Microorganisms

22 pages, 1133 KiB

Open AccessReview

Insights into Chlamydia Development and Host Cells Response

by Shuaini Yang, Jiajia Zeng, Jinxi Yu, Ruoyuan Sun, Yuqing Tuo and Hong Bai

Microorganisms 2024, 12(7), 1302; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms12071302 - 26 Jun 2024

Viewed by 86

Chlamydia infections commonly afflict both humans and animals, resulting in significant morbidity and imposing a substantial socioeconomic burden worldwide. As an obligate intracellular pathogen, Chlamydia interacts with other cell organelles to obtain necessary nutrients and establishes an intracellular niche for the development of [...] Read more.

Chlamydia infections commonly afflict both humans and animals, resulting in significant morbidity and imposing a substantial socioeconomic burden worldwide. As an obligate intracellular pathogen, Chlamydia interacts with other cell organelles to obtain necessary nutrients and establishes an intracellular niche for the development of a biphasic intracellular cycle. Eventually, the host cells undergo lysis or extrusion, releasing infectious elementary bodies and facilitating the spread of infection. This review provides insights into Chlamydia development and host cell responses, summarizing the latest research on the biphasic developmental cycle, nutrient acquisition, intracellular metabolism, host cell fates following Chlamydia invasion, prevalent diseases associated with Chlamydia infection, treatment options, and vaccine prevention strategies. A comprehensive understanding of these mechanisms will contribute to a deeper comprehension of the intricate equilibrium between Chlamydia within host cells and the progression of human disease. Full article

(This article belongs to the Section Medical Microbiology)

► Show Figures

Figure 1

21 pages, 2785 KiB

Open AccessArticle

Varietal Susceptibility of Olive to Pseudomonas savastanoi pv. savastanoi and the Antibacterial Potential of Plant-Based Agents

by Laura Košćak, Janja Lamovšek, Marina Lukić, Tvrtko Karlo Kovačević, Edyta Đermić, Smiljana Goreta Ban, Nikola Major and Sara Godena

Microorganisms 2024, 12(7), 1301; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms12071301 - 26 Jun 2024

Viewed by 102

Abstract

Olive knot disease, caused by the bacterium Pseudomonas savastanoi pv. savastanoi, causes great damage in olive orchards. While control measures of P. savastanoi pv. savastanoi in olive orchards primarily rely on pruning and copper-based treatments, the use of antibiotics as [...] Read more.

Olive knot disease, caused by the bacterium Pseudomonas savastanoi pv. savastanoi, causes great damage in olive orchards. While control measures of P. savastanoi pv. savastanoi in olive orchards primarily rely on pruning and copper-based treatments, the use of antibiotics as bactericidal preparations in agriculture is limited and highly restricted. However, plants are naturally endowed with protective molecules, such as phenolic compounds, which defend them against herbivores, insects, and microorganisms. This research aimed to test the virulence of five strains of P. savastanoi pv. savastanoi isolated from different growing regions and olive varieties, and to examine whether there is a difference in plant susceptibility based on the variety. An additional goal was to test the antimicrobial activity of olive mill wastewater, known for its high content of phenolic compounds, and aqueous garlic hydrolysate, as well as to compare them with a commercial copper-based product, pure hydroxytyrosol, and a standard antibiotic as references. Analysis of knot characteristics showed variations in the virulence of the P. savastanoi pv. savastanoi strains, with the highest virulence being observed for the strain I7L and the lowest virulence for the strain B45C-PR. The olive cultivar Rosinjola displayed higher susceptibility compared to Frantoio, Buža, and Leccino, while cv. Istarska bjelica exhibited the least susceptibility compared to the other investigated olive cultivars. In an attempt to explore alternative solutions for disease control, in vitro tests revealed that the phenol HTyr, GE, and the wastewater with the highest total phenolic content (cv. Istarska bjelica) possess the highest antibacterial activity. This supports the role of polyphenols in host defense, aligning with previous field observations of lower susceptibility of cv. Istarska bjelica to olive knot disease. These findings highlight the complex nature of olive knot interactions with bacterial strains and olive cultivars, simultaneously accentuating and underscoring the importance of considering the host’s defenses as well as bacterial virulence in disease management strategies. Full article

(This article belongs to the Section Plant Microbe Interactions)

22 pages, 1097 KiB

Open AccessReview

Phaseolotoxin: Environmental Conditions and Regulatory Mechanisms Involved in Its Synthesis

by Jackeline Lizzeta Arvizu-Gómez, Alejandro Hernández-Morales, Juan Campos-Guillén, Christian González-Reyes and Juan Ramiro Pacheco-Aguilar

Microorganisms 2024, 12(7), 1300; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms12071300 - 26 Jun 2024

Viewed by 102

Abstract

Phaseolotoxin is an antimetabolite toxin produced by diverse pathovars of Pseudomonas syringae which affects various plants, causing diseases of economic importance. Phaseolotoxin contributes to the systemic dissemination of the pathogen in the plant, therefore it is recognized as a major virulence factor. Genetic [...] Read more.

Phaseolotoxin is an antimetabolite toxin produced by diverse pathovars of Pseudomonas syringae which affects various plants, causing diseases of economic importance. Phaseolotoxin contributes to the systemic dissemination of the pathogen in the plant, therefore it is recognized as a major virulence factor. Genetic traits such as the Pht cluster, appear defining to the toxigenic strains phaseolotoxin producers. Extensive research has contributed to our knowledge concerning the regulation of phaseolotoxin revealing a complex regulatory network that involves processes at the transcriptional and posttranscriptional levels, in which specific and global regulators participate. Even more, significant advances in understanding how specific signals, including host metabolites, nutrient sources, and physical parameters such as the temperature, can affect phaseolotoxin production have been made. A general overview of the phaseolotoxin regulation, focusing on the chemical and physical cues, and regulatory pathways involved in the expression of this major virulence factor will be given in the present work. Full article

(This article belongs to the Section Plant Microbe Interactions)

14 pages, 22850 KiB

Open AccessArticle

Genotyping and Phenotyping of Indigenous Saccharomyces cerevisiae from a New Zealand Organic Winery and Commercial Sources Using Inter-Delta and MALDI-TOF MS Typing

by Junwen Zhang, Jeffrey E. Plowman, Bin Tian, Stefan Clerens and Stephen L. W. On

Microorganisms 2024, 12(7), 1299; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms12071299 - 26 Jun 2024

Viewed by 101

Abstract

We used inter-delta typing (IDT) and MALDI-TOF profiling to characterize the genetic and phenotypic diversity of 45 commercially available winemaking Saccharomyces cerevisiae strains and 60 isolates from an organic winemaker from Waipara, New Zealand, as a stratified approach for predicting the commercial potential [...] Read more.

We used inter-delta typing (IDT) and MALDI-TOF profiling to characterize the genetic and phenotypic diversity of 45 commercially available winemaking Saccharomyces cerevisiae strains and 60 isolates from an organic winemaker from Waipara, New Zealand, as a stratified approach for predicting the commercial potential of indigenous isolates. A total of 35 IDTs were identified from the commercial strains, with another 17 novel types defined among the Waipara isolates. IDT 3 was a common type among strains associated with champagne production, and the only type in commercial strains also observed in indigenous isolates. MALDI-TOF MS also demonstrated its potential in S. cerevisiae typing, particularly when the high-mass region (m/z 2000–20,000) was used, with most indigenous strains from each of two fermentation systems distinguished. Furthermore, the comparison between commercial strains and indigenous isolates assigned to IDT 3 revealed a correlation between the low-mass data (m/z 500–4000) analysis and the recommended use of commercial winemaking strains. Both IDT and MALDI-TOF analyses offer useful insights into the genotypic and phenotypic diversity of S. cerevisiae, with MALDI-TOF offering potential advantages for the prediction of applications for novel, locally isolated strains that may be valuable for product development and diversification. Full article

(This article belongs to the Special Issue Microbiology of Fermented Food and Beverages)

► Show Figures

Figure 1

8 pages, 796 KiB

Open AccessCommunication

Analyzing Cervical Microbiome Composition in HIV-Infected Women with Different HPV Infection Profiles: A Pilot Study in Thailand

by Kanya Preechasuth, Lionel Brazier, Woottichai Khamduang, Sayamon Hongjaisee, Nantawan Wangsaeng and Nicole Ngo-Giang-Huong

Microorganisms 2024, 12(7), 1298; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms12071298 - 26 Jun 2024

Viewed by 98

Abstract

We conducted a pilot study to analyze the microbiome in cervical samples of women living with HIV with various profiles of HPV infections. The participants had an average age of 41.5 years. Sequence analysis of 16S rRNA V3 gene amplicons was performed using [...] Read more.

We conducted a pilot study to analyze the microbiome in cervical samples of women living with HIV with various profiles of HPV infections. The participants had an average age of 41.5 years. Sequence analysis of 16S rRNA V3 gene amplicons was performed using next-generation sequencing technology (Ion Torrent PGM^TM). The bioinformatics pipeline was analyzed using the Find, Rapidly, OTUs with Galaxy Solution system (FROGS). Common genera were determined to identify Community State Types (CSTs). The cervical microbiome profiles showed a dominance of lactobacilli in 56% (five out of nine) of samples. All three women with normal cervical cells and high-risk HPV infection were classified as CST IV, characterized by anaerobic bacteria associated with bacterial vaginitis, such as Gardnerella, Prevotella, Atopobium, and Sneathia. Among the two women with abnormal cervical cells and high-risk HPV infection, one was classified as CST III, and the other had an unclassified profile dominated by L. helveticus. Four women with normal cervical cells and no HPV infection exhibited various CSTs. Our study demonstrated the feasibility of the protocol in analyzing the cervical microbiome. However, further analysis with a larger number of longitudinal samples is necessary to determine the role of cervical microbiota in HPV persistence, clearance, or the development of precancerous lesions. Full article

(This article belongs to the Special Issue Vaginal Microbiome in Women's Health)

► Show Figures

Figure 1

12 pages, 1699 KiB

Open AccessArticle

The Relationship between Biofilm Phenotypes and Biofilm-Associated Genes in Food-Related Listeria monocytogenes Strains

by Alexandra Burdová, Adriana Véghová, Jana Minarovičová, Hana Drahovská and Eva Kaclíková

Microorganisms 2024, 12(7), 1297; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms12071297 - 26 Jun 2024

Viewed by 104

Abstract

Listeria monocytogenes is an important pathogen responsible for listeriosis, a serious foodborne illness associated with high mortality rates. Therefore, L. monocytogenes is considered a challenge for the food industry due to the ability of some strains to persist in food-associated environments. Biofilm production [...] Read more.

Listeria monocytogenes is an important pathogen responsible for listeriosis, a serious foodborne illness associated with high mortality rates. Therefore, L. monocytogenes is considered a challenge for the food industry due to the ability of some strains to persist in food-associated environments. Biofilm production is presumed to contribute to increased L. monocytogenes resistance and persistence. The aims of this study were to (1) assess the biofilm formation of L. monocytogenes isolates from a meat processing facility and sheep farm previously characterized and subjected to whole-genome sequencing and (2) perform a comparative genomic analysis to compare the biofilm formation and the presence of a known set of biofilm-associated genes and related resistance or persistence markers. Among the 37 L. monocytogenes isolates of 15 sequence types and four serogroups involved in this study, 14%, 62%, and 24% resulted in the formation of weak, moderate, and strong biofilm, respectively. Increased biofilm-forming ability was associated with the presence of the stress survival islet 1 (SSI-1), inlL, and the truncated inlA genes. Combining the phenotypic and genotypic data may contribute to understanding the relationships between biofilm-associated genes and L. monocytogenes biofilm-forming ability, enabling improvement in the control of this foodborne pathogen. Full article

(This article belongs to the Section Food Microbiology)

► Show Figures

Figure 1

14 pages, 257 KiB

Open AccessArticle

Investigation of Healthcare-Acquired Infections and Antimicrobial Resistance in an Italian Hematology Department before and during the COVID-19 Pandemic

by Federica Petrone, Carmine Gizzi, Alessandro Andriani, Vincenza Martini, Roberta Sala, Angela Abballe, Lucia Capoccetta, Angela Spicciato, Marco Alfio Cutuli, Antonio Guarnieri, Noemi Venditti, Roberto Di Marco and Giulio Petronio Petronio

Microorganisms 2024, 12(7), 1296; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms12071296 - 26 Jun 2024

Viewed by 140

Abstract

Background: The COVID-19 pandemic has made antibiotic resistance (AMR) and healthcare-acquired infections (HAIs) increasingly serious problems. Point-prevalence Surveys (PPS) and other surveillance techniques are essential for antimicrobial management and prevention. Methods: In a hematology department of an Italian hospital, the prevalence of HAI, [...] Read more.

Background: The COVID-19 pandemic has made antibiotic resistance (AMR) and healthcare-acquired infections (HAIs) increasingly serious problems. Point-prevalence Surveys (PPS) and other surveillance techniques are essential for antimicrobial management and prevention. Methods: In a hematology department of an Italian hospital, the prevalence of HAI, microbiology, and AMR were examined in this retrospective study in two different periods, namely 2019 and 2021 (pre-pandemic and during the pandemic, respectively). Comparisons were made between patient demographics, hospitalization duration, surveillance swabs, and HAIs. Findings: There was no discernible variation in the prevalence of HAI between 2019 and 2021. Higher rates of HAI were connected with longer hospital stays. Variations in antimicrobial susceptibility and species distribution were found by microbiological analysis. Discussion: The incidence of HAI stayed constant during the epidemic. Nevertheless, shifts in antibiotic susceptibility and microbiological profiles highlight the necessity of continuous monitoring and care. Conclusions: Despite the difficulties of COVID-19, ongoing surveillance and infection control initiatives are crucial for halting HAIs and battling antimicrobial resistance (AMR) in healthcare environments. To fully understand the pandemic’s long-term impact on the spread of infectious diseases and antibiotic resistance, more research is required. Full article

(This article belongs to the Collection Advances in Public Health Microbiology)

17 pages, 3310 KiB

Open AccessArticle

Antagonistic Effects of Corynebacterium pseudodiphtheriticum 090104 on Respiratory Pathogens

by Ramiro Ortiz Moyano, Stefania Dentice Maidana, Yoshiya Imamura, Mariano Elean, Fu Namai, Yoshihito Suda, Keita Nishiyama, Vyacheslav Melnikov, Haruki Kitazawa and Julio Villena

Microorganisms 2024, 12(7), 1295; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms12071295 - 26 Jun 2024

Viewed by 199

Abstract

In previous studies, it was demonstrated that Corynebacterium pseudodiphtheriticum 090104, isolated from the human nasopharynx, modulates respiratory immunity, improving protection against infections. Here, the antagonistic effect of the 090104 strain on respiratory pathogens, including Streptococcus pneumoniae, Staphylococcus aureus, Klebsiella pneumoniae, [...] Read more.

In previous studies, it was demonstrated that Corynebacterium pseudodiphtheriticum 090104, isolated from the human nasopharynx, modulates respiratory immunity, improving protection against infections. Here, the antagonistic effect of the 090104 strain on respiratory pathogens, including Streptococcus pneumoniae, Staphylococcus aureus, Klebsiella pneumoniae, Pseudomonas aeruginosa, and Acinetobacter baumannii, was explored. In a series of in vitro studies, the capacity of C. pseudodiphtheriticum 090104, its bacterium-like particles, and its culture supernatants to coaggregate, inhibit the growth, and change the virulent phenotype of pathogenic bacteria was evaluated. The results showed that the 090104 strain was able to exert a bacteriostatic effect on K. pneumoniae and S. pneumoniae growth. In addition, C. pseudodiphtheriticum 090104 coaggregated, inhibited biofilm formation, and induced phenotypic changes in all the respiratory pathogens evaluated. In conclusion, this work demonstrated that, in addition to its beneficial effects exerted by host–microbe interactions, C. pseudodiphtheriticum 090104 can enhance protection against respiratory pathogens through its microbe–microbe interactions. The mechanisms involved in such interactions should be evaluated in future research. Full article

(This article belongs to the Special Issue Applied Microbiome Science and Technology)

► Show Figures

Figure 1

7 pages, 365 KiB

Open AccessCommunication

Evaluation of Bacterial Viability for Fecal Microbiota Transplantation: Impact of Thawing Temperature and Storage Time

by Paolo Bottino, Daria Vay, Christian Leli, Lidia Ferrara, Valentina Pizzo, Franca Gotta, Alessio Raiteri, Fabio Rapallo, Annalisa Roveta, Antonio Maconi and Andrea Rocchetti

Microorganisms 2024, 12(7), 1294; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms12071294 - 25 Jun 2024

Viewed by 182

Abstract

Fecal Microbiota Transplantation (FMT) represents a promising therapeutic tool under study for several purposes and is currently applied to the treatment of recurrent Clostridioides difficile infection. However, since the use of fresh stool was affected by several issues linked to donor screening, the [...] Read more.

Fecal Microbiota Transplantation (FMT) represents a promising therapeutic tool under study for several purposes and is currently applied to the treatment of recurrent Clostridioides difficile infection. However, since the use of fresh stool was affected by several issues linked to donor screening, the development of a frozen stool bank is a reliable option to standardize FMT procedures. Nevertheless, different environmental factors impact microbial viability. Herein, we report the effect of different thawing temperatures and storage conditions on bacterial suspensions in the FMT procedure. In total, 20 stool samples were divided into aliquots and tested across a combination of different storing periods (15, 30; 90 days) and thawing procedures (4 °C overnight, room temperature for 1 h; 37 °C for 5 min). Focusing on storage time, our data showed a significant reduction in viability for aerobic and anaerobic bacteria after thawing for 15 days, while no further reductions were observed until after 90 days. Instead, among the different thawing procedures, no significant differences were observed for aerobic bacteria, while for anaerobes, thawing at 37 °C for 5 min was more effective in preserving the bacterial viability. In conclusion, the frozen fecal microbiota remained viable for at least three months, with an excellent recovery rate in all three thawing conditions. Full article

(This article belongs to the Section Gut Microbiota)

12 pages, 578 KiB

Open AccessArticle

The Diversity of Spotted Fever Group Rickettsia Found in Ixodidae Hard Ticks Removed from Humans in Karachay-Cherkessia, North Caucasus, Russia

by Alexey V. Rakov, Tatiana A. Chekanova, Ketevan Petremgvdlishvili, Svetlana B. Linnik, Khusey Kh. Batchaev and Vasiliy G. Akimkin

Microorganisms 2024, 12(7), 1293; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms12071293 - 25 Jun 2024

Viewed by 193

Abstract

Karachay-Cherkessia is the region in the Russian Federation that has been overlooked in terms of research on the human bacterial pathogens transmitted by ticks. In this study, we investigated the infection status of ticks with Rickettsia, Borrelia, Coxiella burmetii, Anaplasma [...] Read more.

Karachay-Cherkessia is the region in the Russian Federation that has been overlooked in terms of research on the human bacterial pathogens transmitted by ticks. In this study, we investigated the infection status of ticks with Rickettsia, Borrelia, Coxiella burmetii, Anaplasma phagocytophilum, and Ehrlichia chaffeensis/Ehrlichia muris associated with natural focal infections in Karachay-Cherkessia. A total amount of 159 ticks from three species across three genera (Ixodes ricinus, Dermacentor marginatus, Hyalomma scupense) removed from humans were collected for analysis. Additionally, we used 53 individual ticks and 40 tick pools from the vegetation of three species (I. ricinus, D. marginatus, and Rhipicephalus bursa). Screening of the studied pathogens was performed by using commercial qPCR kits. Sanger sequencing utilizing partial sequences of gltA and ompA genes was employed to identify the Rickettsia species. Our findings revealed the presence of DNA from five species within the spotted fever group Rickettsia, namely Rickettsia raoultii, R. slovaca, R. helvetica, R. monacensis, and R. aeschlimannii. Moreover, two distinct genotypes were identified within R. aeschlimannii, R. helvetica, and R. monacensis. Additionally, DNA from Borrelia burgdoferi s.l., B. miyamotoi, and A. phagocytophilum was detected in the tested ticks. This study provides valuable insights into the prevalence and the diversity of bacterial pathogens transmitted by ticks in the Karachay-Cherkessia region. Full article

(This article belongs to the Special Issue One Health Research on Zoonotic Tick-Borne Pathogens)

17 pages, 25932 KiB

Open AccessArticle

Amino Acid-Induced Chemotaxis Plays a Key Role in the Adaptation of Vibrio harveyi from Seawater to the Muscle of the Host Fish

by Xiaoxu Zhang, Zhe Zhang, Qingpi Yan, Ziyan Du, Lingmin Zhao and Yingxue Qin

Microorganisms 2024, 12(7), 1292; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms12071292 - 25 Jun 2024

Viewed by 167

Abstract

Vibrio harveyi is a normal flora in natural marine habitats and a significant opportunistic pathogen in marine animals. This bacterium can cause a series of lesions after infecting marine animals, in which muscle necrosis and ulcers are the most common symptoms. This study [...] Read more.

Vibrio harveyi is a normal flora in natural marine habitats and a significant opportunistic pathogen in marine animals. This bacterium can cause a series of lesions after infecting marine animals, in which muscle necrosis and ulcers are the most common symptoms. This study explored the adaptation mechanisms of V. harveyi from the seawater environment to host fish muscle environment. The comprehensive transcriptome analysis revealed dramatic changes in the transcriptome of V. harveyi during its adaptation to the host fish muscle environment. Based on Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, flagellar assembly, oxidative phosphorylation, bacterial chemotaxis, and two-component systems play crucial roles in V. harveyi’s adaptation to host fish muscle. A comparison of biological phenotypes revealed that V. harveyi displayed a significant increase in flagellar length, swimming, twitching, chemotaxis, adhesion, and biofilm formation after induction by host fish muscle, and its dominant amino acids, especially bacterial chemotaxis induced by host muscle, Ala and Arg. It could be speculated that the enhancement of bacterial chemotaxis induced by amino acids plays a key role in the adaptation of V. harveyi from seawater to the muscle of the host fish. Full article

(This article belongs to the Section Veterinary Microbiology)

► Show Figures

Figure 1

15 pages, 817 KiB

Open AccessArticle

Role of Nedd4L in Macrophage Pro-Inflammatory Polarization Induced by Influenza A Virus and Lipopolysaccharide Stimulation

by Meihong Peng, Cheng Zhao, Fangguo Lu, Xianggang Zhang, Xiaoqi Wang, Li He and Bei Chen

Microorganisms 2024, 12(7), 1291; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms12071291 - 25 Jun 2024

Viewed by 166

Abstract

Influenza A virus (IAV) infection often leads to influenza-associated fatalities, frequently compounded by subsequent bacterial infections, particularly Gram-negative bacterial co-infections. Lipopolysaccharide (LPS), a primary virulence factor in Gram-negative bacteria, plays a crucial role in influenza–bacterial co-infections. However, the precise pathogenic mechanisms underlying the [...] Read more.

Influenza A virus (IAV) infection often leads to influenza-associated fatalities, frequently compounded by subsequent bacterial infections, particularly Gram-negative bacterial co-infections. Lipopolysaccharide (LPS), a primary virulence factor in Gram-negative bacteria, plays a crucial role in influenza–bacterial co-infections. However, the precise pathogenic mechanisms underlying the synergistic effects of viral–bacterial co-infections remain elusive, posing significant challenges for disease management. In our study, we administered a combination of IAV and LPS to mice and examined associated parameters, including the lung function, lung index, wet/dry ratio, serum inflammatory cytokines, Nedd4L expression in lung tissue, and mRNA levels of inflammatory cytokines. Co-infection with IAV and LPS exacerbated lung tissue inflammation and amplified M1 macrophage expression in lung tissue. Additionally, we stimulated macrophages with IAV and LPS in vitro, assessing the inflammatory cytokine content in the cell supernatant and cytokine mRNA expression within the cells. This combined stimulation intensified the inflammatory response in macrophages and upregulated Nedd4L protein and mRNA expression. Subsequently, we used siRNA to knockdown Nedd4L in macrophages, revealing that suppression of Nedd4L expression alleviated the inflammatory response triggered by concurrent IAV and LPS stimulation. Collectively, these results highlight the pivotal role of Nedd4L in mediating the exacerbated inflammatory responses observed in IAV and LPS co-infections. Full article

(This article belongs to the Section Molecular Microbiology and Immunology)

21 pages, 2574 KiB

Open AccessArticle

Development and Evaluation of Bioconverted Milk with Anti-Microbial Effect against Periodontal Pathogens and α-Glucosidase Inhibitory Activity

by Yewon Lee, Yohan Yoon and Kyoung-Hee Choi

Microorganisms 2024, 12(7), 1290; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms12071290 - 25 Jun 2024

Viewed by 385

Abstract

To decrease periodontal pathogens and increase the number of beneficial bacteria, probiotics and bioactive compounds made via microbial bioconversion are recently used. In addition, the interest regarding probiotics-mediated bioconversion with popular medicinal plants is increasing. Artemisia herba-alba, a type of wormwood, has [...] Read more.

To decrease periodontal pathogens and increase the number of beneficial bacteria, probiotics and bioactive compounds made via microbial bioconversion are recently used. In addition, the interest regarding probiotics-mediated bioconversion with popular medicinal plants is increasing. Artemisia herba-alba, a type of wormwood, has recently been attention as a medicinal plant due to its various bioactive compounds. Therefore, we developed bioconverted milk containing A. herba-alba that effectively inhibited periodontal pathogens and α-glucosidase. To select the appropriate lactic acid bacteria for the probiotic candidate strain, 74 strains of lactic acid bacteria were screened. Among them, Lactiplantibacillus plantarum SMFM2016-RK was chosen as the probiotic due to its beneficial characteristics such as high acid and bile tolerance, antioxidant activity, and α-glucosidase inhibition. Based on the minimal bactericidal concentration against three periodontal pathogens, the following appropriate concentrations of Artemisia herba-alba extract were added to milk: 5 mg/mL of A. herba-alba ethanol extract and 25 mg/mL of A. herba-alba hot-water extract. Four bioconverted milks (BM), BM1, BM2, BM3, and BM4, were produced by combining L. plantarum SMFM2016-RK alone, L. plantarum SMFM2016-RK and ethanol extract, L. plantarum SMFM2016-RK and hot-water extract, and L. plantarum SMFM2016-RK with both extracts. As a result of antimicrobial activity, BM3 inhibited the growth of Aggregatibacter actinomycetemcomitans and Porphyromonas gingivalis the most, and BM4 suppressed the growth of Fusobacterium nucleatum the most. In addition, bioconverted milk containing A. herba-alba (BM2, BM3, and BM4) inhibited α-glucosidase more effectively than BM1. The whole genome of L. plantarum SMFM2016-RK was obtained, and 3135 CDS, 67 tRNA, and 16 RNA were predicted. The genome annotation of L. plantarum SMFM2016-RK revealed 11 CDS related to proteolysis and amino acid metabolism and 2 CDS of phenolic acid-metabolizing enzymes. In conclusion, A. herba-alba-added milk bioconverted by L. plantarum SMFM2016-RK displayed both the growth inhibitory effect on periodontal pathogens and the α-glucosidase inhibitory activity; thus, it necessitates to evaluate the effects on the alleviation of periodontal diseases and glycemic control through future animal experiments. Full article

(This article belongs to the Special Issue Plant and Human Probiotics: Consequences on the Autochthonous Microbiota)

27 pages, 2063 KiB

Open AccessArticle

Utilizing Feline Lentiviral Infection to Establish a Translational Model for COVID-19 in People with Human Immunodeficiency Virus Infection

by Shoroq Shatnawi, Sachithra Gunasekara, Laura Bashor, Miruthula Tamil Selvan, Mary Nehring, Shannon Cowan, Jerry Ritchey, Susan VandeWoude, Brianne Taylor, Craig Miller and Jennifer M. Rudd

Microorganisms 2024, 12(7), 1289; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms12071289 - 25 Jun 2024

Viewed by 330

Abstract

People living with human immunodeficiency virus (PLWH) are a significant population globally. Research delineating our understanding of coinfections in PLWH is critical to care for those navigating infection with other pathogens. The recent COVID-19 pandemic underscored the urgent need for studying the effects [...] Read more.

People living with human immunodeficiency virus (PLWH) are a significant population globally. Research delineating our understanding of coinfections in PLWH is critical to care for those navigating infection with other pathogens. The recent COVID-19 pandemic underscored the urgent need for studying the effects of SARS-CoV-2 infections in therapy-controlled and uncontrolled immunodeficiency viral infections. This study established the utility of a feline model for the in vivo study of coinfections. Domestic cats are naturally infected with SARS-CoV-2 and Feline Immunodeficiency Virus, a lentivirus molecularly and pathogenically similar to HIV. In this study, comparisons are made between FIV-positive and FIV-negative cats inoculated with SARS-CoV-2 (B.1.617.2.) in an experimental setting. Of the FIV+ cats, three received Zidovudine (AZT) therapy in the weeks leading up to SARS-CoV-2 inoculation, and two did not. SARS-CoV-2 viral RNA was quantified, histopathologic comparisons of respiratory tissues were made, and T-cell populations were analyzed for immune phenotype shifts between groups. CD4+ T lymphocyte responses varied, with FIV+-untreated cats having the poorest CD4+ response to SARS-CoV-2 infection. While all cats had significant pulmonary inflammation, key histopathologic features of the disease differed between groups. Additionally, viral genomic analysis was performed, and results were analyzed for the presence of emerging, absent, amplified, or reduced mutations in SARS-CoV-2 viral RNA after passage through the feline model. Positive selection is noted, especially in FIV+ cats untreated with AZT, and mutations with potential relevance were identified; one FIV+-untreated cat had persistent, increasing SARS-CoV-2 RNA in plasma five days post-infection. These findings and others support the utility of the feline model for studying coinfection in people with HIV and highlight the importance of antiretroviral therapy in clearing SARS-CoV-2 coinfections to minimize transmission and emergence of mutations that may have deleterious effects. Full article

(This article belongs to the Special Issue Epidemiology of SARS-CoV-2/COVID-19 Infections)

20 pages, 3675 KiB

Open AccessArticle

Proteomics Analysis of Duck Lung Tissues in Response to Highly Pathogenic Avian Influenza Virus

by Periyasamy Vijayakumar, Anamika Mishra, Ram Pratim Deka, Sneha M. Pinto, Yashwanth Subbannayya, Richa Sood, Thottethodi Subrahmanya Keshava Prasad and Ashwin Ashok Raut

Microorganisms 2024, 12(7), 1288; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms12071288 - 25 Jun 2024

Viewed by 203

Abstract

Domestic ducks (Anas platyrhynchos domesticus) are resistant to most of the highly pathogenic avian influenza virus (HPAIV) infections. In this study, we characterized the lung proteome and phosphoproteome of ducks infected with the HPAI H5N1 virus (A/duck/India/02CA10/2011/Agartala) at 12 h, [...] Read more.

Domestic ducks (Anas platyrhynchos domesticus) are resistant to most of the highly pathogenic avian influenza virus (HPAIV) infections. In this study, we characterized the lung proteome and phosphoproteome of ducks infected with the HPAI H5N1 virus (A/duck/India/02CA10/2011/Agartala) at 12 h, 48 h, and 5 days post-infection. A total of 2082 proteins were differentially expressed and 320 phosphorylation sites mapping to 199 phosphopeptides, corresponding to 129 proteins were identified. The functional annotation of the proteome data analysis revealed the activation of the RIG-I-like receptor and Jak-STAT signaling pathways, which led to the induction of interferon-stimulated gene (ISG) expression. The pathway analysis of the phosphoproteome datasets also confirmed the activation of RIG-I, Jak-STAT signaling, NF-kappa B signaling, and MAPK signaling pathways in the lung tissues. The induction of ISG proteins (STAT1, STAT3, STAT5B, STAT6, IFIT5, and PKR) established a protective anti-viral immune response in duck lung tissue. Further, the protein–protein interaction network analysis identified proteins like AKT1, STAT3, JAK2, RAC1, STAT1, PTPN11, RPS27A, NFKB1, and MAPK1 as the main hub proteins that might play important roles in disease progression in ducks. Together, the functional annotation of the proteome and phosphoproteome datasets revealed the molecular basis of the disease progression and disease resistance mechanism in ducks infected with the HPAI H5N1 virus. Full article

(This article belongs to the Special Issue Poultry Pathogens and Poultry Diseases)

19 pages, 1508 KiB

Open AccessArticle

Microbial Community Shifts in Tea Plant Rhizosphere under Seawater Stress: Enrichment of Beneficial Taxa

by Xiaohua Zhang, Haozhen Li, Bin Li, Kangkang Song, Yuxue Sha, Ying Liu, Shaolin Dong, Di Wang and Long Yang

Microorganisms 2024, 12(7), 1287; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms12071287 - 25 Jun 2024

Viewed by 201

Abstract

Seawater intrusion has a significant impact on the irrigation quality of agricultural water, thereby posing a threat to plant growth and development. We hypothesized that the rhizosphere of tea plants harbors beneficial microorganisms, which may improve the tolerance of tea plants to seawater [...] Read more.

Seawater intrusion has a significant impact on the irrigation quality of agricultural water, thereby posing a threat to plant growth and development. We hypothesized that the rhizosphere of tea plants harbors beneficial microorganisms, which may improve the tolerance of tea plants to seawater stress. This study utilized 16s and ITS techniques to analyze microbial community shifts in the tea plant rhizosphere and non-rhizosphere under seawater stress conditions. The findings suggest that seawater stress leads to a reduction in microbial diversity, although the rhizosphere microbial diversity in stressed soils showed a relatively higher level. Moreover, the rhizosphere of the tea plant under seawater stress exhibited an enrichment of plant growth-promoting rhizobacteria alongside a higher presence of pathogenic fungi. Network analysis revealed that seawater stress resulted in the construction of a more complex and stable rhizosphere microbial network compared to normal conditions. Predictions of bacterial potential functions highlighted a greater diversity of functional groups, enhancing resource utilization efficiency. In general, the rhizosphere microorganisms of tea plants are jointly selected by seawater and the host. The microorganisms closely related to the rhizosphere of tea plants are retained and, at the same time, attract beneficial microorganisms that may alleviate stress. These findings provide new insights into plant responses to saline stress and have significant implications for leveraging vegetation to enhance the resilience of coastal saline soils and contribute to economic progress. Full article

(This article belongs to the Special Issue Soil Microbial Communities under Environmental Change)

21 pages, 1028 KiB

Open AccessArticle

Large-Scale Molecular Epidemiological Survey of Blastocystis sp. among Herbivores in Egypt and Assessment of Potential Zoonotic Risk

by Doaa Naguib, Nausicaa Gantois, Jeremy Desramaut, Ruben Garcia Dominguez, Nagah Arafat, Samar Magdy Atwa, Gaël Even, Damien Paul Devos, Gabriela Certad, Magali Chabé and Eric Viscogliosi

Microorganisms 2024, 12(7), 1286; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms12071286 - 25 Jun 2024

Viewed by 207

Abstract

Given the proven zoonotic potential of the intestinal protozoan Blastocystis sp., a fast-growing number of surveys are being conducted to identify potential animal reservoirs for transmission of the parasite. Nevertheless, few epidemiological studies have been conducted on farmed animals in Egypt. Therefore, a [...] Read more.

Given the proven zoonotic potential of the intestinal protozoan Blastocystis sp., a fast-growing number of surveys are being conducted to identify potential animal reservoirs for transmission of the parasite. Nevertheless, few epidemiological studies have been conducted on farmed animals in Egypt. Therefore, a total of 1089 fecal samples were collected from herbivores (sheep, goats, camels, horses, and rabbits) in six Egyptian governorates (Dakahlia, Gharbia, Kafr El Sheikh, Giza, Aswan, and Sharqia). Samples were screened for the presence of Blastocystis sp. by real-time PCR followed by sequencing of positive PCR products and phylogenetic analysis for subtyping of the isolates. Overall, Blastocystis sp. was identified in 37.6% of the samples, with significant differences in frequency between animal groups (sheep, 65.5%; camels, 62.2%; goats, 36.0%; rabbits, 10.1%; horses, 3.3%). Mixed infections were reported in 35.7% of the Blastocystis sp.-positive samples. A wide range of subtypes (STs) with varying frequency were identified from single infections in ruminants including sheep (ST1–ST3, ST5, ST10, ST14, ST21, ST24, ST26, and ST40), goats (ST1, ST3, ST5, ST10, ST26, ST40, ST43, and ST44), and camels (ST3, ST10, ST21, ST24–ST26, ST30, and ST44). Most of them overlapped across these animal groups, highlighting their adaptation to ruminant hosts. In other herbivores, only three and two STs were evidenced in rabbits (ST1–ST3) and horses (ST3 and ST44), respectively. The greater occurrence and wider genetic diversity of parasite isolates among ruminants, in contrast to other herbivores, strongly suggested that dietary habits likely played a significant role in influencing both the colonization rates of Blastocystis sp. and ST preference. Of all the isolates subtyped herein, 66.3% were reported as potentially zoonotic, emphasizing the significant role these animal groups may play in transmitting the parasite to humans. These findings also expand our knowledge on the prevalence, genetic diversity, host specificity, and zoonotic potential of Blastocystis sp. in herbivores. Full article

(This article belongs to the Special Issue Prevention and Control of Zoonotic Pathogen Infection)

21 pages, 1371 KiB

Open AccessArticle

Detection of Klebsiella pneumoniae Carbapenem Resistance Genes by qPCR: Choosing the Right Method for Total DNA Extraction

by Cecilia Heller, Iris Bachmann, Martin Spiegel, Frank T. Hufert and Gregory Dame

Microorganisms 2024, 12(7), 1285; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms12071285 - 25 Jun 2024

Viewed by 210

Abstract

Rapid and accurate detection of Klebsiella pneumoniae carbapenem resistance is important for infection control and targeted antibiotic therapy. PCR-based assay performance heavily depends on the quality and quantity of template DNA. Challenges arise from the necessity to isolate chromosomal and large plasmid-encoded resistance [...] Read more.

Rapid and accurate detection of Klebsiella pneumoniae carbapenem resistance is important for infection control and targeted antibiotic therapy. PCR-based assay performance heavily depends on the quality and quantity of template DNA. Challenges arise from the necessity to isolate chromosomal and large plasmid-encoded resistance genes simultaneously from a limited number of target cells and to remove PCR inhibitors. qPCRs for the detection of K. pneumoniae strains carrying bla_OXA-48, bla_NDM-1, bla_KPC-2, and bla_VIM-1 carbapenemase genes were developed. We compared the performance of template DNA extracted with silica column-based methods, reversed elution systems, and lysis-only methods either from diluted culture fluid or from a synthetic stool matrix which contained PCR inhibitors typically present in stool. The synthetic stool matrix was chosen to mimic K. pneumoniae containing rectal swabs or stool samples in a reproducible manner. For total DNA isolated from culture fluid, resistance gene detection by qPCR was always possible, independent of the extraction method. However, when total DNA was isolated from synthetic stool matrix spiked with K. pneumoniae, most methods were insufficient. The best performance of template DNA was obtained with reversed elution. This highlights the importance of choosing the right DNA extraction method for consistent carbapenem resistance detection by PCR. Full article

(This article belongs to the Section Antimicrobial Agents and Resistance)

21 pages, 1932 KiB

Open AccessArticle

Molecular and Phylogenomic Analysis of a Vancomycin Intermediate Resistance USA300LV Strain in Chile

by Daniela Núñez, Pablo Jiménez, Marcelo Cortez-San Martín, Carolina Cortés, Matías Cárdenas, Sofia Michelson, Tamara Garay, Maggie Vecchiola, Alejandra Céspedes, Jonathan E. Maldonado and Yesseny Vásquez-Martínez

Microorganisms 2024, 12(7), 1284; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms12071284 - 25 Jun 2024

Viewed by 183

Abstract

Antimicrobial resistance is a major global health problem, and, among Gram-positive bacteria, methicillin-resistant Staphylococcus aureus (MRSA) represents a serious threat. MRSA causes a wide range of infections, including bacteremia, which, due to the limited use of β-lactams, is difficult to treat. This study [...] Read more.

Antimicrobial resistance is a major global health problem, and, among Gram-positive bacteria, methicillin-resistant Staphylococcus aureus (MRSA) represents a serious threat. MRSA causes a wide range of infections, including bacteremia, which, due to the limited use of β-lactams, is difficult to treat. This study aimed to analyze 51 MRSA isolates collected in 2018 from samples of patients with bacteremia from two hospitals of the Metropolitan Health Service of Santiago, Chile, both in their resistance profile and in the identification of virulence factors. In addition, genomic characterization was carried out by the WGS of an isolate that was shown to be the one of greatest concern (N°. 42) due to its intermediate resistance to vancomycin, multiple virulence factors and being classified as ST8 PVL-positive. In our study, most of the isolates turned out to be multidrug-resistant, but there are still therapeutic options, such as tetracycline, rifampicin, chloramphenicol and vancomycin, which are currently used for MRSA infections; however, 18% were PVL positive, which suggests greater virulence of these isolates. It was determined that isolate N°42 is grouped within the USA300-LV strains (ST8, PVL+, COMER+); however, it has been suggested that, in Chile, a complete displacement of the PVL-negative ST5 clone has not occurred. Full article

(This article belongs to the Section Medical Microbiology)

8 pages, 6570 KiB

Open AccessCommunication

Quest for the Nitrogen-Metabolic Versatility of Microorganisms in Soil and Marine Ecosystems

by Yongpeng Zhao, Xia Zhu-Barker, Kai Cai, Shuling Wang, Alan L. Wright and Xianjun Jiang

Microorganisms 2024, 12(7), 1283; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms12071283 - 25 Jun 2024

Viewed by 234

Abstract

Whether nitrogen (N)-metabolic versatility is a common trait of N-transforming microbes or if it only occurs in a few species is still unknown. We collected 83 soil samples from six soil types across China, retrieved 19 publicly available metagenomic marine sample data, and [...] Read more.

Whether nitrogen (N)-metabolic versatility is a common trait of N-transforming microbes or if it only occurs in a few species is still unknown. We collected 83 soil samples from six soil types across China, retrieved 19 publicly available metagenomic marine sample data, and analyzed the functional traits of N-transforming microorganisms using metagenomic sequencing. More than 38% and 35% of N-transforming species in soil and marine ecosystems, respectively, encoded two or more N-pathways, although N-transforming species differed greatly between them. Furthermore, in both soil and marine ecosystems, more than 80% of nitrifying and N-fixing microorganisms at the species level were N-metabolic versatile. This study reveals that N-metabolic versatility is a common trait of N-transforming microbes, which could expand our understanding of the functional traits of drivers of nitrogen biogeochemistry. Full article

(This article belongs to the Section Environmental Microbiology)

► Show Figures

Figure 1

16 pages, 3015 KiB

Open AccessArticle

Spatiotemporal Variations in Co-Occurrence Patterns of Planktonic Prokaryotic Microorganisms along the Yangtze River

by Wenran Du, Jiacheng Li, Guohua Zhang, Ke Yu and Shufeng Liu

Microorganisms 2024, 12(7), 1282; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms12071282 - 24 Jun 2024

Viewed by 324

Abstract

Bacteria and archaea are foundational life forms on Earth and play crucial roles in the development of our planet’s biological hierarchy. Their interactions influence various aspects of life, including eukaryotic cell biology, molecular biology, and ecological dynamics. However, the coexistence network patterns of [...] Read more.

Bacteria and archaea are foundational life forms on Earth and play crucial roles in the development of our planet’s biological hierarchy. Their interactions influence various aspects of life, including eukaryotic cell biology, molecular biology, and ecological dynamics. However, the coexistence network patterns of these microorganisms within natural river ecosystems, vital for nutrient cycling and environmental health, are not well understood. To address this knowledge gap, we systematically explored the non-random coexistence patterns of planktonic bacteria and archaea in the 6000-km stretch of the Yangtze River by using high-throughput sequencing technology. By analyzing the O/R ratio, representing the divergence between observed (O%) and random (R%) co-existence incidences, and the module composition, we found a preference of both bacteria and archaea for intradomain associations over interdomain associations. Seasons notably influenced the co-existence of bacteria and archaea, and archaea played a more crucial role in spring as evidenced by their predominant presence of interphyla co-existence and more species as keystone ones. The autumn network was characterized by a higher node or edge number, greater graph density, node degree, degree centralization, and nearest neighbor degree, indicating a more complex and interconnected structure. Landforms markedly affected microbial associations, with more complex networks and more core species found in plain and non-source areas. Distance-decay analysis suggested the importance of geographical distance in shaping bacteria and archaea co-existence patterns (more pronounced in spring). Natural, nutrient, and metal factors, including water temperature, NH₄⁺-N, Fe, Al, and Ni were identified as crucial determinants shaping the co-occurrence patterns. Overall, these findings revealed the dynamics of prokaryotic taxa coexistence patterns in response to varying environmental conditions and further contributed to a broader understanding of microbial ecology in freshwater biogeochemical cycling. Full article

(This article belongs to the Topic The Challenges and Future Trends in Anthropogenic and Natural Pollution Control Engineering)

► Show Figures

Figure 1

26 pages, 1885 KiB

Open AccessReview

Arbuscular Mycorrhizal Fungi as Biostimulant and Biocontrol Agents: A Review

by Mathieu Delaeter, Maryline Magnin-Robert, Béatrice Randoux and Anissa Lounès-Hadj Sahraoui

Microorganisms 2024, 12(7), 1281; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms12071281 - 24 Jun 2024

Viewed by 288

Abstract

Arbuscular mycorrhizal fungi (AMF) are soil microorganisms living in symbiosis with most terrestrial plants. They are known to improve plant tolerance to numerous abiotic and biotic stresses through the systemic induction of resistance mechanisms. With the aim of developing more sustainable agriculture, reducing [...] Read more.

Arbuscular mycorrhizal fungi (AMF) are soil microorganisms living in symbiosis with most terrestrial plants. They are known to improve plant tolerance to numerous abiotic and biotic stresses through the systemic induction of resistance mechanisms. With the aim of developing more sustainable agriculture, reducing the use of chemical inputs is becoming a major concern. After providing an overview on AMF history, phylogeny, development cycle and symbiosis benefits, the current review aims to explore the potential of AMF as biostimulants and/or biocontrol agents. Nowadays, AMF inoculums are already increasingly used as biostimulants, improving mineral nutrient plant acquisition. However, their role as a promising tool in the biocontrol market, as an alternative to chemical phytosanitary products, is underexplored and underdiscussed. Thus, in the current review, we will address the mechanisms of mycorrhized plant resistance to biotic stresses induced by AMF, and highlight the various factors in favor of inoculum application, but also the challenges that remain to be overcome. Full article

(This article belongs to the Special Issue Microbial-Based Plant Biostimulants 2.0)

19 pages, 5029 KiB

Open AccessArticle

Screening of the Biocontrol Efficacy of Potent Trichoderma Strains against Fusarium oxysporum f.sp. ciceri and Scelrotium rolfsii Causing Wilt and Collar Rot in Chickpea

by Ranjna Kumari, Vipul Kumar, Ananta Prasad Arukha, Muhammad Fazle Rabbee, Fuad Ameen and Bhupendra Koul

Microorganisms 2024, 12(7), 1280; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms12071280 - 24 Jun 2024

Viewed by 171

Abstract

Chickpeas contribute to half of the pulses produced in India and are an excellent source of protein, fibers, carbohydrates, minerals, and vitamins. However, the combination of the wilt and root rot diseases drastically lowers its yield. The use of antagonist microbes that restrict [...] Read more.

Chickpeas contribute to half of the pulses produced in India and are an excellent source of protein, fibers, carbohydrates, minerals, and vitamins. However, the combination of the wilt and root rot diseases drastically lowers its yield. The use of antagonist microbes that restrict the growth of other phytopathogens is an ecofriendly approach to combat the serious threats raised by the plant pathogens. Trichoderma spp. are well known as biocontrol agents, especially against soil- and seed-borne phytopathogens. In this study, 21 Trichoderma isolates that were collected from different rhizospheric soils were evaluated against two notorious soil-borne pathogens, such as Fusarium oxysproum f.sp. ciceri and Sclerotium rolfsii. The maximum percentage of inhibition against the tested pathogens was observed in Trichoderma isolate PBT13 (72.97%, 61.1%) followed by PBT3 (72.23%, 59.3%). The mycelial extension rate method, dual culture (antagonism), production of cell-wall degrading enzymes (CWDs), and antifungal metabolites (by GC-MS) were used as selection criteria for potent Trichoderma isolates. Among the 21 isolates, PBT3, PBT4, PBT9, and PBT13 exhibited high antagonistic activity, production of antifungal metabolites, and chitinase and β-1,3-glucanase activity. These four species were subjected to molecular characterization using an internal transcribed spacer (ITS 1 and ITS4). The results of molecular characterization identified the four species as T. virnes, T. asperellum, T. lixii, and T. harzianum. Moreover, significant chitinase and β-1,3-glucanase activities of all Trichoderma isolates were recorded in the growth medium. Trichoderma harzianum (isolate PBT13) was found to exhibit the highest chitinase activity in terms of zone formation (4.40 ± 0.17 cm), whereas Trichoderma virens (isolate PBT3) exhibited the highest β-1,3-glucanase activity1.511 μmole/min. A GC-MS analysis of ethyl extracts from two isolates of Trichoderma (PBT9, PBT13) revealed the presence of 28 VOCs. Overall, this study suggests that these four Trichoderma strains are promising biological control agents (BCAs) and could be developed as bio-pesticides after stringent field trials for the management of soil-borne diseases of chickpeas. Full article

(This article belongs to the Special Issue Soil Fungi in Sustainable Agriculture, 2nd Edition)

19 pages, 2958 KiB

Open AccessReview

Alfalfa Spring Black Stem and Leaf Spot Disease Caused by Phoma medicaginis: Epidemic Occurrence and Impacts

by Yanru Lan, Wennan Zhou, Tingyu Duan, Yanzhong Li, Cory Matthew and Zhibiao Nan

Microorganisms 2024, 12(7), 1279; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms12071279 - 24 Jun 2024

Viewed by 232

Abstract

Alfalfa spring black stem and leaf spot disease (ASBS) is a cosmopolitan soil-borne and seed-borne disease caused by Phoma medicaginis, which adversely affects the yield, and nutritive value and can stimulate production of phyto-oestrogenic compounds at levels that may adversely affect ovulation [...] Read more.

Alfalfa spring black stem and leaf spot disease (ASBS) is a cosmopolitan soil-borne and seed-borne disease caused by Phoma medicaginis, which adversely affects the yield, and nutritive value and can stimulate production of phyto-oestrogenic compounds at levels that may adversely affect ovulation rates in animals. This review summarizes the host range, damage, and symptoms of this disease, and general features of the infection cycle, epidemic occurrence, and disease management. ASBS has been reported from over 40 countries, and often causes severe yield loss. Under greenhouse conditions, reported yield loss was 31–82% for roots, 32–80% for leaves, 21% for stems and 26–28% for seedlings. In field conditions, the forage yield loss is up to 56%, indicating that a single-cut yield of 5302 kg/ha would be reduced to 2347 kg/ha. P. medicaginis can infect up to 50 species of plants, including the genera Medicago, Trifolium, Melilotus, and Vicia. ASBS is more severe during warm spring conditions before the first harvest than in hot summer and cooler winter conditions, and can infect alfalfa roots, stems, leaves, flowers, pods, and seeds, with leaf spot and/or black stem being the most typical symptoms. The primary infection is caused by the overwintering spores and mycelia in the soil, and on seeds and the cortex of dead and dry stems. The use of resistant cultivars is the most economical and effective strategy for the control of ASBS. Although biological control has been studied in the glasshouse and is promising, chemical control is the main control method in agriculture. Full article

(This article belongs to the Special Issue Plant-Microbe Interaction State-of-the-Art Research in China)

► Show Figures

Figure 1

14 pages, 1497 KiB

Open AccessReview

Hemotrophic Mycoplasmas—Vector Transmission in Livestock

by Mareike Arendt, Julia Stadler, Mathias Ritzmann, Julia Ade, Katharina Hoelzle and Ludwig E. Hoelzle

Microorganisms 2024, 12(7), 1278; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms12071278 - 23 Jun 2024

Viewed by 372

Abstract

Hemotrophic mycoplasmas (HMs) are highly host-adapted and specialized pathogens infecting a wide range of mammals including farm animals, i.e., pigs, cattle, sheep, and goats. Although HMs have been known for over 90 years, we still do not know much about the natural transmission [...] Read more.

Hemotrophic mycoplasmas (HMs) are highly host-adapted and specialized pathogens infecting a wide range of mammals including farm animals, i.e., pigs, cattle, sheep, and goats. Although HMs have been known for over 90 years, we still do not know much about the natural transmission routes within herds. Recently, it has been repeatedly discussed in publications that arthropod vectors may play a role in the transmission of HMs from animal to animal. This is mainly since several HM species could be detected in different potential arthropod vectors by PCR. This review summarizes the available literature about the transmission of bovine, porcine, ovine, and caprine HM species by different hematophagous arthropod vectors. Since most studies are only based on the detection of HMs in potential vectors, there are rare data about the actual vector competence of arthropods. Furthermore, there is a need for additional studies to investigate, whether there are biological vectors in which HMs can multiply and be delivered to new hosts. Full article

(This article belongs to the Special Issue Infection and Transmission of Clinical Pathogens in Livestock)

► Show Figures

Figure 1

15 pages, 6225 KiB

Open AccessArticle

Caldanaerobacter subterraneus subsp. keratinolyticus subsp. nov., a Novel Feather-Degrading Anaerobic Thermophile

by Akzhigit Mashzhan, Aida Kistaubayeva, Rubén Javier-López, Akerke Bissenbay and Nils-Kåre Birkeland

Microorganisms 2024, 12(7), 1277; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms12071277 - 23 Jun 2024

Viewed by 395

Abstract

Caldanaerobacter subterraneus subsp. keratinolyticus subsp. nov. strain KAk was found in a geothermal hot spring located in Kazakhstan. Growth occurred at temperatures ranging from 50 to 80 °C, with approximately 70 °C as optimum. It also thrived in pH conditions ranging from 4.0 [...] Read more.

Caldanaerobacter subterraneus subsp. keratinolyticus subsp. nov. strain KAk was found in a geothermal hot spring located in Kazakhstan. Growth occurred at temperatures ranging from 50 to 80 °C, with approximately 70 °C as optimum. It also thrived in pH conditions ranging from 4.0 to 9.0, with the best growth occurring at 6.8. Under optimal conditions in a glucose-containing medium, the cells were predominantly observed singly, in pairs, or less frequently in chains, and did not form endospores. However, under conditions involving growth with merino wool or feathers, or under suboptimal conditions, the cells of strain KAk exhibited a notably elongated and thinner morphology, with lengths ranging from 5 to 8 µm, and spores were observed. The KAk strain exhibited efficient degradation of feather keratin and merino wool at temperatures ranging from 65 to 70 °C. Analysis of the 16S rRNA gene sequence placed KAk within the genus Caldanaerobacter, family Thermoanaerobacteraceae, with the highest similarity to C. subterraneus subsp. tengcongensis MB4^T (98.84% sequence identity). Furthermore, our analysis of the draft genome sequence indicated a genome size of 2.4 Mbp, accompanied by a G+C value of 37.6 mol%. This study elucidated the physiological and genomic characteristics of strain KAk, highlighting its keratinolytic capabilities and distinctiveness compared to other members of the genus Caldanaerobacter. Full article

(This article belongs to the Special Issue Latest Advances in the Microbial Degradation of Hazardous Organic Contaminants)

► Show Figures

Figure 1

20 pages, 7726 KiB

Open AccessReview

Impact of Plant‒Microbe Interactions with a Focus on Poorly Investigated Urban Ecosystems—A Review

by Pamela Monaco, Apollonia Baldoni, Gino Naclerio, Gabriella Stefania Scippa and Antonio Bucci

Microorganisms 2024, 12(7), 1276; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms12071276 - 23 Jun 2024

Viewed by 289

Abstract

The urbanization process, which began with the Industrial Revolution, has undergone a considerable increase over the past few decades. Urbanization strongly affects ecological processes, often deleteriously, because it is associated with a decrease in green spaces (areas of land covered by vegetation), loss [...] Read more.

The urbanization process, which began with the Industrial Revolution, has undergone a considerable increase over the past few decades. Urbanization strongly affects ecological processes, often deleteriously, because it is associated with a decrease in green spaces (areas of land covered by vegetation), loss of natural habitats, increased rates of species extinction, a greater prevalence of invasive and exotic species, and anthropogenic pollutant accumulation. In urban environments, green spaces play a key role by providing many ecological benefits and contributing to human psychophysical well-being. It is known that interactions between plants and microorganisms that occur in the rhizosphere are of paramount importance for plant health, soil fertility, and the correct functioning of plant ecosystems. The growing diffusion of DNA sequencing technologies and “omics” analyses has provided increasing information about the composition, structure, and function of the rhizomicrobiota. However, despite the considerable amount of data on rhizosphere communities and their interactions with plants in natural/rural contexts, current knowledge on microbial communities associated with plant roots in urban soils is still very scarce. The present review discusses both plant‒microbe dynamics and factors that drive the composition of the rhizomicrobiota in poorly investigated urban settings and the potential use of beneficial microbes as an innovative biological tool to face the challenges that anthropized environments and climate change impose. Unravelling urban biodiversity will contribute to green space management, preservation, and development and, ultimately, to public health and safety. Full article

(This article belongs to the Section Plant Microbe Interactions)

13 pages, 5415 KiB

Open AccessArticle

N-Terminal Sequences of Signal Peptides Assuming Critical Roles in Expression of Heterologous Proteins in Bacillus subtilis

by Meijuan Zhang, Jie Zhen, Jia Teng, Xingya Zhao, Xiaoping Fu, Hui Song, Yeni Zhang, Hongchen Zheng and Wenqin Bai

Microorganisms 2024, 12(7), 1275; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms12071275 - 23 Jun 2024

Viewed by 364

Abstract

The N-terminal sequences of proteins and their corresponding encoding sequences may play crucial roles in the heterologous expression. In this study, the secretory expression of alkaline pectin lyase APL in B. subtilis was investigated to explore the effects of the N-terminal 5–7 amino [...] Read more.

The N-terminal sequences of proteins and their corresponding encoding sequences may play crucial roles in the heterologous expression. In this study, the secretory expression of alkaline pectin lyase APL in B. subtilis was investigated to explore the effects of the N-terminal 5–7 amino acid sequences of different signal peptides on the protein expression and secretion. It was identified for the first time that the first five amino acid sequences of the N-terminal of the signal peptide (SP^-LipA) from Bacillus subtilis lipase A play an important role in promoting the expression of APL. Furthermore, it was revealed that SP^-LipA resulted in higher secretory expression compared to other signal peptides in this study primarily due to its encoding of N-terminal amino acids with relatively higher transcription levels and its efficient secretion capacity. Based on this foundation, the recombinant strain constructed in this work achieved a new record for the highest extracellular yields of APL in B. subtilis, reaching 12,295 U/mL, which was 1.9-times higher than that expressed in the recombinant Escherichia coli strain previously reported. The novel theories uncovered in this study are expected to play significant roles in enhancing the expression of foreign proteins both inside and outside of cells. Full article

(This article belongs to the Section Microbial Biotechnology)

► Show Figures

Figure 1

18 pages, 1404 KiB

Open AccessArticle

Exploring Pathogen Presence Prediction in Pastured Poultry Farms through Transformer-Based Models and Attention Mechanism Explainability

by Athish Ram Das, Nisha Pillai, Bindu Nanduri, Michael J. Rothrock, Jr. and Mahalingam Ramkumar

Microorganisms 2024, 12(7), 1274; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms12071274 - 23 Jun 2024

Viewed by 182

Abstract

In this study, we explore how transformer models, which are known for their attention mechanisms, can improve pathogen prediction in pastured poultry farming. By combining farm management practices with microbiome data, our model outperforms traditional prediction methods in terms of the F1 score—an [...] Read more.

In this study, we explore how transformer models, which are known for their attention mechanisms, can improve pathogen prediction in pastured poultry farming. By combining farm management practices with microbiome data, our model outperforms traditional prediction methods in terms of the F1 score—an evaluation metric for model performance—thus fulfilling an essential need in predictive microbiology. Additionally, the emphasis is on making our model’s predictions explainable. We introduce a novel approach for identifying feature importance using the model’s attention matrix and the PageRank algorithm, offering insights that enhance our comprehension of established techniques such as DeepLIFT. Our results showcase the efficacy of transformer models in pathogen prediction for food safety and mark a noteworthy contribution to the progress of explainable AI within the biomedical sciences. This study sheds light on the impact of effective farm management practices and highlights the importance of technological advancements in ensuring food safety. Full article

(This article belongs to the Special Issue Bioinformatics and Omic Data Analysis in Microbial Research)

20 pages, 2603 KiB

Open AccessArticle

Exploring the Microbial Mosaic: Insights into Composition, Diversity, and Environmental Drivers in the Pearl River Estuary Sediments

by Tal Zvi-Kedem, Maya Lalzar, Jing Sun, Jiying Li, Dan Tchernov and Dalit Meron

Microorganisms 2024, 12(7), 1273; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms12071273 - 23 Jun 2024

Viewed by 207

Abstract

River estuaries are dynamic and complex ecosystems influenced by various natural processes, including climatic fluctuations and anthropogenic activities. The Pearl River Estuary (PRE), one of the largest in China, receives significant land-based pollutants due to its proximity to densely populated areas and urban [...] Read more.

River estuaries are dynamic and complex ecosystems influenced by various natural processes, including climatic fluctuations and anthropogenic activities. The Pearl River Estuary (PRE), one of the largest in China, receives significant land-based pollutants due to its proximity to densely populated areas and urban development. This study aimed to characterize the composition, diversity, and distribution patterns of sediment microbial communities (bacteria, archaea, and eukaryotes) and investigated the connection with environmental parameters within the PRE and adjacent shelf. Physicochemical conditions, such as oxygen levels, nitrogen compounds, and carbon content, were analyzed. The study found that the microbial community structure was mainly influenced by site location and core depth, which explained approximately 67% of the variation in each kingdom. Sites and core depths varied in sediment properties such as organic matter content and redox conditions, leading to distinct microbial groups associated with specific chemical properties of the sediment, notably C/N ratio and NH4+ concentration. Despite these differences, certain dominant taxonomic groups were consistently present across all sites: Gammaproteobacteria in bacteria; Bathyarchaeia, Nitrososphaeria, and Thermoplasmata in archaea; and SAR in Eukaryota. The community diversity index was the highest in the bacteria kingdom, while the lowest values were observed at site P03 across the three kingdoms and were significantly different from all other sites. Overall, this study highlights the effect of depth, core depth, and chemical properties on sediment microbiota composition. The sensitivity and dynamism of the microbiota, along with the possibility of identifying specific markers for changes in environmental conditions, is valuable for managing and preserving the health of estuaries and coastal ecosystems. Full article

(This article belongs to the Special Issue Microbial Community Structure in Marine and Coastal Sediments)

Journal Menu

Journal Browser

Microorganisms, Volume 12, Issue 7 (July 2024) – 50 articles

Further Information

Guidelines

MDPI Initiatives

Follow MDPI