyzing daily or weekly fecal samples. After delivery, the germfree infant gastrointestinal tracts were rapidly colonized, and the succession of bacteria in each ecosystem was monitored. During the first few days of life the profiles were simple, but they became more complex as the bacterial diversity increased with time in both babies. Clone libraries of amplified 16S rDNA fragments from baby feces were constructed, and these libraries allowed identification of the bacterial types by comparative DNA sequence analysis; the bacteria identified included members of the genera Bifidobacterium, Ruminococcus, Enterococcus, Clostridium, and Enterobacter. Species most closely related to the genera Bifidobacterium and Ruminococcus in particular dominated the intestinal microbiota based on the stability over time and the numbers, as estimated by the intensities of the bands. However, 19 of the 34 cloned rDNA sequences exhibited less than 97% identity with sequences of known bacteria or cloned sequences in databases. This study showed that using PCR-DGGE and 16S rDNA sequence analysis together resulted in a dynamic description of bacterial colonization in the infant intestinal ecosystem and allowed visualization of bacteria that are difficult to cultivate or to detect by other methods.

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