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19 pages, 3439 KiB  
Article
Effects of Cr Stress on Bacterial Community Structure and Composition in Rhizosphere Soil of Iris tectorum under Different Cultivation Modes
by Zhao Wei, Zhu Sixi, Gu Baojing, Yang Xiuqing, Xia Guodong and Wang Baichun
Microbiol. Res. 2023, 14(1), 243-261; https://doi.org/10.3390/microbiolres14010020 - 14 Feb 2023
Cited by 12 | Viewed by 1788
Abstract
With the rapid development of industry, Cr has become one of the major heavy metal pollutants in soil, severely impacting soil microecology, among which rhizosphere microorganisms can improve the soil microenvironment to promote plant growth. However, how rhizosphere bacterial communities respond to Cr [...] Read more.
With the rapid development of industry, Cr has become one of the major heavy metal pollutants in soil, severely impacting soil microecology, among which rhizosphere microorganisms can improve the soil microenvironment to promote plant growth. However, how rhizosphere bacterial communities respond to Cr stress under different cultivation modes remains to be further studied. Therefore, in this study, a greenhouse pot experiment combined with 16S rRNA high-throughput sequencing technology was used to study the effects of Cr stress at 200 mg kg−1 on the bacterial community structure and diversity in the rhizosphere soil of Iris tectorum under different cultivation modes. The results showed that the rhizosphere bacterial community diversity index (Shannon and Simpson) and abundance index (Ace and Chao) increased significantly with wetland plant diversity under Cr stress. Moreover, the bacterial community changed by 20.1% due to the addition of Cr, further leading to a 15.9% decrease in the common species of the bacterial community, among which Proteobacteria, Actinobacteria, Chloroflexi, and Acidobacteriota accounted for more than 74.8% of the total sequence. However, with the increase in plant diversity, the abundance of rhizosphere-dominant bacteria and plant growth-promoting bacteria communities increased significantly. Meanwhile, the symbiotic network analysis found that under the two cultivation modes, the synergistic effect between the dominant bacteria was significantly enhanced, and the soil microenvironment was improved. In addition, through redundancy analysis, it was found that C, N, and P nutrients in uncontaminated soil were the main driving factors of bacterial community succession in the rhizosphere of I. tectorum, and Cr content in contaminated soil was the main driving factor of bacterial community succession in I. tectorum rhizosphere. In summary, the results of this study will provide a basis for the response of the rhizosphere bacterial community to Cr and the interaction between wetland plants and rhizosphere bacteria in the heavy metal restoration of wetland plants under different cultivation modes. Full article
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14 pages, 2921 KiB  
Article
Bacterial Community Drives the Carbon Source Degradation during the Composting of Cinnamomum camphora Leaf Industrial Extracted Residues
by Hanchang Zhou, Lan Di, Xiaoju Hua, Tao Deng and Xiaodong Wang
Microbiol. Res. 2023, 14(1), 229-242; https://doi.org/10.3390/microbiolres14010019 - 9 Feb 2023
Cited by 2 | Viewed by 1803
Abstract
The increasing production of industrial aromatic plant residues (IAPRs) are potentially environmental risky, and composting is a promising solution to resolve the coming IAPR problems. Carbon source degradation is a basic but important field in compost research; however, we still lack a clear [...] Read more.
The increasing production of industrial aromatic plant residues (IAPRs) are potentially environmental risky, and composting is a promising solution to resolve the coming IAPR problems. Carbon source degradation is a basic but important field in compost research; however, we still lack a clear understanding of carbon source degradation and the corresponding relationship to microbial community variation during IAPR composting, which hampers the improvement of IAPR composting efficiency and the promotion of this technology. In this study, samples were chosen on the first day, the 10th day, the 20th day, and the last day during the composting of Cinnamomum camphora leaf IAPRs, and the microbial community composition, main carbon source composition, and several enzyme activities were measured accordingly. The results showed that during composting, the hemicellulose had the highest reduction (200 g kg−1), followed by cellulose (143 g kg−1), lignin (15.5 g kg−1), starch (5.48 g kg−1), and soluble sugar (0.56 g kg−1), which supported that hemicellulose and cellulose were the main carbon source to microbes during composting. The relative abundance of the main bacterial phylum Firmicute decreased from 85.1% to 40.3% while Actinobactreia increased from 14.4% to 36.7%, and the relative abundance of main fungal class Eurotiomycetes decreased from 60.9% to 19.6% while Sordariomycetes increased from 16.9% to 69.7%. Though principal coordinates analysis found that both bacterial and fungal community composition significantly varied during composting (p < 0.05), structure equation modeling (SEM) supported that bacterial composition rather than fungal counterpart was more responsible for the change in carbon source composition, as the standard total effects offered by bacterial composition (−0.768) was about five times the fungal composition (−0.144). Enzyme2 (comprised of xylanase, laccase, cellulase and manganese peroxidase) provided −0.801 standard total effects to carbon source composition, while Enzyme1 (comprised of lignin peroxidase and polyphenol oxidase) had only 0.172. Furthermore, xylanase and laccase were the only two enzymes appeared in co-occurrence network, clustered with nearly all the carbon sources concerned (except starch) in module-II. Xylanase, hemicellulose, and cellulose were linked to higher numbers of OTUs, more than laccase and other carbon sources. In addition, there were 11 BOTUs but only 1 FOTUs directly interacted to xylanase, hemicellulose, and cellulose simultaneously, three of them were Limnochordaceae and two were Savagea, which highlighted the potential core function in lignocellulose degradation provided by bacterial members, especially Limnochordaceae and Savagea. Thus, the results supported that during composting of Cinnamomum camphora leaf IAPRs, the degradation of dominate carbon sources, hemicellulose and cellulose, was mainly driven by bacterial community rather than fungal community. In addition, the bacterial originated xylanase and laccase played potentially core roles in the functional modules. This research clearly investigated the microbial dynamics of carbon source degradation during the composting of Cinnamomum camphora leaf IAPRs, and offers valuable information about and new insight into future IAPRs waste treatment. Full article
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11 pages, 1481 KiB  
Article
Forces Governing the Transport of Pathogenic and Nonpathogenic Escherichia coli in Nitrogen and Magnesium Doped Biochar Amended Sand Columns
by Katherine Quinn, Sohrab Haghighi Mood, Elizabeth Cervantes, Manuel Garcia Perez and Nehal I. Abu-Lail
Microbiol. Res. 2023, 14(1), 218-228; https://doi.org/10.3390/microbiolres14010018 - 7 Feb 2023
Viewed by 1748
Abstract
Background: Access to safe drinking water remains a global issue with fecal indicator bacteria being major pollutants. Biochars offer low-cost adsorbents for bacterial pathogens. A fundamental understanding of how biochars interact with bacterial pathogens is essential to designing effective biofilters. Methods: Water-saturated sand [...] Read more.
Background: Access to safe drinking water remains a global issue with fecal indicator bacteria being major pollutants. Biochars offer low-cost adsorbents for bacterial pathogens. A fundamental understanding of how biochars interact with bacterial pathogens is essential to designing effective biofilters. Methods: Water-saturated sand columns amended with Magnesium and Nitrogen-doped biochars produced by pyrolysis at 400, 500, 600, and 700 °C were used to Quantify the transport of pathogenic Escherichia coli O157:H7 and nonpathogenic E. coli k12 strains in porous media. Measured data were modeled using DLVO theory of colloidal stability. were explored. Results: (1) Biochar is hydrophobic while sand and bacteria are hydrophilic; (2) all Gibbs free energy values quantified between E. coli O157:H7 and biochar were negative except for biochar produced at 700 °C; (3) all types of forces investigated (van der Waals, electrostatic, and acid-base interactions) played a role in governing the interactions between bacteria and biochar. Conclusions: (1) Adding doped biochar to sand at a 2% weight ratio enhanced the retention of bacterial cells in the sand/biochar columns; (2) bacterial transport is strain-dependent and mediated by various types of forces resulting from interactions between the various functional groups displayed on bacteria and biochar/sand. Our findings emphasize the importance of monitoring biochar’s functionality to eliminate bacterial pollutants from contaminated water. Full article
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13 pages, 867 KiB  
Article
Impact of Temperature on the Bioactive Compound Content of Aqueous Extracts of Humulus lupulus L. with Different Alpha and Beta Acid Content: A New Potential Antifungal Alternative
by Ulin A. Basilio-Cortes, Olivia Tzintzun-Camacho, Onecimo Grimaldo-Juárez, Dagoberto Durán-Hernández, Adabella Suarez-Vargas, Carlos Ceceña Durán, Alexis Salazar-Navarro, Luis A. González-Anguiano and Daniel González-Mendoza
Microbiol. Res. 2023, 14(1), 205-217; https://doi.org/10.3390/microbiolres14010017 - 6 Feb 2023
Cited by 3 | Viewed by 1962
Abstract
Hops contain a wide variety of polyphenolic compounds with diverse antimicrobial properties. This study aimed to evaluate the impact of temperature on the bioactive components of samples of aqueous extracts of hops with different characteristics. A central compound rotating design model was used [...] Read more.
Hops contain a wide variety of polyphenolic compounds with diverse antimicrobial properties. This study aimed to evaluate the impact of temperature on the bioactive components of samples of aqueous extracts of hops with different characteristics. A central compound rotating design model was used in order to obtain optimal conditions of temperature and extract concentration to inhibit Fusarium oxysporum and Alternaria solani. At intermediate temperatures according to the design of experiments, significant effects on antifungal activity were observed. The optimal conditions with antifungal activity were at a concentration of 160 mg/mL and a temperature of 65 °C to obtain mycelial diameters ≤ 25 mm. The bioactive compounds were shown in the FT-IR spectrum after each heat treatment of both samples; significant changes were observed in the bands between 2786 to 3600 cm−1 and 1022 to 1729 cm−1. The content of total phenols and flavonoids showed a concentration increase of 4.54 to 6.24 mg GAE/g and 6.21 to 8.12 mg QE/g from an initial evaluation temperature of 25 °C to 57.5 °C, respectively, benefited by the heating temperature, enhancing antifungal activity. However, when increasing the temperature ≥90 °C, a tendency to decrease the concentration of bioactive compounds was observed, probably due to their denaturation due to the effect of temperature and exposure time, being non-thermolabile compounds at high temperatures. These aqueous extracts are an alternative to effective natural antifungals. Full article
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15 pages, 911 KiB  
Review
Procalcitonin and Adrenomedullin in Infectious Diseases
by Yoshimitsu Kiriyama and Hiromi Nochi
Microbiol. Res. 2023, 14(1), 190-204; https://doi.org/10.3390/microbiolres14010016 - 1 Feb 2023
Viewed by 3163
Abstract
Calcitonin (CT) and adrenomedullin (ADM) are members of the CT family. Procalcitonin (PCT) is a prohormone of CT. Elevations in serum PCT and ADM levels are associated with severe sepsis and coronavirus disease 2019 (COVID-19). PCT enhances sepsis mortality and it binds to [...] Read more.
Calcitonin (CT) and adrenomedullin (ADM) are members of the CT family. Procalcitonin (PCT) is a prohormone of CT. Elevations in serum PCT and ADM levels are associated with severe sepsis and coronavirus disease 2019 (COVID-19). PCT enhances sepsis mortality and it binds to the CGRP receptor, which is a heterodimer of CT receptor-like receptor and receptor activity-modifying protein 1. The N-terminal truncated form of PCT, PCT3-116, is produced by the cleavage of PCT by dipeptidyl peptidase 4 (DPP-4) and is the main form of PCT in serum during sepsis, inducing microvascular permeability. Mid-regional pro-adrenomedullin (MR-proADM) is used instead of ADM as a biological indicator because ADM is rapidly degraded, and MR-proADM is released at the same rate as ADM. ADM reduces endothelial permeability and promotes endothelial stability. Endothelial dysfunction is responsible for multiple organ failure in sepsis and COVID-19 patients. Therefore, ADM may be an important molecule for improving the severity associated with sepsis and COVID-19. This review focuses on the current knowledge of PCT and ADM in sepsis and COVID-19. Full article
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13 pages, 1787 KiB  
Study Protocol
ESBL Displace: A Protocol for an Observational Study to Identify Displacing Escherichia coli Strain Candidates from ESBL-Colonized Travel Returners Using Phenotypic, Genomic Sequencing and Metagenome Analysis
by Michael Schweitzer, Alfredo Mari, Tim Roloff, Esther Künzli, Stefanie Heller, Diana Albertos Torres, Marco Meola, Danica Nogarth, Leanid Laganenka, Lisa Prampolini, Helena M. B. Seth-Smith, Olivia Grüninger, Alexander Gensch, Josiane Reist, Sebastian Bonhoeffer, Wolf-Dietrich Hardt and Adrian Egli
Microbiol. Res. 2023, 14(1), 177-189; https://doi.org/10.3390/microbiolres14010015 - 31 Jan 2023
Viewed by 2290
Abstract
Introduction: Invading extended-spectrum beta-lactamase-producing Escherichia coli (ESBL-PE), non-ESBL E. coli, and other bacteria form a complex environment in the gut. The duration and dynamics of ESBL-PE colonization varies among individuals. Understanding the factors associated with colonization may lead to decolonization strategies. In this [...] Read more.
Introduction: Invading extended-spectrum beta-lactamase-producing Escherichia coli (ESBL-PE), non-ESBL E. coli, and other bacteria form a complex environment in the gut. The duration and dynamics of ESBL-PE colonization varies among individuals. Understanding the factors associated with colonization may lead to decolonization strategies. In this study, we aim to identify (i) single E. coli strains and (ii) microbiome networks that correlate with retention or decline of colonization, and (iii) pan-sensitive E. coli strains that potentially could be used to displace ESBL-PE during colonization. Methods and analysis: We recruit healthy travellers to Southeast Asia for a one-year prospective observational follow-up study. We collect and biobank stool, serum, and peripheral blood mononuclear cells (PBMCs) at predefined timepoints. Additional information is collected with questionnaires. We determine the colonization status with ESBL-PE and non-ESBL E. coli and quantify cell densities in stools and ratios over time. We characterize multiple single bacterial isolates per patient and timepoint using whole genome sequencing (WGS) and 16S/ITS amplicon-based and shotgun metagenomics. We determine phylogenetic relationships between isolates, antimicrobial resistance (AMR; phenotypic and genotypic), and virulence genes. We describe the bacterial and fungal stool microbiome alpha and beta diversity on 16S/ITS metagenomic data. We describe patterns in microbiome dynamics to identify features associated with protection or risk of ESBL-PE colonization. Ethics and dissemination: The study is registered (clinicaltrials.gov; NCT04764500 on 09/02/2019) and approved by the Ethics Committee (EKNZ project ID 2019-00044). We will present anonymized results at conferences and in scientific journals. Bacterial sequencing data will be shared via publicly accessible databases according to FAIR principles. Full article
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16 pages, 1203 KiB  
Article
Whole-Genome Sequence of Aeromonas spp. Isolated from a Dairy Farm in Central Texas
by Toni L. Poole, Wayne D. Schlosser, Tawni L. Crippen, Sonja L. Swiger, Keri N. Norman and Robin C. Anderson
Microbiol. Res. 2023, 14(1), 161-176; https://doi.org/10.3390/microbiolres14010014 - 26 Jan 2023
Viewed by 1983
Abstract
This study investigated the presence of Aeromonas spp. on a dairy farm in central Texas that employed a free-stall management system. A total of 140 samples were collected from areas of two different barns. Twenty-two presumptive Aeromonas isolates were cultured. Phenotypic analysis identified [...] Read more.
This study investigated the presence of Aeromonas spp. on a dairy farm in central Texas that employed a free-stall management system. A total of 140 samples were collected from areas of two different barns. Twenty-two presumptive Aeromonas isolates were cultured. Phenotypic analysis identified five Aeromonas spp. Twenty isolates exhibited β-lactam and one displayed tetracycline resistance. Phylogenetic analysis of the WGS data suggested only four Aeromonas spp. All isolates possessed at least one β-lactam resistance gene and one isolate possessed tet(E). No plasmids were identified from sequence alignments. Virulence genes were identified in all four Aeromonas spp. Mobility elements were identified in three of these, with the exception being A. dhakensis. Four of the transposons identified in this study have been associated with multidrug resistance in Italy, Sweden, and Singapore. There was no significant difference in the proportion of isolates from either barn. The absence of plasmids suggests mobility elements and virulence genes were localized to the chromosome. On a dairy farm of healthy cattle, these 22 Aeromonas isolates were considered normal environmental flora while illustrating the ubiquitous nature of Aeromonas spp. globally. Full article
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13 pages, 993 KiB  
Article
Core Genome Sequencing Analysis of E. coli O157:H7 Unravelling Genetic Relatedness among Strains from Cattle, Beef, and Humans in Bishoftu, Ethiopia
by Fanta D. Gutema, Lieven De Zutter, Denis Piérard, Bruno Hinckel, Hideo Imamura, Geertrui Rasschaert, Reta D. Abdi, Getahun E. Agga and Florence Crombé
Microbiol. Res. 2023, 14(1), 148-160; https://doi.org/10.3390/microbiolres14010013 - 25 Jan 2023
Viewed by 2104
Abstract
E. coli O157:H7 is a known Shiga toxin-producing Escherichia coli (STEC), causing foodborne disease globally. Cattle are the main reservoir and consumption of beef and beef products contaminated with E. coli O157:H7 is an important source of STEC infections in humans. To emphasize [...] Read more.
E. coli O157:H7 is a known Shiga toxin-producing Escherichia coli (STEC), causing foodborne disease globally. Cattle are the main reservoir and consumption of beef and beef products contaminated with E. coli O157:H7 is an important source of STEC infections in humans. To emphasize the cattle-to-human transmission through the consumption of contaminated beef in Bishoftu, Ethiopia, whole-genome sequencing (WGS) was performed on E. coli O157 strains isolated from three sources (cattle, beef, and humans). Forty-four E. coli O157:H7 isolates originating from 23 cattle rectal contents, three cattle hides, five beef carcasses, seven beef cuts at retail shops, and six human stools in Bishoftu between June 2017 and May 2019 were included. This study identified six clusters of closely related E. coli O157:H7 isolates based on core genome multilocus sequence typing (cgMLST) by targeting 2513 loci. A genetic linkage was observed among the isolate genomes from the cattle rectal contents, cattle hides, beef carcasses at slaughterhouses, beef at retail shops, and human stool within a time frame of 20 months. All the strains carried practically the same repertoire of virulence genes except for the stx2 gene, which was present in all but eight of the closely related isolates. All the strains carried the mdfA gene, encoding for the MdfA multi-drug efflux pump. CgMLST analysis revealed genetically linked E. coli O157:H7 isolates circulating in the area, with a potential transmission from cattle to humans through the consumption of contaminated beef and beef products. Full article
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16 pages, 2124 KiB  
Review
Heterosigma akashiwo, a Fish-Killing Flagellate
by Malihe Mehdizadeh Allaf
Microbiol. Res. 2023, 14(1), 132-147; https://doi.org/10.3390/microbiolres14010012 - 25 Jan 2023
Cited by 4 | Viewed by 3516
Abstract
Heterosigma akashiwo is a golden-brown unicellular phytoflagellate with a high potential to create harmful algal blooms (HABs) and kill fish in many coastal regions worldwide, resulting in significant economic losses. Climate change and global warming have been introduced as triggers that impact the [...] Read more.
Heterosigma akashiwo is a golden-brown unicellular phytoflagellate with a high potential to create harmful algal blooms (HABs) and kill fish in many coastal regions worldwide, resulting in significant economic losses. Climate change and global warming have been introduced as triggers that impact the frequency and severity of H. akashiwo and other bloom-forming species in the past decades. In this review paper, the author tried to briefly discuss the morphology and taxonomy of H. akashiwo and show how environmental parameters can influence the physiology and toxicity of this species. Although the toxin production and mechanisms are still a conundrum, the proposed fish-killing mechanisms will be reviewed in the next step. Full article
(This article belongs to the Topic Microorganisms in Aquatic Environments)
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16 pages, 1201 KiB  
Article
Potential Mammalian Vector-Borne Diseases in Live and Wet Markets in Indonesia and Myanmar
by Vincent Nijman, K. A. I. Nekaris, Chris R. Shepherd, Lucy Vigne, Ahmad Ardiansyah, Muhammad Ali Imron, Qinyong Ni, Katherine Hedger, Marco Campera and Thais Q. Morcatty
Microbiol. Res. 2023, 14(1), 116-131; https://doi.org/10.3390/microbiolres14010011 - 22 Jan 2023
Cited by 3 | Viewed by 3284
Abstract
Vector-borne diseases spread from wild animals and their associated ectoparasites to humans and domesticated animals. Wildlife markets are recognized as important areas where this transfer can take place. We assessed the potential for spreading vector-borne diseases in two live and wet markets in [...] Read more.
Vector-borne diseases spread from wild animals and their associated ectoparasites to humans and domesticated animals. Wildlife markets are recognized as important areas where this transfer can take place. We assessed the potential for spreading vector-borne diseases in two live and wet markets in Myanmar (Mong La, on the Myanmar-China border) and Indonesia (Sukahaji in Bandung on the island of Java) by making an inventory of all live and freshly killed wild mammals for sale. For eight mammal families, we quantified the number of animals on offer, and we used a heatmap cluster analysis to map vector-borne diseases that these families may carry. In Myanmar, we observed large numbers of wild pigs and deer (potentially carrying West Nile and various encephalitis viruses) whereas in Indonesia we observed Old World fruit bats (potentially carrying Chikungunya and encephalitis viruses) and squirrels (potentially carrying West Nile and encephalitis viruses). The trade in Indonesia was dominated by live mammals offered for sale as pets, and only Old World fruit bats and squirrels traded for traditional Asian medicine were killed in the markets. The trade in Myanmar was more geared towards wild meat (e.g., wild pigs, deer, primates) and traditional Asian medicine (squirrels). The combined risks of vector-borne diseases spreading from traded animals to human health highlight the need for an integrated approach protecting public health, economic interests and biodiversity. Full article
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12 pages, 3842 KiB  
Article
Species of the Genera Neopestalotiopsis and Alternaria as Dominant Pathogen Species Attacking Mastic Trees (Pistacia lentiscus var. Chia)
by Nathalie N. Kamou, Stefanos Testempasis and Anastasia L. Lagopodi
Microbiol. Res. 2023, 14(1), 104-115; https://doi.org/10.3390/microbiolres14010010 - 21 Jan 2023
Cited by 1 | Viewed by 2177
Abstract
Between 2018 and 2021, several mastic trees (Pistacia lentiscus var. Chia) sampled in the field and the nursery of the Chios Mastiha Growers Association (CMGA) were analyzed to determine the cause of dominant diseases. Symptoms included defoliation, leaf, and twig blight, wilting [...] Read more.
Between 2018 and 2021, several mastic trees (Pistacia lentiscus var. Chia) sampled in the field and the nursery of the Chios Mastiha Growers Association (CMGA) were analyzed to determine the cause of dominant diseases. Symptoms included defoliation, leaf, and twig blight, wilting and/or apoplexy of trees and apoplexy of young hardwood cuttings. Moreover, brown discoloration had also been observed on older woody parts of the trees such as branches and tree trunks. Several pathogens have been isolated and identified as the causing agents. Neopestalotiopsis and Alternaria species were isolated consistently from necrotic tissues of mastic trees (branches, twigs, and leaves) in the field and the nursery. All fungal isolates’ pathogenicity was confirmed by applying Koch’s postulates on young mastic trees under glasshouse conditions. Fungal pathogens were identified by sequence analyses of the ITS, β-tubulin, and histone gene regions. Alternaria species were analyzed further by sequencing the endopolygalacturonase (endoPG) and the Alternaria major allergen (Alta1) genes. More specifically, the isolates were identified as Neopestalotiopsis clavispora, Alternaria arborescens, and A. alternata based on morphological features and sequence analyses. This is the first report of N. clavispora, A. arborescens, and A. alternata on P. lentiscus var. Chia. Full article
(This article belongs to the Special Issue Plants, Mycorrhizal Fungi, and Bacteria)
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13 pages, 1942 KiB  
Communication
Characterization and Hydrocarbon Degradation Potential of Variovorax sp. Strain N23 Isolated from the Antarctic Soil
by Jinyan Liu, Zhisong Cui, Tong Hao, Yingchao Li, Xiao Luan, Ke Feng and Li Zheng
Microbiol. Res. 2023, 14(1), 91-103; https://doi.org/10.3390/microbiolres14010009 - 20 Jan 2023
Cited by 1 | Viewed by 1653
Abstract
Increasing pollution has significantly threatened the Antarctic ecosystem. The contamination of hydrocarbons has drawn a considerable amount of attention owing to their toxicity, recalcitrance, and persistence. Considering the Antarctic Treaty, only indigenous species are allowed to bioremediate the contaminated environment. However, the knowledge [...] Read more.
Increasing pollution has significantly threatened the Antarctic ecosystem. The contamination of hydrocarbons has drawn a considerable amount of attention owing to their toxicity, recalcitrance, and persistence. Considering the Antarctic Treaty, only indigenous species are allowed to bioremediate the contaminated environment. However, the knowledge of the ecological role, physiology, function, and genomics of endemic hydrocarbon consumers is still limited. Here, we investigated the dynamics of phenanthrene-consuming communities derived from the Antarctic soil and found that Variovorax, Rhodocyclaceae, and Hydrogenophaga were differentiated in all the phenanthrene-consuming subcultures. We isolated a pure culture of the key hydrocarbon consumer Variovorax sp. strain N23. Moreover, the result of the polyphasic approach suggested that strain N23 represents a novel species of the genus Variovorax. In addition, the genomic characteristics of this strain revealed incomplete degradation pathways for diverse hydrocarbons. Overall, this study reveals the relatively weak hydrocarbon-degrading potential of the indigenous bacteria and suggests the need for more careful protection of the Antarctic ecosystem. Full article
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11 pages, 1155 KiB  
Review
The Current Level of MALDI-TOF MS Applications in the Detection of Microorganisms: A Short Review of Benefits and Limitations
by Ali Haider, Marianna Ringer, Zsolt Kotroczó, Csilla Mohácsi-Farkas and Tamás Kocsis
Microbiol. Res. 2023, 14(1), 80-90; https://doi.org/10.3390/microbiolres14010008 - 19 Jan 2023
Cited by 16 | Viewed by 7159
Abstract
The available literary data suggest the general applicability and benefits of the Matrix-assisted laser desorption/ionization (MALDI) time-of-flight (TOF) mass spectrometry (MS) in the field of microbiological identification. Due to its high reliability, MALDI-TOF might generally be the alternative to the the16s-rRNA sequence-based and [...] Read more.
The available literary data suggest the general applicability and benefits of the Matrix-assisted laser desorption/ionization (MALDI) time-of-flight (TOF) mass spectrometry (MS) in the field of microbiological identification. Due to its high reliability, MALDI-TOF might generally be the alternative to the the16s-rRNA sequence-based and serological-based methods. The essence of the technique is to map the unique protein pattern of microbes that contributes to characterizing a wide variety of microorganisms, including bacteria, fungi, and viruses. With its application, the well-known bacterial and fungal species can be quickly identified, thus saving time in clinical diagnostics. In recent years, new protocols have appeared for directly identifying pathogenic strains from patient samples (blood, urine, feces), a major milestone in healthcare applications. On the other hand, these applications only have reliable results under certain conditions (homogeneous infection, adequate cell count, appropriate separation technique). This review aims to introduce and summarize those developments that have been enabled for routine application in the field of clinical diagnosis. Full article
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3 pages, 153 KiB  
Editorial
Acknowledgment to the Reviewers of Microbiology Research in 2022
by Microbiology Research Editorial Office
Microbiol. Res. 2023, 14(1), 77-79; https://doi.org/10.3390/microbiolres14010007 - 18 Jan 2023
Viewed by 962
Abstract
High-quality academic publishing is built on rigorous peer review [...] Full article
10 pages, 1659 KiB  
Article
Diagnosis and Stratification of COVID-19 Infections Using Differential Plasma Levels of D-Dimer: A Two-Center Study from Saudi Arabia
by Abdullah Alsrhani, Ahmad Alshomar, Abozer Y Elderdery, Zafar Rasheed and Aisha Farhana
Microbiol. Res. 2023, 14(1), 67-76; https://doi.org/10.3390/microbiolres14010006 - 16 Jan 2023
Cited by 4 | Viewed by 1973
Abstract
Background: D-dimer, generated upon the degradation of fibrin, is extensively used to detect thrombosis in various diseases. It is also explored as a marker for thrombosis in cases with COVID-19 disease. Few studies have confirmed its utility as a marker for assessing disease [...] Read more.
Background: D-dimer, generated upon the degradation of fibrin, is extensively used to detect thrombosis in various diseases. It is also explored as a marker for thrombosis in cases with COVID-19 disease. Few studies have confirmed its utility as a marker for assessing disease severity. Objectives: The current research was undertaken to determine the role of D-dimer in patients with COVID-19 and to investigate any association with the progression and severity of the disease in the Saudi population. Methods: Clinical indices in confirmed COVID-19 patients were collected from tertiary care hospitals in Aljouf and Qassim regions. The plasma D-dimer levels were quantified directly in the samples collected from COVID-19 patients (n = 148) using an immunofluorescence assay, and the data were presented in Fibrinogen Equivalent Units (mg/L). The collected data of D-dimer were analyzed based on COVID-19 severity, age, and the gender of patients. Results: The findings show that the plasma D-dimer concentrations were significantly (p = 0.0027) elevated in COVID-19 cases (n = 148), compared to in the normal healthy uninfected controls (n = 309). Moreover, the D-dimer levels were analyzed according to the severity of the disease in the patients. The data revealed that D-dimer concentrations were significantly increased in patients with mild infection to moderate disease, and the levels were the highest in patients with severe COVID-19 disease (p < 0.05). Our analysis demonstrates that the D-dimer levels have no association with the age or gender of COVID-19 patients (p > 0.05) in the study population. Conclusions: D-dimer can serve as a biomarker not only for the detection of COVID-19 infection, but also for determining the severity of infection of COVID-19 disease. Full article
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