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Microorganisms
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Unveiling the Multiple Aspects of Microbial Ecology
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Unveiling the Multiple Aspects of Microbial Ecology

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

Deadline for manuscript submissions: closed (31 December 2022) | Viewed by 8663

Special Issue Editors

Prof. Dr. Eugenia Bezirtzoglou

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Guest Editor
Laboratory of Hygiene and Environmental Protection, Department of Medicine, Democritus University of Thrace, 68100 Alexandroupolis, Greece
Interests: microbiome; antimicrobials; antibiotics; biofilms
Special Issues, Collections and Topics in MDPI journals
Dr. Christina Tsigalou

E-Mail Website
Guest Editor
Laboratory of Microbiology, Department of Medicine, Democritus University of Thrace, 68100 Alexandroupolis, Greece
Interests: immunology; autoimmunity; diet; microbiome; functional foods; antimicrobials
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Yiannis Kourkoutas

E-Mail Website
Guest Editor
Laboratory of Applied Microbiology & Biotechnology, Department of Molecular Biology & Genetics, Democritus University of Thrace, 68100 Alexandroupolis, Greece
Interests: food microbiome; functional foods; nutrition; fermentation; antimicrobials
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

This Special Issue will collate the latest research on microbiomes, shedding light on their roles and functions in humans, animals, food and the environment. The balance of the microbial ecosystem is of utmost importance to the sustainable maintenance of microbial life. Yet, microbial ecosystems are highly dependent on human activities, environmental factors, stress, phytochemicals and antibiotics. By being in close proximity and interacting, microbes form an ecosystem that stabilizes and becomes resistant to changes in environmental living conditions. The composition of the microbial community and host immune status contribute to their stability. In recent years, studies have highlighted the importance of normal microflora that can protect against infection and the collateral damage of antibiotics.

Important research of both human, animal, food and environmental ecosystems, the conditions affecting them, and how these ecosystems affect health status will also be presented.

Lastly, the awareness of the relationship between the environment, food and health must be continuous throughout the development of permanent surveillance systems and policy strategies.

Topics considered for publication might include:

  • Different human, animal, food and environmental microbiomes;
  • Various mechanisms (ex-immunological, etc.) supporting the normal functionality of microbiomes;
  • Epigenetic factors (ex-nutrition, use of antimicrobials, etc.) and microbiome shifts;
  • Microbiota implications in the prevention, therapy and prognosis of diseases;
  • Potential therapeutic or antimicrobial properties of food and nutritional substances.

Prof. Dr. Eugenia Bezirtzoglou
Dr. Christina Tsigalou
Dr. Yiannis Kourkoutas
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.

Published Papers (5 papers)

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Research

21 pages, 1117 KiB  
Article
Overview of Ecology and Aspects of Antibiotic Resistance in Campylobacter spp. Isolated from Free-Grazing Chicken Tissues in Rural Households
by Argyrios Dermatas, Georgios Rozos, Konstantinos Zaralis, Aikaterini Dadamogia, Konstantina Fotou, Eugenia Bezirtzoglou, Konstantoula Akrida-Demertzi, Panagiotis Demertzis and Chrysoula (Chrysa) Voidarou
Microorganisms 2024, 12(2), 368; https://doi.org/10.3390/microorganisms12020368 - 10 Feb 2024
Viewed by 856
Abstract
Rural households all over the world rear backyard chicken mainly for their own consumption and, to a lesser extent, for barter trade. These chickens represent a staple dish with numerous culinary variations and a cheap source of protein. Although some Campylobacter species, and [...] Read more.
Rural households all over the world rear backyard chicken mainly for their own consumption and, to a lesser extent, for barter trade. These chickens represent a staple dish with numerous culinary variations and a cheap source of protein. Although some Campylobacter species, and particularly Campylobacter jejuni and Campylobacter coli, have been associated with industrial poultry carcasses, studies concerning the ecology of this genus in rural households do not exist. To assess the prevalence of Campylobacter species in the tissues of backyard chickens, samples were collected from birds Gallus domesticus bred in households in the rural area of Epirus (Greece), and Campylobacter strains were isolated by quantitative methods at 37 °C and 42 °C. In total, 256 strains were identified, belonging to 17 Campylobacter species, with C. jejuni and C. coli being the most prevalent. From the four ecological parameters studied (size of the flock, presence of small ruminants in the same household, presence of other poultry species in the same household, and feeding leftovers of the household), the size of the flock and the presence of small ruminants and/or pigs in the same household mostly affected the distribution of these strains. To study the phenotypical resistance against 14 antibiotics, 215 strains were selected. The results showed a high prevalence of multidrug-resistance (MDR) strains extending to all classes of antibiotics. Further genome analysis revealed the presence of genes coding resistance (blaOxA-61, tet(O), tet(A) cmeA, cmeB, cmeC, and gyrA (Thr-86-Ile mutation)), with the efflux pump CmeABC being the most prevalent. All antimicrobial resistance-encoded genes co-circulated, except for blaOXA-61, which moved independently. The minimum inhibitory concentration (MIC) values of two out of three antibiotics (representing different classes) were reduced when the strains tested were exposed to carbonyl cyanide 3-chlorophenylhydrazone (CCCP), a known efflux pump inhibitor. The same result was obtained with the addition of CCCP to the MIC values of bile salts. These results lead to the conclusion that Campylobacter species are present in an impressive diversity in backyard chicken tissues and that they exert a significant resistance to antibiotics, raising a potential danger for public health. Full article
(This article belongs to the Special Issue Unveiling the Multiple Aspects of Microbial Ecology)
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21 pages, 2226 KiB  
Article
Adaptation of Proteome and Metabolism in Different Haplotypes of Rhodosporidium toruloides during Cu(I) and Cu(II) Stress
by Philipp Cavelius, Selina Engelhart-Straub, Alexander Biewald, Martina Haack, Dania Awad, Thomas Brueck and Norbert Mehlmer
Microorganisms 2023, 11(3), 553; https://doi.org/10.3390/microorganisms11030553 - 22 Feb 2023
Cited by 2 | Viewed by 1472
Abstract
Rhodosporidium toruloides is a carotenogenic, oleogenic yeast that is able to grow in diverse environments. In this study, the proteomic and metabolic responses to copper stress in the two haplotypes IFO0559 and IFO0880 were assessed. 0.5 mM Cu(I) extended the lag phase of [...] Read more.
Rhodosporidium toruloides is a carotenogenic, oleogenic yeast that is able to grow in diverse environments. In this study, the proteomic and metabolic responses to copper stress in the two haplotypes IFO0559 and IFO0880 were assessed. 0.5 mM Cu(I) extended the lag phase of both strains significantly, while only a small effect was observed for Cu(II) treatment. Other carotenogenic yeasts such as Rhodotorula mucilaginosa are known to accumulate high amounts of carotenoids as a response to oxidative stress, posed by excess copper ion activity. However, no significant increase in carotenoid accumulation for both haplotypes of R. toruloides after 144 h of 0.5 mM Cu(I) or Cu(II) stress was observed. Yet, an increase in lipid production was detected, when exposed to Cu(II), additionally, proteins related to fatty acid biosynthesis were detected in increased amounts under stress conditions. Proteomic analysis revealed that besides the activation of the enzymatic oxidative stress response, excess copper affected iron–sulfur and zinc-containing proteins and caused proteomic adaptation indicative of copper ion accumulation in the vacuole, mitochondria, and Golgi apparatus. Full article
(This article belongs to the Special Issue Unveiling the Multiple Aspects of Microbial Ecology)
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19 pages, 7933 KiB  
Article
Changes of In Situ Prokaryotic and Eukaryotic Communities in the Upper Sanya River to the Sea over a Nine-Hour Period
by Shijie Bai, Jian Zhang, Xiaoxue Qi, Juntao Zeng, Shijun Wu and Xiaotong Peng
Microorganisms 2023, 11(2), 536; https://doi.org/10.3390/microorganisms11020536 - 20 Feb 2023
Cited by 1 | Viewed by 1548
Abstract
The transition areas of riverine, estuarine, and marine environments are particularly valuable for the research of microbial ecology, biogeochemical processes, and other physical–chemical studies. Although a large number of microbial-related studies have been conducted within such systems, the vast majority of sampling have [...] Read more.
The transition areas of riverine, estuarine, and marine environments are particularly valuable for the research of microbial ecology, biogeochemical processes, and other physical–chemical studies. Although a large number of microbial-related studies have been conducted within such systems, the vast majority of sampling have been conducted over a large span of time and distance, which may lead to separate batches of samples receiving interference from different factors, thus increasing or decreasing the variability between samples to some extent. In this study, a new in situ filtration system was used to collect membrane samples from six different sampling sites along the Sanya River, from upstream freshwater to the sea, over a nine-hour period. We used high-throughput sequencing of 16S and 18S rRNA genes to analyze the diversity and composition of prokaryotic and eukaryotic communities. The results showed that the structures of these communities varied according to the different sampling sites. The α-diversity of the prokaryotic and eukaryotic communities both decreased gradually along the downstream course. The structural composition of prokaryotic and eukaryotic communities changed continuously with the direction of river flow; for example, the relative abundances of Rhodobacteraceae and Flavobacteriaceae increased with distance downstream, while Sporichthyaceae and Comamonadaceae decreased. Some prokaryotic taxa, such as Phycisphaeraceae and Chromobacteriaceae, were present nearly exclusively in pure freshwater environments, while some additional prokaryotic taxa, including the SAR86 clade, Clade I, AEGEAN-169 marine group, and Actinomarinaceae, were barely present in pure freshwater environments. The eukaryotic communities were mainly composed of the Chlorellales X, Chlamydomonadales X, Sphaeropleales X, Trebouxiophyceae XX, Annelida XX, and Heteroconchia. The prokaryotic and eukaryotic communities were split into abundant, common, and rare communities for NCM analysis, respectively, and the results showed that assembly of the rare community assembly was more impacted by stochastic processes and less restricted by species dispersal than that of abundant and common microbial communities for both prokaryotes and eukaryotes. Overall, this study provides a valuable reference and new perspectives on microbial ecology during the transition from freshwater rivers to estuaries and the sea. Full article
(This article belongs to the Special Issue Unveiling the Multiple Aspects of Microbial Ecology)
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18 pages, 2536 KiB  
Article
Effect of Chitosan and Alginate-Based Edible Membranes with Oregano Essential Oil and Olive Oil in the Microbiological, Physicochemical and Organoleptic Characteristics of Mutton
by Anestis Tsitsos, Vangelis Economou, Eirini Chouliara, Georgia Koutouzidou, Georgios Arsenos and Ioannis Ambrosiadis
Microorganisms 2023, 11(2), 507; https://doi.org/10.3390/microorganisms11020507 - 17 Feb 2023
Cited by 2 | Viewed by 1531
Abstract
Edible chitosan or alginate coatings and their combinations with oregano essential oil or olive oil, have been examined for their effect on the microbiological, physicochemical and organoleptic characteristics of mutton. The results indicated that these edible coatings can contribute to maintaining good quality [...] Read more.
Edible chitosan or alginate coatings and their combinations with oregano essential oil or olive oil, have been examined for their effect on the microbiological, physicochemical and organoleptic characteristics of mutton. The results indicated that these edible coatings can contribute to maintaining good quality characteristics and extending mutton shelf-life. The total mesophilic counts in mutton ranged from 3.48 to 8.00 log10 CFU/g, the total psychrophilic counts from 4.00 to 9.50 log10 CFU/g, the B. thermosphacta counts from 2.30 to 7.77 log10 CFU/g and the lactic acid bacteria counts from 2.00 to 5.85 log10 CFU/g. Chitosan coatings significantly (p < 0.05) reduced the total mesophilic, the total psychrophilic (1–2 log10 cfu/g), the B. thermosphacta and the lactic acid bacteria counts in mutton. Alginate exhibited a lower L* value and a higher a* value and chroma compared with the control and chitosan lots. No significant differences were observed in the chemical composition of meat pieces among the experimental groups. Oregano oil positively affected the sensory attributes of meat. The most favourable combination, based on the microbiological counts, the organoleptic characteristics and the shelf-life extension of mutton, was that of chitosan with oregano essential oil. Full article
(This article belongs to the Special Issue Unveiling the Multiple Aspects of Microbial Ecology)
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14 pages, 2592 KiB  
Article
Anti-Inflammatory and Antibacterial Effects and Mode of Action of Greek Arbutus, Chestnut, and Fir Honey in Mouse Models of Inflammation and Sepsis
by Elisavet Stavropoulou, Eleftheria Ieronymaki, Evangelia Dimitroulia, Theodoros C. Constantinidis, Georgia Vrioni, Christos Tsatsanis and Athanasios Tsakris
Microorganisms 2022, 10(12), 2374; https://doi.org/10.3390/microorganisms10122374 - 30 Nov 2022
Cited by 3 | Viewed by 2259
Abstract
Background: Honey has been shown to possess anti-inflammatory and bactericidal properties that may be useful for the prevention and treatment of infections as well as of acute and chronic inflammatory diseases. The antimicrobial potency of honey could be attributed to its physicochemical characteristics [...] Read more.
Background: Honey has been shown to possess anti-inflammatory and bactericidal properties that may be useful for the prevention and treatment of infections as well as of acute and chronic inflammatory diseases. The antimicrobial potency of honey could be attributed to its physicochemical characteristics combined with the presence of certain compounds, such as hydrogen peroxide and polyphenols. Honey’s bacteriostatic or bactericidal capacity varies depending on its composition and the bacterial type of each infection. Nevertheless, not all honey samples possess anti-inflammatory or antibacterial properties and their mechanism of action has not been clearly elucidated. Objectives: We therefore investigated the anti-inflammatory properties of three different honey samples that derived from different geographical areas of Greece and different botanical origins, namely, arbutus, chestnut, and fir; they were compared to manuka honey, previously known for its anti-inflammatory and antibacterial activity. Materials and Methods: To test the anti-inflammatory activity of the different samples, we utilized the in vivo model of LPS-driven inflammation, which induces septic shock without the presence of pathogens. To evaluate the antibacterial action of the same honey preparations, we utilized the cecal-slurry-induced peritonitis model in mice. Since acute inflammation and sepsis reduce the biotransformation capacity of the liver, the expression of key enzymes in the process was also measured. Results: The administration of all Greek honey samples to LPS-stimulated mice revealed a potent anti-inflammatory activity by suppressing the TNFα serum levels and the expression of TNFα and iNOS in the liver at levels comparable to those of the manuka honey, but they had no effect on IL-6 or IL-1β. It was shown that the LPS-induced suppression of CYP1A1 in the liver was reversed by Epirus and Crete fir honey, while, correspondingly, the suppression of CYP2B10 in the liver was reversed by Evros chestnut and Epirus fir honey. The effect of the same honey samples in polymicrobial peritonitis in mice was also evaluated. Even though no effect was observed on the disease severity or peritoneal bacterial load, the bacterial load in the liver was reduced in mice treated with Evros chestnut, Epiros fir, and Crete fir, while the bacterial load in the lungs was reduced in Epirus arbutus, Crete fir, and manuka honey-treated mice. Conclusion: Our findings suggest that these specific Greek honey samples possess distinct anti-inflammatory and antibacterial properties, as evidenced by the reduced production of pro-inflammatory mediators and the impaired translocation of bacteria to tissues in septic mice. Their mode of action was comparable or more potent to those of manuka honey. Full article
(This article belongs to the Special Issue Unveiling the Multiple Aspects of Microbial Ecology)
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