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Life
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Advances in Bacterial Metabolism, Gene Regulation, and Pathogenesis
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Advances in Bacterial Metabolism, Gene Regulation, and Pathogenesis

A special issue of Life (ISSN 2075-1729). This special issue belongs to the section "Genetics and Genomics".

Deadline for manuscript submissions: closed (24 June 2022) | Viewed by 20952

Special Issue Editor

Dr. Cheng-Yen Kao

E-Mail Website
Guest Editor
Institute Microbiology and Immunology, National Yang Ming Chiao Tung University, Taipei 112, Taiwan
Interests: antibiotic resistance; bacterial genomics; bacterial pathogenesis; drug development; gene regulation
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Bacterial factors, such as flagella, pili, adhesins, siderophores, and toxins, are critical for pathogenesis and disease development. In addition, the bacterial stress response enables these bugs to survive fluctuating conditions in their immediate surroundings, which also contributes to bacterial adaptation and persistence in the host. Various bacterial mechanisms and signaling systems recognize different environmental changes, modulate metabolism pathways and gene expression, and mount an appropriate response. Research on virulence factors and stress response has not only increased our understanding of the mechanisms underlying bacterial pathogenesis but has also contributed to identifying novel targets for alternative antibacterial therapy. Therefore, in this Special Issue of Life, we invite researchers to submit their papers to share with us advances in the understanding of bacterial metabolism, gene regulation, and pathogenesis. This Special Issue will comprise the topics below:

  • Metabolomics analysis;
  • Transcriptome analysis of the pathogen;
  • Gene regulation of virulence factors;
  • Chemotaxis and motility;
  • Cell adhesion;
  • Signal transduction;
  • Stress response;
  • Toxin production and secretion;
  • Immune evasion mechanisms.

Dr. Cheng-Yen Kao
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. Life 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 2600 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

  •  metabolomics analysis
  •  transcriptome analysis of the pathogen
  •  gene regulation of virulence factors
  •  chemotaxis and motility
  •  cell adhesion
  •  signal transduction
  •  stress response
  •  toxin production and secretion
  •  immune evasion mechanisms

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Published Papers (7 papers)

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Research

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11 pages, 2959 KiB  
Article
In Situ Monitoring and Quantitative Determination of R27 Plasmid Conjugation
by Marta Gibert, Carlos J. Jiménez, Jaume Comas, Ellen L. Zechner, Cristina Madrid and Carlos Balsalobre
Life 2022, 12(8), 1212; https://doi.org/10.3390/life12081212 - 10 Aug 2022
Viewed by 1739
Abstract
Horizontal gene transfer (HGT) by plasmid conjugation is a major driving force in the spread of antibiotic resistance among Enterobacteriaceae. Most of the conjugation studies are based on calculation of conjugation ratios (number of transconjugants/number of donors) after viable counting of transconjugant [...] Read more.
Horizontal gene transfer (HGT) by plasmid conjugation is a major driving force in the spread of antibiotic resistance among Enterobacteriaceae. Most of the conjugation studies are based on calculation of conjugation ratios (number of transconjugants/number of donors) after viable counting of transconjugant and donor cells. The development of robust, fast and reliable techniques for in situ monitoring and quantification of conjugation ratios might accelerate progress in understanding the impact of this cellular process in the HGT. The IncHI1 plasmids, involved in multiresistance phenotypes of relevant pathogens such as Salmonella and E. coli, are distinguished by the thermosensitivity of their conjugative transfer. Conjugation mediated by IncHI1 plasmids is more efficient at temperatures lower than 30 °C, suggesting that the transfer process takes place during the environmental transit of the bacteria. In this report, we described a methodology to monitor in situ the conjugation process during agar surface matings of the IncHI1 plasmid R27 and its derepressed derivative drR27 at different temperatures. A three-color-labeling strategy was used to visualize the spatial distribution of transconjugants within the heterogeneous environment by epifluorescence and confocal microscopy. Moreover, the fluorescent labelling was also used to quantify conjugation frequencies in liquid media by flow cytometry. Full article
(This article belongs to the Special Issue Advances in Bacterial Metabolism, Gene Regulation, and Pathogenesis)
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9 pages, 1020 KiB  
Article
Differential Gene Expression of Efflux Pumps and Porins in Clinical Isolates of MDR Acinetobacter baumannii
by Khalid I. AlQumaizi, Sunil Kumar, Razique Anwer and Shoeb Mustafa
Life 2022, 12(3), 419; https://doi.org/10.3390/life12030419 - 14 Mar 2022
Cited by 8 | Viewed by 3006
Abstract
Background: Acinetobacter baumannii is an opportunistic pathogen associated with healthcare infections and high mortality rates in intensive care units all over the globe. Porins and efflux pumps over-expression have been reported as contributing factors in escalating drug resistance and rendering treatment ineffective. In [...] Read more.
Background: Acinetobacter baumannii is an opportunistic pathogen associated with healthcare infections and high mortality rates in intensive care units all over the globe. Porins and efflux pumps over-expression have been reported as contributing factors in escalating drug resistance and rendering treatment ineffective. In this study, we investigated the mechanisms of multidrug resistance (MDR) in A. baumannii clinical isolates. Methods: A total of 30 A. baumannii isolates were included in the present study from Nehru Hospital (PGIMER-Chandigarh) located in North India. Kirby Bauer disk diffusion assay and MIC were performed to determine the antimicrobial susceptibility pattern. Screening of beta-lactamases was performed using PCR. Relative gene expression of four RND, one MATE efflux pump, and two outer membrane proteins were determined using RT-PCR. Molecular typing of 22 isolates was carried out using MLST Oxford scheme. Results: CarO porin genes showed over-expression in 63% isolates followed by adeGandabeM efflux pump downregulation/underexpression (<0.5 fold), suggesting the carbapenem-susceptible phenotypic nature of the isolates. High prevalence of VIM-2, NDM-1, and OXA-23 genes was observed in A. baumannii isolates. Interestingly, NDM-1 and OXA-58 were traced in 10 and3 A. baumannii isolates respectively; 13 of 22 (59%) isolates showed novel Sequence Types (STs) in the Multi-Locus Sequence Typing (MLST) analysis. ST 1087 was most commonly found ST among all others (16 STs). Conclusions: This study indicated a possible role of carO porin genes and adeG (RND) andabeM (MATE) efflux pumps in carbapenem susceptibility of A. baumannii. New STs were also reported in the majority of the isolates. Full article
(This article belongs to the Special Issue Advances in Bacterial Metabolism, Gene Regulation, and Pathogenesis)
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15 pages, 2889 KiB  
Article
Maggot Extract Interrupts Bacterial Biofilm Formation and Maturation in Combination with Antibiotics by Reducing the Expression of Virulence Genes
by Mustafa Becerikli, Christoph Wallner, Mehran Dadras, Johannes M. Wagner, Stephanie Dittfeld, Birger Jettkant, Falk Gestmann, Heinz Mehlhorn, Tim Mehlhorn-Diehl, Marcus Lehnhardt and Björn Behr
Life 2022, 12(2), 237; https://doi.org/10.3390/life12020237 - 4 Feb 2022
Cited by 9 | Viewed by 2749
Abstract
Biofilms are aggregates of bacteria encased in an extracellular polymer matrix that acts as a diffusion barrier protecting the microbial community. Bacterial communication occurs by small signaling molecules called quorum sensing (QS) factors, which are involved in the activation of virulence genes and [...] Read more.
Biofilms are aggregates of bacteria encased in an extracellular polymer matrix that acts as a diffusion barrier protecting the microbial community. Bacterial communication occurs by small signaling molecules called quorum sensing (QS) factors, which are involved in the activation of virulence genes and formation of biofilms. Larvae of the green bottle blowfly Lucilia sericata remove necrotic tissue by mechanical action (debridement) and proteolytic digestion. We produced a freeze-dried storable powder from larval extract and investigated its therapeutic effect on biofilms. Larval extract in concentrations of 6 and 12 mg/mL in combination with 0.5% antibiotics (≙50 U/mL penicillin and 50 μg/mL streptomycin) diminished free-floating (planktonic) Pseudomonas aeruginosa maintenance, while it showed no effect on Staphylococcus aureus and was not toxic to dermal cells. We established an ex vivo human dermal wound model. Larval extract in concentrations of 24 and 75 mg/mL in the presence of antibiotics (0.5%) significantly destroyed the biofilm stability of both P. aeruginosa and S. aureus biofilms. Furthermore, SEM analyses revealed crack and gap formations on P. aeruginosa. biofilm surface and decreased expression of P. aeruginosa biofilm maturation and virulence genes (lasR, rhlR and rhlA) was observed after treatment by larval extract in combination with antibiotics. Full article
(This article belongs to the Special Issue Advances in Bacterial Metabolism, Gene Regulation, and Pathogenesis)
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4 pages, 391 KiB  
Communication
Influence of Escherichia coli on Expression of Selected Human Drug Addiction Genes
by Roman Kotłowski
Life 2021, 11(12), 1346; https://doi.org/10.3390/life11121346 - 5 Dec 2021
Viewed by 2304
Abstract
The impact of enteric microflora on the expression of genes associated with cocaine and amphetamine addiction was described. Human genome-wide experiments on RNA transcripts expressed in response to three selected Escherichia coli strains allowed for significant alteration (p > 0.05) of the [...] Read more.
The impact of enteric microflora on the expression of genes associated with cocaine and amphetamine addiction was described. Human genome-wide experiments on RNA transcripts expressed in response to three selected Escherichia coli strains allowed for significant alteration (p > 0.05) of the linear regression model between HT-29 RNA transcripts associated with the KEGG pathway:hsa05030:Cocaine addiction after 3 h stimulation with intracellular pathogenic E. coli strain UM146 versus non-pathogenic E. coli Nissle 1917. Among the features influenced by the UM146 bacterial strain were visual learning, response to the presence of morphine, response to hypoxia, behavioral fear response and cognitive functions. Full article
(This article belongs to the Special Issue Advances in Bacterial Metabolism, Gene Regulation, and Pathogenesis)
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13 pages, 1938 KiB  
Article
Mitotic Arrest-Deficient 2 Like 2 (MAD2L2) Interacts with Escherichia coli Effector Protein EspF
by Amin Tahoun, Hanem El-Sharkawy, Samar M. Moustafa, Lina Jamil M. Abdel-Hafez, Ashraf Albrakati, Manfred Koegl, Juergen Haas, Arvind Mahajan, David L. Gally and Ehab Kotb Elmahallawy
Life 2021, 11(9), 971; https://doi.org/10.3390/life11090971 - 15 Sep 2021
Cited by 2 | Viewed by 2691
Abstract
Enteropathogenic (EPEC) and Enterohemorrhagic (EHEC) Escherichia coli are considered emerging zoonotic pathogens of worldwide distribution. The pathogenicity of the bacteria is conferred by multiple virulence determinants, including the locus of enterocyte effacement (LEE) pathogenicity island, which encodes a type III secretion system (T3SS) [...] Read more.
Enteropathogenic (EPEC) and Enterohemorrhagic (EHEC) Escherichia coli are considered emerging zoonotic pathogens of worldwide distribution. The pathogenicity of the bacteria is conferred by multiple virulence determinants, including the locus of enterocyte effacement (LEE) pathogenicity island, which encodes a type III secretion system (T3SS) and effector proteins, including the multifunctional secreted effector protein (EspF). EspF sequences differ between EPEC and EHEC serotypes in terms of the number and residues of SH3-binding polyproline-rich repeats and N-terminal localization sequence. The aim of this study was to discover additional cellular interactions of EspF that may play important roles in E. coli colonization using the Yeast two-hybrid screening system (Y2H). Y2H screening identified the anaphase-promoting complex inhibitor Mitotic Arrest-Deficient 2 Like 2 (MAD2L2) as a host protein that interacts with EspF. Using LUMIER assays, MAD2L2 was shown to interact with EspF variants from EHEC O157:H7 and O26:H11 as well as EPEC O127:H6. MAD2L2 is targeted by the non-homologous Shigella effector protein invasion plasmid antigen B (IpaB) to halt the cell cycle and limit epithelial cell turnover. Therefore, we postulate that interactions between EspF and MAD2L2 serve a similar function in promoting EPEC and EHEC colonization, since cellular turnover is a key method for bacteria removal from the epithelium. Future work should investigate the biological importance of this interaction that could promote the colonization of EPEC and EHEC E. coli in the host. Full article
(This article belongs to the Special Issue Advances in Bacterial Metabolism, Gene Regulation, and Pathogenesis)
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17 pages, 5484 KiB  
Article
Differential Mucosal Microbiome Profiles across Stages of Human Colorectal Cancer
by Mingqing Zhang, Yongming Lv, Shaobin Hou, Yanfei Liu, Yijia Wang and Xuehua Wan
Life 2021, 11(8), 831; https://doi.org/10.3390/life11080831 - 13 Aug 2021
Cited by 19 | Viewed by 3576
Abstract
Emerging evidences link gut microbiota to colorectal cancer (CRC) initiation and development. However, the CRC stage- and spatial-specific bacterial taxa were less investigated, especially in a Chinese cohort, leading to our incomplete understanding of the functional roles of gut microbiota in promoting CRC [...] Read more.
Emerging evidences link gut microbiota to colorectal cancer (CRC) initiation and development. However, the CRC stage- and spatial-specific bacterial taxa were less investigated, especially in a Chinese cohort, leading to our incomplete understanding of the functional roles of gut microbiota in promoting CRC progression and recurrence. Here, we report the composition and structure of gut microbiota across CRC stages I, II and III, by analyzing the gut mucosal microbiomes of 75 triplet-paired samples collected from on-tumor, adjacent-tumor and off-tumor sites and 26 healthy controls. We observed tumor-specific pattern of mucosal microbiome profiles as CRC progressed and identified ten bacterial taxa with high abundances (>1%) as potential biomarkers for tumor initiation and development. Peptostreptococcus and Parvimonas can serve as biomarkers for CRC stage I. Fusobacterium, Streptococcus, Parvimonas, Burkholderiales, Caulobacteraceae, Delftia and Oxalobacteraceae can serve as biomarkers for CRC stage II, while Fusobacterium, Burkholderiales, Caulobacteraceae, Oxalobacteraceae, Faecalibacterium and Sutterella can serve as biomarkers for CRC stage III. These biomarkers classified CRC stages I, II and III distinguished from each other with an area under the receiver-operating curve (AUC) > 0.5. Moreover, co-occurrence and co-excluding network analysis of these genera showed strong correlations in CRC stage I, which were subsequently reduced in CRC stages II and III. Our findings provide a reference index for stage-specific CRC diagnosis and suggest stage-specific roles of Peptostreptococcus, Fusobacterium, Streptococcus and Parvimonas in driving CRC progression. Full article
(This article belongs to the Special Issue Advances in Bacterial Metabolism, Gene Regulation, and Pathogenesis)
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Review

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15 pages, 367 KiB  
Review
Characteristics of the Skin Microbiome in Selected Dermatological Conditions: A Narrative Review
by Esther Olunoiki, Jacqueline Rehner, Markus Bischoff, Elena Koshel, Thomas Vogt, Jörg Reichrath and Sören L. Becker
Life 2022, 12(9), 1420; https://doi.org/10.3390/life12091420 - 12 Sep 2022
Cited by 8 | Viewed by 3130
Abstract
The skin is the largest and outermost organ of the human body. The microbial diversity of the skin can be influenced by several variable factors such as physiological state, lifestyle, and geographical locations. Recent years have seen increased interest in research aiming at [...] Read more.
The skin is the largest and outermost organ of the human body. The microbial diversity of the skin can be influenced by several variable factors such as physiological state, lifestyle, and geographical locations. Recent years have seen increased interest in research aiming at an improved understanding of the relationship between the human microbiota and several diseases. Albeit understudied, interesting correlations between the skin microbiota and several dermatological conditions have been observed. Studies have shown that a decrease or increase in the abundance of certain microbial communities can be implicated in several dermatological pathologies. This narrative review (i) examines the role of the skin microbiota in the maintenance of skin homeostasis and health, (ii) provides examples on how some common skin diseases (acne inversa, candidiasis, psoriasis) are associated with the dysbiosis of microbial communities, and (iii) describes how recent research approaches used in skin microbiome studies may lead to improved, more sensitive diagnostics and individual therapeutics in the foreseeable future. Full article
(This article belongs to the Special Issue Advances in Bacterial Metabolism, Gene Regulation, and Pathogenesis)
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