The 2nd International Conference (https://shap-conference.com) is one of the activities of the "Sino-Hellenic Academic Project" of the Hellenic Culture Research Centre, the Yellow River Culture Research Centre in Greece and the Collaborative Innovation Centre for Yellow River Culture and Sustainable Development.
At the conference, the results of the application of the unique technology of DNA Sequence Archaeogene, which was applied in collaboration with Professor Ioannis Lyritzis, will be presented on archaeological finds from the Mycenaean settlement at Kastrouli in Fokida. More specifically, through the publication "Whole Genome Sequencing Approach Revealed Microbial Species in Mycenaean Period Associated Residual Plant Biomass: First Results", new technologies for sequencing microbial DNA from archaeological finds will be presented that can provide valuable information for Αrchaeometry.
The Conference is under the auspices of the Ministry of Tourism, the Ministry of Culture and Sports, the Region of Central Greece, the Municipality of Delphi and the Embassy of the People's Republic of China in the Hellenic Republic. In addition, it is officially supported by the European Academy of Sciences and Arts, the Institute of Geology and Geophysics, the Chinese Academy of Sciences, many Greek and foreign Universities, the Hellenic Pharmaceutical Association and other organizations.
The pilot - project started with two drinking water supply systems and two biological treatment plants in Aigio, Achaia and Aghios Nikolaos, Crete.
The implementation process includes:
-the design and development of sampling procedures
-the design and elaboration of the isolation and analysis of the genetic material (DNA) of the samples
- bioinformatics analysis of the data
-the interpretation of the extracted results and their distribution to the stakeholders
The sampling took place in April 2021 by specialized personnel of DNA Sequence and Constrat with guidance at the sampling points by personnel of the municipalities of Aigio and Aghios Nikolaos respectively. For the water supply network, water samples were collected from representative points throughout the network "from source to tap" (boreholes, tanks, settlements’ faucets), while for the biological treatment plant water samples were collected from its entrance and exit to the unit, as well as from all the intermediate stages of treatment. The samples were transferred to the DNA Sequence laboratory where the genetic material (DNA) for each sample was isolated and sequenced. Laboratory analysis of all samples was based on WGS (Whole Genome Sequencing) and 16S rRNA technology which are important tools for the determination of microbial communities in water and wastewater. DNA sequencing was performed using Oxford Nanopore Technologies (ONT) nanofilm technology.
The large volume of data (raw data) was processed and analyzed through the company's bioinformatics platform so that the results are available for quality evaluation. At the end of the procedures, all the information about the project implementation process was communicated to the interested parties via a report. The results were then presented to the stakeholders with the help of a user-friendly online interactive platform, in which the user can navigate and explore the microbial biodiversity that characterizes the sampled point as well as get informed about the detected species (pathogenicity, biofilm formation trend, etc.). Constrat in turn, utilizing the produced results will reinforce and specialize its services in the field of water supply and wastewater systems.
Regarding the results of the analysis, the quality of water reaching the consumer, the effectiveness of chlorination in selected points of the water network, the possibility of sludge bulking occurrence which is caused by the excessive growth of filamentous bacteria extending outside the flocs resulting in decreasing the wastewater treatment efficiency and deteriorating the water quality in the effluent, the comparison of the efficiency between the conventional activated sludge systems and the membrane bioreactors (MBR) methods, were also assessed.
Conventional monitoring methods that target selected, well characterized microorganisms, in addition to the longer time required to yield results, exclude microorganisms that either cannot be cultured or do not pose a high health risk (e.g. unspecified or minor infectivity and/or pathogenicity). The complete metagenomics analysis, offered by DNA Sequence, enables the whole genome of all the microorganisms present in a sample to be sequenced, while through bioinformatics analysis it can distinguish species at strain level and even identify known genes for resistance to antibiotics. Therefore, the ability to detect the entire microbial spectrum in water and wastewater using methods of metagenomics technology comes to complement the already implemented necessary controls to ensure water high quality and safety. The result is to strengthen and expand the ability to make timely decisions where this is deemed appropriate not only to ensure public health but also the proper maintenance and performance of water supply facilities and wastewater treatment plants.
Τwo excellent articles by professor Christos Ouzounis and Dr. Aspasia Chatziefthimiou (pages 4-6, 8).
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"The detection of microbial load in water supply and wastewater treatment systems are constantly evolving processes, necessary for the protection of public health and safety. The spread of the SARS-CoV-2 pandemic has highlighted the need to develop effective biomonitoring methods and the need to broaden the targeted detection of a specific microbial spectrum in water, as defined by current safety protocols (ISO / TC 147 / SC 4). Especially during the last year, urban wastewater has been used as a trustworthy indicator of SARS-CoV-2 strains, both nationally and globally (Alygizakis 2021, Peccia 2020).
DNA Sequence takes microbial detection to the next level, adopting state-of-the-art technologies that allow the identification of all known and unknown microorganisms found in water, air or surface samples, as opposed to the routine control that is usually performed. The approach followed, which is based on innovative methods of Metagenomic analysis and bioinformatics data processing, is very fast. This allows microbial monitoring at checkpoints in almost real time, allowing for timely mediation and action if deemed necessary.
The company, in its two years of life, has established commercial and research collaborations in a wide range of activities, such as health, animal husbandry, water quality control, tourism and the food industry, where it implements the novel Biosurveillance
system it offers. Indicatively, DNASequence has collaborated with INTRAKAT AETE where it evaluated the microbial imprint on the ground of the old airport Ellinikon which is currently under urban reconstruction, while it has signed a collaboration agreement with
the company Constrat that operates in the field of water supply - sewerage, for bio-monitoring of selected water supply and biological treatment in Greece. Sampling isperformed in selected boreholes and wastewater treatment plants in order to identify all
microorganisms and the findings are used complementary to the required indicators to ensure water quality and safety. The future goal is to adopt this model systematically and on a large scale, in order to create an integrated control system for timely detection of the
spread of pathogenic microorganisms throughout the water supply chain.
New generation DNA sequencing technologies, one of which is Metagenomics, are the
future of Biosafety and Bio-monitoring applications. These technologies have already moved
dynamically from purely research towards commercial applications, with examples in critical areas such as water quality assurance (Brumfield 2020), nosocomial infection control(Greninger 2017), and even the International Space Station (Be 2017). The use of
Metagenomics in combination with the effective analysis of complex data produced by Bioinformatics and Artificial Intelligence methods, compose a powerful tool in the detection of unknown biological threats that until recently were invisible through traditional control