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Microorganisms
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Feature Papers in Microbiomes
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Feature Papers in Microbiomes

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

Deadline for manuscript submissions: 30 November 2025 | Viewed by 9475

Special Issue Editor

Dr. Pabulo Rampelotto

E-Mail Website
Guest Editor
Clinical Hospital of Porto Alegre (HCPA), affiliated with the Federal University of Rio Grande do Sul, Porto Alegre 91501-970, Brazil
Interests: microbiome; molecular microbiology; metagenomics; omics; biostatistics; next-generation sequencing; clinical research; bioinformatics; biotechnology; system biology; grand challenges
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The field of microbiome research has experienced exponential growth in the past decade, revolutionizing our understanding of the complex relationships between microorganisms and their hosts. As we approach 2025, taking stock of the latest advancements and emerging trends in this dynamic field is essential. This Special Issue of Microorganisms aims to provide a comprehensive overview of the cutting-edge research and innovative approaches shaping the future of microbiome science through a compilation of timely research articles, reviews, and perspectives that capture the rapidly evolving landscape of microbiomes each year.

The scope of this Special Issue encompasses a wide range of topics, including the application of next-generation sequencing technologies for microbiome profiling, the integration of multi-omics data to unravel the functional potential of microbial communities, the development of computational tools for microbiome data analysis, and the translation of microbiome research into clinical and environmental interventions. We particularly welcome submissions that explore the role of the microbiome in human and animal health and disease, the impact of environmental factors on microbial communities, and the potential of microbiome-based therapies and biotechnological applications.

By fostering interdisciplinary collaboration and knowledge exchange, we aim to advance the field of microbiome research and pave the way for groundbreaking discoveries that will have far-reaching implications for human and animal well-being, environmental sustainability, and the development of innovative biotechnological solutions.

Dr. Pabulo H. Rampelotto
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

  • human microbiome
  • animal microbiome
  • environmental microbiome
  • marine microbiome
  • plant microbiome
  • soil microbiome
  • bioinformatics and computational tools
  • microbial interactions and functions
  • microbiome-associated diseases
  • microbiome-omics technologies
  • multi-omics integration
  • microbial network
  • host–microbiome interactions
  • microbiome-based therapies
  • emerging trends

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Published Papers (7 papers)

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Research

21 pages, 2053 KiB  
Article
The Composition and Function of Bacterial Communities Associated with the Northern Root-Knot Nematode (Meloidogyne hapla) Populations Showing Parasitic Variability
by Isaac Lartey, Gian M. N. Benucci, Terence L. Marsh, Gregory M. Bonito and Haddish Melakeberhan
Microorganisms 2025, 13(3), 487; https://doi.org/10.3390/microorganisms13030487 - 22 Feb 2025
Viewed by 539
Abstract
The co-existence of microbial communities and Meloidogyne hapla populations showing high, medium, and low levels of parasitic variability (PV) in mineral and muck soils with different soil health conditions in Michigan vegetable production fields is established. However, if PV relates or not to [...] Read more.
The co-existence of microbial communities and Meloidogyne hapla populations showing high, medium, and low levels of parasitic variability (PV) in mineral and muck soils with different soil health conditions in Michigan vegetable production fields is established. However, if PV relates or not to bacterial communities is unknown. This study characterized bacterial communities present on and in the body of nine M. hapla field and greenhouse sub-populations isolated from the mineral and muck fields. We utilized a high throughput sequencing of 16S rDNA. Results showed a variable composition (or abundance) of 65 genera in the field and 61 genera in the greenhouse isolates, with 12 genera of unknown and the rest belonging to 14 known functional groups. The medium- and low-PV populations shared more bacterial composition than either one with the high-PV population. Thus, laying a foundation for an in-depth understanding of if the observed associations have any role in cause-and-effect relationships with M. hapla PV. Full article
(This article belongs to the Special Issue Feature Papers in Microbiomes)
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16 pages, 3310 KiB  
Article
Antibiotic Resistance Profiles and Genomic Analysis of Endophytic Bacteria Isolates from Wild Edible Fungi in Yunnan
by Shuqiong Yi, Haiyan Wu, Yingting Lin, Xiaoyan Cha and Ying Shang
Microorganisms 2025, 13(2), 361; https://doi.org/10.3390/microorganisms13020361 - 7 Feb 2025
Viewed by 773
Abstract
The use of antibiotics has led to the emergence of antibiotic resistance, posing significant challenges in the prevention, control, and treatment of microbial diseases, while threatening public health, the environment, and food safety. In this study, the antibiotic resistance phenotypes and genotypes of [...] Read more.
The use of antibiotics has led to the emergence of antibiotic resistance, posing significant challenges in the prevention, control, and treatment of microbial diseases, while threatening public health, the environment, and food safety. In this study, the antibiotic resistance phenotypes and genotypes of 56 endophytic bacteria isolates from three species of wild edible fungi in Yunnan were analyzed using the Kirby-Bauer disk diffusion method and PCR amplification. The results revealed that all isolates were sensitive to ofloxacin, but resistance was observed against 17 other antibiotics. Specifically, 55, 53, and 51 isolates exhibited resistance to amoxicillin, penicillin, and vancomycin, respectively. Antibiotic resistance gene (ARG) detection indicated that the sulfonamide sul1 gene had the highest detection rate (53.57%). Excluding the ARG that was not detected, the lowest detection rates were the sulfonamide sul2 and sul3 genes, both at 1.79%. Among six tetracycline resistance genes, only tetK and tetM were detected. For β-lactam antibiotics, blaTEM, blaVIM, and blaSHV genes were present, while blaOXA was absent. In aminoglycoside resistance genes, aadB was not detected, while detection rates for aac(3′)-IIa, acrB, and aadA1 were 3.57%, 1.79%, and 37.5%, respectively. The chloramphenicol Cat gene was detected at a rate of 14.29%, whereas floR was absent. For polypeptide resistance, VanC was detected at 3.57%, with EmgrB not detected. All three quinolone genes were detected, with detection rates of 8.92% for GyrA, 39.29% for GyrB, and 37.5% for ParC. Through phylogenetic analysis, 12 isolates that are closely related to ten common foodborne pathogenic bacteria were further selected for whole-genome sequencing and assembly. Gene annotations revealed that each isolate contained more than 15 ARGs and over 30 virulence factors. Notably, the detection rate of antibiotic resistance phenotypes was higher than that of genotypes, highlighting the importance of studying phenotypic antibiotic resistance that lacks identifiable ARGs. This study enriches the research on endophytes in wild edible fungi and provides new data for microbial ecology and antibiotic resistance research. It also offers critical insights for monitoring microbial antibiotic resistance in wild edible fungi and potentially other food sources, contributing to more effective strategies for ecological protection, sustainable agricultural development, and public health security. Full article
(This article belongs to the Special Issue Feature Papers in Microbiomes)
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21 pages, 15157 KiB  
Article
Microbial Dynamics: Assessing Skincare Regimens’ Impact on the Facial Skin Microbiome and Skin Health Parameters
by Nicole Wagner, Valerie Diane Valeriano, Samuel Diou-Hirtz, Evelina Björninen, Ulf Åkerström, Lars Engstrand, Ina Schuppe-Koistinen and Johanna Maria Gillbro
Microorganisms 2024, 12(12), 2655; https://doi.org/10.3390/microorganisms12122655 - 21 Dec 2024
Viewed by 1754
Abstract
The human skin microbiome, a complex ecosystem of microbes, plays a pivotal role in skin health. This study aimed to investigate the impact of two skincare regimens, with preservatives (CSPs) and preservative-free (PFPs), on the skin microbiome in correlation to skin quality. double-blind [...] Read more.
The human skin microbiome, a complex ecosystem of microbes, plays a pivotal role in skin health. This study aimed to investigate the impact of two skincare regimens, with preservatives (CSPs) and preservative-free (PFPs), on the skin microbiome in correlation to skin quality. double-blind randomized cosmetic studywith a split-face design was conducted on 26 female participants. Microbial diversity and abundance were analyzed using 16S rRNA amplicon sequence data and skin quality utilizing the Antera 3D skin camera. We confirmed earlier studies on the identification of major skin microbial taxa at the genus level, including Cutibacterium acnes, Corynebacterium, and Neisseriaceae as a predominant part of the facial skin microbiome. Furthermore, microbiome profile-based subgrouping was employed, which revealed that the cluster, characterized by the Neisseriaceae family as its predominant organism, exhibited significant reduction in folds count, fine lines, and redness after application of PFP compared to CSP. A Spearman correlation analysis highlighted the correlation between changes in specific bacteria and skin quality parameters such as redness, pores, and texture in the context of comparing PFP and CSP. Overall, the PFP treatment demonstrated a greater number of significant correlations between bacterial changes and skin quality compared to the CSP treatment, suggesting a distinct impact of the preservative-free skincare regimen on the skin microbiome and skin quality. Our study provides insights into different microbiome-centered approaches to improve our understanding of the skin microbiome’s interplay with skin quality but also highlights the need for larger, comprehensive research to further understand the microbiome’s role in dermatology. Full article
(This article belongs to the Special Issue Feature Papers in Microbiomes)
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10 pages, 1943 KiB  
Article
Towards Reliable Methodology: Microbiome Analysis of Fresh Frozen vs. Formalin-Fixed Paraffin-Embedded Bladder Tissue Samples: A Feasibility Study
by Dominik Enderlin, Uwe Bieri, Jana Gadient, Yasser Morsy, Michael Scharl, Jan Hendrik Rüschoff, Lukas John Hefermehl, Anna Nikitin, Janine Langenauer, Daniel Stephan Engeler, Beat Förster, Fabian Obrecht, Jonathan Surber, Thomas Paul Scherer, Daniel Eberli and Cédric Poyet
Microorganisms 2024, 12(12), 2594; https://doi.org/10.3390/microorganisms12122594 - 15 Dec 2024
Viewed by 1500
Abstract
Studies have shown that the human microbiome influences the response to systemic immunotherapy. However, only scarce data exist on the impact of the urinary microbiome on the response rates of bladder cancer (BC) to local Bacillus Calmette-Guérin instillation therapy. We launched the prospective [...] Read more.
Studies have shown that the human microbiome influences the response to systemic immunotherapy. However, only scarce data exist on the impact of the urinary microbiome on the response rates of bladder cancer (BC) to local Bacillus Calmette-Guérin instillation therapy. We launched the prospective SILENT-EMPIRE study in 2022 to address this question. We report the results of the pilot study of SILENT-EMPIRE, which aimed to compare the microbiome between fresh frozen (FF) and formalin-fixed paraffin-embedded (FFPE) samples in the cancerous tissue and adjacent healthy tissue of BC patients. Our results show that alpha diversity is increased in FF samples compared to FFPE (coverage index p = 0.041, core abundance index p = 0.008). No significant differences concerning alpha diversity could be detected between cancerous and non-cancerous tissue in the same BC patients. This study demonstrates that microbiome analysis from both FF and FFPE samples is feasible. Implementing this finding could aid in the translation of research findings into clinical practice. Full article
(This article belongs to the Special Issue Feature Papers in Microbiomes)
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18 pages, 1726 KiB  
Article
In Silico Analysis of Probiotic Bacteria Changes Across COVID-19 Severity Stages
by Clarissa Reginato Taufer, Juliana da Silva and Pabulo Henrique Rampelotto
Microorganisms 2024, 12(11), 2353; https://doi.org/10.3390/microorganisms12112353 - 18 Nov 2024
Viewed by 1006
Abstract
The gut microbiota plays a crucial role in modulating the immune response during COVID-19, with several studies reporting significant alterations in specific bacterial genera, including Akkermansia, Bacteroides, Bifidobacterium, Faecalibacterium, Lactobacillus, Oscillospira, and Ruminococcus. These genera are [...] Read more.
The gut microbiota plays a crucial role in modulating the immune response during COVID-19, with several studies reporting significant alterations in specific bacterial genera, including Akkermansia, Bacteroides, Bifidobacterium, Faecalibacterium, Lactobacillus, Oscillospira, and Ruminococcus. These genera are symbionts of the gut microbiota and contribute to host health. However, comparing results across studies is challenging due to differences in analysis methods and reference databases. We screened 16S rRNA raw datasets available in public databases on COVID-19, focusing on the V3–V4 region of the bacterial genome. In total, seven studies were included. All samples underwent the same bioinformatics pipeline, evaluating the differential abundance of these seven bacterial genera at each level of severity. The reanalysis identified significant changes in differential abundance. Bifidobacterium emerged as a potential biomarker of disease severity and a therapeutic target. Bacteroides presented a complex pattern, possibly related to disease-associated inflammation or opportunistic pathogen growth. Lactobacillus showed significant changes in abundance across the COVID-19 stages. On the other hand, Akkermansia and Faecalibacterium did not show significant differences, while Oscillospira and Ruminococcus produced statistically significant results but with limited relevance to COVID-19 severity. Our findings reveal new insights into the differential abundance of key bacterial genera in COVID-19, particularly Bifidobacterium and Bacteroides. Full article
(This article belongs to the Special Issue Feature Papers in Microbiomes)
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11 pages, 1024 KiB  
Article
Oxford Nanopore Technology-Based Identification of an Acanthamoeba castellanii Endosymbiosis in Microbial Keratitis
by Sebastian Alexander Scharf, Lennart Friedrichs, Robert Bock, Maria Borrelli, Colin MacKenzie, Klaus Pfeffer and Birgit Henrich
Microorganisms 2024, 12(11), 2292; https://doi.org/10.3390/microorganisms12112292 - 12 Nov 2024
Cited by 2 | Viewed by 1161
Abstract
(1) Background: Microbial keratitis is a serious eye infection that carries a significant risk of vision loss. Acanthamoeba spp. are known to cause keratitis and their bacterial endosymbionts can increase virulence and/or treatment resistance and thus significantly worsen the course of the disease. [...] Read more.
(1) Background: Microbial keratitis is a serious eye infection that carries a significant risk of vision loss. Acanthamoeba spp. are known to cause keratitis and their bacterial endosymbionts can increase virulence and/or treatment resistance and thus significantly worsen the course of the disease. (2) Methods and Results: In a suspected case of Acanthamoeba keratitis, in addition to Acanthamoeba spp., an endosymbiont of acanthamoebae belonging to the taxonomic order of Holosporales was detected by chance in a bacterial 16S rDNA-based pan-PCR and subsequently classified as Candidatus Paracaedibacter symbiosus through an analysis of an enlarged 16S rDNA region. We used Oxford Nanopore Technology to evaluate the usefulness of whole-genome sequencing (WGS) as a one-step diagnostics method. Here, Acanthamoeba castellanii and the endosymbiont Candidatus Paracaedibacter symbiosus could be directly detected at the species level. No other microbes were identified in the specimen. (3) Conclusions: We recommend the introduction of WGS as a diagnostic approach for keratitis to replace the need for multiple species-specific qPCRs in future routine diagnostics and to enable an all-encompassing characterisation of the polymicrobial community in one step. Full article
(This article belongs to the Special Issue Feature Papers in Microbiomes)
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22 pages, 2751 KiB  
Article
Unveiling Emerging Opportunistic Fish Pathogens in Aquaculture: A Comprehensive Seasonal Study of Microbial Composition in Mediterranean Fish Hatcheries
by Dimitrios Skliros, Maria Kostakou, Constantina Kokkari, Maria Ioanna Tsertou, Christina Pavloudi, Haris Zafeiropoulos, Pantelis Katharios and Emmanouil Flemetakis
Microorganisms 2024, 12(11), 2281; https://doi.org/10.3390/microorganisms12112281 - 10 Nov 2024
Viewed by 1964
Abstract
The importance of microbial communities in fish hatcheries for fish health and welfare has been recognized, with several studies mapping these communities during healthy rearing conditions and disease outbreaks. In this study, we analyzed the bacteriome of the live feeds, such as microalgae, [...] Read more.
The importance of microbial communities in fish hatcheries for fish health and welfare has been recognized, with several studies mapping these communities during healthy rearing conditions and disease outbreaks. In this study, we analyzed the bacteriome of the live feeds, such as microalgae, rotifers, and Artemia, used in fish hatcheries that produce Mediterranean species. Our goal was to provide baseline information about their structure, emphasizing in environmental putative fish pathogenic bacteria. We conducted 16S rRNA amplicon Novaseq sequencing for our analysis, and we inferred 46,745 taxonomically annotated ASVs. Results showed that incoming environmental water plays a significant role in the presence of important taxa that constitute presumptive pathogens. Bio-statistical analyses revealed a relatively stable bacteriome among seasonal samplings for every hatchery but a diverse bacteriome between sampling stations and a distinct core bacteriome for each hatchery. Analysis of putative opportunistic fish pathogenic genera revealed some co-occurrence correlation events and a high average relative abundance of Vibrio, Tenacibaculum, and Photobacterium genera in live feeds, reaching a grand mean average of up to 7.3% for the hatchery of the Hellenic Center of Marine Research (HCMR), 12% for Hatchery A, and 11.5% for Hatchery B. Mapping the bacteriome in live feeds is pivotal for understanding the marine environment and distinct aquaculture practices and can guide improvements in hatchery management, enhancing fish health and sustainability in the Mediterranean region. Full article
(This article belongs to the Special Issue Feature Papers in Microbiomes)
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