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Microbiol. Res., Volume 13, Issue 3 (September 2022) – 22 articles

Cover Story (view full-size image): Everything that connects the intestine to the liver contributes to the realization of the gut–liver axis, an extremely dynamic system that plays a crucial role in the development and progression of portal hypertension in patients with advanced chronic liver disease. The intestinal barrier and the hepatic sinusoid system are the two hinges of the firewall that contains and controls bacterial translocation. Any impairment in the communication between these components of the gut–liver axis gives rise to a vicious cycle, leading to portal hypertension and its complications. The gut microbiome has recently emerged as a promising therapeutic tool for the near future, with a major clinical impact on portal hypertension through the modulation of the gut–liver axis. View this paper
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14 pages, 890 KiB  
Article
Assessment of Antimicrobial Efficiency of Pistacia lentiscus and Fortunella margarita Essential Oils against Spoilage and Pathogenic Microbes in Ice Cream and Fruit Juices
by Gregoria Mitropoulou, Haido Bardouki, Manolis Vamvakias, Panayiotis Panas, Panagiotis Paraskevas and Yiannis Kourkoutas
Microbiol. Res. 2022, 13(3), 667-680; https://doi.org/10.3390/microbiolres13030048 - 16 Sep 2022
Cited by 9 | Viewed by 2296
Abstract
Nowadays, the use of antimicrobial natural agents as alternative food preservatives represents an intriguing case. The purpose of this study was to investigate possible antimicrobial activity of Pistacia lentiscus and Fortunella margarita essential oils (EOs) and to evaluate their commercial potential in the [...] Read more.
Nowadays, the use of antimicrobial natural agents as alternative food preservatives represents an intriguing case. The purpose of this study was to investigate possible antimicrobial activity of Pistacia lentiscus and Fortunella margarita essential oils (EOs) and to evaluate their commercial potential in the food industry. The main constituents identified by GC/MS in Pistacia lentiscus EO were a-pinene (67.7%), myrcene (18.8%), and β-pinene (3.0%), whereas limonene (93.8%) and myrcene (2.7%) were the dominant compounds in Fortunella margarita EO. The antimicrobial properties were initially assayed and the minimum inhibitory, non-inhibitory, and minimum lethal concentration values against the EscherichiacoliListeria monocytogenes, Pseudomonas fragi, Aspergillus niger, and Saccharomyces cerevisiae were determined using a previously published model, combining absorbance measurements with the common dilution method and non-linear regression analysis to fit the data. Their efficiency was further validated in ice cream containing 0.2% (w/w) Pistacia lentiscus, 0.006% (w/w) Fortunella margarita EOs and 2% (w/w) aqueous residue of F. margarita EO deliberately inoculated with 4 logcfu/g EscherichiacoliListeria monocytogenes or Pseudomonas fragi, separately. Similarly, the activity of the oils was monitored in fruit juice (lemon, apple, and blackcurrant) containing 0.2% (w/w) Pistacia lentiscus, 0.006% (w/w) Fortunella margarita EOs and 2% (w/w) aqueous residue of F. margarita EO deliberately spiked with 100 spores/mL of Aspergillus niger or 4 logcfu/mL of Saccharomyces cerevisiae, separately. The results showed that microbial viable counts in the supplemented products ranged at significantly lower levels compared to the control samples during storage. Overall, the data indicated that both EOs constitute effective antimicrobial sources with many potent applications in the food industry. Full article
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12 pages, 2440 KiB  
Article
Molecular Character of Mylonchulus hawaiiensis and Morphometric Differentiation of Six Mylonchulus (Nematoda; Order: Mononchida; Family: Mylonchulidae) Species Using Multivariate Analysis
by Ebrahim Shokoohi and Ngonidzashe Moyo
Microbiol. Res. 2022, 13(3), 655-666; https://doi.org/10.3390/microbiolres13030047 - 14 Sep 2022
Cited by 6 | Viewed by 1831
Abstract
Mononchida members are predatory nematodes with the potential to reduce the number of plant-parasitic nematodes in the soil. During a survey on Mononchida in Iran, several populations of Mylonchulus were recovered from various localities. A population of M. hawaiiensis was studied using 18S [...] Read more.
Mononchida members are predatory nematodes with the potential to reduce the number of plant-parasitic nematodes in the soil. During a survey on Mononchida in Iran, several populations of Mylonchulus were recovered from various localities. A population of M. hawaiiensis was studied using 18S rDNA. The phylogenetic analysis using Bayesian inference placed the sequenced M. hawiinesis (OP210758) together with other M. hawaiiensis from Japan (AB361438-AB361442) with a 1.00 posterior probability support. In addition, morphological differences between six Mylonchulus (Nematoda; order: Mononchida; Family: Mylonchulidae) populations were investigated in Iran using discriminant analyses (DA), PERMANOVA, and principal coordinate analysis (PCoA). The purpose was to evaluate the efficacy of PCoA and DA in separating the Mylonchulus species, namely M. sigmaturus, M. paitensis, M. lacustris, M. brachyuris, M. kermaninesis, and M. hawaiiensis. To achieve this, 16 morphometric measurements (body length, a, b, c, c′, V, G1, G2, buccal cavity length, buccal cavity width, dorsal tooth apex, dorsal tooth length, neck length, amphid from anterior end, rectum, and tail length) were made on 160 specimens. The analysis of variance showed that all features were significantly different among the species, except a, b, and the amphid position from the anterior end and tail length. The stepwise discriminant analysis revealed that body length, tail length, neck length, and c′ value were the four most discriminating variables useful to distinguish clearly the six species of Mylonchulus. The variables with strong discriminatory power correctly classified 98.87% of individuals from Iran’s sample of known Mylonchulus species. The results provide a morphometric basis for effectively distinguishing Mylonchulus species. Full article
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12 pages, 4230 KiB  
Article
Evaluation of Different Molecular Markers for Genotyping Non-Saccharomyces Wine Yeast Species
by Aspasia Nisiotou, Emanouela Gyftogianni and Georgios Banilas
Microbiol. Res. 2022, 13(3), 643-654; https://doi.org/10.3390/microbiolres13030046 - 8 Sep 2022
Cited by 1 | Viewed by 2244
Abstract
Wine quality is determined by the particular yeast strains prevailing at various stages of fermentation. Therefore, the ability to make an easy, fast, and unambiguous discrimination of yeasts at the strain level is of great importance. Here, the tandem repeat-tRNA (TRtRNA) method with [...] Read more.
Wine quality is determined by the particular yeast strains prevailing at various stages of fermentation. Therefore, the ability to make an easy, fast, and unambiguous discrimination of yeasts at the strain level is of great importance. Here, the tandem repeat-tRNA (TRtRNA) method with the 5GAC or ISSR-MB primer sets and random amplified polymorphic DNA (RAPD) analysis with (GTG)3, R5, and RF2 oligonucleotides were tested on various non-Saccharomyces wine yeast species. The TRtRNA-PCR employing ISSR-MB showed the highest capacity in discriminating Lachancea thermotolerans and Metschnikowia pulcherrima isolates. RAPD with RF2 was the most efficient method in resolving Starmerella bacillaris isolates, although it produced few polymorphic bands. RAPD with R5 showed the highest capacity to discriminate among the Issatchenkia orientalis, Hanseniaspora guilliermondii, and Pichia anomala isolates. RAPD with either R5 or RF2 exhibited the highest ability to discriminate among the Torulaspora delbrueckii isolates. RAPD with (GTG)3 was the most discriminating method for the H. uvarum isolates. Here we concluded that both TRtRNA-PCR and RAPD-PCR offer rapid means for typing non-Saccharomyces species. However, each method performs better for a given species when paired with a particular primer set. The present results can be useful in wine research for the fast fingerprinting of non-Saccharomyces yeasts. Full article
(This article belongs to the Collection Microbiology and Technology of Fermented Foods)
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17 pages, 697 KiB  
Article
The Effect of Heavy Metals on Microbial Communities in Industrial Soil in the Area of Piekary Śląskie and Bukowno (Poland)
by Anna Katarzyna Jarosławiecka and Zofia Piotrowska-Seget
Microbiol. Res. 2022, 13(3), 626-642; https://doi.org/10.3390/microbiolres13030045 - 7 Sep 2022
Cited by 16 | Viewed by 3859
Abstract
The aim of this study was to determine the activity and structure of microbial communities in soils contaminated with heavy metals (HMs). To achieve this goal, soil samples were taken from two contaminated sites (i.e., Piekary Śląskie and Bukowno) in Poland. A wide [...] Read more.
The aim of this study was to determine the activity and structure of microbial communities in soils contaminated with heavy metals (HMs). To achieve this goal, soil samples were taken from two contaminated sites (i.e., Piekary Śląskie and Bukowno) in Poland. A wide range of methods were applied, including: total and metal-tolerant culturable bacteria enumeration; microbial community structure analysis using the phospholipid fatty acid method (PLFA); denaturing gradient gel electrophoresis (PCR-DGGE); and metabolic activity using BIOLOG and EcoPlateTM. Our studies showed that HMs negatively affected microbial community structure and activity in polluted soils. Apart from the contamination with HMs, other soil parameters like soil pH and water also impacted microbial community structure and growth. Metal-tolerant bacterial strains were isolated, identified and tested for presence of genes encoding HM tolerance using the polymerase chain reaction (PCR) methodology. Contamination with HMs in the tested areas was found to lead to development of metallotolerant bacteria with multiple tolerances toward Zn, Ni, Cd and Cu. Different genes (e.g., czcA, cadA and nccA) encoding HM efflux pumps were detected within isolated bacteria. Culturable bacteria isolated belonged to Proteobacteria, Actinobacteria and Bacteroidetes genera. Among non-culturable bacteria in soil samples, a significant fraction of the total bacteria and phyla, such as Gemmatimonadetes and Acidobacteria, were found to be present in all studied soils. In addition, bacteria of the Chloroflexi genus was present in soil samples from Piekary Śląskie, while bacteria of the Firmicutes genus were found in soil samples from Bukowno. Full article
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6 pages, 836 KiB  
Communication
Assessment of Quality and Safety Criteria of Raw Milk Samples from Different Dairy Farms
by Pierina Visciano and Maria Schirone
Microbiol. Res. 2022, 13(3), 620-625; https://doi.org/10.3390/microbiolres13030044 - 28 Aug 2022
Cited by 1 | Viewed by 2172
Abstract
Ten dairy farms supplying raw milk to the dairy industry were investigated to determine compliance with the safety criteria (plate count at 30 °C and somatic cell count) of Regulation (EC) 853/2004. The relationship of such criteria with lipid and protein percentages was [...] Read more.
Ten dairy farms supplying raw milk to the dairy industry were investigated to determine compliance with the safety criteria (plate count at 30 °C and somatic cell count) of Regulation (EC) 853/2004. The relationship of such criteria with lipid and protein percentages was also evaluated. The results demonstrated a great variability due to the different management systems of each dairy farm, with regard to the milking hygiene, the health status of the animals, and the prevention measures against mastitis. Moreover, in some dairy farms, the somatic cell counts were positively correlated with the quality components of raw milk as well as the plate count at 30 °C. Full article
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11 pages, 1175 KiB  
Article
Patterns of Presentation of Drug-Resistant Tuberculosis in Nigeria: A Retrospective File Review
by Olanrewaju Oladimeji, Yasir Othman, Kelechi Elizabeth Oladimeji, Bamidele Paul Atiba, Victor Abiola Adepoju and Babatunde Adeniran Odugbemi
Microbiol. Res. 2022, 13(3), 609-619; https://doi.org/10.3390/microbiolres13030043 - 21 Aug 2022
Cited by 5 | Viewed by 2913
Abstract
Background: An understanding of the patterns of drug-resistant tuberculosis (DR-TB) is needed to develop the best diagnostic tools and decide on optimal treatment combination therapies for the management of DR-TB in Nigeria. Objective: We aimed to investigate patterns of DR-TB for the five [...] Read more.
Background: An understanding of the patterns of drug-resistant tuberculosis (DR-TB) is needed to develop the best diagnostic tools and decide on optimal treatment combination therapies for the management of DR-TB in Nigeria. Objective: We aimed to investigate patterns of DR-TB for the five first-line anti-TB drugs over a period of seven years (2010–2016) and the associated clinical and socio-demographic factors. Methods: A retrospective study recruited 2555 DR-TB patients between 2010 and 2016 across the six geopolitical treatment zones in Nigeria. We determined DR-TB patterns based on standard case definition and their association with demographic and clinical information. Data were analyzed using Statistical Package for Social Sciences (SPSS) software. Independent predictors of DR-TB patterns/types were determined using bivariate and multivariate analyses with a statistical significance of p < 0.05 and a 95% confidence interval. Results: The majority of the participants were males, 66.93% (1710), 31–40 years old, 35.19% (899), previously treated, 77.10% (1909), had received at least two treatments, 411 (49.94%) and were multi-drug resistant, 61.41% (1165). The Southwest zone had the highest number of DR-TB cases, 36.92%. We found an upward trend in the prevalence of DR-TB from 2010 to 2016. Participants who had received one previous treatment showed statistically significant higher rifampicin resistance (59.68%), those with two previous treatments reported a statistically significant higher polydrug resistance (78.57%), and those with three or more previous treatments had a statistically significant higher multidrug resistance (19.83%) (χ2 = 36.39; p = 0.001). Mono-drug resistance and rifampicin resistance were statistically significantly higher in the southwest zone (29.48% and 34.12% respectively), polydrug resistance in the northcentral (20.69%) and south-south zones (20.69%), and multidrug resistance in the southwest (30.03%) and northcentral zones (19.18%) (χ2 = 98.26; p = 0.001). Conclusions: We present patterns of DR-TB across the six geopolitical zones in Nigeria. Clinicians should weigh in on these patterns while deciding on the best first-line drug combinations to optimize treatment outcomes for DR-TB patients. A national scale-up plan for DST services should focus on patients with previous multiple exposures to anti-TB treatments and on those in the Northeastern zone of the country. Full article
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11 pages, 1058 KiB  
Article
Antepartum Antibiotic Therapy under 34 Weeks of Gestation and Its Impact on Early-Onset Neonatal Infection and Maternal Vaginal Microbiota
by Junsuke Muraoka, Masatoki Kaneko, Koutaro Doi, Yuki Kodama and Hiroshi Sameshima
Microbiol. Res. 2022, 13(3), 598-608; https://doi.org/10.3390/microbiolres13030042 - 21 Aug 2022
Cited by 1 | Viewed by 2001
Abstract
The use of prenatal antibiotics should be carefully considered, owing to their potential adverse effects on neonatal outcomes. This study aimed to identify the contributing factors to early-onset neonatal infection and to determine the influence of antepartum antibiotics on women and neonates. This [...] Read more.
The use of prenatal antibiotics should be carefully considered, owing to their potential adverse effects on neonatal outcomes. This study aimed to identify the contributing factors to early-onset neonatal infection and to determine the influence of antepartum antibiotics on women and neonates. This study included 127 pregnant women without obvious intra-amniotic infection on admission, who delivered under 34 weeks of gestation. Information on maternal and neonatal characteristics was obtained from their medical charts. Vaginal swabs were taken from all women on admission. In total, 29 (22.8%) neonates developed early-onset infection. Multivariate analysis revealed that antepartum antibiotics were the most strongly associated factor for early-onset neonatal infection (odds ratio, 11.2; 95% confidence interval, 4.08–31.02). The frequency of early-onset neonatal infection was significantly higher in women who received antibiotic therapy than in those who did not; no significant difference in prolonging their gestation or neonatal morbidities was observed. The prevalence of women who hosted vaginal microorganisms on admission was similar to that in women whose infants subsequently developed early-onset neonatal infection compared with that of women whose infants did not. Among infants of the 40 women who received antepartum antibiotic therapy, 21 developed early-onset infection. Of the women who delivered these 21 infants, 62% (13/21) showed reduced lactobacilli and 43% (9/21) had resistant bacterial strains in their vaginal microbiota at the time of delivery. The use of antepartum antibiotics is the most strongly associated factor in early-onset neonatal infection; it does not prolong gestation and would change the vaginal environment. Full article
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14 pages, 1061 KiB  
Article
Isolation of a Marine Bacterium and Application of Its Bioflocculant in Wastewater Treatment
by Tsolanku Sidney Maliehe, Kgabo Moganedi, Peter Masoko and Tlou Nelson Selepe
Microbiol. Res. 2022, 13(3), 584-597; https://doi.org/10.3390/microbiolres13030041 - 21 Aug 2022
Cited by 1 | Viewed by 2315
Abstract
Bioflocculation has become the method of choice in wastewater treatment because of its effectiveness, environmental friendliness and innocuousness to humans. In this study, the bioflocculant-producing bacterium was isolated and its bioflocculant was used in wastewater treatment. The isolate was identified by 16S rRNA [...] Read more.
Bioflocculation has become the method of choice in wastewater treatment because of its effectiveness, environmental friendliness and innocuousness to humans. In this study, the bioflocculant-producing bacterium was isolated and its bioflocculant was used in wastewater treatment. The isolate was identified by 16S rRNA gene sequencing analysis. Its culture conditions (inoculum size, carbon and nitrogen sources, pH, temperature and time) were optimised using the one-factor-at-a-time assay. The cytotoxicity of the bioflocculant was assessed on human colorectal adenocarcinoma cells (Caco2) by tetrazolium-based colorimetric method. The ability of the bioflocculant to reduce biochemical oxygen demand (BOD) and chemical oxygen demand (COD) in wastewater was evaluated using Jar test. The bacterium was identified as Bacillus subtilis CSM5 and the maximum flocculating activity of 92% was observed when fructose and urea were used as nutrients and the culture conditions were adjusted to 30 °C, pH 9, 160 rpm and 72 h of incubation. Caco2 exhibited 90% viability when the highest bioflocculant concentration of 200 µg/µL was used. The reduction of BOD and COD was achieved at 59 ± 3.1 and 75 ± 0.4%, respectively. In conclusion, B. subtilis CSM5 is a good candidate for bioflocculant production and its bioflocculant has good potential for use in wastewater treatment. Full article
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10 pages, 936 KiB  
Article
Prevalence of Intestinal Parasites in HIV/AIDS-Infected Patients Attending Clinics in Selected Areas of the Eastern Cape
by Anozie Ifeoma, Teke Apalata, Boyisi Aviwe, Olanrewaju Oladimeji and Dominic T. Abaver
Microbiol. Res. 2022, 13(3), 574-583; https://doi.org/10.3390/microbiolres13030040 - 19 Aug 2022
Cited by 8 | Viewed by 4158
Abstract
Introduction: Intestinal parasites in HIV and AIDS patients increase the risk of gastroenteritis, adding to the complexity of the virus. According to the literature, their interactions are one of the factors leading to HIV replication and progression of AIDS in Africa. Chronic immunosuppression [...] Read more.
Introduction: Intestinal parasites in HIV and AIDS patients increase the risk of gastroenteritis, adding to the complexity of the virus. According to the literature, their interactions are one of the factors leading to HIV replication and progression of AIDS in Africa. Chronic immunosuppression caused by HIV infection makes people vulnerable to parasitic infections, and this is associated with a CD4+ cell count of less than 100. The study describes the prevalence of intestinal parasites in patients attending HIV/AIDS clinics in certain areas of the Eastern Cape. Methods: A cross-sectional study was conducted among 600 patients from HIV/AIDS clinics in the Eastern Cape. Tambo Municipality and Amatole Municipality were the municipalities covered. These included the Ngangalizwe Community Clinic, Tsolo Gateway Clinic, Idutywa Health Centre, and Nqamakwe Health Centre. The stools of 600 participants were examined using direct wet saline/iodine embedding, formal ether concentration technique, and modified Ziehl–Neelsen methods. Results: The mean age of the study participants was 28.2 years. They were predominantly female (79.9%), mostly single (63.6%), and lived in rural (65.2%) and urban areas (34.8%). The prevalence of intestinal parasites was determined to be 30% (180/600) after screening 600 stool samples. The most frequently detected parasites were Ascaris lumbricoides (55.9%), Balantidium coli (15.1%), Entamoeba coli (11.3%), Diphyllobothrium latum (4.3%), Taenia species (3.8%), Schistosoma mansoni (1.6%), and Cryptosporidium spp. (1.6%). Males were affected more frequently (39.2%) than females (27.9%). The difference was statistically significant (p = 0.017). Among the identified intestinal parasites, A. lumbricoides, B. coli, and Taenia spp. were found at all four sites. Conclusion: This study has shed light on the high burden of intestinal parasites in HIV/AIDS patients in the Eastern Cape. Medication adherence, deworming, and sanitary hygiene practices are needed to enhance the control of infection in the affected communities and hence contribute to the control of the HIV pandemic. Full article
(This article belongs to the Topic Host–Parasite Interactions)
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18 pages, 3127 KiB  
Article
Tolerance and Cadmium (Cd) Immobilization by Native Bacteria Isolated in Cocoa Soils with Increased Metal Content
by Pedro F. Feria-Cáceres, Lucas Penagos-Velez and Claudia X. Moreno-Herrera
Microbiol. Res. 2022, 13(3), 556-573; https://doi.org/10.3390/microbiolres13030039 - 14 Aug 2022
Cited by 7 | Viewed by 2612
Abstract
Twelve cadmium native bacteria previously isolated in soils of cocoa farms located in the western Colombian Andes (Santander), and tolerant to 2500 µM CdCl2 (120 mg Cd/L), were chosen in order to test their tolerance and Cd immobilization using liquid culture medium [...] Read more.
Twelve cadmium native bacteria previously isolated in soils of cocoa farms located in the western Colombian Andes (Santander), and tolerant to 2500 µM CdCl2 (120 mg Cd/L), were chosen in order to test their tolerance and Cd immobilization using liquid culture medium (Nutritive broth) at different concentrations of heavy metals. Furthermore, in the greenhouse experiments, the strains Exiguobacterium sp. (11-4A), Klebsiella variicola sp. (18-4B), and Enterobacter sp. (29-4B) were applied in combined treatments using CCN51 cacao genotype seeds grown in soil with different concentrations of Cd. All bacterial strains’ cell morphologies were deformed in TEM pictures, which also identified six strain interactions with biosorption and four strain capacities for bioaccumulation; FT-IR suggested that the amide, carbonyl, hydroxyl, ethyl, and phosphate groups on the bacteria biomass were the main Cd binding sites. In the pot experiments, the concentration of Cd was distributed throughout the cacao plant, but certain degrees of immobilization of Cd can occur in soil to prevent an increase in this level in roots with the presence of Klebsiella sp. Full article
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17 pages, 782 KiB  
Review
Influence of Gut–Liver Axis on Portal Hypertension in Advanced Chronic Liver Disease: The Gut Microbiome as a New Protagonist in Therapeutic Management
by Francesco Santopaolo, Gaetano Coppola, Lucia Giuli, Antonio Gasbarrini and Francesca Romana Ponziani
Microbiol. Res. 2022, 13(3), 539-555; https://doi.org/10.3390/microbiolres13030038 - 12 Aug 2022
Cited by 5 | Viewed by 2832
Abstract
Clinically significant portal hypertension is associated with most complications of advanced chronic liver disease (ACLD), including variceal bleeding, ascites, spontaneous bacterial peritonitis, hepatorenal syndrome, and hepatic encephalopathy. Gut dysbiosis is a hallmark of ACLD with portal hypertension and consists of the overgrowth of [...] Read more.
Clinically significant portal hypertension is associated with most complications of advanced chronic liver disease (ACLD), including variceal bleeding, ascites, spontaneous bacterial peritonitis, hepatorenal syndrome, and hepatic encephalopathy. Gut dysbiosis is a hallmark of ACLD with portal hypertension and consists of the overgrowth of potentially pathogenic bacteria and a decrease in autochthonous bacteria; additionally, congestion makes the intestinal barrier more permeable to bacteria and their products, which contributes to the development of complications through inflammatory mechanisms. This review summarizes current knowledge on the role of the gut–liver axis in the pathogenesis of portal hypertension, with a focus on therapies targeting portal hypertension and the gut microbiota. The modulation of the gut microbiota on several levels represents a major challenge in the upcoming years; in-depth characterization of the molecular and microbiological mechanisms linking the gut–liver axis to portal hypertension in a bidirectional relationship could pave the way to the identification of new therapeutic targets for innovative therapies in the management of ACLD. Full article
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9 pages, 956 KiB  
Article
Transmission Patterns of Clostridioides difficile in a Non-Epidemic Setting Based on WGS Analysis
by Virginie Courbin, Killian Le Neindre, Jeanne Couturier, Cécile Gateau, Rabab Syed Zaidi, Anlyata Youssouf and Frédéric Barbut
Microbiol. Res. 2022, 13(3), 530-538; https://doi.org/10.3390/microbiolres13030037 - 10 Aug 2022
Cited by 1 | Viewed by 1946
Abstract
Clostridioides difficile is a major nosocomial pathogen and has a considerable burden on healthcare systems. Our objective was to determine the transmission patterns of C. difficile in a non-epidemic setting using whole-genome multi-locus sequence typing (wgMLST) and core-genome single-nucleotide polymorphism (cgSNP) analyses. A [...] Read more.
Clostridioides difficile is a major nosocomial pathogen and has a considerable burden on healthcare systems. Our objective was to determine the transmission patterns of C. difficile in a non-epidemic setting using whole-genome multi-locus sequence typing (wgMLST) and core-genome single-nucleotide polymorphism (cgSNP) analyses. A retrospective study was conducted in a 650-bed university hospital between January 2016 and February 2017. In total, 191 strains isolated from 169 symptomatic C. difficile infection (CDI) patients were analyzed by WGS. Sequences were compared using wgMLST and cgSNP analyses. Genetic data and ward movements were then combined to identify the transmission rate and the type of transmission. The transmission rate varied from 55/169 (19.5%) (wgMLST) to 33/169 (32.5%) (cgSNP). Most transmission was considered cryptic, irrespective of the genetic analysis (38/55 [69.1%] by wgMLST to 25/33 [75.8%] by cgSNP). No transmission within the same ward was observed. In a non-epidemic setting, most C. difficile transmission occurs from sources other than symptomatic CDI patients. Full article
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7 pages, 1033 KiB  
Case Report
Longitudinally Extensive Transverse Myelitis Associated with Cytomegalovirus Infection in an Immunocompetent Patient
by Raul Montalvo and María-Fernanda Sánchez Vidal
Microbiol. Res. 2022, 13(3), 523-529; https://doi.org/10.3390/microbiolres13030036 - 8 Aug 2022
Viewed by 2647
Abstract
Longitudinally extensive transverse myelitis (LETM) associated with cytomegalovirus infection is extremely rare and is, mainly observed in immunocompetent people. A 55-year-old woman with no evidence of immunosuppression was admitted with paresthesia in the lower limbs for 15 days, difficulty walking, fecal incontinence, and [...] Read more.
Longitudinally extensive transverse myelitis (LETM) associated with cytomegalovirus infection is extremely rare and is, mainly observed in immunocompetent people. A 55-year-old woman with no evidence of immunosuppression was admitted with paresthesia in the lower limbs for 15 days, difficulty walking, fecal incontinence, and acute urinary retention. Magnetic resonance imaging (MRI) in the T2 sequence showed signs of hyperintensity in the cervical and thoracic cord. The serological study showed IgM antibodies to cytomegalovirus, and the result of the FilmArray meningitis/encephalitis panel showed the presence of cytomegalovirus. She received treatment with methylprednisolone and ganciclovir with a favorable outcome. This case highlights the importance of investigating treatable causes in patients with longitudinally extensive transverse myelitis with acute presentation. Full article
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9 pages, 6416 KiB  
Article
Effect of Two Strains of Beauveria bassiana on the Fecundity of Nezara viridula L. (Heteroptera: Pentatomidae)
by Maribel Portilla, Gadi V. P. Reddy and Moukaram Tertuliano
Microbiol. Res. 2022, 13(3), 514-522; https://doi.org/10.3390/microbiolres13030035 - 4 Aug 2022
Cited by 4 | Viewed by 2074
Abstract
The southern green stink bug (SGSB) Nezara viridula (L.) (Heteroptera: Pentatomidae), has become a significant pest of soybean and cotton in southern Central America and in the lower mid-southern U.S. A laboratory colony of SGSB was used to evaluate the effect of two [...] Read more.
The southern green stink bug (SGSB) Nezara viridula (L.) (Heteroptera: Pentatomidae), has become a significant pest of soybean and cotton in southern Central America and in the lower mid-southern U.S. A laboratory colony of SGSB was used to evaluate the effect of two isolates of Beauveria bassiana (Balsamo-Crivelli) Vuillemin (Hypocreales: Cordycipitaceae) including the commercial strain GHA and the Mississippi Delta native NI8 strain on the fecundity of this pest. Water control, Tween-80, and four concentrations of each strain (n × 104, 105, 106, and 107) were evaluated. Both native and commercial isolates with the highest concentrations were susceptible to the SGSB. Females, however, were much more pathogenic to both strains than males. Lethal concentration of the native strain (236 spores/mm2) was 1.4-fold lower (326 spores/mm2) than the GHA strain for females evaluated 20 d post-exposure. Greater concentrations (1.1 × 107 spores/mm2, 5.2 × 106 spores/mm2) were required to kill males with both strains native and commercial, respectively. For controls and lower concentrations, cumulative fecundity ranged from 1178 to 2082 eggs/10 couples/life reproduction, compared with 597 and 673 eggs/10 couples sprayed (n × 106 and 107) with the native NI8, respectively, and 386 eggs/10 couples sprayed (n × 107) with the commercial GHA. Full article
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14 pages, 1681 KiB  
Article
Effects of Different Nutritional Zinc Forms on the Proliferation of Beneficial Commensal Microorganisms
by Viviana Molnar-Nagy, Ko-Hua Tso, Jeffrey W. Hall, Guillermo Tellez-Isaias, Xochitl Hernandez-Velasco, Sherry Layton and Zsofia Bata
Microbiol. Res. 2022, 13(3), 500-513; https://doi.org/10.3390/microbiolres13030034 - 30 Jul 2022
Cited by 4 | Viewed by 1799
Abstract
This study compared the minimal inhibition concentrations (MICs) and their effects on the growth kinetics of seven different types of zinc (Zn) compounds and Na2EDTA in the case of three typical commensal beneficial microorganisms (Bacillus subtilis, Lactococcus lactis, [...] Read more.
This study compared the minimal inhibition concentrations (MICs) and their effects on the growth kinetics of seven different types of zinc (Zn) compounds and Na2EDTA in the case of three typical commensal beneficial microorganisms (Bacillus subtilis, Lactococcus lactis, and Saccharomyces cerevisiae). The seven Zn compounds included ZnSO4, four Zn–amino acid chelates, and two Zn–EDTA complexes. Both MICs and growth kinetic parameters indicated that different microorganisms show different sensitivities; for example, B. subtilis, L. lactis, and S. cerevisiae were most sensitive to ZnSO4, Na2EDTA, and Zn(NH3)2(Gly)2, respectively. Both ZnEDTA and Zn(NH3)2(Lys)2 improved the growth rate of all beneficial commensal intestinal microorganisms at low concentrations (5–10 mg/L) and showed low toxicity towards all tested strains. At higher concentrations (100–500 mg/L), all compounds decreased the growth rate and increased the lag phase. In conclusion, both growth kinetic parameters and MICs tested effectively measured the inhibitory effects of the test materials; however, growth kinetics provides a more detailed picture of the concentration-dependent effects and those on the mechanisms of microbial growth inhibition. Full article
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20 pages, 2621 KiB  
Article
Assessment of Bacteriocin-Antibiotic Synergy for the Inhibition and Disruption of Biofilms of Listeria monocytogenes and Vancomycin-Resistant Enterococcus
by Joanna Ivy Irorita Fugaban, Jorge Enrique Vazquez Bucheli, Wilhelm Heinrich Holzapfel and Svetoslav Dimitrov Todorov
Microbiol. Res. 2022, 13(3), 480-499; https://doi.org/10.3390/microbiolres13030033 - 29 Jul 2022
Cited by 3 | Viewed by 2026
Abstract
In this study, we have evaluated the effects of previously characterized bacteriocins produced by E. faecium strains ST651ea, ST7119ea, and ST7319ea, against biofilm formation and biofilms formed by L. monocytogenes ATCC15313 and vancomycin-resistant E. faecium VRE19. The effects of bacteriocins on the biofilms [...] Read more.
In this study, we have evaluated the effects of previously characterized bacteriocins produced by E. faecium strains ST651ea, ST7119ea, and ST7319ea, against biofilm formation and biofilms formed by L. monocytogenes ATCC15313 and vancomycin-resistant E. faecium VRE19. The effects of bacteriocins on the biofilms formed by L. monocytogenes ATCC151313 were evaluated by crystal violet assay and further confirmed by quantifying viable cells and cell metabolic activities through flow cytometry and TTC assay, respectively, indicating that bacteriocin activities required to completely eradicate biofilms are at least 1600 AU mL−1, 3200 AU mL−1, and 6400 AU mL−1, respectively for each bacteriocin evaluated. Furthermore, bacteriocins ST651ea and ST7119ea require at least 6400 AU mL−1 to completely eradicate the viability of cells within the biofilms formed by E. faecium VRE19, while bacteriocin ST7319ea requires at least 12800 AU mL−1 to obtain the same observations. Assessment of synergistic activities between selected conventional antibiotics (ciprofloxacin and vancomycin) with these bacteriocins was carried out to evaluate their effects on biofilm formation and pre-formed biofilms of both test microorganisms. Results showed that higher concentrations are needed to completely eradicate metabolic activities of cells within pre-formed biofilms in contrast with the biofilm formation abilities of the strains. Furthermore, synergistic activities of bacteriocins with both ciprofloxacin and vancomycin are more evident against vancomycin-resistant E. faecium VRE19 rather than L. monocytogenes ATCC15313. These observations can be further explored for possible applications of these combinations of antibiotics as a possible treatment of clinically relevant pathogens. Full article
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14 pages, 2021 KiB  
Article
Options for Increasing the Rate of Bioleaching of Arsenic Containing Copper Concentrate
by Alena Artykova, Yuliya Elkina, Aleksandra Nechaeva, Vitaliy Melamud, Anna Boduen and Aleksandr Bulaev
Microbiol. Res. 2022, 13(3), 466-479; https://doi.org/10.3390/microbiolres13030032 - 28 Jul 2022
Cited by 7 | Viewed by 1821
Abstract
In the present work the effect of alkaline sulfide leaching (ASL) on the extraction of copper and zinc from low-grade copper concentrate containing chalcopyrite, tennantite, sphalerite, and pyrite during batch and continuous bioleaching experiments was studied. It was demonstrated that ASL and further [...] Read more.
In the present work the effect of alkaline sulfide leaching (ASL) on the extraction of copper and zinc from low-grade copper concentrate containing chalcopyrite, tennantite, sphalerite, and pyrite during batch and continuous bioleaching experiments was studied. It was demonstrated that ASL and further bioleaching may be a promising approach for treatment of copper–zinc concentrates containing tennantite as this approach allows increasing copper extraction degree in comparison to one-stage bioleaching by 1.6–2.3 times. Thus, ASL was shown to be effective for pretreatment of tennantite containing concentrates to improve bioleaching for copper extraction. At the same time, ASL led to decrease in zinc extraction by 1.4–1.5 times. Therefore, the development of combined hydrometallurgical processes including ASL and bioleaching for effective metal leaching requires further studies to avoid negative effect on zinc extraction. Full article
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48 pages, 2737 KiB  
Review
Streptomyces: Still the Biggest Producer of New Natural Secondary Metabolites, a Current Perspective
by Lavinia Donald, Atanas Pipite, Ramesh Subramani, Jeremy Owen, Robert A. Keyzers and Taitusi Taufa
Microbiol. Res. 2022, 13(3), 418-465; https://doi.org/10.3390/microbiolres13030031 - 1 Jul 2022
Cited by 54 | Viewed by 11707
Abstract
There is a real consensus that new antibiotics are urgently needed and are the best chance for combating antibiotic resistance. The phylum Actinobacteria is one of the main producers of new antibiotics, with a recent paradigm shift whereby rare actinomycetes have been increasingly [...] Read more.
There is a real consensus that new antibiotics are urgently needed and are the best chance for combating antibiotic resistance. The phylum Actinobacteria is one of the main producers of new antibiotics, with a recent paradigm shift whereby rare actinomycetes have been increasingly targeted as a source of new secondary metabolites for the discovery of new antibiotics. However, this review shows that the genus Streptomyces is still the largest current producer of new and innovative secondary metabolites. Between January 2015 and December 2020, a significantly high number of novel Streptomyces spp. have been isolated from different environments, including extreme environments, symbionts, terrestrial soils, sediments and also from marine environments, mainly from marine invertebrates and marine sediments. This review highlights 135 new species of Streptomyces during this 6-year period with 108 new species of Streptomyces from the terrestrial environment and 27 new species from marine sources. A brief summary of the different pre-treatment methods used for the successful isolation of some of the new species of Streptomyces is also discussed, as well as the biological activities of the isolated secondary metabolites. A total of 279 new secondary metabolites have been recorded from 121 species of Streptomyces which exhibit diverse biological activity. The greatest number of new secondary metabolites originated from the terrestrial-sourced Streptomyces spp. Full article
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41 pages, 10342 KiB  
Review
Microbiological Aspects of Unique, Rare, and Unusual Fatty Acids Derived from Natural Amides and Their Pharmacological Profile
by Valery M. Dembitsky
Microbiol. Res. 2022, 13(3), 377-417; https://doi.org/10.3390/microbiolres13030030 - 26 Jun 2022
Cited by 5 | Viewed by 3304
Abstract
In the proposed review, the pharmacological profile of unique, rare, and unusual fatty acids derived from natural amides is considered. These amides are produced by various microorganisms, lichens, and fungi. The biological activity of some natural fatty acid amides has been determined by [...] Read more.
In the proposed review, the pharmacological profile of unique, rare, and unusual fatty acids derived from natural amides is considered. These amides are produced by various microorganisms, lichens, and fungi. The biological activity of some natural fatty acid amides has been determined by their isolation from natural sources, but the biological activity of fatty acids has not been practically studied. According to QSAR data, the biological activity of fatty acids is shown, which demonstrated strong antifungal, antibacterial, antiviral, antineoplastic, anti-inflammatory activities. Moreover, some fatty acids have shown rare activities such as antidiabetic, anti-infective, anti-eczematic, antimutagenic, and anti-psoriatic activities. For some fatty acids that have pronounced biological properties, 3D graphs are shown that show a graphical representation of unique activities. These data are undoubtedly of both theoretical and practical interest for chemists, pharmacologists, as well as for the pharmaceutical industry, which is engaged in the synthesis of biologically active drugs. Full article
(This article belongs to the Topic Microbiology Metabolomics)
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11 pages, 3737 KiB  
Article
Wide Spectrum Potent Antimicrobial Efficacy of Wound Dressings Impregnated with Cuprous Oxide Microparticles
by Gadi Borkow, Tohar Roth and Alexander Kalinkovich
Microbiol. Res. 2022, 13(3), 366-376; https://doi.org/10.3390/microbiolres13030029 - 24 Jun 2022
Cited by 3 | Viewed by 1955
Abstract
Copper has intrinsic antimicrobial properties. Wound dressings impregnated with cuprous oxide microparticles (hereafter termed COD) have been cleared for the management of acute and chronic wounds by the FDA and other regulatory bodies. The COD reduced the viable microbial titers of a wide [...] Read more.
Copper has intrinsic antimicrobial properties. Wound dressings impregnated with cuprous oxide microparticles (hereafter termed COD) have been cleared for the management of acute and chronic wounds by the FDA and other regulatory bodies. The COD reduced the viable microbial titers of a wide spectrum of microbes by more than 10,000-fold (4-logs) within 3 h of exposure at 37 °C (p < 0.001). Similar microbial titer reductions were achieved by 3-year naturally aged COD dressings, showing the stability of the biocidal efficacy over time. The potent biocidal efficacy of the COD was maintained even after 7 daily consecutive inoculations of the dressings with ~106 CFU. COD with an adhesive contour blocked the passage of bacteria from the exterior environment to the wound bed side of the dressing even after 7 daily consecutive inoculations of different bacteria on the outer surface of the dressings. Taken together, the study demonstrates the wide spectrum potent in vitro biocidal efficacy of the cuprous oxide impregnated dressings against a wide panel of microorganisms. Full article
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16 pages, 6092 KiB  
Article
Glucosylceramides from Cladosporium and Their Roles in Fungi–Plant Interaction
by Mariana Ingrid Dutra da Silva Xisto, Mariana Collodetti Bernardino, Rodrigo Rollin-Pinheiro, Caroline Barros Montebianco, Andrêina Paula da Silva, Renata Oliveira Rocha Calixto, Bianca Braz Mattos, Maite Freitas Silva Vaslin and Eliana Barreto-Bergter
Microbiol. Res. 2022, 13(3), 350-365; https://doi.org/10.3390/microbiolres13030028 - 24 Jun 2022
Viewed by 2125
Abstract
Cladosporium species are widely distributed filamentous fungi. One of the most important species is C. herbarum, which is related to infections in a variety of plants and of concern in plantations. Fungal cerebrosides, such as glucosylceramide (GlcCer), have been described as playing [...] Read more.
Cladosporium species are widely distributed filamentous fungi. One of the most important species is C. herbarum, which is related to infections in a variety of plants and of concern in plantations. Fungal cerebrosides, such as glucosylceramide (GlcCer), have been described as playing important roles in fungal growth and pathogenesis, but GlcCer from C. herbarum has not been characterized so far. For this reason, the present study aimed to elucidate the chemical structure of GlcCer from C. herbarum and its role in the interaction with Passiflora edulis. Mass spectrometry characterization of purified GlcCer revealed two major molecular ions, m/z 760 and m/z 774, and it reacts with monoclonal anti-GlcCer antibodies and is exposed on the fungal surface. P. edulis treatment with GlcCer induced increased levels of superoxide as well as the expression of some genes related to plant defense, such as PR3, POD, LOX and PAL. GlcCer also enhanced growth parameters, such as plant height and root weight. All these results suggest that C. herbarum GlcCer can stimulate plant defense mechanisms, which could help plants to face fungal infections. Full article
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8 pages, 529 KiB  
Article
The Emergence of Carbapenem-Resistant Gram-Negative Bacteria in Mizoram, Northeast India
by Vanlalruati S. C. Ralte, Archana Loganathan, Prasanth Manohar, Christine Vanlalbiakdiki Sailo, Zothan Sanga, Lalremruata Ralte, John Zothanzama, Sebastian Leptihn, Ramesh Nachimuthu and Nachimuthu Senthil Kumar
Microbiol. Res. 2022, 13(3), 342-349; https://doi.org/10.3390/microbiolres13030027 - 22 Jun 2022
Cited by 5 | Viewed by 3414
Abstract
(Background) Numerous reports on carbapenem resistance in different parts of India have been published, yet there are insufficient studies on the prevalence of antibiotic resistance in the northeast region of the country. This study evaluated the emergence of carbapenem resistance in the clinical [...] Read more.
(Background) Numerous reports on carbapenem resistance in different parts of India have been published, yet there are insufficient studies on the prevalence of antibiotic resistance in the northeast region of the country. This study evaluated the emergence of carbapenem resistance in the clinical isolates collected in Mizoram. (Results) A total of 141 Gram-negative clinical isolates were collected from the two hospitals, including the Civil Hospital in Lunglei and the Synod Hospital in Aizawl. The isolates include Escherichia coli (n = 62, 43.9%), Klebsiella spp. (n = 43, 30.4%), Pseudomonas aeruginosa (n = 9, 6.3%), Serratia marcescens (n = 3, 2.1%), Proteus mirabilis (n = 2, 1.4%), Shigella spp. (n = 4, 2.8%), Enterobacter spp. (n = 6, 4.2%) and Acinetobacter spp. (n = 12, 8.5%). The isolates were found to be resistant to meropenem (11%), colistin (48%), tigecycline (25%) and cefotaxime (50%). A total of four E. coli and one Shigella sonnei encoded the blaOXA-48-like gene. The blaCTX-M-1 gene was detected in 13 isolates, of which eight were E. coli, two Shigella flexneri, and one isolates each of K. pneumoniae, K. oxytoca and Shigella sonnei, respectively. (Conclusion) Carbapenem-resistant Enterobacteriaceae are common among other parts of India, despite limited access to antibiotics, the emergence of resistance in the northeastern region is worrying. Full article
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