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A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Microbiology".

Deadline for manuscript submissions: 20 December 2024 | Viewed by 11829

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Dr. Nicole Hansmeier

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Guest Editor

Luther College at the University of Regina, Regina, SK S4S 0A2, Canada
Interests: genomics; proteomics; transcriptomics; metabolomics; lipidomics; interactomics; microorganism

Special Issue Information

Dear Colleagues,

Microorganisms face a wide variety of challenges in their natural habitats, ranging from harsh environmental conditions, harmful pollutants to host defense systems. To address these challenges, microorganisms developed diverse strategies, including dedicated genetic mechanisms, complex metabolic adaptations or biofilm formation.

Omics methodologies encompassing genomics, transcriptomics, proteomics, lipidomics and metabolomics have become invaluable for elucidating microbial adaptations.

This current Special Issue entitled “Microbial Omics” of the International Journal of Molecular Sciences invites you to contribute research and review papers showcasing the use of omics technologies and methodologies to explore microbial physiology, adaptions or interactions at the molecular level, in response to challenges to their survival (e.g., environmental exposures, pollutants, antimicrobials and host defense systems).

Dr. Nicole Hansmeier
Guest Editor

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Keywords

omics technologies
omics methodologies
microorganisms
proteomics
genomics
transcriptomics

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Published Papers (9 papers)

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Research

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16 pages, 7530 KiB

Open AccessArticle

Microbial Diversity and Biodegradation Mechanism of Microorganisms in the Dingtao M2 Tomb

by Yu Wang, Cen Wang, Lilong Hou, Xinyu Yang, Chenghao Li, Shengkuan Cui, Cuilian Ma, Ling Wang, Lu Zhang, Yuanyuan Liu, Hong Guo and Jiao Pan

Int. J. Mol. Sci. 2024, 25(22), 12270; https://doi.org/10.3390/ijms252212270 - 15 Nov 2024

Viewed by 252

Abstract

The Dingtao M2 tomb, the largest and best-preserved imperial “Huangchangticou” tomb in China, holds great significance for its conservation. Currently, varying degrees of microbial degradation are occurring on the surfaces of the M2 tomb. This study aimed to determine the microbial diversity of the M2 tomb and its surrounding environment during July 2021 and August 2022. High-throughput metagenomic sequencing revealed that the dominant fungus on the surface of the tomb chamber was Dacrymyces stillatus (DTT1) in July 2021, which changed to Talaromyces pinophilus (DTT2) in August 2022. Enzymatic activities for cellulose and lignin degradation suggested that DTT1 has high levels of manganese peroxidase, lignin peroxidase, laccase, and cellulase. The wood of the tomb contained higher levels of Fe²⁺ and Ca²⁺, and experiments with different concentration gradients of these ions in the culture medium revealed that DTT1 exhibited greater activity of cellulose and lignin degradation in environments with higher concentrations of Fe²⁺ and Ca²⁺. DTT2 degraded both cellulose and lignin. Lastly, a laboratory plate inhibition experiment demonstrated that isothiazolinone fungicide had a significant fungicidal effect on these two dominant fungi. This study provides valuable data and a theoretical basis for the preservation of the M2 tomb and other wooden cultural relics. Full article

(This article belongs to the Special Issue Microbial Omics)

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16 pages, 3937 KiB

Open AccessArticle

Assessment of Skimmed Milk Flocculation for Bacterial Enrichment from Water Samples, and Benchmarking of DNA Extraction and 16S rRNA Databases for Metagenomics

by Deyan Donchev, Ivan Stoikov, Antonia Diukendjieva and Ivan N. Ivanov

Int. J. Mol. Sci. 2024, 25(19), 10817; https://doi.org/10.3390/ijms251910817 - 8 Oct 2024

Viewed by 605

Abstract

Water samples for bacterial microbiome studies undergo biomass concentration, DNA extraction, and taxonomic identification steps. Through benchmarking, we studied the applicability of skimmed milk flocculation (SMF) for bacterial enrichment, an adapted in-house DNA extraction protocol, and six 16S rRNA databases (16S-DBs). Surface water samples from two rivers were treated with SMF and vacuum filtration (VF) and subjected to amplicon or shotgun metagenomics. A microbial community standard underwent five DNA extraction protocols, taxonomical identification with six different 16S-DBs, and evaluation by the Measurement Integrity Quotient (MIQ) score. In SMF samples, the skimmed milk was metabolized by members of lactic acid bacteria or genera such as Polaromonas, Macrococcus, and Agitococcus, resulting in increased relative abundance (p < 0.5) up to 5.0 log fold change compared to VF, rendering SMF inapplicable for bacterial microbiome studies. The best-performing DNA extraction protocols were FastSpin Soil, the in-house method, and EurX. All 16S-DBs yielded comparable MIQ scores within each DNA extraction kit, ranging from 61–66 (ZymoBIOMICs) up to 80–82 (FastSpin). DNA extraction kits exert more bias toward the composition than 16S-DBs. This benchmarking study provided valuable information to inform future water metagenomic study designs. Full article

(This article belongs to the Special Issue Microbial Omics)

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18 pages, 28117 KiB

Open AccessArticle

A Well-Established Gut Microbiota Enhances the Efficiency of Nutrient Metabolism and Improves the Growth Performance of Trachinotus ovatus

by Miao Kong, Wendong Zhao, Cong Wang, Jie Qi, Jinxiang Liu and Quanqi Zhang

Int. J. Mol. Sci. 2024, 25(10), 5525; https://doi.org/10.3390/ijms25105525 - 18 May 2024

Cited by 2 | Viewed by 1170

Abstract

The gut microbiota has become an essential component of the host organism and plays a crucial role in the host immune system, metabolism, and physiology. Nevertheless, our comprehension of how the fish gut microbiota contributes to enhancing nutrient utilization in the diet and improving host growth performance remains unclear. In this study, we employed a comprehensive analysis of the microbiome, metabolome, and transcriptome to analyze intestines of the normal control group and the antibiotic-treated model group of T. ovatus to investigate how the gut microbiota enhances fish growth performance and uncover the underlying mechanisms. First, we found that the growth performance of the control group was significantly higher than that of the antibiotic-treated model under the same feeding conditions. Subsequent multiomics analyses showed that the gut microbiota can improve its own composition by mediating the colonization of some probiotics represented by Lactobacillus in the intestine, improving host metabolic efficiency with proteins and lipids, and also influencing the expression of genes in signaling pathways related to cell proliferation, which together contribute to the improved growth performance of T. ovatus. Our results demonstrated the important contribution of gut microbiota and its underlying molecular mechanisms on the growth performance of T. ovatus. Full article

(This article belongs to the Special Issue Microbial Omics)

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17 pages, 10696 KiB

Open AccessArticle

Large-Scale Biogeographical Shifts of Abundance of Antibiotic Resistance Genes and Marine Bacterial Communities as Their Carriers along a Trophic Gradient

by Mia Dželalija, Željana Fredotović, Nikolina Udiković-Kolić, Hrvoje Kalinić, Slaven Jozić, Ivica Šamanić, Marin Ordulj and Ana Maravić

Int. J. Mol. Sci. 2024, 25(1), 654; https://doi.org/10.3390/ijms25010654 - 4 Jan 2024

Viewed by 1541

Abstract

The role of marine environments in the global spread of antibiotic resistance still remains poorly understood, leaving gaps in the One Health-based research framework. Antibiotic resistance genes (ARGs) encoding resistance to five major antibiotic classes, including sulfonamides (sul1, sul2), tetracyclines (tetA, tetB), β-lactams (bla_CTX-M, bla_TEM bla_VIM), macrolides (ermB, mphA), aminoglycosides (aac3-2), and integrase gene (intl1) were quantified by RT-qPCR, and their distribution was investigated in relation to environmental parameters and the total bacterial community in bottom layer and surface waters of the central Adriatic (Mediterranean), over a 68 km line from the wastewater-impacted estuary to coastal and pristine open sea. Seasonal changes (higher in winter) were observed for antibiotic resistance frequency and the relative abundances of ARGs, which were generally higher in eutrophic coastal areas. In particular, intl1, followed by bla_TEM and bla_VIM, were strongly associated with anthropogenic influence and Gammaproteobacteria as their predominant carriers. Water column stratification and geographic location had a significant influence on ARGs distribution in the oligotrophic zone, where the bacterial community exhibited a seasonal shift from Gammaproteobacteria in winter to Marine group II in summer. Full article

(This article belongs to the Special Issue Microbial Omics)

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26 pages, 18281 KiB

Open AccessArticle

Comparative Analysis of Differential Cellular Transcriptome and Proteome Regulation by HIV-1 and HIV-2 Pseudovirions in the Early Phase of Infection

by Tamás Richárd Linkner, Viktor Ambrus, Balázs Kunkli, Zsófia Ilona Szojka, Gergő Kalló, Éva Csősz, Ajneesh Kumar, Miklós Emri, József Tőzsér and Mohamed Mahdi

Int. J. Mol. Sci. 2024, 25(1), 380; https://doi.org/10.3390/ijms25010380 - 27 Dec 2023

Viewed by 1685

Abstract

In spite of the similar structural and genomic organization of human immunodeficiency viruses type 1 and 2 (HIV-1 and HIV-2), striking differences exist between them in terms of replication dynamics and clinical manifestation of infection. Although the pathomechanism of HIV-1 infection is well characterized, relatively few data are available regarding HIV-2 viral replication and its interaction with host–cell proteins during the early phase of infection. We utilized proteo-transcriptomic analyses to determine differential genome expression and proteomic changes induced by transduction with HIV-1/2 pseudovirions during 8, 12 and 26 h time-points in HEK-293T cells. We show that alteration in the cellular milieu was indeed different between the two pseudovirions. The significantly higher number of genes altered by HIV-2 in the first two time-points suggests a more diverse yet subtle effect on the host cell, preparing the infected cell for integration and latency. On the other hand, GO analysis showed that, while HIV-1 induced cellular oxidative stress and had a greater effect on cellular metabolism, HIV-2 mostly affected genes involved in cell adhesion, extracellular matrix organization or cellular differentiation. Proteomics analysis revealed that HIV-2 significantly downregulated the expression of proteins involved in mRNA processing and translation. Meanwhile, HIV-1 influenced the cellular level of translation initiation factors and chaperones. Our study provides insight into the understudied replication cycle of HIV-2 and enriches our knowledge about the use of HIV-based lentiviral vectors in general. Full article

(This article belongs to the Special Issue Microbial Omics)

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27 pages, 2669 KiB

Open AccessArticle

RpoS-Regulated Genes and Phenotypes in the Phytopathogenic Bacterium Pectobacterium atrosepticum

by Olga Petrova, Elizaveta Semenova, Olga Parfirova, Ivan Tsers, Natalia Gogoleva, Yuri Gogolev, Yevgeny Nikolaichik and Vladimir Gorshkov

Int. J. Mol. Sci. 2023, 24(24), 17348; https://doi.org/10.3390/ijms242417348 - 11 Dec 2023

Cited by 1 | Viewed by 1590

Abstract

The alternative sigma factor RpoS is considered to be one of the major regulators providing stress resistance and cross-protection in bacteria. In phytopathogenic bacteria, the effects of RpoS have not been analyzed with regard to cross-protection, and genes whose expression is directly or indirectly controlled by RpoS have not been determined at the whole-transcriptome level. Our study aimed to determine RpoS-regulated genes and phenotypes in the phytopathogenic bacterium Pectobacterium atrosepticum. Knockout of the rpoS gene in P. atrosepticum affected the long-term starvation response, cross-protection, and virulence toward plants with enhanced immune status. The whole-transcriptome profiles of the wild-type P. atrosepticum strain and its ΔrpoS mutant were compared under different experimental conditions, and functional gene groups whose expression was affected by RpoS were determined. The RpoS promoter motif was inferred within the promoter regions of the genes affected by rpoS deletion, and the P. atrosepticum RpoS regulon was predicted. Based on RpoS-controlled phenotypes, transcriptome profiles, and RpoS regulon composition, the regulatory role of RpoS in P. atrosepticum is discussed. Full article

(This article belongs to the Special Issue Microbial Omics)

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18 pages, 1840 KiB

Open AccessArticle

miRNA Expression Signatures Induced by Chicken Astrovirus Infection in Chickens

by Joanna Sajewicz-Krukowska, Paweł Mirosław, Jan P. Jastrzębski, Katarzyna Domańska-Blicharz, Karolina Tarasiuk and Barbara Marzec-Kotarska

Int. J. Mol. Sci. 2023, 24(20), 15128; https://doi.org/10.3390/ijms242015128 - 12 Oct 2023

Viewed by 1403

Abstract

miRNAs represent ubiquitous regulators of gene expression and play an important and pivotal regulatory role in viral disease pathogenesis and virus–host interactions. Although previous studies have provided basic data for understanding the role of miRNAs in the molecular mechanisms of viral infection in birds, the role of miRNAs in the regulation of host responses to chicken astrovirus (CAstV) infection in chickens is not yet understood. In our study, we applied next-generation sequencing to profile miRNA expression in CAstV-infected chickens and to decipher miRNA-targeted specific signaling pathways engaged in potentially vital virus-infection biological processes. Among the 1354 detected miRNAs, we identified 58 mature miRNAs that were significantly differentially expressed in infected birds. Target prediction resulted in 4741 target genes. GO and KEGG pathway enrichment analyses showed that the target genes were mainly involved in the regulation of cellular processes and immune responses. Full article

(This article belongs to the Special Issue Microbial Omics)

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19 pages, 4422 KiB

Open AccessArticle

Proteomics Investigation of the Impact of the Enterococcus faecalis Secretome on MCF-7 Tumor Cells

by Moudi A. Alwehaibi, Mysoon M. Al-Ansari, Assim A. Alfadda, Reem Al-Malki, Afshan Masood, Anas M. Abdel Rahman and Hicham Benabdelkamel

Int. J. Mol. Sci. 2023, 24(19), 14937; https://doi.org/10.3390/ijms241914937 - 5 Oct 2023

Cited by 2 | Viewed by 2272

Abstract

Breast cancer is the most prevalent form of cancer among women. The microenvironment of a cancer tumor is surrounded by various cells, including the microbiota. An imbalance between microbes and their host may contribute to the development and spread of breast cancer. Therefore, the objective of this study is to investigate the influence of Enterococcus faecalis on a breast cancer cell line (MCF-7) to mimic the luminal A subtype of breast cancer, using an untargeted proteomics approach to analyze the proteomic profiles of breast cancer cells after their treatment with E. faecalis in order to understand the microbiome and its role in the development of cancer. The breast cancer cell line MCF-7 was cultured and then treated with a 10% bacterial supernatant at two time points (24 h and 48 h) at 37 °C in a humidified incubator with 5% CO₂. Proteins were then extracted and separated using two-dimensional difference (2D-DIGE) gel electrophoresis, and the statistically significant proteins (p-value < 0.05, fold change > 1.5) were identified via matrix-assisted laser desorption/ionization–time-of-flight mass spectrometry (MALDI-TOF-MS). The protein fingerprints showed a differential protein expression pattern in the cells treated with E. faecalis for 24 and 48 h compared with the control. We found 58 statistically significant proteins changes in the MCF-7 breast cancer cells affected by E. faecalis. Kilin and transgelin were upregulated after 24 h of treatment and could be used as diagnostic and prognostic markers for breast cancer. In addition, another protein involved in the inhibition of cell proliferation was coiled-coil domain-containing protein 154. The protein markers identified in this study may serve as possible biomarkers for breast cancer progression. This promotes their future uses as important therapeutic goals in the treatment and diagnosis of cancer and increases our understanding of the breast microbiome and its role in the development of cancer. Full article

(This article belongs to the Special Issue Microbial Omics)

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Review

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18 pages, 369 KiB

Open AccessReview

The Oral Microbiota, Microbial Metabolites, and Immuno-Inflammatory Mechanisms in Cardiovascular Disease

by Zheng Wang, Robert C. Kaplan, Robert D. Burk and Qibin Qi

Int. J. Mol. Sci. 2024, 25(22), 12337; https://doi.org/10.3390/ijms252212337 - 17 Nov 2024

Viewed by 372

Abstract

Cardiovascular diseases (CVDs) remain a leading cause of global morbidity and mortality. Recent advancements in high-throughput omics techniques have enhanced our understanding of the human microbiome’s role in the development of CVDs. Although the relationship between the gut microbiome and CVDs has attracted considerable research attention and has been rapidly evolving in recent years, the role of the oral microbiome remains less understood, with most prior studies focusing on periodontitis-related pathogens. In this review, we summarized previously reported associations between the oral microbiome and CVD, highlighting known CVD-associated taxa such as Porphyromonas gingivalis, Fusobacterium nucleatum, and Aggregatibacter actinomycetemcomitans. We also discussed the interactions between the oral and gut microbes. The potential mechanisms by which the oral microbiota can influence CVD development include oral and systemic inflammation, immune responses, cytokine release, translocation of oral bacteria into the bloodstream, and the impact of microbial-related products such as microbial metabolites (e.g., short-chain fatty acids [SCFAs], trimethylamine oxide [TMAO], hydrogen sulfide [H₂S], nitric oxide [NO]) and specific toxins (e.g., lipopolysaccharide [LPS], leukotoxin [LtxA]). The processes driven by these mechanisms may contribute to atherosclerosis, endothelial dysfunction, and other cardiovascular pathologies. Integrated multi-omics methodologies, along with large-scale longitudinal population studies and intervention studies, will facilitate a deeper understanding of the metabolic and functional roles of the oral microbiome in cardiovascular health. This fundamental knowledge will support the development of targeted interventions and effective therapies to prevent or reduce the progression from cardiovascular risk to clinical CVD events. Full article

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