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Applied Microbiology
Special Issues
Microbiome in Ecosystem 3.0
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Microbiome in Ecosystem 3.0

A special issue of Applied Microbiology (ISSN 2673-8007).

Deadline for manuscript submissions: 31 October 2024 | Viewed by 2227

Special Issue Editor

Dr. Bong-Soo Kim

E-Mail Website
Guest Editor
Department of Life Science, Multidisciplinary Genome Institute, Hallym University, Chuncheon 24252, Republic of Korea
Interests: microbiome; metagenomics; homeostasis; disease; ecosystem
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

This Special Issue is the continuation of our previous special issue “Microbiome in Ecosystem” and “Microbiome in Ecosystem 2.0”.

The microbiome consists of complex microbes and related molecules. Recently, the microbiome has been applied to various fields in order to develop a novel way for maintaining homeostasis or the balance of ecosystems. The understanding of the microbiome’s interaction with its habitats including its host is still limited. This Special Issue is devoted to publishing original research and review articles on various aspects of the microbiome in ecosystems. Topics of interest include, but are not restricted to, novel methods for understanding the microbiome, the role of the microbiome in ecosystems, microbe–microbe interactions in the microbiome, microbe–host interactions, and microbe–environment interactions in various ecosystems.

Dr. Bong-Soo Kim
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at mdpi.longhoe.net 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. Applied Microbiology is an international peer-reviewed open access quarterly 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 1000 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
  • metagenomics
  • ecosystem

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Published Papers (2 papers)

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Research

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11 pages, 1567 KiB  
Article
Predicting Microbiome Growth Dynamics under Environmental Perturbations
by George Sun and Yi-Hui Zhou
Appl. Microbiol. 2024, 4(2), 948-958; https://doi.org/10.3390/applmicrobiol4020064 - 10 Jun 2024
Viewed by 493
Abstract
MicroGrowthPredictor is a model that leverages Long Short-Term Memory (LSTM) networks to predict dynamic changes in microbiome growth in response to varying environmental perturbations. In this article, we present the innovative capabilities of MicroGrowthPredictor, which include the integration of LSTM modeling with a [...] Read more.
MicroGrowthPredictor is a model that leverages Long Short-Term Memory (LSTM) networks to predict dynamic changes in microbiome growth in response to varying environmental perturbations. In this article, we present the innovative capabilities of MicroGrowthPredictor, which include the integration of LSTM modeling with a novel confidence interval estimation technique. The LSTM network captures the complex temporal dynamics of microbiome systems, while the novel confidence intervals provide a robust measure of prediction uncertainty. We include two examples—one illustrating the human gut microbiota composition and diversity due to recurrent antibiotic treatment and the other demonstrating the application of MicroGrowthPredictor on an artificial gut dataset. The results demonstrate the enhanced accuracy and reliability of the LSTM-based predictions facilitated by MicroGrowthPredictor. The inclusion of specific metrics, such as the mean square error, validates the model’s predictive performance. Our model holds immense potential for applications in environmental sciences, healthcare, and biotechnology, fostering advancements in microbiome research and analysis. Moreover, it is noteworthy that MicroGrowthPredictor is applicable to real data with small sample sizes and temporal observations under environmental perturbations, thus ensuring its practical utility across various domains. Full article
(This article belongs to the Special Issue Microbiome in Ecosystem 3.0)
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Review

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15 pages, 1563 KiB  
Review
Reassessing Gout Management through the Lens of Gut Microbiota
by Jean Demarquoy and Oumaima Dehmej
Appl. Microbiol. 2024, 4(2), 824-838; https://doi.org/10.3390/applmicrobiol4020057 - 22 May 2024
Viewed by 539
Abstract
Gout, recognized as the most common form of inflammatory arthritis, arises from the accumulation of uric acid crystals, leading to intense pain, particularly in the big toe. This condition has traditionally been associated with the overproduction or reduced clearance of uric acid. Recent [...] Read more.
Gout, recognized as the most common form of inflammatory arthritis, arises from the accumulation of uric acid crystals, leading to intense pain, particularly in the big toe. This condition has traditionally been associated with the overproduction or reduced clearance of uric acid. Recent studies, however, have underscored the significant role of the gut microbiota in uric acid metabolism, impacting both its production and elimination. This emerging understanding suggests that maintaining gut health could offer innovative approaches to treating gout, complementing traditional dietary and pharmacological interventions. It highlights the potential of probiotics or microbiome-based therapies, indicating a future where treatments are tailored to an individual’s microbiome. This offers a fresh perspective on gout management and underscores the broader influence of the microbiota on health and disease. Full article
(This article belongs to the Special Issue Microbiome in Ecosystem 3.0)
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