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Microorganisms
Special Issues
The Microbiome in Ecosystems
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The Microbiome in Ecosystems

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

Deadline for manuscript submissions: 31 October 2025 | Viewed by 4043

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,

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. Our 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 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
  • ecosystems
  • microbe–microbe interactions
  • microbe–host interactions
  • microbe–environment interactions

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Published Papers (5 papers)

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Research

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14 pages, 3035 KiB  
Article
Microbiome-Induced Microenvironmental Changes Before and After Breast Cancer Treatment
by Jeongshin An, Hyungju Kwon, Young Ju Kim and Byung-In Moon
Microorganisms 2025, 13(5), 1057; https://doi.org/10.3390/microorganisms13051057 - 1 May 2025
Viewed by 327
Abstract
Breast cancer treatment, including surgery, chemotherapy, radiotherapy, and endocrine therapy, can affect the microbiome and microenvironment of the human body. The present study examined how the microbiome changes before and after treatment in patients with breast cancer and explored variations in the expression [...] Read more.
Breast cancer treatment, including surgery, chemotherapy, radiotherapy, and endocrine therapy, can affect the microbiome and microenvironment of the human body. The present study examined how the microbiome changes before and after treatment in patients with breast cancer and explored variations in the expression of putative proteins linked to these shifts. Forty-five patients enrolled in this study, and blood samples were collected and sequenced to analyze microbiome composition. Using these sequences, we estimated and compared the putative protein expression levels. In addition, complete blood count results were analyzed to evaluate treatment-induced alterations. The findings indicate that treatment leads to microbiome modifications associated with changes in the human microenvironment. Moreover, key putative proteins involved in these processes were identified. This study provides valuable insights into how breast cancer treatment affects the microbiome and helps elucidate the potential role of microbial protein expression in patient outcomes. Full article
(This article belongs to the Special Issue The Microbiome in Ecosystems)
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20 pages, 2180 KiB  
Article
Characterization and Assembly Dynamics of the Microbiome Associated with Swine Anaerobic Lagoon Manure Treated with Biochar
by A. Nathan Frazier, William Willis, Heather Robbe, Anna Ortiz and Jacek A. Koziel
Microorganisms 2025, 13(4), 758; https://doi.org/10.3390/microorganisms13040758 - 27 Mar 2025
Viewed by 380
Abstract
Biochar has significant potential for livestock microbiomes and crop agriculture regarding greenhouse gas emissions reduction. Therefore, a pilot study was designed to investigate the effect of biochar application on the surface of swine manure from an open lagoon and the associated microbial communities. [...] Read more.
Biochar has significant potential for livestock microbiomes and crop agriculture regarding greenhouse gas emissions reduction. Therefore, a pilot study was designed to investigate the effect of biochar application on the surface of swine manure from an open lagoon and the associated microbial communities. Samples were collected from four different treatment groups: control (n = 4), coarse biochar (n = 4), fine biochar (n = 4), and ultra-fine biochar (n = 4). Additionally, aged manure in bulk was collected (n = 4) to assess alterations from the control group. The method of 16S rRNA amplicon sequencing along with microbial analyses was performed. Diversity was significantly different between aged manure in bulk samples and all treatment groups (Kruskal–Wallis; p < 0.05). Additionally, distinct community compositions were seen using both weighted and unweighted UniFrac distance matrices (PERMANOVA; p < 0.01). Differential abundance analysis revealed four distinct features within all treatment groups that were enriched (q < 0.001): Idiomarina spp., Geovibrio thiophilus, Parapusillimonas granuli, and an uncultured Gammaproteobacteria species. Similarly, Comamonas spp. and Brumimicrobium aurantiacum (q-value < 0.001) were significantly depleted by all the treatments. Stochastic and functional analyses revealed that biochar treatments were not deterministically altering assembly patterns, and functional redundancy was evident regardless of compositional shifts. Full article
(This article belongs to the Special Issue The Microbiome in Ecosystems)
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20 pages, 2697 KiB  
Article
The Microbiome of an Outpatient Sports Medicine Clinic During a Global Pandemic: Effects of Implementation of a Microbiome-Specific Cleaning Program
by Greer Russell, Rabia Alegoz, Kelley Hester, Kayla L. Sierzega, Martin J. Szul, Nathaniel Hubert, Timothy Rylander, Sarah Jensen, Mae J. Ciancio, Kristina Martinez-Guryn and Christian C. Evans
Microorganisms 2025, 13(4), 737; https://doi.org/10.3390/microorganisms13040737 - 25 Mar 2025
Viewed by 314
Abstract
Outpatient healthcare facilities represent potential sources of healthcare-associated infections (HAIs). The purpose of this study was to survey high-contact surfaces in an outpatient physical therapy clinic, characterize the microbiome of those surfaces, and investigate the effects of a microbiome-specific cleaning and hygiene plan. [...] Read more.
Outpatient healthcare facilities represent potential sources of healthcare-associated infections (HAIs). The purpose of this study was to survey high-contact surfaces in an outpatient physical therapy clinic, characterize the microbiome of those surfaces, and investigate the effects of a microbiome-specific cleaning and hygiene plan. Hand sanitizer containing a fluorescent probe used by patients and staff identified surface contact. High-contact surfaces were analyzed for bacterial DNA and SARS-CoV-2. A microbiome-specific cleaning and hygiene plan was developed based on initial analysis. After the implementation of the revised cleaning regimen, microbial community diversity and predicted metagenome content (PICRUSt) were employed for differential analysis. Patients had greater surface contact than staff. Ralstonia pickettii was the dominant species pre-cleaning, comprising 49.76% of the total, and observed on 79.5% of surfaces. The cleaning and hygiene plan significantly increased Shannon diversity, and R. pickettii decreased to 4.05% of total bacteria. SARS-CoV-2 was not observed on any surfaces. This study found ecological dominance by a single species in this outpatient clinic, suggesting a potential source of HAIs. However, a microbiome-specific cleaning strategy was successful in diversifying the microbiome and reducing ecological dominance. Additional research is needed to confirm these findings. Full article
(This article belongs to the Special Issue The Microbiome in Ecosystems)
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19 pages, 4449 KiB  
Article
Variations in the Bacterial, Fungal, and Protist Communities and Their Interactions Within Sediment Affected by the Benthic Organism, Snail Bellamya purificata
by Yiran Hou, Yiyun Zhang, Rui Jia, Linjun Zhou, Bing Li and Jian Zhu
Microorganisms 2024, 12(12), 2550; https://doi.org/10.3390/microorganisms12122550 - 11 Dec 2024
Viewed by 808
Abstract
In aquatic benthic environments, benthic organisms have been found to regulate important biogeochemical characteristics and perform key ecosystem functions. To further explore the ecological impact of the snail Bellamya purificata’s, presence on the benthic environment, we employed high-throughput sequencing technology to investigate [...] Read more.
In aquatic benthic environments, benthic organisms have been found to regulate important biogeochemical characteristics and perform key ecosystem functions. To further explore the ecological impact of the snail Bellamya purificata’s, presence on the benthic environment, we employed high-throughput sequencing technology to investigate its effects on the bacterial, fungal, and protist communities in sediment and their intrinsic interactions. Our findings revealed that B. purificata’s presence significantly enhanced the diversity and evenness of the fungal community while simultaneously decreasing the diversity and richness of the protist community, and it also altered the composition and relative abundance of the dominant phyla across the bacterial, fungal, and protist communities. The snail B. purificata considerably altered the co-occurrence networks of the microbial communities, particularly by enhancing the intrinsic complexity of the protist community and by strengthening the interconnections among the protist, bacterial, and fungal communities. Notably, the proportions of specialists within the sediment bacterial, fungal, and protist communities declined due to the snail B. purificata. Its presence also notably expanded the habitat niche breadth for sediment bacteria and protists. In terms of community assembly, B. purificata shifted the fungal community assembly from being dominated by stochastic processes to being dominated by deterministic processes, whereas the protist community assembly shifted from deterministic processes to being dominated by stochastic processes. The mainly altered ecological processes in the fungal and protist assemblies were drift and homogenizing selection. Additionally, the presence of B. purificata resulted in a notable reduction in the sediment ON level and a significant increase in the ammonia, FA, and EN concentrations. Sediment properties, particularly FA and nitrate, were strongly correlated with microbial communities and were key contributors to changes in microbial community dynamics. These research findings not only broadened our understanding of the ecological impacts of B. purificata on benthic microbial communities but also highlighted its substantial potential in enhancing microbial community stability. Full article
(This article belongs to the Special Issue The Microbiome in Ecosystems)
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Review

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19 pages, 2464 KiB  
Review
Plasma Optimization as a Novel Tool to Explore Plant–Microbe Interactions in Climate Smart Agriculture
by Binoop Mohan, Chandrima Karthik, Doni Thingujam, Karolina M. Pajerowska-Mukhtar, Vinoy Thomas and M Shahid Mukhtar
Microorganisms 2025, 13(1), 146; https://doi.org/10.3390/microorganisms13010146 - 13 Jan 2025
Viewed by 997
Abstract
Plasma treatment has emerged as a promising tool for manipulating plant microbiomes and metabolites. This review explores the diverse applications and effects of plasma on these biological systems. It is hypothesized that plasma treatment will not induce substantial changes in the composition of [...] Read more.
Plasma treatment has emerged as a promising tool for manipulating plant microbiomes and metabolites. This review explores the diverse applications and effects of plasma on these biological systems. It is hypothesized that plasma treatment will not induce substantial changes in the composition of plant microbiomes or the concentration of plant metabolites. We delve into the mechanisms by which plasma can regulate microbial communities, enhance antimicrobial activity, and recruit beneficial microbes to mitigate stress. Furthermore, we discuss the optimization of plasma parameters for effective microbiome interaction and the role of plasmids in plant–microbe interactions. By characterizing plasmidome responses to plasma exposure and investigating transcriptional and metabolomic shifts, we provide insights into the potential of plasma as a tool for engineering beneficial plant–microbe interactions. The review presented herein demonstrates that plasma treatment induces substantial changes in both microbial community composition and metabolite levels, thereby refuting our initial hypothesis. Finally, we integrate plasmidome, transcriptome, and metabolome data to develop a comprehensive understanding of plasma’s effects on plant biology and explore future perspectives for agricultural applications. Full article
(This article belongs to the Special Issue The Microbiome in Ecosystems)
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