Collection and Processing of Microbial Samples

2013 ◽  
pp. 89-130
Author(s):  
Samir Deshpande
Keyword(s):  
Microbial Samples

scholarly journals Influence of local tetracycline on the microbiota of alveolar osteitis in rats

2008 ◽  
Vol 19 (2) ◽  
pp. 119-123 ◽  
Author(s):  
Joseane Maria Dias Bosco ◽  
Sérgio Ricardo de Oliveira ◽  
Álvaro Francisco Bosco ◽  
Christiane Marie Schweitzer ◽  
Elerson Gaetti Jardim Júnior
Keyword(s):  
Aqueous Solution ◽  
Wistar Rats ◽  
Blood Agar ◽  
Selective Media ◽  
Sterile Saline ◽  
Alveolar Osteitis ◽  
Microbial Samples

The aim of the present study was to evaluate the effects of local tetracycline on the occurrence of alveolar osteitis in rats, and on the microbiota associated to this infection. Forty Wistar rats were randomly assigned to 4 groups (n=10): I - the rats had the maxillary right incisor extracted and the alveolar wound did not receive any treatment; II - adrenaline and Ringer-PRAS were introduced into the alveolar wound; III - the alveolar wound was irrigated with sterile saline; and IV - the alveolar wound was irrigated with an aqueous solution of tetracycline. Microbial samples from the alveolar wounds were collected 2 days after surgery and inoculated on blood agar (with and without 8 µg/mL of tetracycline) and other selective media, and were incubated in either aerobiosis or anaerobiosis at 37ºC, for 2 to 14 days. It was verified that tetracycline reduced the occurrence of alveolar osteitis in the rats and caused significant changes in the microbiota of the surgical sites, decreasing the number of anaerobes and increasing the participation of tetracycline-resistant and multi-resistant microorganisms.

scholarly journals Bacteremic sepsis leads to higher mortality when adjusting for confounders with propensity score matching

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Lisa Mellhammar ◽  
Fredrik Kahn ◽  
Caroline Whitlow ◽  
Thomas Kander ◽  
Bertil Christensson ◽  
...  
Keyword(s):  
Intensive Care ◽  
Clinical Review ◽  
Pathogen Detection ◽  
Mortality Rates ◽  
Blood Cultures ◽  
Population Heterogeneity ◽  
Sepsis Diagnosis ◽  
Culture Positive ◽  
Culture Negative ◽  
Microbial Samples

AbstractOne can falsely assume that it is well known that bacteremia is associated with higher mortality in sepsis. Only a handful of studies specifically focus on the comparison of culture-negative and culture-positive sepsis with different conclusions depending on study design. The aim of this study was to describe outcome for critically ill patients with either culture-positive or -negative sepsis in a clinical review. We also aimed to identify subphenotypes of sepsis with culture status included as candidate clinical variables. Out of 784 patients treated in intensive care with a sepsis diagnosis, blood cultures were missing in 140 excluded patients and 95 excluded patients did not fulfill a sepsis diagnosis. Of 549 included patients, 295 (54%) had bacteremia, 90 (16%) were non-bacteremic but with relevant pathogens detected and in 164 (30%) no relevant pathogen was detected. After adjusting for confounders, 90-day mortality was higher in bacteremic patients, 47%, than in non-bacteremic patients, 36%, p = 0.04. We identified 8 subphenotypes, with different mortality rates, where pathogen detection in microbial samples were important for subphenotype distinction and outcome. In conclusion, bacteremic patients had higher mortality than their non-bacteremic counter-parts and bacteremia is more common in sepsis when studied in a clinical review. For reducing population heterogeneity and improve the outcome of trials and treatment for sepsis, distinction of subphenotypes might be useful and pathogen detection an important factor.

A Full-Ocean-Depth Sampler for Hadal Microbes Based on Multistage Membrane Filters With In-Situ Preservation

2021 ◽  
Vol 55 (2) ◽  
pp. 25-34
Author(s):  
Jiawang Chen ◽  
Weitao He ◽  
Peng Zhou ◽  
Jiasong Fang ◽  
Dahai Zhang ◽  
...  
Keyword(s):  
Ribonucleic Acid ◽  
Gene Pool ◽  
Special Structure ◽  
High Quality ◽  
Mariana Trench ◽  
Membrane Filters ◽  
In Situ Preservation ◽  
Microbial Samples ◽  
Flow Pump

Abstract In order to obtain high-quality microbial samples from the hadal zone, which has a depth of over 6,000 m, a full-ocean-depth sampler with the function of in-situ filtration and preservation was developed. A flow pump and several membrane filters were used for in-situ filtration under the sea. With a multistage filtering structure, the microbes can be initially screened according to their sizes. To avoid the degradation of microbial ribonucleic acid (RNA), a special structure was designed to inject the RNAlater solution into the samples immediately after the filtration. The sampler was tested in our laboratory and deployed during Mariana TS-15 in 2019. It was installed on a hadal lander of Shanghai Ocean University and deployed at MBR02 (11.371°N, 142.587°E, 10,931 m) in the Mariana Trench. A total of 20 L of in-situ seawater was filtered, and membranes with pore sizes of 3 and 0.2 μm were preserved. The study is expected to provide important support for the establishment of a hadal microbial gene pool.

scholarly journals In vitro evaluation of the effectiveness of the chemomechanical preparation against Enterococcus faecalis after single- or multiple-visit root canal treatment

2007 ◽  
Vol 21 (4) ◽  
pp. 308-313 ◽  
Author(s):  
Eduardo Diogo Gurgel-Filho ◽  
Nilton Vivacqua-Gomes ◽  
Brenda Paula Figueiredo de Almeida Gomes ◽  
Caio Cezar Randi Ferraz ◽  
Alexandre Augusto Zaia ◽  
...  
Keyword(s):  
Calcium Hydroxide ◽  
Enterococcus Faecalis ◽  
Root Canal ◽  
Control Groups ◽  
Single Visit ◽  
Root Canals ◽  
Multiple Visit ◽  
Microbial Samples ◽  
Chlorhexidine Gel

The purpose was to assess the elimination of Enterococcus faecalis in vitro in human mandibular premolars after chemomechanical preparation with or without the use of a calcium hydroxide dressing. After 60 days of contamination with E. faecalis, the root canals were prepared using the Crown-Down technique combined with 2% chlorhexidine gel irrigation. Then, the specimens were divided into two experimental groups, treated in a single visit or in multiple visits, and two control groups. The multiple-visit group received a dressing with calcium hydroxide for 14 days (CalenTM) and the single-visit group did not receive any medication. In the two control groups, the canals were filled with BHI after chemomechanical preparation with 2% chlorhexidine gel or distilled water. Microbial samples were taken from the root canals for colony forming unit count for each phase of the treatment using sterile paper points inside the root canal lumen. Data were ranked and analyzed by the Kruskal-Wallis statistical test. The residual microbial colonies were then assessed. The results showed that chemomechanical preparation using 2% chlorhexidine gel with no intra-canal dressing reduced by 100% the E. faecalis contamination of the root canal lumen. The calcium-hydroxide group that received the 14-day intra-canal dressing allowed a small number of bacteria to grow between visits, but without statistical differences between groups.

scholarly journals Community-curated and standardised metadata of published ancient metagenomic samples with AncientMetagenomeDir

2020 ◽  
Author(s):  
James A. Fellows Yates ◽  
Aida Andrades Valtueña ◽  
Ashild J. Vågene ◽  
Becky Cribdon ◽  
Irina M. Velsko ◽  
...  
Keyword(s):  
Large Scale ◽  
Genetic Data ◽  
Data Retrieval ◽  
Data Sources ◽  
Valuable Data ◽  
Dna And Rna ◽  
Wide Range ◽  
Evolutionary Studies ◽  
Meta Analyses ◽  
Microbial Samples

ABSTRACTAncient DNA and RNA are valuable data sources for a wide range of disciplines. Within the field of ancient metagenomics, the number of published genetic datasets has risen dramatically in recent years, and tracking this data for reuse is particularly important for large-scale ecological and evolutionary studies of individual microbial taxa, microbial communities, and metagenomic assemblages. AncientMetagenomeDir (archived at https://doi.org/10.5281/zenodo.3980833) is a collection of indices of published genetic data deriving from ancient microbial samples that provides basic, standardised metadata and accession numbers to allow rapid data retrieval from online repositories. These collections are community-curated and span multiple sub-disciplines in order to ensure adequate breadth and consensus in metadata definitions, as well as longevity of the database. Internal guidelines and automated checks to facilitate compatibility with established sequence-read archives and term-ontologies ensure consistency and interoperability for future meta-analyses. This collection will also assist in standardising metadata reporting for future ancient metagenomic studies.

scholarly journals Fungi and Oomycetes in the Irrigation Water of Forest Nurseries

Forests ◽  
2020 ◽  
Vol 11 (4) ◽  
pp. 459 ◽  
Author(s):  
Adas Marčiulynas ◽  
Diana Marčiulynienė ◽  
Jūratė Lynikienė ◽  
Artūras Gedminas ◽  
Miglė Vaičiukynė ◽  
...  
Keyword(s):  
Irrigation Water ◽  
Plant Pathogens ◽  
High Throughput Sequencing ◽  
Irrigation System ◽  
Tree Seedlings ◽  
High Quality ◽  
Forest Nurseries ◽  
Study Sites ◽  
Microbial Samples

The aim of the present study was to assess fungal and oomycete communities in the irrigation water of forest nurseries, focusing on plant pathogens in the hope of getting a better understanding of potential pathogenic microorganisms and spreading routes in forest nurseries. The study sites were at Anykščiai, Dubrava, Kretinga and Trakai state forest nurseries in Lithuania. For the collection of microbial samples, at each nursery five 100-L water samples were collected from the irrigation ponds and filtered. Following DNA isolation from the irrigation water filtrate samples, these were individually amplified using ITS rDNA as a marker and subjected to PacBio high-throughput sequencing. Clustering in the SCATA pipeline and the taxonomic classification of 24,006 high-quality reads showed the presence of 1286 non-singleton taxa. Among those, 895 were representing fungi and oomycetes. The detected fungi were 57.3% Ascomycota, 38.1% Basidiomycota, 3.1% Chytridiomycota, 0.8% Mucoromycota and 0.7% Oomycota. The most common fungi were Malassezia restricta E. Guého, J. Guillot & Midgley (20.1% of all high-quality fungal sequences), Pezizella discreta (P. Karst.) Dennis (10.8%) and Epicoccum nigrum Link (4.9%). The most common oomycetes were Phytopythium cf. citrinum (B. Paul) Abad, de Cock, Bala, Robideau, Lodhi & Lévesque (0.4%), Phytophthora gallica T. Jung & J. Nechwatal (0.05%) and Peronospora sp. 4248_322 (0.05%). The results demonstrated that the irrigation water used by forest nurseries was inhabited by a species-rich but largely site-specific communities of fungi. Plant pathogens were relatively rare, but, under suitable conditions, these can develop rapidly, spread efficiently through the irrigation system and be a threat to the production of high-quality tree seedlings.

scholarly journals A machine learning framework to determine geolocations from metagenomic profiling

2020 ◽  
Vol 15 (1) ◽  
Author(s):  
Lihong Huang ◽  
Canqiang Xu ◽  
Wenxian Yang ◽  
Rongshan Yu
Keyword(s):  
Machine Learning ◽  
Prediction Models ◽  
Geographic Origin ◽  
Training Data ◽  
Metagenomic Data ◽  
Training Dataset ◽  
Kriging Interpolation ◽  
Learning Framework ◽  
Testing Data ◽  
Microbial Samples

Abstract Background Studies on metagenomic data of environmental microbial samples found that microbial communities seem to be geolocation-specific, and the microbiome abundance profile can be a differentiating feature to identify samples’ geolocations. In this paper, we present a machine learning framework to determine the geolocations from metagenomics profiling of microbial samples. Results Our method was applied to the multi-source microbiome data from MetaSUB (The Metagenomics and Metadesign of Subways and Urban Biomes) International Consortium for the CAMDA 2019 Metagenomic Forensics Challenge (the Challenge). The goal of the Challenge is to predict the geographical origins of mystery samples by constructing microbiome fingerprints.First, we extracted features from metagenomic abundance profiles. We then randomly split the training data into training and validation sets and trained the prediction models on the training set. Prediction performance was evaluated on the validation set. By using logistic regression with L2 normalization, the prediction accuracy of the model reaches 86%, averaged over 100 random splits of training and validation datasets.The testing data consists of samples from cities that do not occur in the training data. To predict the “mystery” cities that are not sampled before for the testing data, we first defined biological coordinates for sampled cities based on the similarity of microbial samples from them. Then we performed affine transform on the map such that the distance between cities measures their biological difference rather than geographical distance. After that, we derived the probabilities of a given testing sample from unsampled cities based on its predicted probabilities on sampled cities using Kriging interpolation. Results show that this method can successfully assign high probabilities to the true cities-of-origin of testing samples. Conclusion Our framework shows good performance in predicting the geographic origin of metagenomic samples for cities where training data are available. Furthermore, we demonstrate the potential of the proposed method to predict metagenomic samples’ geolocations for samples from locations that are not in the training dataset.

scholarly journals Autonomous Microbial Sampler (AMS), a device for the uncontaminated collection of multiple microbial samples from submarine hydrothermal vents and other aquatic environments

2006 ◽  
Vol 53 (5) ◽  
pp. 894-916 ◽  
Author(s):  
Craig D. Taylor ◽  
Kenneth W. Doherty ◽  
Stephen J. Molyneaux ◽  
Archie T. Morrison ◽  
John D. Billings ◽  
...  
Keyword(s):  
Hydrothermal Vents ◽  
Aquatic Environments ◽  
Microbial Samples
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