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Microorganisms
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Applied Microbiome Science and Technology
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Applied Microbiome Science and Technology

A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Microbial Biotechnology".

Deadline for manuscript submissions: 31 March 2025 | Viewed by 3540

Special Issue Editor

Prof. Dr. Eric (Chun-Ming) Huang

E-Mail Website1 Website2
Guest Editor
Department of Biomedical Sciences and Engineering, National Central University, Taoyuan 32001, Taiwan
Interests: skin microbiome; acne vaccine; beneficial microbes
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The microbiome represents the entire collection of microbes that play a critical role in the host–environment complex. Investigating the interactions between the microbiome, host, and environment and their impact on host biological mechanisms reveals new pathways or indications for monitoring health and disease. These new pathways can largely expand the big data obtained from the microbiome. Scientists may apply machine learning to analyze these microbiome data and develop next-generation therapeutics such as digital therapeutics (DTx). DTx delivers evidence-based software-driven therapeutics which can be used to create new formulas for personalized medicine in humans. DTx has also been used to accelerate plant disease diagnostics and increase yields. In this Special Issue, we aim to collect the most recent insights in applied microbiome science and technology. We welcome all types of manuscript, including original articles, reviews, and editorials, addressing one or more of the following objectives:

  • New pathways in the microbiome–host–environment complex;
  • Remote diagnostics for humans (such as telemedicine), plants, or environments;
  • Digital therapeutics for the health of humans, plants, or environments.

Prof. Dr. Eric (Chun-Ming) Huang
Guest Editor

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 submissions that pass pre-check are 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. Microorganisms is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). 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

  • microbiome-host-environment
  • diagnostics for humans, plants or environments
  • digital therapeutics for health of humans, plants, or environments

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Further information on MDPI's Special Issue polices can be found here.

Published Papers (2 papers)

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Research

17 pages, 3310 KiB  
Article
Antagonistic Effects of Corynebacterium pseudodiphtheriticum 090104 on Respiratory Pathogens
by Ramiro Ortiz Moyano, Stefania Dentice Maidana, Yoshiya Imamura, Mariano Elean, Fu Namai, Yoshihito Suda, Keita Nishiyama, Vyacheslav Melnikov, Haruki Kitazawa and Julio Villena
Microorganisms 2024, 12(7), 1295; https://doi.org/10.3390/microorganisms12071295 - 26 Jun 2024
Viewed by 1524
Abstract
In previous studies, it was demonstrated that Corynebacterium pseudodiphtheriticum 090104, isolated from the human nasopharynx, modulates respiratory immunity, improving protection against infections. Here, the antagonistic effect of the 090104 strain on respiratory pathogens, including Streptococcus pneumoniae, Staphylococcus aureus, Klebsiella pneumoniae, [...] Read more.
In previous studies, it was demonstrated that Corynebacterium pseudodiphtheriticum 090104, isolated from the human nasopharynx, modulates respiratory immunity, improving protection against infections. Here, the antagonistic effect of the 090104 strain on respiratory pathogens, including Streptococcus pneumoniae, Staphylococcus aureus, Klebsiella pneumoniae, Pseudomonas aeruginosa, and Acinetobacter baumannii, was explored. In a series of in vitro studies, the capacity of C. pseudodiphtheriticum 090104, its bacterium-like particles, and its culture supernatants to coaggregate, inhibit the growth, and change the virulent phenotype of pathogenic bacteria was evaluated. The results showed that the 090104 strain was able to exert a bacteriostatic effect on K. pneumoniae and S. pneumoniae growth. In addition, C. pseudodiphtheriticum 090104 coaggregated, inhibited biofilm formation, and induced phenotypic changes in all the respiratory pathogens evaluated. In conclusion, this work demonstrated that, in addition to its beneficial effects exerted by host–microbe interactions, C. pseudodiphtheriticum 090104 can enhance protection against respiratory pathogens through its microbe–microbe interactions. The mechanisms involved in such interactions should be evaluated in future research. Full article
(This article belongs to the Special Issue Applied Microbiome Science and Technology)
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13 pages, 2364 KiB  
Article
Extraction Methods Determine the Quality of Soil Microbiota Acquisition
by Zhuoxin Liu, Chi Zhang, Jiejia Ma, Qianze Peng, Xiaohua Du, Shu’e Sun, Ju’e Cheng, Weiye Peng, Lijie Chen, Zepei Gu, Weixing Zhang, Pin Su and Deyong Zhang
Microorganisms 2024, 12(2), 403; https://doi.org/10.3390/microorganisms12020403 - 17 Feb 2024
Cited by 1 | Viewed by 1488
Abstract
The soil microbiome plays a key role in plant health. Native soil microbiome inoculation, metagenomic profiling, and high-throughput cultivation require efficient microbe extraction. Sonication and oscillation are the most common methods used to extract soil microbiomes. However, the extraction efficiency of these methods [...] Read more.
The soil microbiome plays a key role in plant health. Native soil microbiome inoculation, metagenomic profiling, and high-throughput cultivation require efficient microbe extraction. Sonication and oscillation are the most common methods used to extract soil microbiomes. However, the extraction efficiency of these methods has not been investigated in full. In this study, we compared the culturable microbe numbers, community structures, and alpha diversities among the different methods, including sonication, oscillation, and centrifugation, and their processing times. The study results showed that sonication significantly increases the culturable colony number compared with oscillation and centrifugation. Furthermore, the sonication strategy was found to be the main factor influencing extraction efficiency, but increased sonication time can aid in recovery from this impact. Finally, the extraction processing times were found to have a significant negative relationship with α-diversity among the extracted microbiota. In conclusion, sonication is the main factor for enriching in situ microbiota, and increased extraction time significantly decreases the α-diversity of the extracted microbiota. The results of this study provide insights into the isolation and utilization of different microorganism sources. Full article
(This article belongs to the Special Issue Applied Microbiome Science and Technology)
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