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Microorganisms
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Omics Research in Microbial Ecology
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Omics Research in Microbial Ecology

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

Deadline for manuscript submissions: closed (15 March 2025) | Viewed by 8621

Special Issue Editors

Dr. Andrey Plotnikov

E-Mail Website
Guest Editor
Institute for Cellular and Intracellular Symbiosis, Ural Branch of the Russian Academy of Sciences, 460000 Orenburg, Russia
Interests: microbial communities in salt water; microbial communities in meromictic lakes; water protist communities; halophilic protists; symbioses between protists and bacteria
Dr. Natalia Gogoleva

E-Mail Website
Guest Editor
Research Department for Limnology, University of Innsbruck, Mondsee 5310, Austria
Interests: molecular mechanisms of the host-microbial interactions; microbial adaptation to extreme environmental conditions, interactions in microbial communities

Special Issue Information

Dear Colleagues,

Omics technologies such as genomics, metagenomics, transcriptomics, and metabolomics, among others, have revolutionized microbial ecology as a scientific discipline. These omics technologies provide new and deep insights into the structure and functioning of microbial communities, net interactions between microorganisms of different taxa, and a complex symbiotic relationship between different members of natural and host-associated communities. Due to the development of metagenomics and metatranscriptomics over the last decade, a microbiome as a set of autochthonous and allochthonous microbes has been revealed in phylogenetically distant organisms ranging from protists to animals and land plants. Omics technologies are currently the most popular tools in different branches of microbial ecology, as they are used in various applications from the fundamental hypothesis of the emergence of multi-cellular organisms to practically oriented studies in medicine, animal husbandry, and crop production.

Thus, this Special Issue welcomes research and review articles devoted to new findings in different fields of microbial ecology obtained using modern omics technologies, including, but not restricted to, genomics, metagenomics, transcriptomics, metabolomics, etc. All kinds of microorganisms might be an object of such studies including viruses, prokaryotes, fungi, algae, and protists. The most in demand are articles describing new results from cutting-edge research on microbial communities and microbiomes in newly studied organisms (from protists to plants and animals), common and rare ecosystems, and healthy and sick humans and animals. We are also soliciting methodological papers devoted to benefits and limitations of omics technologies in microbial ecology, especially multi-omics approaches.

Dr. Andrey Plotnikov
Dr. Natalia Gogoleva
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 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

  • microbial ecology
  • omics technology
  • omics data
  • microbiome
  • microbial communities
  • microbial symbioses
  • genomics
  • transcriptomics
  • metagenomics
  • proteomics
  • metabolomics
  • host-associated microbial community
  • water microorganisms
  • soil microorganisms
  • microbes associated with plants
  • microbes associated with animals
  • bacteria
  • archaea
  • fungi
  • algae
  • protists
  • viruses

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Published Papers (5 papers)

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Research

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16 pages, 5397 KiB  
Article
Genetic Evolution of Antibiotic Resistance and Virulence Genes in Escherichia coli Isolates from a Chinese Hospital over a 12-Year Period
by Chengjie Feng, Hongbing Jia, Qian Yang and Qinghua Zou
Microorganisms 2025, 13(4), 954; https://doi.org/10.3390/microorganisms13040954 - 21 Apr 2025
Viewed by 182
Abstract
Escherichia coli is a significant pathogen capable of inducing a variety of infections in both human and animal hosts. Despite its clinical significance, there is a lack of longitudinal research aimed at elucidating the genomic attributes that facilitate antimicrobial resistance and clonal dissemination [...] Read more.
Escherichia coli is a significant pathogen capable of inducing a variety of infections in both human and animal hosts. Despite its clinical significance, there is a lack of longitudinal research aimed at elucidating the genomic attributes that facilitate antimicrobial resistance and clonal dissemination in this bacterium. In this study, we investigated the genetic dynamics of antibiotic resistance and virulence factors within a collection of 137 E. coli isolates retrieved from a Chinese hospital over a 12-year period. Notably, a substantial increase in resistance to various antibiotics, including broad-spectrum β-lactams, aminoglycosides, and quinolones, was observed. Additionally, our study revealed the acquisition of diverse antibiotic resistance and virulence genes across different sequence types (STs). Among the STs, ST131 emerged as the most prevalent, exhibiting a high level of multidrug resistance. In contrast, ST73 and ST12 demonstrated a higher prevalence of virulence genes, suggestive of a potential trade-off between antibiotic resistance and virulence. What’s more, we identified significant intra-clonal diversification and convergence of antibiotic resistance and virulence traits within the dominant ST131 group. These findings underscore the importance of longitudinal studies in understanding the evolution of bacterial pathogens and the necessity for ongoing research to inform public health strategies. Full article
(This article belongs to the Special Issue Omics Research in Microbial Ecology)
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20 pages, 5097 KiB  
Article
Combined Analysis of Transcriptomes and Metabolomes Reveals Key Genes and Substances That Affect the Formation of a Multi-Species Biofilm by Nine Gut Bacteria
by Ting Zhang, Zhangming Pei, Hongchao Wang, Jianxin Zhao, Wei Chen and Wenwei Lu
Microorganisms 2025, 13(2), 234; https://doi.org/10.3390/microorganisms13020234 - 22 Jan 2025
Cited by 1 | Viewed by 879
Abstract
Biofilms are one of the ways microorganisms exist in natural environments. In recent years, research has gradually shifted its focus to exploring the complexity and interactions of multi-species biofilms. A study showed that nine gut bacteria can form a multi-species biofilm on wheat [...] Read more.
Biofilms are one of the ways microorganisms exist in natural environments. In recent years, research has gradually shifted its focus to exploring the complexity and interactions of multi-species biofilms. A study showed that nine gut bacteria can form a multi-species biofilm on wheat fibers (M9 biofilm). However, the previous study did not clarify the reasons why M9 exhibited a better biofilm formation ability than the mono-species biofilms. In this study, the gene expression levels and metabolic accumulation of the M9 multi-species biofilm and biofilms of each individual bacterium were analyzed using transcriptomes and metabolomes. The differentially expressed genes (DEGs) showed that there were 740 common DEGs that existed in all of the nine groups, and they could regulate five pathways related to bacterial motility, cellular communication, and signal transduction. The metabolome results revealed that many peptides/amino acids and derivatives were produced in the M9 biofilm. Furthermore, purine metabolism was significantly enhanced in the M9 biofilm. L-arginine, l-serine, guanosine, and hypoxanthine were the common differentially accumulated metabolites (DAMs). The combined analysis of the transcriptomes and metabolomes showed that there were 26 common DEGs highly correlated with the four common DAMs, and they were involved in five metabolic pathways related to amino acids and purines. These results indicate that M9 can regulate multi-species biofilm formation by modulating genes related to bacterial motility, cellular communication, signal transduction, and the metabolism of amino acids and purines. This study provides insights into the interactions of microbial biofilms. Full article
(This article belongs to the Special Issue Omics Research in Microbial Ecology)
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13 pages, 3495 KiB  
Article
Characteristics and Differences in the Antler Velvet Microbiota During Regeneration
by Yongxiang Li, Yuhang Zhu, Bo Yang, Shaochen Yu, Songze Li, André-Denis G. Wright, Rui Du, Huazhe Si and Zhipeng Li
Microorganisms 2025, 13(1), 36; https://doi.org/10.3390/microorganisms13010036 - 27 Dec 2024
Viewed by 862
Abstract
The skin surface has a complex and dynamic ecosystem inhabited by a diverse microbiota. The wound formed by antler velvet shedding can naturally achieve regenerative restoration, but the changes in microbial composition that occur during antler velvet regeneration are largely unknown. In this [...] Read more.
The skin surface has a complex and dynamic ecosystem inhabited by a diverse microbiota. The wound formed by antler velvet shedding can naturally achieve regenerative restoration, but the changes in microbial composition that occur during antler velvet regeneration are largely unknown. In this study, we analyzed the antler velvet microbiota of sika deer at 15 days (Half) and 30 days (Full) post-pedicle casting using 16S rRNA gene sequencing. A total of 2659 OTUs were identified, which were assigned to 26 phyla, 304 families, and 684 genera. The core microbiota of the two groups were mainly composed of Atopostipes spp., Corynebacterium spp., Burkholderia spp., Staphylococcus spp., and Paracoccus spp. In comparison with the Full group, the Shannon, Simpson, Ace, and Chao 1 indices were significantly decreased in the Half group (p < 0.05). Principal coordinate analysis showed that there were significant differences in the microbial community between the Half and Full groups based on Bray–Curtis dissimilarity, weighted Unifrac distance, and unweighted Unifrac distance (p < 0.05). The relative abundances of bacteria belonging to the genera Staphylococcus, Romboutsia_B, and Dietzia increased significantly in the Half group, while the abundances of bacteria belonging to the genera Atopostipes, Psychrobacter, and Faecousia increased significantly in the Full group (p < 0.05). Correlation analysis showed that the relative abundances of bacteria belonging to the genera Staphylococcus, Romboutsia_B, and Dietzia positively correlated with arginine and proline metabolism (p < 0.05). These findings demonstrate that antler velvet regeneration is accompanied by distinct changes in microbial composition and highlight the potential roles of key taxonomy in wound healing and tissue regeneration. Full article
(This article belongs to the Special Issue Omics Research in Microbial Ecology)
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21 pages, 4998 KiB  
Article
The Cultivation of Halophilic Microalgae Shapes the Structure of Their Prokaryotic Assemblages
by Elena A. Selivanova, Michail M. Yakimov, Vladimir Y. Kataev, Yuri A. Khlopko, Alexander S. Balkin and Andrey O. Plotnikov
Microorganisms 2024, 12(10), 1947; https://doi.org/10.3390/microorganisms12101947 - 26 Sep 2024
Cited by 1 | Viewed by 1467
Abstract
The influence of microalgae on the formation of associated prokaryotic assemblages in halophilic microbial communities is currently underestimated. The aim of this study was to characterize shifts in prokaryotic assemblages of halophilic microalgae upon their transition to laboratory cultivation. Monoalgal cultures belonging to [...] Read more.
The influence of microalgae on the formation of associated prokaryotic assemblages in halophilic microbial communities is currently underestimated. The aim of this study was to characterize shifts in prokaryotic assemblages of halophilic microalgae upon their transition to laboratory cultivation. Monoalgal cultures belonging to the classes Chlorodendrophyceae, Bacillariophyceae, Trebouxiophyceae, and Chlorophyceae were isolated from habitats with intermediate salinity, about 100 g/L, nearby Elton Lake (Russia). Significant changes were revealed in the structure of algae-associated prokaryotic assemblages, indicating that microalgae supported sufficiently diverse and even communities of prokaryotes. Despite some similarities in their prokaryotic assemblages, taxon-specific complexes of dominant genera were identified for each microalga species. These complexes were most different among Alphaproteobacteria, likely due to their close association with microalgae. Other taxon-specific bacteria included members of phylum Verrucomicrobiota (Coraliomargarita in assemblages of Navicula sp.) and class Gammaproteobacteria (Salinispirillum in microbiomes of A. gracilis). After numerous washings of algal cells, only alphaproteobacteria Marivibrio remained in all assemblages of T. indica, likely due to a firm attachment to the microalgae cells. Our results may be useful for further efforts to develop technologies applied for industrial cultivation of halophilic microalgae and for developing approaches to obtain new prokaryotes with a microalgae-associated lifestyle. Full article
(This article belongs to the Special Issue Omics Research in Microbial Ecology)
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Review

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22 pages, 432 KiB  
Review
Revisiting the Intestinal Microbiome and Its Role in Diarrhea and Constipation
by Mihaela Adela Iancu, Monica Profir, Oana Alexandra Roşu, Ruxandra Florentina Ionescu, Sanda Maria Cretoiu and Bogdan Severus Gaspar
Microorganisms 2023, 11(9), 2177; https://doi.org/10.3390/microorganisms11092177 - 29 Aug 2023
Cited by 27 | Viewed by 4074
Abstract
The gut microbiota represents a community of microorganisms (bacteria, fungi, archaea, viruses, and protozoa) that colonize the gut and are responsible for gut mucosal structural integrity and immune and metabolic homeostasis. The relationship between the gut microbiome and human health has been intensively [...] Read more.
The gut microbiota represents a community of microorganisms (bacteria, fungi, archaea, viruses, and protozoa) that colonize the gut and are responsible for gut mucosal structural integrity and immune and metabolic homeostasis. The relationship between the gut microbiome and human health has been intensively researched in the past years. It is now widely recognized that gut microbial composition is highly responsible for the general health of the host. Among the diseases that have been linked to an altered gut microbial population are diarrheal illnesses and functional constipation. The capacity of probiotics to modulate the gut microbiome population, strengthen the intestinal barrier, and modulate the immune system together with their antioxidant properties have encouraged the research of probiotic therapy in many gastrointestinal afflictions. Dietary and lifestyle changes and the use of probiotics seem to play an important role in easing constipation and effectively alleviating diarrhea by suppressing the germs involved. This review aims to describe how probiotic bacteria and the use of specific strains could interfere and bring benefits as an associated treatment for diarrhea and constipation. Full article
(This article belongs to the Special Issue Omics Research in Microbial Ecology)
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