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Special Issue "Analysing Bacterial Infection, Microbiome Characterics and Small Molecules in Diagnostics: Emerging Options"

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Microbiology".

Deadline for manuscript submissions: 31 October 2020.

Special Issue Editors

Prof. Dr. Hans-Peter Deigner
Website
Guest Editor
Hochschule Furtwangen, Institute of Precision Medicine, Furtwangen, Germany
Interests: diagnostic assays; new biomarker approaches; small molecule quantification; endogenous metabolites
Dr. Esra Aǧel
Website
Guest Editor
TUBITAK Marmara Research Center, Kocaeli, Turkey
Interests: Microbiology; Moleculer microbiology; Infection diseases Loop Mediated isothermal amplification (LAMP) method; RT-PCR; Point of care (POC); Labonadisc; Aptasensor
Dr. Markus Egert
Website
Guest Editor
Hochschule Furtwangen, Furtwangen, Germany

Special Issue Information

Dear Colleagues,

The conserved nature of host responses offers new approaches for diagnostic development in infectious diseases. Routine diagnostic methods are very useful but do not provide enough sensitivity and specificity. For many decades, a diverse range of analytical targets such as metabolites, nucleic acids, proteins are established as biomarkers now also including parts of the microbiome and one objective of this special issue will be evaluation of the role of emerging host and microbial biomarkers in diagnosis of infectious diseases.

In fact, the development of universal and reliable methods to detect biomarkers for diagnostics and prognostics and the search for highly specific and sensitive biomarkers for infectious diseases and beyond have posed the biggest challenges and options now include analysis of the structure and functionality of complex microbial communities in the human microbiome.

Aptamers for instance are now providing opportunities for quantitative diagnostic assays although translation into practice remains challenging in many cases. Aptamers are highly stable, short nucleic acid sequences capable of binding to the target with high affinity and specificity; small molecules that are problematic for toxins, proteins, cells, and even antibodies can be targeted by aptamers.  The technology (applied in chip- or horizontal flow tests), the target analyte can be quickly detected of target molecules in quantitative and multiplex formats, also on-site in miniaturized portable systems requiring less reagents, energy, and no special infrastructure and laborious/long sample preparation. These systems provide a high level of integration and automation. Emerging options for quantification of large and in small molecules by additional novel approaches will also be covered by this special issue.

Prof. Dr. Hans-Peter Deigner
Dr. Esra Aǧel
Dr. Markus Egert
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All papers will be peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • Assay systems development
  • Point-of-care testing
  • Metabolomic and proteomic approaches
  • Host response diagnostics
  • Infectious diseases diagnostics
  • Small molecule biomarkers
  • Gene expression profiling

Published Papers (3 papers)

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Research

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Open AccessArticle
How Do Trichoderma Genus Fungi Win a Nutritional Competition Battle against Soft Fruit Pathogens? A Report on Niche Overlap Nutritional Potentiates
Int. J. Mol. Sci. 2020, 21(12), 4235; https://doi.org/10.3390/ijms21124235 - 14 Jun 2020
Abstract
We present a case study report into nutritional competition between Trichoderma spp. isolated from wild raspberries and fungal phytopathogenic isolates (Colletotrichum sp., Botrytis sp., Verticillium sp. and Phytophthora sp.), which infect soft fruit ecological plantations. The competition was evaluated on the basis [...] Read more.
We present a case study report into nutritional competition between Trichoderma spp. isolated from wild raspberries and fungal phytopathogenic isolates (Colletotrichum sp., Botrytis sp., Verticillium sp. and Phytophthora sp.), which infect soft fruit ecological plantations. The competition was evaluated on the basis of nutritional potentiates. Namely, these were consumption and growth, calculated on the basis of substrate utilization located on Biolog® Filamentous Fungi (FF) plates. The niche size, total niche overlap and Trichoderma spp. competitiveness indices along with the occurrence of a stressful metabolic situation towards substrates highlighted the unfolding step-by-step approach. Therefore, the Trichoderma spp. and pathogen niche characteristics were provided. As a result, the substrates in the presence of which Trichoderma spp. nutritionally outcompete pathogens were denoted. These were adonitol, D-arabitol, i-erythritol, glycerol, D-mannitol and D-sorbitol. These substrates may serve as additives in biopreparations of Trichoderma spp. dedicated to plantations contaminated by phytopathogens of the genera Colletotrichum sp., Botrytis sp., Verticillium sp. and Phytophthora sp. Full article
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Open AccessArticle
Epidemiological and Genomic Characterization of Campylobacter jejuni Isolates from a Foodborne Outbreak at Hangzhou, China
Int. J. Mol. Sci. 2020, 21(8), 3001; https://doi.org/10.3390/ijms21083001 - 24 Apr 2020
Cited by 3
Abstract
Background: Foodborne outbreaks caused by Campylobacter jejuni have become a significant public health problem worldwide. Applying genomic sequencing as a routine part of foodborne outbreak investigation remains in its infancy in China. We applied both traditional PFGE profiling and genomic investigation to understand [...] Read more.
Background: Foodborne outbreaks caused by Campylobacter jejuni have become a significant public health problem worldwide. Applying genomic sequencing as a routine part of foodborne outbreak investigation remains in its infancy in China. We applied both traditional PFGE profiling and genomic investigation to understand the cause of a foodborne outbreak in Hangzhou in December 2018. Method: A total of 43 fecal samples, including 27 sick patients and 16 canteen employees from a high school in Hangzhou city in Zhejiang province, were recruited. Routine real-time fluorescent PCR assays were used for scanning the potential infectious agents, including viral pathogens (norovirus, rotavirus, adenovirus, and astrovirus), and bacterial pathogens (Salmonella, Shigella, Campylobacter jejuni, Vibrio parahaemolyticus and Vibrio cholerae). Bacterial selection medium was used to isolate and identify the positive bacteria identified by molecular test. Pulsed field gel electrophoresis (PFGE), and next generation sequencing (NGS) were applied to fifteen recovered C. jejuni isolates to further understand the case linkage of this particular outbreak. Additionally, we retrieved reference genomes from the NCBI database and performed a comparative genomics analysis with the examined genomes produced in this study. Results: The analyzed samples were found to be negative for the queried viruses. Additionally, Salmonella, Shigella, Vibrio parahaemolyticus and Vibrio cholera were not detected. Fifteen C. jejuni strains were identified by the real-time PCR assay and bacterial selection medium. These C. jejuni strains were classified into two genetic profiles defined by the PFGE. Out of fifteen C. jejuni strains, fourteen have a unified consistent genotype belonging to ST2988, and the other strain belongs to ST8149, with a 66.7% similarity in comparison with the rest of the strains. Moreover, all fifteen strains harbored blaOXA-61 and tet(O), in addition to a chromosomal mutation in gyrA (T86I). The examined fourteen strains of ST2988 from CC354 clone group have very minimal genetic difference (3~66 SNPs), demonstrated by the phylogenomic investigation. Conclusion: Both genomic investigation and PFGE profiling confirmed that C. jejuni ST2988, a new derivative from CC354, was responsible for the foodborne outbreak Illustrated in this study. Full article
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Review

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Open AccessReview
Research Advances of Beneficial Microbiota Associated with Crop Plants
Int. J. Mol. Sci. 2020, 21(5), 1792; https://doi.org/10.3390/ijms21051792 - 05 Mar 2020
Abstract
Plants are associated with hundreds of thousands of microbes that are present outside on the surfaces or colonizing inside plant organs, such as leaves and roots. Plant-associated microbiota plays a vital role in regulating various biological processes and affects a wide range of [...] Read more.
Plants are associated with hundreds of thousands of microbes that are present outside on the surfaces or colonizing inside plant organs, such as leaves and roots. Plant-associated microbiota plays a vital role in regulating various biological processes and affects a wide range of traits involved in plant growth and development, as well as plant responses to adverse environmental conditions. An increasing number of studies have illustrated the important role of microbiota in crop plant growth and environmental stress resistance, which overall assists agricultural sustainability. Beneficial bacteria and fungi have been isolated and applied, which show potential applications in the improvement of agricultural technologies, as well as plant growth promotion and stress resistance, which all lead to enhanced crop yields. The symbioses of arbuscular mycorrhizal fungi, rhizobia and Frankia species with their host plants have been intensively studied to provide mechanistic insights into the mutual beneficial relationship of plant–microbe interactions. With the advances in second generation sequencing and omic technologies, a number of important mechanisms underlying plant–microbe interactions have been unraveled. However, the associations of microbes with their host plants are more complicated than expected, and many questions remain without proper answers. These include the influence of microbiota on the allelochemical effect caused by one plant upon another via the production of chemical compounds, or how the monoculture of crops influences their rhizosphere microbial community and diversity, which in turn affects the crop growth and responses to environmental stresses. In this review, first, we systematically illustrate the impacts of beneficial microbiota, particularly beneficial bacteria and fungi on crop plant growth and development and, then, discuss the correlations between the beneficial microbiota and their host plants. Finally, we provide some perspectives for future studies on plant–microbe interactions. Full article
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