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Analysis of Peptidomimetic Toxicity in E. coli Bacterial Cells—Studies on Selected Strains

A special issue of Materials (ISSN 1996-1944). This special issue belongs to the section "Biomaterials".

Deadline for manuscript submissions: closed (31 January 2022) | Viewed by 24651

Special Issue Editor

Department of Animal Nutrition, The Kielanowski Institute of Animal Physiology and Nutrition, Polish Academy of Sciences, 05-110 Jabłonna, Poland
Interests: nanoparticles; coumarin derivatives, oxidative stress in gram negative and positive bacteria; smart and multifunctional properties of ionic liquids and peptidomimetics; DNA etheno and prophano adducts
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Special Issue Information

Dear Colleagues,

Peptidomimetics are molecules whose structure and function are similar to those of peptides. They are an important group of compounds with biological, microbiological, anti-inflammatory, and anti-cancer properties. Therefore, studies on new peptidomimetics, which load the effect of native peptides, whose half-life in the body is much longer due to structural modifications, are extremely important. A preliminary study of new potential antimicrobial drugs was performed. Special emphasis was placed on the selection of the structure of α-aminoamides with the highest biological activity against different types of Gram-stained bacteria by lipopolysaccharide (LPS). Herein, Escherichia coli model strains K12 (without LPS in its structure) and R1–R4 (with different length LPS in its structure) were used. The presented work showed that the antibacterial activity of α-aminoamides depends on their structure and affects the LPS of bacteria. Moreover, the influence of various newly synthesized α-aminoamides on bacteria possessing smooth and rough LPS and oxidative damage of plasmid. DNA caused by all newly obtained compounds was indicated. We also measured the damage of isolated plasmid DNA using modeling of E. coli strains from Fpg enzymes caused by target compounds. Presented studies clearly explain that α-aminoamides they can be used as substitutes for antibiotics. The chemical and biological activity of the analyzed α-aminoamides was associated with short alkyl chain and different isocyanide molecules in their structure such as tetr-butyl isocyanide or 2,5-dimethoxybenzyl isocyanide. The observed results are especially important in the case of the increasing resistance of bacteria to various drugs and antibiotics.

This Special Issue is looking for new compounds that could replace antibiotics in terms of their biofunctionality, structure, and toxicity to pathogenic bacterial strains that infect our body. For many years, lengthy and costly research has been carried out in the search for such substances. An alternative to such research are compounds that occur naturally and are called peptidomimetics, which are similar in structure to commonly used antibiotics, but different in the nature of their functioning, because they are more specific and toxic to bacterial cells, such as coumarins and their derivatives and α-aminoamides. This Special Issue comprehensively discusses the latest achievements in the field of innovative methods of analyzing and assessing the toxicity of these compounds based on MIC and MBC tests and the use of the Fpg enzyme from the BER system, which is a repair glycosylase with two activities of glycosylase and AP-lyase. These simple screening tests show how inexpensive and easy it is to assess the toxicity of structurally complex compounds in model bacterial cells from the E.coli group, which can naturally replace "slowly useless" antibiotics. Coumarins are natural compounds that were detected in 80 species of plants. They have numerous applications including in the medical, food, tobacco, perfumery, and spirit industries. They show anti-swelling and diastolic effects. However, excess consumption of coumarins may adversely affect our health, because they are easily absorbed from the intestines into the lymph and blood, causing cirrhosis of the liver. A preliminary study of α-aminoamids and its derivatives as new potential antimicrobial drugs containing carboxylic acid, ester, or isocyanide group was also performed to determine their basic structure related to their biological features against various types of Gram-stained bacteria by lipopolysaccharide (LPS). In our research, we hypothesized that the toxicity (antibacterial activity) of both types of analyzed compounds are antagonistic compounds to many of the currently used antibiotics. The high biological activity of the selected coumarin peptidomimetic and α-aminoamides was associated with the identification of the so-called magic methyl groups, which substantially change the biochemical properties of target compounds. Investigating the effects of these compounds is particularly important in the era of increasingly common resistance in bacteria.

Prof. Dr. Paweł Kowalczyk
Guest Editor

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Keywords

  • oxidative stress
  • coumarin derivatives
  • Fpg protein—formamidopyrimidine DNA N-glycosylase/AP lyase
  • LPS—lipopolysaccharide
  • α-aminoamides (AAAs)

Published Papers (10 papers)

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Research

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15 pages, 2452 KiB  
Article
The Synthesis and Evaluation of Amidoximes as Cytotoxic Agents on Model Bacterial E. coli Strains
by Jan Samsonowicz-Górski, Paweł Kowalczyk, Dominik Koszelewski, Anna Brodzka, Mateusz Szymczak, Karol Kramkowski and Ryszard Ostaszewski
Materials 2021, 14(24), 7577; https://0-doi-org.brum.beds.ac.uk/10.3390/ma14247577 - 09 Dec 2021
Cited by 11 | Viewed by 2199
Abstract
The biological research on newly synthesized amidoximes, Boc-protected amidoximes and Boc-derived amidines, obtained by a reduction of the parent amidoximes is reported, herein. Due to the presence of a free amino group in both amidines and amidoximes, these compounds can undergo various chemical [...] Read more.
The biological research on newly synthesized amidoximes, Boc-protected amidoximes and Boc-derived amidines, obtained by a reduction of the parent amidoximes is reported, herein. Due to the presence of a free amino group in both amidines and amidoximes, these compounds can undergo various chemical reactions such as N-alkylation and N-acylation. One such reaction is Boc-protection, often used in organic synthesis to protect the amino and imino groups. Until now, Boc-protected amidoximes have not been tested for biological activity. Amidoxime derivatives were tested on bacterial E. coli strains. Initial cellular studies tests and digestion with Fpg after the modification of bacterial DNA, suggest that these compounds may have greater potential as antibacterial agents compared to antibiotics such as ciprofloxacin (ci), bleomycin (b) and cloxacillin (cl). The described compounds are highly specific for pathogenic E. coli strains on the basis of the model strains used and may be used in the future as new substitutes for commonly used antibiotics in clinical and hospital infections in the pandemic era. Full article
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17 pages, 3512 KiB  
Article
The Synthesis and Evaluation of Aminocoumarin Peptidomimetics as Cytotoxic Agents on Model Bacterial E. coli Strains
by Paweł Kowalczyk, Monika Wilk, Parul Parul, Mateusz Szymczak, Karol Kramkowski, Stanisława Raj, Grzegorz Skiba, Dorota Sulejczak, Patrycja Kleczkowska and Ryszard Ostaszewski
Materials 2021, 14(19), 5725; https://0-doi-org.brum.beds.ac.uk/10.3390/ma14195725 - 30 Sep 2021
Cited by 15 | Viewed by 1553
Abstract
This work presents the successful synthesis of a library of novel peptidomimetics via Ugi multicomponent reaction. Most of these peptidomimetics contain differently substituted aminocoumarin; 7-amino-4-methylcoumarin and 7-amino-4-(trifluoromethyl) coumarin. Inspired by the biological properties of coumarin derivatives and peptidomimetics, we proposed the synthesis of [...] Read more.
This work presents the successful synthesis of a library of novel peptidomimetics via Ugi multicomponent reaction. Most of these peptidomimetics contain differently substituted aminocoumarin; 7-amino-4-methylcoumarin and 7-amino-4-(trifluoromethyl) coumarin. Inspired by the biological properties of coumarin derivatives and peptidomimetics, we proposed the synthesis of coumarin incorporated peptidomimetics. We studied the potential of synthesized compounds as antimicrobial drugs on model E. coli bacterial strains (k12 and R2–R4). To highlight the importance of coumarin in antimicrobial resistance, we also synthesized the structurally similar peptidomimetics, using benzylamine. Preliminary cellular studies suggest that the compounds with coumarin derivatives have more potential as antimicrobial agents compared to the compounds without coumarin. We also analyzed the effect of aldehyde, free acid group and ester group on the course of their antimicrobial properties. Full article
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18 pages, 7041 KiB  
Article
Pyridine Derivatives—A New Class of Compounds That Are Toxic to E. coli K12, R2–R4 Strains
by Dominik Koszelewski, Ryszard Ostaszewski, Paweł Śmigielski, Anastasiia Hrunyk, Karol Kramkowski, Łukasz Laskowski, Magdalena Laskowska, Rafał Lizut, Mateusz Szymczak, Jacek Michalski, Kamil Gawin and Paweł Kowalczyk
Materials 2021, 14(18), 5401; https://0-doi-org.brum.beds.ac.uk/10.3390/ma14185401 - 18 Sep 2021
Cited by 14 | Viewed by 2026
Abstract
A preliminary study of 2-amino-4-aryl-3,5-dicarbonitrile-6-thiopyridines as new potential antimicrobial drugs was performed. Special emphasis was placed on the selection of the structure of target pyridine derivatives with the highest biological activity against different types of Gram-stained bacteria by lipopolysaccharide (LPS). Herein, Escherichia coli [...] Read more.
A preliminary study of 2-amino-4-aryl-3,5-dicarbonitrile-6-thiopyridines as new potential antimicrobial drugs was performed. Special emphasis was placed on the selection of the structure of target pyridine derivatives with the highest biological activity against different types of Gram-stained bacteria by lipopolysaccharide (LPS). Herein, Escherichia coli model strains K12 (without LPS in its structure) and R2–R4 (with different lengths of LPS in its structure) were used. Studied target compounds were provided with yields ranging from 53% to 91% by the lipase-catalyzed one pot multicomponent reaction of various aromatic aldehydes with malononitrile, and thiols. The presented work showed that the antibacterial activity of the studied pyridines depends on their structure and affects the LPS of bacteria. Moreover, the influence of the pyridines on bacteria possessing smooth and rough LPS and oxidative damage to plasmid DNA caused by investigated compounds was indicated. Additionally, the modification of the bacterial DNA with the tested compounds was performed to detect new potential oxidative damages, which are recognized by the Fpg protein. The obtained damage modification values of the analyzed compounds were compared with the modifications after antibiotics were used in this type of research. The presented studies demonstrate that 2-amino-4-aryl-3,5-dicarbonitrile-6-thiopyridines can be used as substitutes for known antibiotics. The observed results are especially important in the case of the increasing resistance of bacteria to various drugs and antibiotics. Full article
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18 pages, 4010 KiB  
Article
Protective Action of L. salivarius SGL03 and Lactoferrin against COVID-19 Infections in Human Nasopharynx
by Marzena Kucia, Ewa Wietrak, Mateusz Szymczak, Michał Majchrzak and Paweł Kowalczyk
Materials 2021, 14(11), 3086; https://0-doi-org.brum.beds.ac.uk/10.3390/ma14113086 - 04 Jun 2021
Cited by 3 | Viewed by 2286
Abstract
In this study, we used live viral particles from oral secretions from 17 people infected with SARS-CoV-2 and from 17 healthy volunteers, which were plated on a suitable medium complete for all microorganisms and minimal for L.salivarius growth. Both types of media [...] Read more.
In this study, we used live viral particles from oral secretions from 17 people infected with SARS-CoV-2 and from 17 healthy volunteers, which were plated on a suitable medium complete for all microorganisms and minimal for L.salivarius growth. Both types of media also contained an appropriately prepared vector system pGEM-5Zf (+) based on the lactose operon (beta-galactosidase system). Incubation was carried out on both types of media for 24 h with the addition of 200 μL of Salistat SGL03 solution in order to test its inhibitory effect on the coronavirus contained in the oral mucosa and nasopharynx, visible as light blue virus particles on the test plates, which gradually disappeared in the material collected from infected persons over time. Regardless of the conducted experiments, swabs were additionally taken from the nasopharynx of infected and healthy people after rinsing the throat and oral mucosa with Salistat SGL03. In both types of experiments, after 24 h of incubation on appropriate media with biological material, we did not find any virus particles. Results were also confirmed by MIC and MBC tests. Results prove that lactoferrin, as one of the ingredients of the preparation, is probably a factor that blocks the attachment of virus particles to the host cells, determining its anti-viral properties. The conducted preliminary experiments constitute a very promising model for further research on the anti-viral properties of the ingredients contained in the Salistat SGL03 dietary supplement. Full article
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25 pages, 1810 KiB  
Article
δ-Lactones—A New Class of Compounds That Are Toxic to E. coli K12 and R2–R4 Strains
by Paweł Kowalczyk, Barbara Gawdzik, Damian Trzepizur, Mateusz Szymczak, Grzegorz Skiba, Stanisława Raj, Karol Kramkowski, Rafał Lizut and Ryszard Ostaszewski
Materials 2021, 14(11), 2956; https://0-doi-org.brum.beds.ac.uk/10.3390/ma14112956 - 30 May 2021
Cited by 23 | Viewed by 2657
Abstract
Lactones are among the well-known organic substances with a specific taste and smell. They are characterized by antibacterial, antiviral, anti-inflammatory, and anti-cancer properties. In recent years, among this group of compounds, new biologically active substances have been searched by modifying the main (leading) [...] Read more.
Lactones are among the well-known organic substances with a specific taste and smell. They are characterized by antibacterial, antiviral, anti-inflammatory, and anti-cancer properties. In recent years, among this group of compounds, new biologically active substances have been searched by modifying the main (leading) structure with new analogs with stronger or different responses that may have a toxic effect on the cells of pathogenic bacteria and constitute an alternative to commonly used antibiotics. A preliminary study of δ-lactone derivatives as new potential candidates for antibacterial drugs was conducted. Particular emphasis was placed on the selection of the structure of lactones with the highest biological activity, especially those with fluorine in their structure as a substituent in terms of action on bacterial lipopolysaccharide (LPS) in the model strains of Escherichia coli K12 (without LPS in its structure) and R2–R4 (LPS of different lengths in its structure). In the presented studies, on the basis of the conducted MIC and MBC tests, it was shown that the antibacterial (toxic) activity of lactones depends on their structure and the length of the bacterial LPS in the membrane of specific strains. Moreover, oxidative damage of bacterial DNA isolated from bacteria after modification with newly synthesized compounds after application of the repair enzyme Fpg glycosylase was analyzed. The analyzed damage values were compared with the modification with appropriate antibiotics: ciprofloxacin, bleomycin, and cloxacillin. The presented research clearly shows that lactone derivatives can be potential candidates as substitutes for drugs, e.g., the analyzed antibiotics. Their chemical and biological activity is related to coumarin derivatives and the corresponding δ-lactone groups in the structure of the substituent. The observed results are of particular importance in the case of increasing bacterial resistance to various drugs and antibiotics, especially in nosocomial infections and neoplasms, and in the era of a microbial pandemic. Full article
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18 pages, 692 KiB  
Article
Impact of the Diet on the Formation of Oxidative Stress and Inflammation Induced by Bacterial Biofilm in the Oral Cavity
by Ilona Rowińska, Adrianna Szyperska-Ślaska, Piotr Zariczny, Robert Pasławski, Karol Kramkowski and Paweł Kowalczyk
Materials 2021, 14(6), 1372; https://0-doi-org.brum.beds.ac.uk/10.3390/ma14061372 - 12 Mar 2021
Cited by 7 | Viewed by 2245
Abstract
The diet is related to the diversity of bacteria in the oral cavity, and the less diverse microbiota of the oral cavity may favor the growth of pathogenic bacteria of all bacterial complexes. Literature data indicate that disturbances in the balance of the [...] Read more.
The diet is related to the diversity of bacteria in the oral cavity, and the less diverse microbiota of the oral cavity may favor the growth of pathogenic bacteria of all bacterial complexes. Literature data indicate that disturbances in the balance of the bacterial flora of the oral cavity seem to contribute to both oral diseases, including periodontitis, and systemic diseases. If left untreated, periodontitis can damage the gums and alveolar bones. Improper modern eating habits have an impact on the oral microbiome and the gut microbiome, which increase the risk of several chronic diseases, including inflammatory bowel disease, obesity, type 2 diabetes, cardiovascular disease and cancer. The subject of our consideration is the influence of the traditional diet on the formation of oxidative stress and inflammation caused by bacterial biofilm in the oral cavity. Through dental, biomedical and laboratory studies, we wanted to investigate the effect of individual nutrients contained in specific diets on the induction of oxidative stress inducing inflammation of the soft tissues in the oral cavity in the presence of residual supra- and subgingival biofilm. In our research we used different types of diets marked as W, T, B, F and noninvasively collected biological material in the form of bacterial inoculum from volunteers. The analyzed material was grown on complete and selective media against specific strains of all bacterial complexes. Additionally, the zones of growth inhibition were analyzed based on the disc diffusion method. The research was supplemented with dental and periodontological indicators. The research was supplemented by the application of molecular biology methods related to bacterial DNA isolation, PCR reactions and sequencing. Such selected methods constitute an ideal screening test for the analysis of oral bacterial microbiota. The obtained results suggest that certain types of diet can be an effective prophylaxis in the treatment of civilization diseases such as inflammation of the oral cavity along with periodontal tissues and gingival pockets. Full article
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14 pages, 1689 KiB  
Article
Comparison of Osmotic Resistance, Shape and Transmembrane Potential of Erythrocytes Collected from Healthy and Fed with High Fat-Carbohydrates Diet (HF-CD) Pigs—Protective Effect of Cistus incanus L. Extracts
by Sylwia Cyboran-Mikołajczyk, Robert Pasławski, Urszula Pasławska, Kacper Nowak, Michał Płóciennik, Katarzyna Męczarska, Jan Oszmiański, Dorota Bonarska-Kujawa, Paweł Kowalczyk and Magdalena Wawrzyńska
Materials 2021, 14(4), 1050; https://0-doi-org.brum.beds.ac.uk/10.3390/ma14041050 - 23 Feb 2021
Cited by 1 | Viewed by 2024
Abstract
Long-term high fat-carbohydrates diet (HF-CD) contributes to the formation of irreversible changes in the organism that lead to the emergence of civilization diseases. In this study, the impact of three-month high-fat diet on the physical properties of erythrocytes (RBCs) was studied. Furthermore, the [...] Read more.
Long-term high fat-carbohydrates diet (HF-CD) contributes to the formation of irreversible changes in the organism that lead to the emergence of civilization diseases. In this study, the impact of three-month high-fat diet on the physical properties of erythrocytes (RBCs) was studied. Furthermore, the biological activity of Cistus incanus L. extracts, plant known with high pro-health potential, in relation to normal and HF-CD RBCs, was determined. Obtained results have shown that, applied HF-CD modified shape, membrane potential and osmotic resistance of erythrocytes causing changes in membrane lipid composition and the distribution of lipids. The impact of HF-CD on physical properties of RBCs along with atherosclerotic lesions of the artery was visible, despite the lack of statistically significant changes in blood morphology and plasma lipid profile. This suggests that erythrocytes may be good markers of obesity-related diseases. The studies of biological activity of Cistus incanus L. extracts have demonstrated that they may ameliorate the effect of HF-CD on erythrocytes through the membrane-modifying and antioxidant activity. Full article
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20 pages, 3445 KiB  
Article
1,2-Diarylethanols—A New Class of Compounds That Are Toxic to E. coli K12, R2–R4 Strains
by Paweł Kowalczyk, Damian Trzepizur, Mateusz Szymczak, Grzegorz Skiba, Karol Kramkowski and Ryszard Ostaszewski
Materials 2021, 14(4), 1025; https://0-doi-org.brum.beds.ac.uk/10.3390/ma14041025 - 22 Feb 2021
Cited by 16 | Viewed by 2282
Abstract
An initial study of 1,2-diarylethanols derivatives as new potential antibacterial drugs candidates was conducted. Particular emphasis was placed on the selection of the structure of 1,2-diarylethanols with the highest biological activity of lipopolysaccharides (LPS) in the model strains of Escherichia coli K12 (without [...] Read more.
An initial study of 1,2-diarylethanols derivatives as new potential antibacterial drugs candidates was conducted. Particular emphasis was placed on the selection of the structure of 1,2-diarylethanols with the highest biological activity of lipopolysaccharides (LPS) in the model strains of Escherichia coli K12 (without LPS in its structure) and R2–R4 (with different lengths of LPS in its structure). In the presented studies, based on the conducted minimum inhibitory concentration (MIC) and MBC tests, it was demonstrated that the antibacterial (toxic) effect of 1,2-diarylethanols depends on their structure and the length of LPS bacteria in the membrane of specific strains. Moreover, the oxidative damage of bacterial DNA isolated from bacteria after modification with newly synthesized compounds after application of the repair enzyme Fpg glycosylases was analysed. The analysed damage values were compared with modification with appropriate antibiotics; bacterial DNA after the use of kanamycin, streptomycin, ciprofloxacin, bleomycin and cloxicillin. The presented research clearly shows that 1,2-diarylethanol derivatives can be used as potential candidates for substitutes for new drugs, e.g., the analysed antibiotics. Their chemical and biological activity is related to two aromatic groups and the corresponding chemical groups in the structure of the substituent. The observed results are particularly important in the case of increasing bacterial resistance to various drugs and antibiotics, especially in nosocomial infections and neoplasms, and in the era of pandemics caused by microorganisms. Full article
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23 pages, 1898 KiB  
Article
α-Amidoamids as New Replacements of Antibiotics—Research on the Chosen K12, R2–R4 E. coli Strains
by Paweł Kowalczyk, Arleta Madej, Mateusz Szymczak and Ryszard Ostaszewski
Materials 2020, 13(22), 5169; https://0-doi-org.brum.beds.ac.uk/10.3390/ma13225169 - 16 Nov 2020
Cited by 19 | Viewed by 2063
Abstract
A preliminary study of α-amidoamids as new potential antimicrobial drugs was performed. Special emphasis was placed on selection of structure of α-amidoamids with the highest biological activity against different types of Gram-stained bacteria by lipopolysaccharide (LPS). Herein, Escherichia coli model strains K12 (without [...] Read more.
A preliminary study of α-amidoamids as new potential antimicrobial drugs was performed. Special emphasis was placed on selection of structure of α-amidoamids with the highest biological activity against different types of Gram-stained bacteria by lipopolysaccharide (LPS). Herein, Escherichia coli model strains K12 (without LPS in its structure) and R1–R4 (with different length LPS in its structure) were used. The presented work showed that the antibacterial activity of α-amidoamids depends on their structure and affects the LPS of bacteria. Moreover, the influence of various newly synthesized α-amidoamids on bacteria possessing smooth and rought LPS and oxidative damage of plasmid DNA caused by all newly obtained compounds was indicated. The presented studies clearly explain that α-amidoamids can be used as substitutes for antibiotics. The chemical and biological activity of the analysed α-amidoamids was associated with short alkyl chain and different isocyanides molecules in their structure such as: tetr-butyl isocyanide or 2,5-dimethoxybenzyl isocyanide. The observed results are especially important in the case of the increasing resistance of bacteria to various drugs and antibiotics. Full article
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Review

Jump to: Research

33 pages, 1388 KiB  
Review
The Influence of Diet on Oxidative Stress and Inflammation Induced by Bacterial Biofilms in the Human Oral Cavity
by Ilona Rowińska, Adrianna Szyperska-Ślaska, Piotr Zariczny, Robert Pasławski, Karol Kramkowski and Paweł Kowalczyk
Materials 2021, 14(6), 1444; https://0-doi-org.brum.beds.ac.uk/10.3390/ma14061444 - 16 Mar 2021
Cited by 13 | Viewed by 4283
Abstract
The article is a concise compendium of knowledge on the etiology of pathogenic microorganisms of all complexes causing oral diseases. The influence of particular components of the diet and the role of oxidative stress in periodontal diseases were described. The study investigated the [...] Read more.
The article is a concise compendium of knowledge on the etiology of pathogenic microorganisms of all complexes causing oral diseases. The influence of particular components of the diet and the role of oxidative stress in periodontal diseases were described. The study investigated the bacteriostatic effect of the diet of adults in in vivo and in vitro tests on the formation of bacterial biofilms living in the subgingival plaque, causing diseases called periodontitis. If left untreated, periodontitis can damage the gums and alveolar bones. Anaerobic bacteria, called periopathogens or periodontopathogens, play a key role in the etiopathogenesis of periodontitis. The most important periopathogens of the oral microbiota are bacteria of all complexes, including the red complex. The obtained results suggest the possibility of using a specific diet in the prevention and treatment of periodontal diseases-already treated as a disease of civilization. The quoted article is an innovative compilation of knowledge on this subject and it can be a valuable source of knowledge for professional hygienists, dentists, peridontologists, dentistry students and anyone who cares about proper oral hygiene. The obtained results suggest the possibility of using this type of diet in the prophylaxis of the oral cavity in order to avoid periodontitis. Full article
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