Journal Description
Microbiology Research
Microbiology Research
is an international, scientific, peer-reviewed open access journal published monthly online by MDPI (from Volume 11 Issue 2-2020).
- Open Access— free for readers, with article processing charges (APC) paid by authors or their institutions.
- High Visibility: indexed within Scopus, ESCI (Web of Science), Embase, and other databases.
- Rapid Publication: manuscripts are peer-reviewed and a first decision is provided to authors approximately 15.4 days after submission; acceptance to publication is undertaken in 2.7 days (median values for papers published in this journal in the second half of 2024).
- Recognition of Reviewers: APC discount vouchers, optional signed peer review, and reviewer names published annually in the journal.
Impact Factor:
2.1 (2023);
5-Year Impact Factor:
2.0 (2023)
Latest Articles
Effect of Carotenoid Composition on Stability and Light-Induced Oxidative Damage of the LH2 Complexes Isolated from Ectothiorhodospira haloalkaliphila
Microbiol. Res. 2025, 16(2), 36; https://doi.org/10.3390/microbiolres16020036 (registering DOI) - 2 Feb 2025
Abstract
►
Show Figures
Earlier, it has been shown that carotenoid-dependent singlet oxygen photogeneration in LH2 of Ectothiorhodospira haloalkaliphila leads to damage to pigments and protein. Present work continues this investigation using LH2 complexes with altered carotenoid composition: carotenoid-less LH2, and LH2 complexes with incorporated neurosporene, spheroidene,
[...] Read more.
Earlier, it has been shown that carotenoid-dependent singlet oxygen photogeneration in LH2 of Ectothiorhodospira haloalkaliphila leads to damage to pigments and protein. Present work continues this investigation using LH2 complexes with altered carotenoid composition: carotenoid-less LH2, and LH2 complexes with incorporated neurosporene, spheroidene, or rhodopin (LH2-Neu, LH2-Sph, or LH2-Rho, respectively). This work provides the first data on the products (hydroperoxides of organic molecules, most likely components of the protein matrix of the complexes) of the interaction of singlet oxygen with LH2 components with a modified carotenoid composition; the ability of various carotenoids to both influence the stability of LH2 and participate in oxidative damage to the complexes is assessed. It was shown that inhibition of carotenoid synthesis led to a decrease in LH2 thermal stability and reduced the light-induced oxidative damage to bacteriochlorophyll and protein. Re-incorporation of exogenous carotenoids did not return stability of the complexes but reduced the tendency of complexes to aggregate, and (in the case of LH2-Rho) reactivated both photooxidation of bacteriochlorophyll and photoproduction of organic hydroperoxides. It was concluded that carotenoids play an important role in comple x stability and are capable of inducing oxidative damage to LH2 components through singlet oxygen photogeneration.
Full article
Open AccessArticle
Biological Control of Sclerotinia sclerotiorum on Greenhouse Lettuce Using Trichoderma koningiopsis Agg
by
Snježana Topolovec-Pintarić, Ana Maria Kovaček, Olga Malev, Ivana Kušan, Neven Matočec, Ana Pošta, Lucia Pole and Armin Mešić
Microbiol. Res. 2025, 16(2), 35; https://doi.org/10.3390/microbiolres16020035 - 31 Jan 2025
Abstract
The lettuce drop or white mold is an economically important disease as the causal fungus Sclerotinia sclerotiorum can infect the lettuce at any stage of plant development. Polyphagous nature of S. sclerotiorum, the longevity of soil-borne sclerotia and air-borne ascospores makes the
[...] Read more.
The lettuce drop or white mold is an economically important disease as the causal fungus Sclerotinia sclerotiorum can infect the lettuce at any stage of plant development. Polyphagous nature of S. sclerotiorum, the longevity of soil-borne sclerotia and air-borne ascospores makes the control difficult. Chemical fungicides are available only for foliar application against infections by ascospores so, the development of bio-control is of great importance. We tested antagonism of native isolate T. koningiopsis agg. (Hypocreales) (STP8) under laboratory and greenhouse environments. In vitro tests showed excellent STP8 antagonisms to S. sclerotiorum evidencing hyperparasitic activity on mycelia and sclerotia as well as antibiosis. The sclerotia were completely degraded after two months. In the greenhouse, infection of lettuce with S. sclerotiorum was reduced by treating the seedlings with an STP8 spore suspension. Uninfected plants treated with STP8 were of the best quality based on morphological parameters, confirming the ability of STP8 to promote lettuce growth. Even the infected lettuce treated with STP8 were healthier and in better condition than the control lettuce, suggesting that STP8 was also enhancing plant defense system.
Full article
(This article belongs to the Collection Microorganisms and Their Incredible Potential to Face Societal Challenges)
►▼
Show Figures
Figure 1
Open AccessArticle
Enterobacter soli Strain AF-22b-4245: Study of the Genome and the Effect on Wheat Growth
by
Ekaterina Alexeevna Sokolova, Olga Viktorovna Mishukova, Inna Viktorovna Khlistun, Irina Nikolaevna Tromenschleger, Evgeniya Vladimirovna Chumanova and Elena Nikolaevna Voronina
Microbiol. Res. 2025, 16(2), 34; https://doi.org/10.3390/microbiolres16020034 - 30 Jan 2025
Abstract
►▼
Show Figures
Background: In this work the plant growth-promoting (PGP) qualities of the Enterobacter soli strain AF-22b-4245 were studied, including screening tests for PGP, whole genome sequencing (WGS) and genome annotation, and greenhouse experiments on wheat. A gene table was formed that allows us to
[...] Read more.
Background: In this work the plant growth-promoting (PGP) qualities of the Enterobacter soli strain AF-22b-4245 were studied, including screening tests for PGP, whole genome sequencing (WGS) and genome annotation, and greenhouse experiments on wheat. A gene table was formed that allows us to evaluate the potential PGP properties of a microorganism based on the results of genome-wide sequencing. Results: Based on the results of screening tests and genome annotation, it can be concluded that the E. soli strain AF-22b-4245 strain may have PGP properties, which consist in the ability to survive in arid and saline soils contaminated with copper, arsenic, lead, and chromium soils, form biofilms, produce phytohormones, siderophores, and solubilize phosphorus. Based on the results of experiments on wheat, the E. soli strain AF-22b-4245 increases the efficiency of mineral fertilizers; this effect persists even in conditions of drought and excess salt. It has been shown that E. soli A F22b-4245 can compensate for the lack of soluble phosphorus in the mineral fertilizer, probably by solubilizing insoluble forms in the soil.
Full article
Figure 1
Open AccessArticle
Sex Differences and Pathogen Patterns in Surgically Treated Aortic Valve Endocarditis over 15 Years
by
Elisa Mikus, Mariafrancesca Fiorentino, Diego Sangiorgi, Antonino Costantino, Simone Calvi, Elena Tenti, Elena Tremoli, Alberto Tripodi and Carlo Savini
Microbiol. Res. 2025, 16(2), 33; https://doi.org/10.3390/microbiolres16020033 - 29 Jan 2025
Abstract
►▼
Show Figures
Background: Infective endocarditis (IE) is a serious public health concern due to its high morbidity and lethality. This study investigates epidemiological trends in aortic valve endocarditis, focusing on sex-related differences in microbial etiology and surgical outcomes over a 15-year period. Methods: From January
[...] Read more.
Background: Infective endocarditis (IE) is a serious public health concern due to its high morbidity and lethality. This study investigates epidemiological trends in aortic valve endocarditis, focusing on sex-related differences in microbial etiology and surgical outcomes over a 15-year period. Methods: From January 2010 to January 2024, 608 patients underwent cardiac surgery for IE at our center. Of these, 274 patients received isolated aortic valve replacement. This retrospective, single-center study analyzes these cases. Results: Despite a decline in overall aortic valve replacement surgeries, a significant increase in surgeries due to aortic valve endocarditis was observed (p < 0.001). Both sexes showed a rising incidence of aortic valve endocarditis, with females undergoing surgery at an older age, particularly in native valve cases (p = 0.008). In prosthetic valve cases, this age difference was less pronounced (p = 0.050). While sex did not influence microbial etiology in native valve endocarditis, females with prosthetic valves were more frequently infected by Streptococcus (p = 0.033). Staphylococcus aureus infections increased in native valves (p = 0.016). Conclusions: Over 15 years, surgical aortic valve endocarditis has risen in both sexes. Males are more often affected by native valve cases, while females develop it later. Neither gender nor microbial etiology independently predicts death.
Full article
Figure 1
Open AccessArticle
In Vitro Evaluation of the Antiviral Properties of Exogenous mRNA Encoding the Human MxA Protein
by
Marina A. Plotnikova, Ekaterina A. Romanovskaya-Romanko, Anastasia A. Pulkina, Marina A. Shuklina, Anna-Polina S. Shurygina and Sergey A. Klotchenko
Microbiol. Res. 2025, 16(2), 32; https://doi.org/10.3390/microbiolres16020032 - 25 Jan 2025
Abstract
►▼
Show Figures
MxA is a cytoplasmic protein induced in human cells exposed to type I and III interferons. It can inhibit various viruses, including influenza A, by blocking the early steps of the viral replication cycle. The rapid advancement of mRNA-based technology has allowed us
[...] Read more.
MxA is a cytoplasmic protein induced in human cells exposed to type I and III interferons. It can inhibit various viruses, including influenza A, by blocking the early steps of the viral replication cycle. The rapid advancement of mRNA-based technology has allowed us to evaluate the antiviral activity of MxA-mRNA, encoding intracellular MxA protein, and explore its potential as a therapeutic agent. In this study, we used in vitro transfection methods to obtain functional, mature MxA-mRNA and evaluate its activity within cells. We also observed an undesirable cellular response to transfection with exogenous mRNAs, which involved interferon III induction and reduced cell viability. Nevertheless, preventive administration of MxA-mRNA led to a specific 10–80-fold decrease in influenza A and B levels in cell supernatants—an effect not observed with the control GFP-Luc-mRNA. Additionally, we investigated the antiviral activity of MxA-mRNA against RNA viruses, such as SARS-CoV-2 and both serotypes of RSV, but we could not demonstrate a significant virus-specific effect of exogenous mRNA on their replication. We believe that mRNAs that encode native antiviral proteins have great therapeutic potential.
Full article
Figure 1
Open AccessCase Report
First Isolation, Molecular Identification, and Phylogenetic Characterization of A3B5 Very Virulent Infectious Bursal Disease Virus in Pullets in Chile
by
Leandro Cádiz, Miguel Guzmán, Paola Rivera, Fernando Navarrete, Paulina Torres and Héctor Hidalgo
Microbiol. Res. 2025, 16(2), 31; https://doi.org/10.3390/microbiolres16020031 - 23 Jan 2025
Abstract
Infectious bursal disease virus (IBDV) is an important pathogen affecting the poultry industry worldwide. IBDV serotype 1, including classical virulent strains (cvIBDV), variant strains (varIBDV), and very virulent strains (vvIBDV), is pathogenic for chickens. IBDV mainly infects immature B-lymphocytes in the bursa of
[...] Read more.
Infectious bursal disease virus (IBDV) is an important pathogen affecting the poultry industry worldwide. IBDV serotype 1, including classical virulent strains (cvIBDV), variant strains (varIBDV), and very virulent strains (vvIBDV), is pathogenic for chickens. IBDV mainly infects immature B-lymphocytes in the bursa of Fabricius, weakening the humoral immune response and leading to secondary infections and increased morbidity and mortality. The Laboratory of Avian Pathology received ten live 8-week-old pullets from a laying hen operation experiencing increased mortality, prostration, diarrhea, and sudden death. Upon necropsy, the affected birds presented swollen, hemorrhagic, and edematous bursa of Fabricius, as well as hemorrhage in the breast and thigh muscles. RT-PCR confirmed that the samples from the bursa of Fabricius were positive for IBDV. Phylogenetic analysis of the VP1 and VP2 gene nucleotide sequences classified the strain, isolated in embryonated chicken eggs, as the A3B5 genotype. Amino acid sequence analysis of the VP2 hypervariable region revealed the presence of amino acid residues commonly found in vvIBDV. Additional studies are required to investigate the epidemiological situation of this genotype in Chile and to evaluate current vaccination plans and their effectiveness against new variants.
Full article
Open AccessArticle
Trends and Patterns of Antimicrobial Resistance in a Tertiary Care Hospital in Bangladesh
by
Sangjukta Roy, Hridika Talukder Barua, Mohammad Julhas Sujan, Akram Hossain, Shyamal Kumar Paul, Syeda Anjuman Nasreen, Salma Ahmed, Nazia Haque, Zakir Hossain Habib, Aninda Rahman, S. M. Shahriar Rizvi, Md. Abul Hasnat, Soo Young Kwon, John Stelling, Sanjay Gautam, Alina Shaw, Florian Marks and Nimesh Poudyal
Microbiol. Res. 2025, 16(2), 30; https://doi.org/10.3390/microbiolres16020030 - 23 Jan 2025
Abstract
Introduction: Antimicrobial resistance (AMR) is a global public health issue, particularly in resource-limited, low- to middle-income countries like Bangladesh. In this study, we analyze and present four years of data on AMR from a tertiary care hospital in Bangladesh to inform policymakers and
[...] Read more.
Introduction: Antimicrobial resistance (AMR) is a global public health issue, particularly in resource-limited, low- to middle-income countries like Bangladesh. In this study, we analyze and present four years of data on AMR from a tertiary care hospital in Bangladesh to inform policymakers and the wider community. Methods: In a retrospective cross-sectional study, we collected data for 4403 bacterial isolates reported between January 2017 and February 2020 at Mymensingh Medical College Hospital (MMCH), Bangladesh. All data were entered, cleaned, and analyzed using the software Stata Version-16.0, WHONET, a microbiology laboratory data management solution, and Quick Analysis of Antimicrobial Patterns and Trends (QAAPT), an AMR data visualization platform. Results: The bacteria were most commonly isolated from urine (71.66%, n = 3155), followed by pus (11.63%, n = 512), sputum (6.70%, n = 295), wound swabs (6.70%, n = 295), stool (1.91%, n = 84), endotracheal aspirate (1.20%, n = 53), and blood (0.20%, n = 9). Gram-negative bacteria predominated in all samples. Escherichia coli was the most common Gram-negative bacterium (31.30%, n = 1378), while Staphylococcus aureus was the most common Gram-positive bacterium (4.38%, n = 193). Antimicrobial susceptibility testing (AST) showed that multidrug resistance in Gram-negative bacteria such as E. coli, Klebsiella sp., and Acinetobacter sp. was common. S. aureus exhibited high resistance rates for beta-lactams, macrolides, and quinolones. In the urine samples, E. coli demonstrated high resistance to antibiotics like amoxicillin/clavulanic acid, ciprofloxacin, ceftriaxone, and cefuroxime (60–100%). Critical and high-priority pathogens as listed by the WHO constituted approximately 60% of the isolates. The AMR trends over three months showed increased resistance to amoxicillin/clavulanic acid for E. coli and to cefuroxime for Klebsiella sp. For S. aureus, the resistance to ciprofloxacin increased over three years, while the resistance to azithromycin decreased. Conclusions: There is a rise in bacterial resistance to the available antibiotics, with a significant prevalence of critical and high-priority pathogens in Bangladesh. We recommend vigilant AMR surveillance and stewardship programs to control the AMR in this country.
Full article
Open AccessArticle
Zoonotic Foodborne Infections in a Tertiary Healthcare Setting: Clinical and Epidemiological Aspects of Campylobacter and Salmonella Infection in Northern Portugal in 2010–2020
by
Maria Inês Matos, Rafael Rocha, João Pinto, André Guimarães, Rita Lino, Maria Helena Rocha, Marta Patacho, Raquel Duro, Lurdes Santos and Jorge Almeida
Microbiol. Res. 2025, 16(2), 29; https://doi.org/10.3390/microbiolres16020029 - 23 Jan 2025
Abstract
►▼
Show Figures
This study aimed to describe the epidemiology, clinical presentation, and management of Campylobacter sp. and Salmonella sp. infections in a tertiary hospital in Northern Portugal (2010–2020) and identify factors associated with reporting, invasive disease, and hospitalization. A retrospective review included patients with Campylobacter
[...] Read more.
This study aimed to describe the epidemiology, clinical presentation, and management of Campylobacter sp. and Salmonella sp. infections in a tertiary hospital in Northern Portugal (2010–2020) and identify factors associated with reporting, invasive disease, and hospitalization. A retrospective review included patients with Campylobacter sp. (2015–2020) or Salmonella sp. infections (2010–2020). Reported cases were cross-referenced with the National Epidemiological Surveillance System. A total of 742 patients were included: 342 with Campylobacter sp., 392 with non-typhoidal Salmonella (NTS), and 15 with typhoidal Salmonella (TS). Immunosuppression was present in 16.7% of cases. NTS infections were invasive in 21.4% of cases, compared to 4.0% for Campylobacter. Macrolide resistance in Campylobacter reached 10%, particularly in C. coli, while multidrug resistance (MDR) was observed in 37.8% of NTS isolates. Immunocompromised patients accounted for over 70% of relapses in Campylobacter disease. Reporting rates were low: 32.8% for NTS, 30.6% for Campylobacter, and 14.3% for TS. Reporting was associated with male sex, no immunosuppression, hospitalization, and non-MDR organisms. In conclusion, immunocompromised patients face higher risks of invasive and relapsing disease. High rates of MDR in NTS limit treatment options. Underreporting remains significant, underscoring the need for improved awareness and reporting to inform public health strategies.
Full article
Figure 1
Open AccessArticle
Roles of Whole-Genome Sequencing in Determining Transmission and Risk Factors Associated with Carbapenem-Resistant Organisms at a Vietnam HealthCare Center of Orphan Children
by
Van Kim Nguyen, Pirom Noisumdaeng, Katiya Ivanovitch, Eugene Athan, Larry Croft, Phuong Toai Nguyen and Huu Phuc Pham Nguyen
Microbiol. Res. 2025, 16(1), 28; https://doi.org/10.3390/microbiolres16010028 - 20 Jan 2025
Abstract
►▼
Show Figures
Antimicrobial resistance is one of the most concerning public health issues in Vietnam due to antibiotic-resistant Gram-negative bacteria, including carbapenem-resistant organisms (CROs), which might appear in remote areas in Vietnam. At this center, we performed a cross-sectional study and collected fecal samples from
[...] Read more.
Antimicrobial resistance is one of the most concerning public health issues in Vietnam due to antibiotic-resistant Gram-negative bacteria, including carbapenem-resistant organisms (CROs), which might appear in remote areas in Vietnam. At this center, we performed a cross-sectional study and collected fecal samples from humans (20 healthcare workers (HCWs) and 67 residents) and 175 environmental samples, with rectal and environment swabs, as data for this study, from September 2022 to December 2022. We conducted microbiological testing, including the MELAB Chromogenic CARBA agar plates, blood agar plates, and the BD PhoenixTM Automated Microbiology System to screen, isolate, and identify bacterial species and phenotypic tests for the antimicrobial susceptibility of carbapenem-resistant bacteria and the whole-genome sequencing for 12 CROs chosen to confirm the CRO transmission between HCWs and residents. The study findings showed that the prevalence and risk factors associated with CRO colonization were detected in HCWs, residents, and the environment in the Center of Care and Protection of Orphan Children. CRO transmission happened between HCWs and residents detected with WGS analysis. Whole-genome sequencing (WGS) plays a significant role in CRO control and prevention and reduces CRO transmission/colonization in this center and other healthcare settings.
Full article
Figure 1
Open AccessArticle
Prevalence and Antibiotic Resistance of Salmonella spp. and Campylobacter spp. Isolated from Retail Chickens in Saudi Arabia
by
Sulaiman F. Aljasir and Sahar A. Allam
Microbiol. Res. 2025, 16(1), 27; https://doi.org/10.3390/microbiolres16010027 - 19 Jan 2025
Abstract
Foodborne pathogens such as Salmonella spp.and Campylobacter spp. pose significant threats to the safety of broiler meat worldwide. However, data on their prevalence in retail chicken meat in Saudi Arabia are scarce. This context mainly concerns the vast poultry market in Saudi Arabia,
[...] Read more.
Foodborne pathogens such as Salmonella spp.and Campylobacter spp. pose significant threats to the safety of broiler meat worldwide. However, data on their prevalence in retail chicken meat in Saudi Arabia are scarce. This context mainly concerns the vast poultry market in Saudi Arabia, which may double by 2030. The overall objective of this study was to determine the prevalence and antibiotic resistance of Salmonella spp. and Campylobacter spp. in retail chickens from small, medium-sized, and large production companies in Saudi Arabia. Of the 212 chicken samples tested, Salmonella was detected in 9.3% of samples, all identified as Salmonella enterica serovar Enteritidis. Campylobacter was more prevalent, found in 35.8% of samples, with Campylobacter jejuni accounting for 26.4% and Campylobacter coli for 9.3%. Pathogen prevalence was higher in small-scale than in medium-sized and large producers. Salmonella Enteritidis isolates were resistant to nalidixic acid (90%), amoxicillin-clavulanic acid, and tetracycline (70%). Most Campylobacter coli isolates (90%) exhibited resistance to erythromycin, clindamycin, and gentamicin, followed by tetracycline (80%). Campylobacter jejuni isolates showed high resistance to erythromycin, clindamycin, tetracycline, azithromycin, and nalidixic acid (75–92%). Multidrug resistance (MDR) was observed in all Campylobacter jejuni isolates, 90% of Campylobacter coli isolates, and 70% of Salmonella isolates. These findings underscore the urgent need for adherence to food safety guidelines, particularly in small-scale poultry farms. The pervasive presence of MDR Salmonella spp. and Campylobacter spp. in broiler meat calls for enhanced surveillance, stricter enforcement of food safety practices, and public health initiatives to mitigate the risk of foodborne diseases in Saudi Arabia.
Full article
(This article belongs to the Collection Public Health and Quality Aspects Related to Animal Productions)
Open AccessArticle
Antifungal and Antibacterial Activity of Aqueous and Ethanolic Extracts of Different Rosa rugosa Parts
by
Žaneta Maželienė, Jolita Kirvaitienė, Kamilė Kaklauskienė, Rasa Volskienė and Asta Aleksandravičienė
Microbiol. Res. 2025, 16(1), 26; https://doi.org/10.3390/microbiolres16010026 - 18 Jan 2025
Abstract
With the rising incidence of drug-resistant pathogens, focus should be placed on biologically active compounds derived from plant species used in herbal medicine, as these compounds may provide a new source of antifungal and antibacterial activities. The aim of this study was to
[...] Read more.
With the rising incidence of drug-resistant pathogens, focus should be placed on biologically active compounds derived from plant species used in herbal medicine, as these compounds may provide a new source of antifungal and antibacterial activities. The aim of this study was to evaluate the antifungal and antibacterial activity of ethanol and aqueous extracts from different parts of Rosa rugosa. In order to evaluate the antimicrobial activity of the extracts of R. rugosa rose hips, flowers, petals, leaves, stems, and roots, a laboratory microbiological test was performed using the well diffusion method in agar. A rotary evaporator was used for extract concentration and extractant removal. Antimicrobial activity was tested against one fungus, four Gram-positive, and four Gram-negative bacteria. The leaf extracts exhibited the strongest antimicrobial activity, followed by the extracts from the petals and rose hips, while weaker activity was observed in the root extracts. The extracts from the stems and rose hips showed the weakest effect. Ethanol extracts were more effective than water extracts. Aqueous and ethanolic extracts of R. rugosa parts demonstrated antifungal activity against Candida albicans, with ethanol extracts proving to be more effective. Among all the R. rugosa parts analyzed, the petals exhibited the strongest antifungal activity.
Full article
(This article belongs to the Special Issue Antifungal Activities of Plant Extracts)
►▼
Show Figures
Figure 1
Open AccessArticle
Cultivatable Bacteriota of Chronic Wound of Patients with Diabetic Foot Syndrome with Critical Limb Ischemia Based on Wound Biopsy in Peri-Revascularization Period
by
Syedah Sarah Hussaini, Fran Dominic Grubesa, Mateusz Gajda, Martyna Schönborn, Katarzyna Bogucka, Mikołaj Maga, Paweł Maga and Jadwiga Wójkowska-Mach
Microbiol. Res. 2025, 16(1), 25; https://doi.org/10.3390/microbiolres16010025 - 18 Jan 2025
Abstract
►▼
Show Figures
Diabetic foot syndrome is often associated with inflammation. The aim of this study was to evaluate the impact of improved blood supply on the change in the clinical status and culturable bacteriota of chronic wounds. Patients with diabetic foot and peripheral arterial disease
[...] Read more.
Diabetic foot syndrome is often associated with inflammation. The aim of this study was to evaluate the impact of improved blood supply on the change in the clinical status and culturable bacteriota of chronic wounds. Patients with diabetic foot and peripheral arterial disease with a Rutherford score of 5 or 6 were included (n = 23). The blood supply to the limb was assessed with laboratory tests and two time-point qualitative cultures using a wound biopsy. The baseline parameters of the blood supply to the limb were Transcutaneous Oxygen Perfusion (TCPO2) of 15.0 mmHg, an Ankle Brachial Index (ABI) of 0.7, and a Toe Brachial Index (TBI) of 0.1, with an average Wound, Infection, Inflammation (WIfI) score of 5.7 (high). The most frequently isolated pathogens were Staphylococcus aureus (26.1%), followed by the Enterobacteriaceae family and Pseudomonas spp. (13.0%, each). Negative cultures were present in 47.8% (n = 11). The control parameters of blood supply improved; TCPO2 was 38.5 mmHg, the ABI was 0.9, and the TBI was 0.3, with a reduction in the average WIfI score to 3.7 (mild), while total colony-forming units (CFUs) increased by 13.5%. No cases of reocclusion or restenosis were observed during the study; however, small amputations were performed in two patients (8.7%). Five (21.7%) ulcers were significantly reduced and two (8.7%) progressed, while a negative culture at follow-up was obtained in five fewer patients than at baseline and nine patients presented growth despite having an initial negative result. Quantitative reduction was obtained in four (17.4%) cases. Pathogen distribution at follow-up resembled baseline findings. Optimizing clinical environments (enhancing blood flow and controlling inflammation) in general over focusing singularly on microbiota composition or revascularization seems to be crucial and arguably outweighed the impact of microbial change alone; in particular, reperfusion may increase the conditions to bacterial growth at the first stage.
Full article
Figure 1
Open AccessReview
Relationship Between Human Microbiome and Helicobacter pylori
by
Giada La Placa, Marcello Covino, Marcello Candeli, Antonio Gasbarrini, Francesco Franceschi and Giuseppe Merra
Microbiol. Res. 2025, 16(1), 24; https://doi.org/10.3390/microbiolres16010024 - 17 Jan 2025
Abstract
The enteric microbiota influences gene expression in the colonic epithelium. H. pylori (Helicobacter pylori) affects gastric growth factors, cytokines, and tumor cell markers, potentially benefiting the host. The interaction between H. pylori and human microbiota is complex but appears beneficial in gastric disease
[...] Read more.
The enteric microbiota influences gene expression in the colonic epithelium. H. pylori (Helicobacter pylori) affects gastric growth factors, cytokines, and tumor cell markers, potentially benefiting the host. The interaction between H. pylori and human microbiota is complex but appears beneficial in gastric disease development. This publication discusses the human microbiota, gastric microbiome, chronic H. pylori colonization, and the bacterium’s role in gastric disease. The interplay between the gastric bacterium and human microbiota during infection is also explored. The human gut has the most abundant and complex microbial community and performs vital roles in food digestion and nutrient uptake, extraction of absorbable vitamins, and inhibition of pathogen colonization. Helicobacter pylori is a highly specialized human gastric pathogen, predominantly colonizing the gastric mucus layer, on or adherent to the underlying gastric epithelial cell surfaces. Many studies have suggested that the gastric microbiome is related to H. pylori infection, and some bacterial species can be used for the detection or diagnosis of H. pylori infection. Human microbiome and genome analysis has revolutionized our understanding of the intricate relationship between humans and their associated microbial communities. The integration of microbiome data has displayed promising capabilities in occult disease detection, unveiling previously hidden pathologies and providing opportunities for early intervention. These groundbreaking discoveries have paved the way for novel therapeutic strategies and a deeper comprehension of the interconnected nature of the human microbiome and overall health.
Full article
Open AccessArticle
Isolation of Bacillus paralichenifromis BL-1 and Its Potential Application in Producing Bioflocculants Using Phenol Saline Wastewater
by
Tao Zhang, Rongkai Guo, Fanshu Liu, Lei Zhang, Linxiao Li, Rongfei Zhang, Chaogang Shao, Junbo Zhou, Fan Ding and Lan Yu
Microbiol. Res. 2025, 16(1), 23; https://doi.org/10.3390/microbiolres16010023 - 17 Jan 2025
Abstract
►▼
Show Figures
Phenolic compounds are harmful organic pollutants found in wastewater from the chemical and pharmaceutical industries, which are frequently accompanied by high saline concentrations. Microorganism-based biodegradation represents an environmentally friendly and cost-effective strategy for phenol removal. In this study, we isolated a bioflocculant-producing Bacillus
[...] Read more.
Phenolic compounds are harmful organic pollutants found in wastewater from the chemical and pharmaceutical industries, which are frequently accompanied by high saline concentrations. Microorganism-based biodegradation represents an environmentally friendly and cost-effective strategy for phenol removal. In this study, we isolated a bioflocculant-producing Bacillus paralicheniformis BL-1 that is capable of phenol degradation in high-salinity conditions. Differential gene expression analysis revealed the down-regulation of genes related to the synthesis of extracellular polymeric substances and the up-regulation of poly-γ-glutamate biosynthesis in 10% NaCl conditions. These findings indicate that poly-γ-glutamate is the main large biomolecule produced by B. paralicheniformis BL-1. A further investigation suggested that salinity stress resulted in the down-regulated expression of the genes involved in iron homeostasis. Therefore, alleviating iron limitation by supplying excess iron could improve cell growth and, thus, increase the phenol removal rate and flocculating activity. The productivity of poly-γ-glutamate reached 2.23 g/L, and the phenol removal rate reached 73.83% in the synthetic medium supplemented with 10% NaCl, 500 mg/L phenol, and 250 μM FeCl3.
Full article
Figure 1
Open AccessArticle
Gut Microbiome Profiles in Colorectal Cancer Patients in Iraq
by
Fatima J. Kadhim, Zahid S. Aziz and Khalid S. Ibrahim
Microbiol. Res. 2025, 16(1), 22; https://doi.org/10.3390/microbiolres16010022 - 16 Jan 2025
Abstract
Colorectal cancer (CRC) is the third most commonly diagnosed cancer globally, and is a significant contributor to both morbidity and mortality rates. Emerging research has promptly highlighted the potential role of the gut microbiome in the development and progression of CRC. This study
[...] Read more.
Colorectal cancer (CRC) is the third most commonly diagnosed cancer globally, and is a significant contributor to both morbidity and mortality rates. Emerging research has promptly highlighted the potential role of the gut microbiome in the development and progression of CRC. This study aims to investigate the differences in gut microbiota between CRC patients and healthy individuals in Iraq, using 16S rRNA metagenomic sequencing on Illumina NovaSeq (PE250-Seq). A total of 21 stool samples were analyzed: 12 from early-stage CRC patients and nine from healthy controls. Bacterial DNA was extracted, followed by 16S rRNA amplicon sequencing to profile the microbial communities. The results indicated significant differences between the fecal microbiome of the two groups. Remarkably, CRC patients exhibited a marked reduction in Bacteroidota and an increase in Verrucomicrobiota compared to healthy controls. At the genus level, Prevotella, Faecalibacterium, Roseburia, Barnesiella, Eubacterium Lachnospiraceae_UCG_004, and Lachnospira were significantly less abundant in CRC patients compared to the healthy individuals, while Actinomyces, Monoglobus, Desulfovibrio, Akkermansia, and Bacteroides were highly enriched. In addition, diversity analyses further indicated decreased α-diversity and distinct β-diversity patterns in the CRC patients, suggesting significant shifts in the gut microbial composition. These findings underscore the potential of microbiome-based diagnostics and therapeutic strategies, with microbial alterations serving as biomarkers for CRC diagnosis. Further research needs to focus on elucidating the causal relationships and therapeutic potential of these microbiome changes in CRC management.
Full article
(This article belongs to the Topic High-Throughput Analyses as a Multi-Faceted Approach for Characterizing the Human Microbiota)
►▼
Show Figures
Figure 1
Open AccessArticle
Indicators of the Microbial Corrosion of Steel Induced by Sulfate-Reducing Bacteria Under the Influence of Certain Drugs
by
Nataliia Tkachuk, Liubov Zelena and Yaroslav Novikov
Microbiol. Res. 2025, 16(1), 21; https://doi.org/10.3390/microbiolres16010021 - 16 Jan 2025
Abstract
►▼
Show Figures
Microorganisms cause microbiologically influenced corrosion, for the prevention of which bactericide inhibitors are used. The aim of the work was to study in vitro the sensitivity of SRB Desulfovibrio oryzae NUChC SRB1 to different concentrations of dimethyl sulfoxide (DMSO), and evaluate the indicators
[...] Read more.
Microorganisms cause microbiologically influenced corrosion, for the prevention of which bactericide inhibitors are used. The aim of the work was to study in vitro the sensitivity of SRB Desulfovibrio oryzae NUChC SRB1 to different concentrations of dimethyl sulfoxide (DMSO), and evaluate the indicators of the microbial corrosion of steel induced by this bacterium in the presence of the pharmaceutical drugs DMSO and paracetamol. The sensitivity of SRB D. oryzae to 1–100% DMSO (v/v) was studied via the dilution method in Postgate’s “C” liquid medium. The corrosion activity of D. oryzae against steel 3 was investigated under DMSO and paracetamol treatment at a final concentration of 45% (v/v) and 0.2% (w/v), respectively, according to the ability of bacteria to form a biofilm on the surface of the steel samples (via the crystal violet method) and the effect on the corrosion rate (via the gravimetric method). It was revealed that DMSO affected D. oryzae NUChC SRB1 and exhibited bactericidal properties (at a concentration range of 10–100%, v/v) and antibiofilm properties (at a concentration of 45%, v/v). Despite its antibiofilm properties confirmed by the reduction in bacterial biofilm mass, anticorrosion features were not observed in the model 35-day conditions of the microbial corrosion of steel in an anaerobic environment with bacterial sulfate reduction. Paracetamol (0.2%, w/v) did not affect biofilm formation by SRB under these conditions, and significantly contributed to an increase in the rate of the microbial corrosion of steel. The prospect of further research is to assess the effect of DMSO and paracetamol on the indicators of microbial corrosion induced by SRB under the influence of the concentrations of these compounds found in wastewater, to clarify the possible additional causes of damage to the equipment of treatment plants. Further research should also be directed at investigating the antimicrobial properties of complexes of compounds with DMSO, which should be considered as an ecological solution to the problem of microbiologically influenced corrosion prevention.
Full article
Figure 1
Open AccessArticle
Detection and Characterization of Escherichia coli and Escherichia coli O157:H7 in Human, Animal, and Food Samples from Kirkuk Province, Iraq
by
Hayman Abdullah Ameen Altaie, Maroua Gdoura Ben Amor, Burhan Ahmed Mohammed and Radhouane Gdoura
Microbiol. Res. 2025, 16(1), 20; https://doi.org/10.3390/microbiolres16010020 - 16 Jan 2025
Abstract
This study aims to investigate the prevalence of E. coli and E. coli O157:H7 in 353 samples collected in Kirkuk from human stool, animal feces, raw and pasteurized milk, and beef hamburgers. E. coli was isolated using conventional methods and identified with the
[...] Read more.
This study aims to investigate the prevalence of E. coli and E. coli O157:H7 in 353 samples collected in Kirkuk from human stool, animal feces, raw and pasteurized milk, and beef hamburgers. E. coli was isolated using conventional methods and identified with the Enterosystem Kit 18R. Suspected E. coli O157:H7 were confirmed serologically and tested for antimicrobial resistance and virulence genes (stx1, stx2, eaeA, and hlyA). The overall prevalence rates of 20.4% for E. coli and 7.9% for E. coli O157:H7 were found, with the highest prevalence in human stool. The antimicrobial susceptibility profile of 28 E. coli O157:H7 isolates revealed significant resistance and sensitivity patterns, highlighting important implications for public health. The isolates demonstrated complete sensitivity to gentamicin (100%), while also showing high sensitivity to ciprofloxacin (92.86%), ceftriaxone (85.71%), and amikacin (64.29%). Conversely, the isolates exhibited notable resistance to tetracycline (85.71%), ampicillin (75.00%), sulfamethoxazole (71.43%), and streptomycin (67.86%). All the E. coli O157:H7 strains isolated in this study were positive for stx1 and/or stx2, as well as the eaeA gene, and are referred to as enterohemorrhagic (EHEC) strains. In order to highlight the genotypic variability among the EHEC E. coli O157:H7 isolates, five virulence profiles were identified, with profile III (stx2, eaeA, and hlyA) being the most common (35.7%). This profile was closely associated with diarrheic humans, while profile V (stx1, eaeA) was prevalent in animal feces and products. These findings may raise awareness of the risks associated with this pathogen, helping to reduce the incidence of E. coli-related diseases and to protect human health.
Full article
(This article belongs to the Collection Public Health and Quality Aspects Related to Animal Productions)
Open AccessArticle
Molecular Diversity of Arbuscular Mycorrhizal Fungi Associated with the Rhizosphere of Vachellia seyal Del. from Selected Saline Soils in Senegal
by
Anicet Georges Bruno Manga, Godar Sene, André Amakobo Diatta, Tahir Abdoulaye Diop, Gérard Barroso and Diederik van Tuinen
Microbiol. Res. 2025, 16(1), 19; https://doi.org/10.3390/microbiolres16010019 - 16 Jan 2025
Abstract
►▼
Show Figures
Drought and salinity are major environmental constraints that severely limit crop production, particularly in arid and semi-arid zones. We investigated the genetic diversity of arbuscular mycorrhizal fungi isolated from the rhizosphere of Vachellia seyal in three different soils from Senegal with varying levels
[...] Read more.
Drought and salinity are major environmental constraints that severely limit crop production, particularly in arid and semi-arid zones. We investigated the genetic diversity of arbuscular mycorrhizal fungi isolated from the rhizosphere of Vachellia seyal in three different soils from Senegal with varying levels of salinity. Soil and root samples were collected from under V. seyal and in the vicinity of the trees. After DNA extraction, nested PCR, and sequencing of the large subunit region of the rRNA gene, different phylotypes from rhizospheric soils, roots, and spores were compared by phylogeny in order to investigate the role of salinity in arbuscular fungal diversity. This study revealed several unidentified arbuscular fungi and a particularly high host specificity in V. seyal roots. The vast majority of operational taxonomic units (OTUs) isolated in this study had no homologous sequences in the databases.
Full article
Figure 1
Open AccessCommunication
Copper Tolerance of Trichoderma koningii Tk10
by
Kehe Fu, Lili Fan, Jiaming Ji and Xiayu Qiu
Microbiol. Res. 2025, 16(1), 18; https://doi.org/10.3390/microbiolres16010018 - 15 Jan 2025
Abstract
►▼
Show Figures
Copper (Cu) is an essential micronutrient for all living organisms, serving as a cofactor for numerous enzymes. However, excessive copper concentrations can be harmful. To investigate copper tolerance in fungi, a copper-tolerant strain was isolated from soil and identified as Trichoderma koningii Tk10,
[...] Read more.
Copper (Cu) is an essential micronutrient for all living organisms, serving as a cofactor for numerous enzymes. However, excessive copper concentrations can be harmful. To investigate copper tolerance in fungi, a copper-tolerant strain was isolated from soil and identified as Trichoderma koningii Tk10, with optimized culture conditions being established. Additionally, copper-related genes were analyzed through whole-genome sequencing. The results indicated that Tk10 exhibits a maximum copper tolerance of 5.4 mmol/L and a maximum adsorption rate of 51.5% under optimal cultivation conditions. Whole-genome sequencing revealed six genes associated with copper tolerance, including one superoxide dismutase gene, one peroxidase gene, and three catalase genes linked to copper stress. Furthermore, the enzyme activities of the catalase, superoxide dismutase, and peroxidase significantly increased, reaching levels that were 8.02, 4.12, and 3.88 times higher than those observed in the control group, respectively. A real-time quantitative PCR analysis indicated that three of these genes were significantly upregulated in response to copper stress. The findings of this study provide valuable insights into copper tolerance in filamentous fungi.
Full article
Figure 1
Open AccessArticle
Epidemiological Analysis of a K. pneumoniae NDM Outbreak in a Temporary Ward for Patients with Primary COVID-19 Infection
by
Agata Pruss, Klaudia Miładowska, Helena Masiuk, Paweł Kwiatkowski, Joanna Jursa-Kulesza, Bartosz Wojciuk, Stefania Giedrys-Kalemba and Barbara Dołęgowska
Microbiol. Res. 2025, 16(1), 17; https://doi.org/10.3390/microbiolres16010017 - 12 Jan 2025
Abstract
►▼
Show Figures
The COVID-19 pandemic made the medical community realize how large a problem it would face. The epidemiological situation forced the opening of additional wards, the so-called “COVID wards”, where an increase in the rate of coexisting bacterial infections was observed. We report a
[...] Read more.
The COVID-19 pandemic made the medical community realize how large a problem it would face. The epidemiological situation forced the opening of additional wards, the so-called “COVID wards”, where an increase in the rate of coexisting bacterial infections was observed. We report a hospital outbreak due to New Delhi carbapenemases producing K. pneumoniae clones. Twenty-eight K. pneumoniae strains were analyzed from patients with primary COVID-19 infection. The drug susceptibility of the strains was determined by the diffusion–circulation method and E-test. Phenotypic and PCR methods confirmed the production of carbapenemases. The phylogenetic similarity of the obtained strains was examined using pulsed-field electrophoresis. Most strains were isolated from bronchoalveolar lavage. All isolates obtained were resistant to β-lactams and fluoroquinolones. All strains produced New Delhi carbapenemases and were classified into two genetic clusters, A and B. Eight risk factors for secondary bacterial infection were analyzed. Following an intervention involving hand hygiene, strict contact prevention, and cleaning of the hospital environment and medical devices, this outbreak was successfully brought under control.
Full article
Figure 1
Highly Accessed Articles
Latest Books
E-Mail Alert
News
Topics
Topic in
Antibiotics, Antioxidants, JoF, Microbiology Research, Microorganisms
Redox in Microorganisms, 2nd Edition
Topic Editors: Michal Letek, Volker BehrendsDeadline: 31 July 2025
Topic in
JoF, Microbiology Research, Microorganisms, Pathogens
Pathophysiology and Clinical Management of Fungal Infections
Topic Editors: Allan J. Guimarães, Marcos de Abreu AlmeidaDeadline: 30 November 2025
Topic in
Applied Microbiology, Fermentation, Foods, Microbiology Research, Microorganisms
Fermented Food: Health and Benefit
Topic Editors: Niel Van Wyk, Alice VilelaDeadline: 31 December 2025
Topic in
Applied Microbiology, Microbiology Research, Microorganisms, IJMS
New Challenge on Plant–Microbe Interactions
Topic Editors: Wenfeng Chen, Junjie ZhangDeadline: 31 January 2026
Conferences
Special Issues
Special Issue in
Microbiology Research
Veterinary Microbiology and Diagnostics
Guest Editor: Seyed Ali GhorashiDeadline: 28 February 2025
Special Issue in
Microbiology Research
Probiotic Applications in Aquaculture
Guest Editors: Chun-Hung Liu, Shao-Yang HuDeadline: 31 March 2025
Special Issue in
Microbiology Research
Antileishmanial Agents
Guest Editor: Edson Roberto da SilvaDeadline: 31 May 2025
Topical Collections
Topical Collection in
Microbiology Research
Microbiology and Technology of Fermented Foods
Collection Editor: Salam A. Ibrahim
Topical Collection in
Microbiology Research
Public Health and Quality Aspects Related to Animal Productions
Collection Editors: Beniamino T. Cenci-Goga, Massimo Zerani, Luca Grispoldi
Topical Collection in
Microbiology Research
Microorganisms and Their Incredible Potential to Face Societal Challenges
Collection Editor: Mireille Fouillaud