Absence of Yersinia pestis-specific DNA in human teeth from five European excavations of putative plague victims

Microbiology ◽  
2004 ◽  
Vol 150 (2) ◽  
pp. 341-354 ◽  
Author(s):  
M. Thomas P. Gilbert ◽  
Jon Cuccui ◽  
William White ◽  
Niels Lynnerup ◽  
Richard W. Titball ◽  
...  
Keyword(s):  
Yersinia Pestis ◽  
Ancient Dna ◽  
Dna Sequences ◽  
Bacterial Species ◽  
Collaborative Study ◽  
Independent Research ◽  
Human Teeth ◽  
Bacterial Dna ◽  
Embedding Technique ◽  
Positive Results

This study reports the results of a collaborative study undertaken by two independent research groups to (a) confirm recent PCR-based detection of Yersinia pestis DNA in human teeth from medieval plague victims in France, and (b) to extend these observations over five different European burial sites believed to contain plague victims dating from the late 13th to 17th centuries. Several different sets of primers were used, including those previously documented to yield positive results on ancient DNA extracts. No Y. pestis DNA could be amplified from DNA extracted from 108 teeth belonging to 61 individuals, despite the amplification of numerous other bacterial DNA sequences. Several methods of extracting dentine prior to the DNA extraction were also compared. PCR for bacterial 16S rDNA indicated the presence of multiple bacterial species in 23 out of 27 teeth DNA extracts where dentine was extracted using previously described methods. In comparison, positive results were obtained from only five out of 44 teeth DNA extracts for which a novel contamination-minimizing embedding technique was used. Therefore, high levels of environmental bacterial DNA are present in DNA extracts where previously described methods of tooth manipulation are used. To conclude, the absence of Y. pestis-specific DNA in an exhaustive search using specimens from multiple putative European plague burial sites does not allow us to confirm the identification of Y. pestis as the aetiological agent of the Black Death and subsequent plagues. In addition, the utility of the published tooth-based ancient DNA technique used to diagnose fatal bacteraemias in historical epidemics still awaits independent corroboration.

scholarly journals Electrochemical profiles of bacteria isolated from crude oil on simple benzene compounds detection

2021 ◽  
Vol 948 (1) ◽  
pp. 012026
Author(s):  
A A Ghozali ◽  
D Iswantini ◽  
C Kusmana ◽  
N Nurhidayat
Keyword(s):  
Crude Oil ◽  
Polyaromatic Hydrocarbons ◽  
Bacterial Species ◽  
Media Culture ◽  
Bacterial Dna ◽  
Growth Assay ◽  
Cyclic Voltammetry Method ◽  
Benzene Toluene ◽  
Positive Results ◽  
Benzene Compounds

Abstract Five polyaromatic hydrocarbons (PAHs) degrading bacterial species had been isolated from crude oil samples. All bacteria were positive Gram-stained, except one; and had positive results on the catalase test. After sequencing bacterial DNA, three bacterial genera were obtained with 99-100% certainty, namely: Pseudomonas sp., Staphylococcus sp., and Bacillus sp. All bacteria were known strongly to form a biofilm, thus can be applied for biosensing and/or bioremediation techniques. Using minimal mineral media growth assay as media culture, all bacteria were able to degrade naphthalene and anthracene, Staphylococcus sp. shown the strong degradation affinity. Meanwhile, Bacillus sp. tended to form strong biofilm. Electrochemical data were obtained with the cyclic voltammetry method, with a scan rate of 100 mV/s. Voltammogram profiles of all bacteria against simple benzene compounds (benzene, toluene, and xylene; concentration for each compound 1μL/mL) showed irreversible oxidation peaks at 0.20-0.40 V ppm of the analyte, producing current 50-100 μA. The measurements were taken when the solution was more stable (±10 seconds) after vigorous shaking to homogenize benzene compounds and introducing O2 into the solution. The peaks were decreasing over the next cycles, indicating the lower bioavailability of benzene compounds to be degraded with O2.

Systematic benchmark of ancient DNA read mapping

2021 ◽  
Author(s):  
Adrien Oliva ◽  
Raymond Tobler ◽  
Alan Cooper ◽  
Bastien Llamas ◽  
Yassine Souilmi
Keyword(s):  
Ancient Dna ◽  
Dna Sequences ◽  
Population Genetic ◽  
Reference Genome ◽  
Population Data ◽  
Human Populations ◽  
Current Standard ◽  
Read Mapping ◽  
Reference Bias ◽  
The Impact

Abstract The current standard practice for assembling individual genomes involves mapping millions of short DNA sequences (also known as DNA ‘reads’) against a pre-constructed reference genome. Mapping vast amounts of short reads in a timely manner is a computationally challenging task that inevitably produces artefacts, including biases against alleles not found in the reference genome. This reference bias and other mapping artefacts are expected to be exacerbated in ancient DNA (aDNA) studies, which rely on the analysis of low quantities of damaged and very short DNA fragments (~30–80 bp). Nevertheless, the current gold-standard mapping strategies for aDNA studies have effectively remained unchanged for nearly a decade, during which time new software has emerged. In this study, we used simulated aDNA reads from three different human populations to benchmark the performance of 30 distinct mapping strategies implemented across four different read mapping software—BWA-aln, BWA-mem, NovoAlign and Bowtie2—and quantified the impact of reference bias in downstream population genetic analyses. We show that specific NovoAlign, BWA-aln and BWA-mem parameterizations achieve high mapping precision with low levels of reference bias, particularly after filtering out reads with low mapping qualities. However, unbiased NovoAlign results required the use of an IUPAC reference genome. While relevant only to aDNA projects where reference population data are available, the benefit of using an IUPAC reference demonstrates the value of incorporating population genetic information into the aDNA mapping process, echoing recent results based on graph genome representations.

scholarly journals Rapid Identification of Bacterial Species with Bacterial DNA Microarray in Cirrhotic Patients with Spontaneous Bacterial Peritonitis

2009 ◽  
Vol 48 (1) ◽  
pp. 3-10 ◽  
Author(s):  
Takaaki Sugihara ◽  
Masahiko Koda ◽  
Yoshiko Maeda ◽  
Tomomitsu Matono ◽  
Takakazu Nagahara ◽  
...  
Keyword(s):  
Dna Microarray ◽  
Spontaneous Bacterial Peritonitis ◽  
Bacterial Species ◽  
Rapid Identification ◽  
Bacterial Dna ◽  
Bacterial Peritonitis ◽  
Cirrhotic Patients

scholarly journals A Genomic Distance Based on MUM Indicates Discontinuity between Most Bacterial Species and Genera

2008 ◽  
Vol 191 (1) ◽  
pp. 91-99 ◽  
Author(s):  
Marc Deloger ◽  
Meriem El Karoui ◽  
Marie-Agnès Petit
Keyword(s):  
Dna Sequences ◽  
Dna Content ◽  
Core Genome ◽  
Biological Diversity ◽  
Bacterial Species ◽  
Genomic Distance ◽  
The Core ◽  
Intraspecies Diversity ◽  
Genome Level ◽  
Definition Of

ABSTRACT The fundamental unit of biological diversity is the species. However, a remarkable extent of intraspecies diversity in bacteria was discovered by genome sequencing, and it reveals the need to develop clear criteria to group strains within a species. Two main types of analyses used to quantify intraspecies variation at the genome level are the average nucleotide identity (ANI), which detects the DNA conservation of the core genome, and the DNA content, which calculates the proportion of DNA shared by two genomes. Both estimates are based on BLAST alignments for the definition of DNA sequences common to the genome pair. Interestingly, however, results using these methods on intraspecies pairs are not well correlated. This prompted us to develop a genomic-distance index taking into account both criteria of diversity, which are based on DNA maximal unique matches (MUM) shared by two genomes. The values, called MUMi, for MUM index, correlate better with the ANI than with the DNA content. Moreover, the MUMi groups strains in a way that is congruent with routinely used multilocus sequence-typing trees, as well as with ANI-based trees. We used the MUMi to determine the relatedness of all available genome pairs at the species and genus levels. Our analysis reveals a certain consistency in the current notion of bacterial species, in that the bulk of intraspecies and intragenus values are clearly separable. It also confirms that some species are much more diverse than most. As the MUMi is fast to calculate, it offers the possibility of measuring genome distances on the whole database of available genomes.

Hybridization capture of Larix candidate adaptive genes from sedimentary ancient DNA.

2021 ◽  
Author(s):  
Stefano Meucci ◽  
Luise Schulte ◽  
Kathleen R. Stoof-Leichsenring ◽  
Stefan Kruse ◽  
Konstantin Krutovsky ◽  
...  
Keyword(s):  
Ancient Dna ◽  
Dna Sequences ◽  
Environmental Changes ◽  
Genetic Material ◽  
Siberian Larch ◽  
Shotgun Sequencing ◽  
Adaptive Genetic Variation ◽  
Hybridization Capture ◽  
Sequencing Method ◽  
Larch Species

<p>Siberian larch forests dominate large areas of northern Russia and contribute important roles for the world´s ecosystem. In order to understand the past dynamics of larches and their adaptive genetic variation, sedimentary ancient DNA (sedaDNA) extracted from lake sediment cores is a crucial source of genetic material. The difficulty of retrieving extremely rare DNA sequences from samples reaching back up to 25000 years in age, is challenging. Previous studies (Schulte et al.) showed that the hybridization capture allowed an enrichment of targeted sequences by several orders of magnitude in comparison to shotgun sequencing method. Therefore, we established for the first time, a hybridization capture method targeting 65 candidate adaptive genes laying on the Larix nuclear genome. Our preliminary results showed the ability of our newly established method to enrich extremely rare DNA sequences of the targeted Larix candidate adaptive genes, which were not retrieved by shotgun sequencing method applied on the same samples. Furthermore, the results allowed to detect and compare specific nucleotide polymorphism of adaptive candidate genes among sedaDNA samples distributed in space and time. The establishment of this new method is laying the basis to investigate possible adaptive variation of larch species acquired across the dry and cold conditions of the Last Glacial Maximum (LGM); as well as their possible advantages or disadvantages in relation to the current environmental changes toward dry and warm conditions.</p>

scholarly journals Quantifying and reducing spurious alignments for the analysis of ultra-short ancient DNA sequences

BMC Biology ◽  
2018 ◽  
Vol 16 (1) ◽  
Author(s):  
Cesare de Filippo ◽  
Matthias Meyer ◽  
Kay Prüfer
Keyword(s):  
Ancient Dna ◽  
Dna Sequences

RAZOR™ EX Anthrax Air Detection System for Detection of Bacillus anthracis Spores from Aerosol Collection Samples: Collaborative Study

2013 ◽  
Vol 96 (2) ◽  
pp. 392-398 ◽  
Author(s):  
Ted Hadfield ◽  
Valorie Ryan ◽  
Usha K Spaulding ◽  
Kristine M Clemens ◽  
Irene M Ota ◽  
...  
Keyword(s):  
Confidence Interval ◽  
Bacillus Anthracis ◽  
Detection System ◽  
Collaborative Study ◽  
Probability Of Detection ◽  
Data Sets ◽  
Method Performance ◽  
Bacillus Anthracis Spores ◽  
Phosphate Buffered Saline ◽  
Positive Results

Abstract The RAZOR™ EX Anthrax Air Detection System was validated in a collaborative study for the detection of Bacillus anthracis in aerosol collection buffer. Phosphate-buffered saline was charged with 1 mg/mL standardized dust to simulate an authentic aerosol collection sample. The dust-charged buffer was spiked with either B. anthracis Ames at 2000 spores/mL or Bacillus cereus at 20 000 spores/mL. Twelve collaborators participated in the study, with four collaborators at each of three sites. Each collaborator tested 12 replicates of B. anthracis in dust-charged buffer and 12 replicates of B. cereus in dust-charged buffer. All samples sets were randomized and blind-coded. All collaborators produced valid data sets (no collaborators displayed systematic errors) and there was only one invalid data point. After unblinding, the analysis revealed a cross-collaborator probability of detection (CPOD) of 1.00 (144 positive results from 144 replicates, 95% confidence interval 0.975–1.00) for the B. anthracis samples and a CPOD of 0.00 (0 positive results from 143 replicates, 95% confidence interval 0.00–0.0262) for the B. cereus samples. These data meet the requirements of AOAC Standard Method Performance Requirement 2010.003, developed by the Stakeholder Panel on Agent Detection Assays.

scholarly journals How, when, and where relic DNA biases estimates of microbial diversity

2017 ◽  
Author(s):  
JT Lennon ◽  
ME Muscarella ◽  
SA Muscarella ◽  
BK Lehmkuhl
Keyword(s):  
Microbial Diversity ◽  
Dna Sequences ◽  
Species Abundance ◽  
Rrna Gene ◽  
Bacterial Dna ◽  
Soil Sediment ◽  
Species Abundance Distributions ◽  
Abundance And Diversity ◽  
Dna Pool ◽  
Biased Estimates

Extracellular or “relic” DNA is one of the largest pools of nucleic acids in the mbiosphere1,2. Relic DNA can influence a number of important ecological and evolutionary processes, but it may also bias estimates of microbial abundance and diversity, which has implications for understanding environmental, engineered, and host-associated ecosystems. We developed models capturing the fundamental processes that regulate the size and composition of the relic DNA pools to identify scenarios leading to biased estimates of biodiversity. Our models predict that bias increases with relic DNA pool size, but only when the species abundance distributions (SAD) of relic and intact DNA are distinct from one another. We evaluated our model predictions by quantifying relic DNA and assessing its contribution to bacterial diversity using 16S rRNA gene sequences collected from different ecosystem types, including soil, sediment, water, and the mammalian gut. On average, relic DNA made up 33 % of the total bacterial DNA pool, but exceeded 80 % in some samples. Despite its abundance, relic DNA had no effect on estimates of taxonomic and phylogenetic diversity, even in ecosystems where processes such as the physical protection of relic DNA are common and predicted by our models to generate bias. Rather, our findings are consistent with the expectation that relic DNA sequences degrade in proportion to their abundance and therefore may contribute minimally to estimates of microbial diversity.

scholarly journals Oral Dextran Sulfate Sodium Administration Induces Peripheral Spondyloarthritis Features in SKG Mice Accompanied by Intestinal Bacterial Translocation and Systemic Th1 and Th17 Cell Activation.

2021 ◽  
Author(s):  
Yuya Tabuchi ◽  
Masao Katsushima ◽  
Yuri Nishida ◽  
Mirei Shirakashi ◽  
Hideaki Tsuji ◽  
...  
Keyword(s):  
Bacterial Translocation ◽  
Whole Blood ◽  
Th17 Cell ◽  
Cell Activation ◽  
Dextran Sulfate ◽  
Dextran Sulfate Sodium ◽  
Quantitative Polymerase Chain Reaction ◽  
Bacterial Species ◽  
Bacterial Dna ◽  
Anti Fungal

Abstract Background: Spondyloarthritis (SpA) is an autoimmune and autoinflammatory musculoskeletal disease characterised by systemic enthesitis. Recent research has focused on subclinical inflammatory bowel disease (IBD) in SpA pathogenesis. SKG mice, harbouring the Zap70 W163C mutation, increase autoreactive Th17 cells intrinsically, and show SpA features, including enteritis, after peritoneal injection of β-1,3- glucan under SPF conditions. In a conventional environment, they exhibit spontaneous arthritis with fungal factors. This study aimed to clarify whether oral dextran sulfate sodium (DSS) administration, utilised in IBD model mice, can provoke SpA features in SKG mice under SPF conditions, focusing on the relationship between gut microorganisms and SpA pathogenesis.Methods: SKG and BALB/c mice were administered oral DSS, and their body weights, arthritis, and enthesitis scores were recorded. In another cohorts, antibiotics (meropenem and vancomycin) or an anti-fungal agent (amphotericin B) were administered orally before DSS administration. The splenic Th1 and Th17 cell populations were examined before and after DSS administration using flow cytometry. Furthermore, the amount of circulating bacterial DNA in whole blood was measured by absolute quantitative polymerase chain reaction (qPCR), and the number and characteristics of bacterial species corresponding to these circulating DNA were analised by next-generation sequencing (NGS).Results: Ankle enthesitis as a peripheral SpA feature was elicited in half of DSS-administered SKG mice, and none of the BALB/c mice. Pre-administration of antibiotics suppressed enthesitis, whilst an anti-fungal agent could not. Th1 and Th17 cell levels in the spleen increased after DSS administration, and this was suppressed by pre-administration of antibiotics. SKG mice have a larger amount of bacterial DNA in whole blood than BALB/c mice before and one day after the initiation of DSS administration. The number of bacterial species in whole blood increased after DSS administration in SKG and BALB/c mice. Some genera and species significantly specific to the DSS-treated SKG mice group were also detected. Conclusion: Oral DSS administration alone elicited peripheral enthesitis in SKG mice with bacterial translocation accompanied by increased splenic Th1 and Th17 cell levels. Pre-administration of antibiotics ameliorated these DSS-induced SpA features. These findings suggest that intestinal bacterial leakage plays a pivotal role in SpA pathogenesis.

scholarly journals Evaluating Flinders Technology Associates card for transporting bacterial isolates and retrieval of bacterial DNA after various storage conditions

2020 ◽  
Vol 13 (10) ◽  
pp. 2243-2251
Author(s):  
Azhar G. Shalaby ◽  
Neveen R. Bakry ◽  
Abeer A. E. Mohamed ◽  
Ashraf A. Khalil
Keyword(s):  
Nucleic Acid ◽  
Bacterial Species ◽  
Storage Conditions ◽  
Animal Origin ◽  
Cell Detection ◽  
Bacterial Cells ◽  
Gram Positive ◽  
Bacterial Dna ◽  
Gram Negative ◽  
Fta Cards

Background and Aim: Flinders Technology Associates (FTA) cards simplify sample storage, transport, and extraction by reducing cost and time for diagnosis. This study evaluated the FTA suitability for safe transport and storage of Gram-positive and Gram-negative bacterial cells of animal origin on its liquid culture form and from organ impression smears (tissues) under the same routine condition of microbiological laboratory along with detecting their nucleic acid over different storage conditions. Materials and Methods: Increase in bacterial count from 104 to 107 (colony-forming units/mL) of 78 isolates representing seven bacterial species was applied onto cards. FTA cards were grouped and inoculated by these bacteria and then stored at different conditions of 24-27°C, 4°C, and –20°C for 24 h, for 2 weeks, for 1 and 3 month storage, respectively. Bacteriological examination was done, after which bacterial DNA was identified using specific primers for each bacterial type and detected by polymerase chain reaction (PCR). Results: The total percentage of recovered bacteria from FTA cards was 66.7% at 24-27–C for 24 h, the detection limit was 100% in Gram-positive species, while it was 57.4% in Gram-negative ones. Regarding viable cell detection from organ impression smears, it was successful under the previous conditions. No live bacterial cells were observed by bacteriological isolation rather than only at 24-27°C for 24 h storage. All bacterial DNA were sufficiently confirmed by the PCR technique at different conditions. Conclusion: Overall, the FTA card method was observed to be a valid tool for nucleic acid purification for bacteria of animal origin in the form of culture or organ smears regardless of its Gram type and is used for a short time only 24 h for storage and transport of live bacteria specifically Gram-positive type. Moreover, the bacterial nucleic acid was intact after storage in –20°C for 3 months and was PCR amplifiable.

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