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Microorganisms, Volume 12, Issue 2 (February 2024) – 189 articles

Cover Story (view full-size image): Extracellular vesicles (EVs) are small membrane-enclosed structures that play a crucial role in facilitating intracellular communication via the transport of proteins, lipids, DNA, rRNA, and miRNAs. EVs have been exploited by a wide range of viruses in order to egress from the host cell and eventually evade the host immune response. Due to the cross-talk between pathways involved in EV biogenesis and the replication of a number of viruses, EVs can incorporate viral fragments, proteins, RNA or entire virions within themselves. Thus, the host immune system often remains unaware of the trafficking of these viral components. Owing to this intricate relationship between Evs and viruses, numerous studies have identified various EV-mediated viral infections and interrogated how Evs can alter the overall spread and longevity of viruses. View this paper
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16 pages, 2628 KiB  
Article
Bacillus amyloliquefaciens Probiotics Mix Supplementation in a Broiler Leaky Gut Model
by Darwin Horyanto, Yadav S. Bajagai, Advait Kayal, Juhani von Hellens, Xiaojing Chen, Thi Thu Hao Van, Anita Radovanović and Dragana Stanley
Microorganisms 2024, 12(2), 419; https://doi.org/10.3390/microorganisms12020419 - 19 Feb 2024
Viewed by 898
Abstract
The supplementation of antimicrobial growth promoters (AGPs) has been banned in many countries because of the emergence of antimicrobial-resistant pathogens in poultry products and the environment. Probiotics have been broadly studied and demonstrated as a promising AGP substitute. Our study is centred on [...] Read more.
The supplementation of antimicrobial growth promoters (AGPs) has been banned in many countries because of the emergence of antimicrobial-resistant pathogens in poultry products and the environment. Probiotics have been broadly studied and demonstrated as a promising AGP substitute. Our study is centred on the effects of a multi-strain Bacillus-based probiotic product on broiler production performance and gut microbial profile in a dexamethasone-induced leaky gut challenge. Two hundred and fifty-six broiler chicks were hatched and randomly assigned into four groups (wheat-soybean meal basal diet (BD) = non-supplemented control (C), BD supplemented with dexamethasone in week 4 (CD), BD containing a probiotic from day one (P), and BD containing a probiotic from day one and supplemented with dexamethasone during challenge week 4 (PD)). The production performance and caecal, gizzard, jejunal lumen and jejunal mucosa swab microbiota were studied by 16S rRNA gene sequencing. The Bacillus probiotic product significantly improved production performance and altered caecal gut microbiota (p ≤ 0.05), but no significant impact on microbiota was observed in other gut sections. Full article
(This article belongs to the Section Gut Microbiota)
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16 pages, 3028 KiB  
Article
Disinfection of Bacteria in Aerosols by Applying High Voltage to Stranded Wire Electrodes
by Takahisa Ueno, Konosuke Takada, Shohei Zaizen, Takashi Sakugawa, Junko Ninomiya and Takashi Furukawa
Microorganisms 2024, 12(2), 418; https://doi.org/10.3390/microorganisms12020418 - 19 Feb 2024
Viewed by 659
Abstract
The inactivation of airborne pathogenic microorganisms is crucial to attenuate the dissemination of infectious diseases induced by airborne pathogens. Conventional air disinfection methodologies, such as ultraviolet (UV) irradiation and ozone treatment, have demonstrated limited efficacy. Consequently, we investigated the potential of employing pulsed [...] Read more.
The inactivation of airborne pathogenic microorganisms is crucial to attenuate the dissemination of infectious diseases induced by airborne pathogens. Conventional air disinfection methodologies, such as ultraviolet (UV) irradiation and ozone treatment, have demonstrated limited efficacy. Consequently, we investigated the potential of employing pulsed voltages to effectively eradicate bacteria within aerosols. Our inquiry revealed that the bacterial disinfection rate increased proportionally with elevated applied voltage and frequency. For instance, when a pulsed voltage of 20 kV and a frequency of 500 Hz were applied, a substantial disinfection rate exceeding 6.0 logarithmic units was attained. Furthermore, with the utilization of the stranded wire anodes, the disinfection intensity could be augmented by up to 2.0 logarithmic units compared with the solid wire configuration. Through the utilization of a stranded wire electrode model, we scrutinized the electric field encompassing the electrode, revealing a non-uniform electric field with the stranded wire electrode. This observation indicated an amplified bacterial disinfection effect, aligning with our experimental outcomes. These findings significantly enhance our comprehension of efficacious approaches to electrically disinfecting airborne bacteria. Full article
(This article belongs to the Special Issue Disinfection and Sterilization of Microorganisms)
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14 pages, 1221 KiB  
Article
Analysis of Vaginal Microbiota Variations in the Third Trimester of Pregnancy and Their Correlation with Preterm Birth: A Case-Control Study
by Catalin Prodan-Barbulescu, Felix Bratosin, Roxana Folescu, Estera Boeriu, Zoran Laurentiu Popa, Cosmin Citu, Adrian Ratiu, Ovidiu Rosca and Adrian Cosmin Ilie
Microorganisms 2024, 12(2), 417; https://doi.org/10.3390/microorganisms12020417 - 19 Feb 2024
Viewed by 746
Abstract
This study conducted a detailed analysis of the vaginal microbiota in pregnant women to explore its correlation with preterm birth (PTB) outcomes. The primary objective was to identify microbial variations associated with increased PTB risk. Secondary objectives included investigating how changes in microbial [...] Read more.
This study conducted a detailed analysis of the vaginal microbiota in pregnant women to explore its correlation with preterm birth (PTB) outcomes. The primary objective was to identify microbial variations associated with increased PTB risk. Secondary objectives included investigating how changes in microbial composition relate to the local immune environment and PTB. Utilizing a retrospective case–control design, the study involved pregnant women with liveborn infants between 2019 and 2023. In total, 89 women who delivered preterm and 106 term deliveries were included. Data collection focused on third-trimester vaginal cultures. Statistically significant differences were observed between the preterm and full-term groups in several areas. The median white blood cell count (10.2 × 103/mm3 vs. 7.6 × 103/mm3, p = 0.009) and neutrophil count (7.2 × 103/mm3 vs. 5.1 × 103/mm3, p < 0.001) were higher in the preterm group. Vaginal pH was also elevated in preterm births (5.6 vs. 4.4, p < 0.001), with a higher prevalence of bacterial vaginosis (29.2% vs. 12.3%, p = 0.001) as indicated by the Nugent Score. The study noted a significant association of PTB with the presence of Candida spp. (OR = 1.84, p = 0.018), Gardnerella vaginalis (OR = 2.29, p = 0.003), Mycoplasma hominis (OR = 1.97, p = 0.007), and Ureaplasma urealyticum (OR = 2.43, p = 0.001). Conversely, a reduction in Lactobacillus spp. correlated with a decreased PTB risk (OR = 0.46, p = 0.001). The study provides compelling evidence that specific vaginal microbiota components, particularly certain pathogenic bacteria and an altered Lactobacillus profile, are significantly associated with PTB risk. These findings highlight the potential of targeting microbial factors in strategies aimed at reducing PTB rates. Further research is necessary to fully understand the complex interplay between microbial dynamics, host immunity, and PTB outcomes. Full article
(This article belongs to the Special Issue Vaginal Microbiome in Women's Health)
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18 pages, 10092 KiB  
Article
Genetic and Evolutionary Analysis of Porcine Deltacoronavirus in Guangxi Province, Southern China, from 2020 to 2023
by Biao Li, Yeheng Gao, Yan Ma, Kaichuang Shi, Yuwen Shi, Shuping Feng, Yanwen Yin, Feng Long and Wenchao Sun
Microorganisms 2024, 12(2), 416; https://doi.org/10.3390/microorganisms12020416 - 19 Feb 2024
Viewed by 590
Abstract
Porcine deltacoronavirus (PDCoV) has shown large-scale global spread since its discovery in Hong Kong in 2012. In this study, a total of 4897 diarrheal fecal samples were collected from the Guangxi province of China from 2020 to 2023 and tested using RT-qPCR. In [...] Read more.
Porcine deltacoronavirus (PDCoV) has shown large-scale global spread since its discovery in Hong Kong in 2012. In this study, a total of 4897 diarrheal fecal samples were collected from the Guangxi province of China from 2020 to 2023 and tested using RT-qPCR. In total, 362 (362/4897, 7.39%) of samples were positive for PDCoV. The S, M, and N gene sequences were obtained from 34 positive samples after amplification and sequencing. These PDCoV gene sequences, together with other PDCoV S gene reference sequences from China and other countries, were analyzed. Phylogenetic analysis revealed that the Chinese PDCoV strains have diverged in recent years. Bayesian analysis revealed that the new China 1.3 lineage began to diverge in 2012. Comparing the amino acids of the China 1.3 lineage with those of other lineages, the China 1.3 lineage showed variations of mutations, deletions, and insertions, and some variations demonstrated the same as or similar to those of the China 1.2 lineage. In addition, recombination analysis revealed interlineage recombination in CHGX-MT505459-2019 and CHGX-MT505449-2017 strains from Guangxi province. In summary, the results provide new information on the prevalence and evolution of PDCoV in Guangxi province in southern China, which will facilitate better comprehension and prevention of PDCoV. Full article
(This article belongs to the Special Issue The Pathogenic Epidemiology of Important Swine Diseases)
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17 pages, 19177 KiB  
Article
Antibacterial Mechanisms and Antivirulence Activities of Oridonin against Pathogenic Aeromonas hydrophila AS 1.1801
by Lunji Wang, Huijuan Li, Jinhao Chen, Yi Wang, Yuqing Gu and Min Jiu
Microorganisms 2024, 12(2), 415; https://doi.org/10.3390/microorganisms12020415 - 19 Feb 2024
Viewed by 835
Abstract
Aeromonas hydrophila, a Gram-negative bacterium widely found in freshwater environments, acts as a common conditional pathogen affecting humans, livestock, and aquatic animals. In this study, the impact of oridonin, an ent-kaurane diterpenoid compound derived from Rabdosia rubescens, on the virulence [...] Read more.
Aeromonas hydrophila, a Gram-negative bacterium widely found in freshwater environments, acts as a common conditional pathogen affecting humans, livestock, and aquatic animals. In this study, the impact of oridonin, an ent-kaurane diterpenoid compound derived from Rabdosia rubescens, on the virulence factors of A. hydrophila AS 1.1801 and its antibacterial mechanism was elucidated. The minimum inhibitory concentration (MIC) of oridonin against A. hydrophila AS 1.1801 was 100 μg/mL. Oridonin at inhibitory concentrations could significantly increase the electrical conductivity in the supernatant and escalate nucleic acid leakage (p < 0.01). This effect was concomitant with observed distortions in bacterial cells, the formation of cytoplasmic cavities, cellular damage, and pronounced inhibition of protein and nucleic acid synthesis. Additionally, oridonin at inhibitory levels exhibited a noteworthy suppressive impact on A. hydrophila AS 1.1801 across biofilm formation, motility, hemolytic activity, lipase activity, and protease activity (p < 0.05), demonstrating a dose-dependent enhancement. qRT-PCR analysis showed that the gene expression of luxR, qseB and omp were significantly downregulated after oridonin treatment in A. hydrophila AS 1.1801 (p < 0.05). Our results indicated that oridonin possessed significant antibacterial and anti-virulence effects on A. hydrophila AS 1.1801. Full article
(This article belongs to the Special Issue Advances in Novel Antibacterial Agents)
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12 pages, 305 KiB  
Article
Antimicrobial Resistance Profile of Group B Streptococci Colonization in a Sample Population of Pregnant Women from Romania
by Aida Petca, Florica Șandru, Silvius Negoiță, Mihai Cristian Dumitrașcu, Daiana Anne-Marie Dimcea, Tiberiu Nedelcu, Claudia Mehedințu, Marinela Magdalena Filipov and Răzvan-Cosmin Petca
Microorganisms 2024, 12(2), 414; https://doi.org/10.3390/microorganisms12020414 - 19 Feb 2024
Viewed by 762
Abstract
Group B Streptococcus (GBS) represents one of the leading causes of life-threatening invasive disease in pregnant women and neonates. Rates of GBS colonization vary by region, but studies on maternal GBS status are limited in Romania. This study aims to identify the prevalence [...] Read more.
Group B Streptococcus (GBS) represents one of the leading causes of life-threatening invasive disease in pregnant women and neonates. Rates of GBS colonization vary by region, but studies on maternal GBS status are limited in Romania. This study aims to identify the prevalence of colonization with GBS and whether the obstetrical characteristics are statistically associated with the study group’s antimicrobial susceptibility patterns of tested GBS strains. This observational study was conducted between 1 May and 31 December 2021 at The Department of Obstetrics and Gynecology at Elias University Emergency Hospital (EUEH) in Bucharest, Romania. A total of 152 samples were positive for GBS and included in the study according to the inclusion criteria. As a result, the prevalence of colonized patients with GBS was 17.3%. GBS isolated in this population had the highest resistance to erythromycin (n = 38; 25%), followed by clindamycin (n = 36; 23.7%). Regarding the susceptibility patterns of tested strains to penicillin, the 152 susceptible strains had MIC breakpoints less than 0.06 μg/μL. The susceptibility patterns of tested strains to linezolid indicated three resistant strains with low levels of resistance (MICs ranging between 2 and 3 μg/μL). Multidrug resistance (at least three antibiotic classes) was not observed. In conclusion, although GBS naturally displays sensitivity to penicillin, the exact bacterial susceptibility testing should be performed in all cases where second-line therapy is taken into consideration for treatment. We acknowledge the need for future actions to limit multidrug-resistant bacteria. Full article
(This article belongs to the Special Issue State-of-the-Art Parasitic and Bacterial Infections in Romania)
20 pages, 3994 KiB  
Article
Targeted Isolation of Antibiofilm Compounds from Halophytic Endophyte Bacillus velezensis 7NPB-3B Using LC-HR-MS-Based Metabolomics
by Sanju Singh, Elizabeth Nwagwu, Louise Young, Pankaj Kumar, Pramod B. Shinde and RuAngelie Edrada-Ebel
Microorganisms 2024, 12(2), 413; https://doi.org/10.3390/microorganisms12020413 - 19 Feb 2024
Viewed by 893
Abstract
The discovery of new natural products has become more challenging because of the re-isolation of compounds and the lack of new sources. Microbes dwelling in extreme conditions of high salinity and temperature are huge prospects for interesting natural metabolites. In this study, the [...] Read more.
The discovery of new natural products has become more challenging because of the re-isolation of compounds and the lack of new sources. Microbes dwelling in extreme conditions of high salinity and temperature are huge prospects for interesting natural metabolites. In this study, the endophytic bacteria Bacillus velezensis 7NPB-3B isolated from the halophyte Salicornia brachiata was screened for its biofilm inhibition against methicillin-resistant Staphylococcus aureus (MRSA). The fractionation of the crude extract was guided by bioassay and LC-HRMS-based metabolomics using multivariate analysis. The 37 fractions obtained by high-throughput chromatography were dereplicated using an in-house MS-Excel macro coupled with the Dictionary of Natural Products database. Successive bioactivity-guided separation yielded one novel compound (1), a diketopiperazine (m/z 469.258 [M − H]) with an attached saturated decanoic acid chain, and four known compounds (25). The compounds were identified based on 1D- and 2D-NMR and mass spectrometry. Compounds 1 and 5 exhibited excellent biofilm inhibition properties of >90% against the MRSA pathogen at minimum inhibition concentrations of 25 and 35 µg/mL, respectively. The investigation resulted in the isolation of a novel diketopiperazine from a bacterial endophyte of an untapped plant using an omics approach. Full article
(This article belongs to the Section Antimicrobial Agents and Resistance)
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13 pages, 3215 KiB  
Article
Identification of Genes Associated with Resistance to Persulcatusin, a Tick Defensin from Ixodes persulcatus
by So Shimoda, Junya Ito, Tasuke Ando, Ryuta Tobe, Kiyotaka Nakagawa and Hiroshi Yoneyama
Microorganisms 2024, 12(2), 412; https://doi.org/10.3390/microorganisms12020412 - 19 Feb 2024
Viewed by 814
Abstract
Antimicrobial peptides (AMPs) are present in a wide range of plants, animals, and microorganisms. Since AMPs are characterized by their effectiveness against emergent antibiotic-resistant bacteria, they are attracting attention as next-generation antimicrobial compounds that could solve the problem of drug-resistant bacteria. Persulcatusin (IP), [...] Read more.
Antimicrobial peptides (AMPs) are present in a wide range of plants, animals, and microorganisms. Since AMPs are characterized by their effectiveness against emergent antibiotic-resistant bacteria, they are attracting attention as next-generation antimicrobial compounds that could solve the problem of drug-resistant bacteria. Persulcatusin (IP), an antibacterial peptide derived from the hard tick Ixodes persulcatus, shows high antibacterial activity against various Gram- positive bacteria as well as multidrug-resistant bacteria. However, reports on the antibacterial action and resistance mechanisms of IP are scarce. In this study, we spontaneously generated mutants showing increased a minimum inhibitory concentration (MIC) of IP and analyzed their cross-resistance to other AMPs and antibiotics. We also used fluorescent probes to investigate the target of IP activity by evaluating IP-induced damage to the bacterial cytoplasmic membrane. Our findings suggest that the antimicrobial activity of IP on bacterial cytoplasmic membranes occurs via a mechanism of action different from that of known AMPs. Furthermore, we screened for mutants with high susceptibility to IP using a transposon mutant library and identified 16 genes involved in IP resistance. Our results indicate that IP, like other AMPs, depolarizes the bacterial cytoplasmic membrane, but it may also alter membrane structure and inhibit cell-wall synthesis. Full article
(This article belongs to the Special Issue Antimicrobial Peptides: Therapeutic Potentials 2.0)
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23 pages, 586 KiB  
Review
Probiotics’ Effects in the Treatment of Anxiety and Depression: A Comprehensive Review of 2014–2023 Clinical Trials
by Ermis Merkouris, Theodora Mavroudi, Daniil Miliotas, Dimitrios Tsiptsios, Aspasia Serdari, Foteini Christidi, Triantafyllos K. Doskas, Christoph Mueller and Konstantinos Tsamakis
Microorganisms 2024, 12(2), 411; https://doi.org/10.3390/microorganisms12020411 - 19 Feb 2024
Viewed by 2404
Abstract
Changes in the gut microbiome can affect cognitive and psychological functions via the microbiota–gut–brain (MGB) axis. Probiotic supplements are thought to have largely positive effects on mental health when taken in sufficient amounts; however, despite extensive research having been conducted, there is a [...] Read more.
Changes in the gut microbiome can affect cognitive and psychological functions via the microbiota–gut–brain (MGB) axis. Probiotic supplements are thought to have largely positive effects on mental health when taken in sufficient amounts; however, despite extensive research having been conducted, there is a lack of consistent findings on the effects of probiotics on anxiety and depression and the associated microbiome alterations. The aim of our study is to systematically review the most recent literature of the last 10 years in order to clarify whether probiotics could actually improve depression and anxiety symptoms. Our results indicate that the majority of the most recent literature suggests a beneficial role of probiotics in the treatment of depression and anxiety, despite the existence of a substantial number of less positive findings. Given probiotics’ potential to offer novel, personalized treatment options for mood disorders, further, better targeted research in psychiatric populations is needed to address concerns about the exact mechanisms of probiotics, dosing, timing of treatment, and possible differences in outcomes depending on the severity of anxiety and depression. Full article
(This article belongs to the Special Issue Probiotics: The Current State of Scientific Knowledge)
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11 pages, 293 KiB  
Review
Assessment of Strategies for Preserving Swine Viral RNA Targets in Diagnostic Specimens
by Berenice Munguía-Ramírez, Luis Giménez-Lirola and Jeffrey Zimmerman
Microorganisms 2024, 12(2), 410; https://doi.org/10.3390/microorganisms12020410 - 18 Feb 2024
Viewed by 644
Abstract
Successful downstream molecular analyses of viral ribonucleic acid (RNA) in diagnostic laboratories, e.g., reverse transcription-quantitative polymerase chain reaction (RT-qPCR) or next-generation sequencing, are dependent on the quality of the RNA in the specimen. In swine specimens, preserving the integrity of RNA requires proper [...] Read more.
Successful downstream molecular analyses of viral ribonucleic acid (RNA) in diagnostic laboratories, e.g., reverse transcription-quantitative polymerase chain reaction (RT-qPCR) or next-generation sequencing, are dependent on the quality of the RNA in the specimen. In swine specimens, preserving the integrity of RNA requires proper sample handling at the time the sample is collected on the farm, during transport, and in the laboratory until RNA extraction is performed. Options for proper handling are limited to maintaining the cold chain or using commercial specimen storage matrices. Herein, we reviewed the refereed literature for evidence that commercial specimen storage matrices can play a role in preserving swine viral RNA in clinical specimens. Refereed publications were included if they compared RNA detection in matrix-treated vs. untreated samples. At present, the small number of refereed studies and the inconsistency in reported results preclude the routine use of commercial specimen storage matrices. For example, specimen storage matrices may be useful under specific circumstances, e.g., where it is mandatory to render the virus inactive. In a broader view, statistically sound side-by-side comparisons between specimens, viral RNA targets, and storage conditions are needed to establish if, when, and how commercial specimen storage matrices could be used in diagnostic medicine. Full article
(This article belongs to the Special Issue Diagnosis and Treatment of Mammalian Infectious Diseases)
15 pages, 2829 KiB  
Article
Possible Role of CHAD Proteins in Copper Resistance
by Gabriela González-Madrid, Claudio A. Navarro, José Acevedo-López, Luis H. Orellana and Carlos A. Jerez
Microorganisms 2024, 12(2), 409; https://doi.org/10.3390/microorganisms12020409 - 18 Feb 2024
Viewed by 639
Abstract
Conserved Histidine Alpha-helical Domain (CHAD) proteins attached to the surface of polyphosphate (PolyP) have been studied in some bacteria and one archaeon. However, the activity of CHAD proteins is unknown beyond their interaction with PolyP granules. By using bioinformatic analysis, we report that [...] Read more.
Conserved Histidine Alpha-helical Domain (CHAD) proteins attached to the surface of polyphosphate (PolyP) have been studied in some bacteria and one archaeon. However, the activity of CHAD proteins is unknown beyond their interaction with PolyP granules. By using bioinformatic analysis, we report that several species of the biomining acidophilic bacteria contain orthologs of CHAD proteins with high sequence identity. Furthermore, the gene coding for the CHAD protein is in the same genetic context of the enzyme polyphosphate kinase (PPK), which is in charge of PolyP synthesis. Particularly, the group of ppk and CHAD genes is highly conserved. Metallosphaera sedula and other acidophilic archaea used in biomining also contain CHAD proteins. These archaea show high levels of identity in genes coding for a cluster having the same organization. Amongst these genes are chad and ppx. In general, both biomining bacteria and archaea contain high PolyP levels and are highly resistant to heavy metals. Therefore, the presence of this conserved genetic organization suggests a high relevance for their metabolism. It has been formerly reported that a crystallized CHAD protein contains a copper-binding site. Based on this previous knowledge, in the present report, it was determined that all analyzed CHAD proteins are very conserved at their structural level. In addition, it was found that the lack of YgiF, an Escherichia coli CHAD-containing protein, decreases copper resistance in this bacterium. This phenotype was not only complemented by transforming E. coli with YgiF but also by expressing CHAD from Acidithiobacillus ferrooxidans in it. Interestingly, the strains in which the possible copper-binding sites were mutated were also more metal sensitive. Based on these results, we propose that CHAD proteins are involved in copper resistance in microorganisms. These findings are very interesting and may eventually improve biomining operations in the future. Full article
(This article belongs to the Section Microbial Biotechnology)
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11 pages, 2813 KiB  
Article
Pseudidiomarina fusca sp. nov., Isolated from the Surface Seawater of the Western Pacific Ocean
by Yaru Wang, Xiaolei Wang, Xueyu Gao, Jingjing He, Xiaoyu Yang, Yunxiao Zhang, Xiaohua Zhang and Xiaochong Shi
Microorganisms 2024, 12(2), 408; https://doi.org/10.3390/microorganisms12020408 - 18 Feb 2024
Viewed by 651
Abstract
The Gram-negative marine bacterium GXY010T, which has been isolated from the surface seawater of the western Pacific Ocean, is aerobic, non-motile and non-flagellated. Strain GXY010T exhibits growth across a temperature range of 10–42 °C (optimal at 37 °C), pH tolerance [...] Read more.
The Gram-negative marine bacterium GXY010T, which has been isolated from the surface seawater of the western Pacific Ocean, is aerobic, non-motile and non-flagellated. Strain GXY010T exhibits growth across a temperature range of 10–42 °C (optimal at 37 °C), pH tolerance from 7.0 to 11.0 (optimal at 7.5) and a NaCl concentration ranging from 1.0 to 15.0% (w/v, optimal at 5.0%). Ubiquinone-8 (Q-8) was the predominant isoprenoid quinone in strain GXY010T. The dominant fatty acids (>10%) of strain GXY010T were iso-C15:0 (14.65%), summed feature 9 (iso-C17:1 ω9c and/or 10-methyl C16:0) (12.41%), iso-C17:0 (10.85%) and summed feature 3 (C16:1 ω7c and/or C16:1 ω6c) (10.41%). Phosphatidylethanolamine (PE), phosphatidylglycerol (PG), diphosphatidylglycerol (DPG), unidentifiable glycolipid (GL) and four non-identifiable aminolipids (AL1-AL4) were the predominant polar lipids of strain GXY010T. The genomic DNA G+C content was identified as a result of 48.0% for strain GXY010T. The strain GXY010T genome consisted of 2,766,857 bp, with 2664 Open Reading Frames (ORFs), including 2586 Coding sequences (CDSs) and 78 RNAs. Strain GXY010T showed Average Nucleotide Identity (ANI) values of 73.4% and 70.6% and DNA–DNA hybridization (DDH) values of 19.2% and 14.5% with reference species Pseudidiomarina tainanensis MCCC 1A02633T (=PIN1T) and Pseudidiomarina taiwanensis MCCC 1A00163T (=PIT1T). From the results of the polyphasic analysis, a newly named species, Pseudidiomarina fusca sp. nov. within the genus Pseudidiomarina, was proposed. The type strain of Pseudidiomarina fusca is GXY010T (=JCM 35760T = MCCC M28199T = KCTC 92693T). Full article
(This article belongs to the Special Issue Marine Microorganisms and Ecology)
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14 pages, 1853 KiB  
Communication
Comparative Study of Mycobacterium bovis and Mycobacterium avium subsp. paratuberculosis In Vitro Infection in Bovine Bone Marrow Derived Macrophages: Preliminary Results
by Benedetta Amato, Dorotea Ippolito, Maria Vitale, Rosa Alduina, Paola Galluzzo, Elisabetta Gerace, Flavia Pruiti Ciarello, Michele Fiasconaro, Vincenza Cannella and Vincenzo Di Marco Lo Presti
Microorganisms 2024, 12(2), 407; https://doi.org/10.3390/microorganisms12020407 - 17 Feb 2024
Viewed by 741
Abstract
Bovine tuberculosis and paratuberculosis are endemic in many areas worldwide. This work aims to study cytokines production and gene expression profiles of bovine macrophages infected with Mycobacterium bovis and Mycobacterium paratuberculosis subsp. avium (MAP) strains to identify potential diagnostic biomarkers. Bovine bone marrow [...] Read more.
Bovine tuberculosis and paratuberculosis are endemic in many areas worldwide. This work aims to study cytokines production and gene expression profiles of bovine macrophages infected with Mycobacterium bovis and Mycobacterium paratuberculosis subsp. avium (MAP) strains to identify potential diagnostic biomarkers. Bovine bone marrow stem cells were differentiated into macrophages and subsequently infected in vitro with different spoligotypes of M. bovis and MAP field strains (as single infections and coinfections), using different multiplicity of infection. Supernatant and cell pellets were collected 24 h, 48 h, and one week post-infection. Preliminarily, gene expression on cell pellets of IL-1β, IL-2, INFγ, IL-6, IL-10, IL-12, and TNFα was assessed by qRT-PCR one week p.i. Subsequently, IL-1β and IL-6 were measured by ELISA and qRT-PCR to investigated their production retrospectively 24 h and 48 h p.i. A variability in macrophages response related to the concentration of mycobacteria, the coinfection with MAP, and M. bovis spoligotypes was identified. An early and constant IL-6 increase was observed in the M. bovis infection. A lower increase in IL-1β was also detected at the highest concentration of the two M. bovis spoligotypes one week post-infection. IL-6 and IL-1 β production was reduced and differently expressed in the MAP infection. IL-6 appeared to be the earliest cytokines produced by bovine macrophages infected with M. bovis. Full article
(This article belongs to the Section Veterinary Microbiology)
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15 pages, 345 KiB  
Article
In Vitro Interaction between Mycoplasma agalactiae and Small Ruminants’ Endogenous Bacterial Strains of Enterococcus spp. and Coagulase-Negative Staphylococcus
by Marion Toquet, Esther Bataller, Raquel Toledo-Perona, Jesús Gomis, Antonio Contreras, Antonio Sánchez, Estrella Jiménez-Trigos and Ángel Gómez-Martín
Microorganisms 2024, 12(2), 406; https://doi.org/10.3390/microorganisms12020406 - 17 Feb 2024
Viewed by 587
Abstract
Recently, an antimicrobial effect on Mycoplasma agalactiae (Ma), the main etiological agent of contagious agalactia (CA), was reported in vitro with strains of Enterococcus spp. from ovine and caprine milk. The aim of this work was to evaluate the interaction of Ma with [...] Read more.
Recently, an antimicrobial effect on Mycoplasma agalactiae (Ma), the main etiological agent of contagious agalactia (CA), was reported in vitro with strains of Enterococcus spp. from ovine and caprine milk. The aim of this work was to evaluate the interaction of Ma with the same Enterococcus spp. isolated from other anatomical locations (vagina) and other bacterial populations present in milk, such as coagulase-negative staphylococci (CNS). The vaginal Enterococcus strains and the raw milk CNS were isolated from sheep and goats. Experimental in vitro conditions were prepared to assess the growth of Ma with and without the presence of these strains. The selected vaginal strains were identified as Enterococcus (E.) hirae and E. mundtii, and the strains of CNS were identified as Staphylococcus petrasii. Different interactions of Ma with ovine and caprine wild vaginal strains of Enterococcus and dairy strains of CNS are described for the first time: Ma can grow exponentially during 15 h with the selected strains, although with certain strains, its optimal growth can be negatively affected (p < 0.05). The colonization and/or excretion of Ma could, therefore, be influenced by certain endogenous bacterial strains. Our results increase the knowledge about possible bacterial ecology dynamics surrounding CA. Full article
(This article belongs to the Section Veterinary Microbiology)
19 pages, 9010 KiB  
Article
Fungal-Bacterial Combinations in Plant Health under Stress: Physiological and Biochemical Characteristics of the Filamentous Fungus Serendipita indica and the Actinobacterium Zhihengliuella sp. ISTPL4 under In Vitro Arsenic Stress
by Neha Sharma, Monika Koul, Naveen Chandra Joshi, Laurent Dufossé and Arti Mishra
Microorganisms 2024, 12(2), 405; https://doi.org/10.3390/microorganisms12020405 - 17 Feb 2024
Viewed by 969
Abstract
Fungal-bacterial combinations have a significant role in increasing and improving plant health under various stress conditions. Metabolites secreted by fungi and bacteria play an important role in this process. Our study emphasizes the significance of secondary metabolites secreted by the fungus Serendipita indica [...] Read more.
Fungal-bacterial combinations have a significant role in increasing and improving plant health under various stress conditions. Metabolites secreted by fungi and bacteria play an important role in this process. Our study emphasizes the significance of secondary metabolites secreted by the fungus Serendipita indica alone and by an actinobacterium Zhihengliuella sp. ISTPL4 under normal growth conditions and arsenic (As) stress condition. Here, we evaluated the arsenic tolerance ability of S. indica alone and in combination with Z. sp. ISTPL4 under in vitro conditions. The growth of S. indica and Z. sp. ISTPL4 was measured in varying concentrations of arsenic and the effect of arsenic on spore size and morphology of S. indica was determined using confocal microscopy and scanning electron microscopy. The metabolomics study indicated that S. indica alone in normal growth conditions and under As stress released pentadecanoic acid, glycerol tricaprylate, L-proline and cyclo(L-prolyl-L-valine). Similarly, d-Ribose, 2-deoxy-bis(thioheptyl)-dithioacetal were secreted by a combination of S. indica and Z. sp. ISTPL4. Confocal studies revealed that spore size of S. indica decreased by 18% at 1.9 mM and by 15% when in combination with Z. sp. ISTPL4 at a 2.4 mM concentration of As. Arsenic above this concentration resulted in spore degeneration and hyphae fragmentation. Scanning electron microscopy (SEM) results indicated an increased spore size of S. indica in the presence of Z. sp. ISTPL4 (18 ± 0.75 µm) compared to S. indica alone (14 ± 0.24 µm) under normal growth conditions. Our study concluded that the suggested combination of microbial consortium can be used to increase sustainable agriculture by combating biotic as well as abiotic stress. This is because the metabolites released by the microbial combination display antifungal and antibacterial properties. The metabolites, besides evading stress, also confer other survival strategies. Therefore, the choice of consortia and combination partners is important and can help in developing strategies for coping with As stress. Full article
(This article belongs to the Section Microbial Biotechnology)
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19 pages, 1389 KiB  
Article
Select Cover Crop Residue and Soil Microbiomes Contribute to Suppression of Fusarium Root and Crown Rot in Barley and Soybean
by Harini S. Aiyer, Andrew McKenzie-Gopsill, Aaron Mills and Adam John Foster
Microorganisms 2024, 12(2), 404; https://doi.org/10.3390/microorganisms12020404 - 17 Feb 2024
Viewed by 704
Abstract
Fusarium root and crown rot (FRCR) negatively impact several economically important plant species. Cover crops host different soil and residue microbiomes, thereby potentially influencing pathogen load and disease severity. The carryover effect of cover crops on FRCR in barley and soybean was investigated. [...] Read more.
Fusarium root and crown rot (FRCR) negatively impact several economically important plant species. Cover crops host different soil and residue microbiomes, thereby potentially influencing pathogen load and disease severity. The carryover effect of cover crops on FRCR in barley and soybean was investigated. Field trials were conducted in Prince Edward Island, Canada. Two cover crops from each plant group, including forbs, brassicas, legumes, and grasses, were grown in a randomized complete block design with barley and soybean planted in split plots the following year. Barley and soybean roots were assessed for FRCR through visual disease rating and Fusarium spp. were isolated from diseased tissue. Fungal and bacterial communities in cover crop residues were quantified using amplicon sequencing. The disease-suppressive effects of soil were tested in greenhouse studies. The results indicated that sorghum-sudangrass-associated microbiomes suppress Fusarium spp., leading to reduced FRCR in both barley and soybean. The oilseed radish microbiome had the opposite effect, consequently increasing FRCR incidence in barley and soybean. The results from this study indicate that cover crop residue and the associated soil microbiome influence the incidence and severity of FRCR in subsequent crops. This information can be used to determine cover cropping strategies in barley and soybean production systems. Full article
(This article belongs to the Special Issue The Effect of Soil Microbes on Plant Growth and Crop Protection)
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13 pages, 2364 KiB  
Article
Extraction Methods Determine the Quality of Soil Microbiota Acquisition
by Zhuoxin Liu, Chi Zhang, Jiejia Ma, Qianze Peng, Xiaohua Du, Shu’e Sun, Ju’e Cheng, Weiye Peng, Lijie Chen, Zepei Gu, Weixing Zhang, Pin Su and Deyong Zhang
Microorganisms 2024, 12(2), 403; https://doi.org/10.3390/microorganisms12020403 - 17 Feb 2024
Viewed by 569
Abstract
The soil microbiome plays a key role in plant health. Native soil microbiome inoculation, metagenomic profiling, and high-throughput cultivation require efficient microbe extraction. Sonication and oscillation are the most common methods used to extract soil microbiomes. However, the extraction efficiency of these methods [...] Read more.
The soil microbiome plays a key role in plant health. Native soil microbiome inoculation, metagenomic profiling, and high-throughput cultivation require efficient microbe extraction. Sonication and oscillation are the most common methods used to extract soil microbiomes. However, the extraction efficiency of these methods has not been investigated in full. In this study, we compared the culturable microbe numbers, community structures, and alpha diversities among the different methods, including sonication, oscillation, and centrifugation, and their processing times. The study results showed that sonication significantly increases the culturable colony number compared with oscillation and centrifugation. Furthermore, the sonication strategy was found to be the main factor influencing extraction efficiency, but increased sonication time can aid in recovery from this impact. Finally, the extraction processing times were found to have a significant negative relationship with α-diversity among the extracted microbiota. In conclusion, sonication is the main factor for enriching in situ microbiota, and increased extraction time significantly decreases the α-diversity of the extracted microbiota. The results of this study provide insights into the isolation and utilization of different microorganism sources. Full article
(This article belongs to the Special Issue Applied Microbiome Science and Technology)
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20 pages, 3401 KiB  
Article
The Effects of Silver Nanoparticles (AgNPs) on Thermophilic Bacteria: Antibacterial, Morphological, Physiological and Biochemical Investigations
by Israt Jahan, Fatma Matpan Bekler, Ahmed Tunç and Kemal Güven
Microorganisms 2024, 12(2), 402; https://doi.org/10.3390/microorganisms12020402 - 17 Feb 2024
Viewed by 821
Abstract
Since thermophilic microorganisms are valuable sources of thermostable enzymes, it is essential to recognize the potential toxicity of silver nanoparticles used in diverse industrial sectors. Thermophilic bacteria Geobacillus vulcani 2Cx, Bacillus licheniformis 3CA, Paenibacillus macerans 3CA1, Anoxybacillus ayderensis FMB1, and Bacillus paralicheniformis FMB2-1 [...] Read more.
Since thermophilic microorganisms are valuable sources of thermostable enzymes, it is essential to recognize the potential toxicity of silver nanoparticles used in diverse industrial sectors. Thermophilic bacteria Geobacillus vulcani 2Cx, Bacillus licheniformis 3CA, Paenibacillus macerans 3CA1, Anoxybacillus ayderensis FMB1, and Bacillus paralicheniformis FMB2-1 were selected, and their MIC and MBC values were assessed by treatment with AgNPs in a range of 62.5–1500 μg mL−1. The growth inhibition curves showed that the G. vulcani 2Cx, and B. paralicheniformis FMB2-1 strains were more sensitive to AgNPs, demonstrating a reduction in population by 71.1% and 31.7% at 62.5 μg mL−1 and by 82.9% and 72.8% at 250 μg mL−1, respectively. TEM and FT-IR analysis revealed that AgNPs caused structural damage, cytoplasmic leakage, and disruption of cellular integrity. Furthermore, cell viability showed a significant decrease alongside an increase in superoxide radical (SOR; O2) production. β-galactosidase biosynthesis decreased to 28.8% level at 500 μg mL−1 AgNPs for G. vulcani 2Cx, 32.2% at 250 μg mL−1 for A. ayderensis FMB1, and 38.8% only at 62.5 μg mL−1, but it was completely inhibited at 500 μg mL−1 for B. licheniformis 3CA. Moreover, B. paralicheniformis FMB2-1 showed a significant decrease to 11.2% at 125 μg mL−1. This study is the first to reveal the toxic effects of AgNPs on thermophilic bacteria. Full article
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15 pages, 1264 KiB  
Article
Serotype Distribution and Antimicrobial Susceptibility Pattern of Streptococcus pneumoniae in COVID-19 Pandemic Era in Brazil
by Samanta C. G. Almeida, Ana Paula S. de Lemos, Ana Luiza Bierrenbach, José Cássio de Moraes and Maria Cristina de Cunto Brandileone
Microorganisms 2024, 12(2), 401; https://doi.org/10.3390/microorganisms12020401 - 17 Feb 2024
Viewed by 722
Abstract
Despite the introduction of the pneumococcal vaccine, Streptococcus pneumoniae remains a cause of invasive diseases in Brazil. This study provides the distribution of serotypes and antimicrobial susceptibility patterns for pneumococcal isolates before and during the years of the COVID-19 pandemic in two age [...] Read more.
Despite the introduction of the pneumococcal vaccine, Streptococcus pneumoniae remains a cause of invasive diseases in Brazil. This study provides the distribution of serotypes and antimicrobial susceptibility patterns for pneumococcal isolates before and during the years of the COVID-19 pandemic in two age groups, <5 and ≥50 years. This is a national laboratory-based surveillance study that uses data from the Brazilian national laboratory for invasive S. pneumoniae from the pre-COVID-19 (January 2016 to January 2020) and COVID-19 (February 2020 to May 2022) periods. Antimicrobial resistance was evaluated by disk diffusion and minimum inhibitory concentration. The year 2020 was marked by a 44.6% reduction in isolates received and was followed by an upward trend from 2021 onwards, which became evident in 2022. No differences were observed in serotypes distribution between the studied periods. The COVID-19 period was marked by the high prevalence of serotypes 19A, 3, and 6C in both age groups. Serotypes 19A and 6C were related to non-antimicrobial susceptibility. We observed a reduction in S. pneumoniae, without changes in serotypes distribution and epidemiological capsular switch during the COVID-19 period. We observed elevated resistance rates, mainly to penicillin and ceftriaxone for non-meningitis cases in children under 5 years of age. Full article
(This article belongs to the Section Public Health Microbiology)
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16 pages, 3213 KiB  
Article
African Swine Fever Virus I267L Is a Hemorrhage-Related Gene Based on Transcriptome Analysis
by Yuan Wen, Xianghan Duan, Jingjing Ren, Jing Zhang, Guiquan Guan, Yi Ru, Dan Li and Haixue Zheng
Microorganisms 2024, 12(2), 400; https://doi.org/10.3390/microorganisms12020400 - 17 Feb 2024
Viewed by 780
Abstract
African swine fever (ASF) is an acute and severe disease transmitted among domestic pigs and wild boars. This disease is notorious for its high mortality rate and has caused great losses to the world’s pig industry in the past few years. After infection, [...] Read more.
African swine fever (ASF) is an acute and severe disease transmitted among domestic pigs and wild boars. This disease is notorious for its high mortality rate and has caused great losses to the world’s pig industry in the past few years. After infection, pigs can develop symptoms such as high fever, inflammation, and acute hemorrhage, finally leading to death. African swine fever virus (ASFV) is the causal agent of ASF; it is a large DNA virus with 150–200 genes. Elucidating the functions of each gene could provide insightful information for developing prevention and control methods. Herein, to investigate the function of I267L, porcine alveolar macrophages (PAMs) infected with an I267L-deleted ASFV strain (named ∆I267L) and wild-type ASFV for 18 h and 36 h were taken for transcriptome sequencing (RNA-seq). The most distinct different gene that appeared at both 18 hpi (hours post-infection) and 36 hpi was F3; it is the key link between inflammation and coagulation cascades. KEGG analysis (Kyoto encyclopedia of genes and genomes analysis) revealed the complement and coagulation cascades were also significantly affected at 18 hpi. Genes associated with the immune response were also highly enriched with the deletion of I267L. RNA-seq results were validated through RT-qPCR. Further experiments confirmed that ASFV infection could suppress the induction of F3 through TNF-α, while I267L deletion partially impaired this suppression. These results suggest that I267L is a pathogenicity-associated gene that modulates the hemorrhages of ASF by suppressing F3 expression. This study provides new insights into the molecular mechanisms of ASFV pathogenicity and potential targets for ASFV prevention and control. Full article
(This article belongs to the Special Issue Advances in African Swine Fever Virus)
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15 pages, 2808 KiB  
Article
Molecular Characterization of ‘Candidatus Phytoplasma prunorum’ in the Czech Republic and Susceptibility of Apricot Rootstocks to the Two Most Abundant Haplotypes
by Tomáš Kiss, Dana Šafářová, Milan Navrátil and Tomáš Nečas
Microorganisms 2024, 12(2), 399; https://doi.org/10.3390/microorganisms12020399 - 17 Feb 2024
Viewed by 640
Abstract
Candidatus Phytoplasma prunorum’ is one of the most destructive pathogens of Prunus species, where susceptible species render unproductive several years after infection. In epidemiology, the molecular characterization of phytoplasmas is based on sequence analysis of variable nonribosomal genes. In this study aceF [...] Read more.
Candidatus Phytoplasma prunorum’ is one of the most destructive pathogens of Prunus species, where susceptible species render unproductive several years after infection. In epidemiology, the molecular characterization of phytoplasmas is based on sequence analysis of variable nonribosomal genes. In this study aceF, pnp, imp and secY genes were used for characterization of the ‘Ca. P. prunorum’ genotypes present in the Czech Republic. In total, 56 plant and 33 vector (Cacopsylla pruni) samples positive to ‘Ca. P. prunorum’ collected in seven localities were used in the study. Based on sequence analysis, four aceF, two pnp, six imp, and three secY genotypes were identified in analyzed samples. The most abundant in both plant and insect samples were the A6, P2, I4, and S2 genotypes. Most of the Czech ‘Ca. P. prunorum’ haplotypes clustered together in the haplotype network analysis. Next, two isolates representing the two most abundant Czech haplotypes (A6-P2-I4-S2 and A5-P2-I4-S2) were used in the susceptibility test of three apricot rootstock types (St. Julien A, M-VA-1, GF-305). Susceptibility was analyzed by phytoplasma quantification using quantitative real-time PCR and evaluation of symptom manifestation. Based on the results, the influence of the rootstock type on the phytoplasma titer and symptom manifestation was greater than of the phytoplasma isolate, while the year of analysis had no influence on the results. The results also showed that the phytoplasma titer is increasing in plant tissues during the vegetation period. Full article
(This article belongs to the Special Issue Phytoplasma Diseases of Trees and Shrubs)
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18 pages, 2148 KiB  
Article
The Microbial Community Structure in the Rhizosphere of Theobroma cacao L. and Euterpe oleracea Mart. Is Influenced by Agriculture System in the Brazilian Amazon
by Rosiane do Socorro dos Reis de Sousa, Giulia Victória Silva Lima, Josinete Torres Garcias, Graziane de Oliveira Gomes, Jackeline Rossetti Mateus, Lucimar Di Paula dos Santos Madeira, Lucy Seldin, Hervé Louis Ghislain Rogez and Joana Montezano Marques
Microorganisms 2024, 12(2), 398; https://doi.org/10.3390/microorganisms12020398 - 17 Feb 2024
Viewed by 857
Abstract
This study tested the hypothesis that cocoa monoculture (MS) and cocoa-açai agroforestry systems (AFS) may influence the microbial community structure and populations of plant growth-promoting bacteria (PGPR). Accordingly, the aim was to analyze the microbial community structure and PGPR populations in different agroecosystems [...] Read more.
This study tested the hypothesis that cocoa monoculture (MS) and cocoa-açai agroforestry systems (AFS) may influence the microbial community structure and populations of plant growth-promoting bacteria (PGPR). Accordingly, the aim was to analyze the microbial community structure and PGPR populations in different agroecosystems in the Brazilian Amazon. To achieve this, the rhizosphere microbial community of cocoa and açai plants in both Amazonian seasons (dry and rainy) was analyzed using culture-dependent (PGPR screening) and -independent methods [PCR-DGGE based on rrs, alp, nifH gene, and intergenic region (ITS) of fungi]. Concerning PGPR screening, out of 48 isolated bacterial strains, 25% were capable of siderophore production, 29% of mineralized organic phosphate, 8% of inorganic phosphate solubilization, and 4% of indole acetic acid production. Moreover, 17% of isolates could inhibit the growth of various phytopathogenic fungi. Statistical analyses of DGGE fingerprints (p < 0.05) showed that bacterial and fungal community structures in the rhizosphere were influenced by the seasons, supporting the results of the physicochemical analysis of the environment. Furthermore, as hypothesized, microbial communities differed statistically when comparing the MS and AFS. These findings provide important insights into the influence of climate and cultivation systems on soil microbial communities to guide the development of sustainable agricultural practices. Full article
(This article belongs to the Special Issue Rhizosphere Microbial Community 2.0)
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15 pages, 1940 KiB  
Article
Analysis of Culturable Bacterial Diversity of Pangong Tso Lake via a 16S rRNA Tag Sequencing Approach
by Pooja Yadav, Joyasree Das, Shiva S. Sundharam and Srinivasan Krishnamurthi
Microorganisms 2024, 12(2), 397; https://doi.org/10.3390/microorganisms12020397 - 17 Feb 2024
Viewed by 928
Abstract
The Pangong Tso lake is a high-altitude freshwater habitat wherein the resident microbes experience unique selective pressures, i.e., high radiation, low nutrient content, desiccation, and temperature extremes. Our study attempts to analyze the diversity of culturable bacteria by applying a high-throughput amplicon sequencing [...] Read more.
The Pangong Tso lake is a high-altitude freshwater habitat wherein the resident microbes experience unique selective pressures, i.e., high radiation, low nutrient content, desiccation, and temperature extremes. Our study attempts to analyze the diversity of culturable bacteria by applying a high-throughput amplicon sequencing approach based on long read technology to determine the spectrum of bacterial diversity supported by axenic media. The phyla Pseudomonadota, Bacteriodetes, and Actinomycetota were retrieved as the predominant taxa in both water and sediment samples. The genera Hydrogenophaga and Rheinheimera, Pseudomonas, Loktanella, Marinomonas, and Flavobacterium were abundantly present in the sediment and water samples, respectively. Low nutrient conditions supported the growth of taxa within the phyla Bacteriodetes, Actinomycetota, and Cyanobacteria and were biased towards the selection of Pseudomonas, Hydrogenophaga, Bacillus, and Enterococcus spp. Our study recommends that media formulations can be finalized after analyzing culturable diversity through a high-throughput sequencing effort to retrieve maximum species diversity targeting novel/relevant taxa. Full article
(This article belongs to the Special Issue Microbial Diversity in Extreme Environments 2.0)
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12 pages, 4096 KiB  
Article
Analysis of Antibiotic Resistance Genes in Water Reservoirs and Related Wastewater from Animal Farms in Central China
by Yapei Rui and Gang Qiu
Microorganisms 2024, 12(2), 396; https://doi.org/10.3390/microorganisms12020396 - 16 Feb 2024
Viewed by 811
Abstract
This study aimed to explore the phenotype and relationship of drug resistance genes in livestock and poultry farm wastewater and drinking water reservoirs to provide evidence for the transmission mechanisms of drug resistance genes, in order to reveal the spread of drug resistance [...] Read more.
This study aimed to explore the phenotype and relationship of drug resistance genes in livestock and poultry farm wastewater and drinking water reservoirs to provide evidence for the transmission mechanisms of drug resistance genes, in order to reveal the spread of drug resistance genes in wastewater from intensive farms in Central China to urban reservoirs that serve as drinking water sources and provide preliminary data for the treatment of wastewater from animal farms to reduce the threat to human beings. DNA extraction and metagenomic sequencing were performed on eight groups of samples collected from four water reservoirs and four related wastewaters from animal farms in Central China. Metagenomic sequencing showed that the top 20 AROs with the highest abundance were vanT_gene, vanY_gene, adeF, qacG, Mtub_rpsL_STR, vanY_gene_, vanW_gene, Mtub_murA_FOF, vanY_gene, vanH_gene, FosG, rsmA, qacJ, RbpA, vanW_gene, aadA6, vanY_gene, sul4, sul1, and InuF. The resistance genes mentioned above belong to the following categories of drug resistance mechanisms: antibiotic target replacement, antibiotic target protection, antibiotic inactivation, and antibiotic efflux. The resistomes that match the top 20 genes are Streptococcus agalactiae and Streptococcus anginosus; Enterococcus faecalis; Enterococcus faecium; Actinomyces viscosus and Bacillus cereus. Enterococcus faecium; Clostridium tetani; Streptococcus agalactiae and Streptococcus anginosus; Streptococcus agalactiae and Streptococcus anginosus; Acinetobacter baumannii, Bifidobacterium bifidum, Bifidobacterium breve, Bifidobacterium longum, Corynebacterium jeikeium, Corynebacterium urealyticum, Mycobacterium kansasii, Mycobacterium tuberculosis, Schaalia odontolytica, and Trueperella pyogenes; Mycobacterium avium and Mycobacterium tuberculosis; Aeromonas caviae, Enterobacter hormaechei, Vibrio cholerae, Vibrio metoecus, Vibrio parahaemolyticus, and Vibrio vulnificus; Pseudomonas aeruginosa and Pseudomonas fluorescens; Staphylococcus aureus and Staphylococcus equorum; M. avium, Achromobacter xylosoxidans, and Acinetobacter baumannii; Sphingobium yanoikuyae, Acinetobacter indicus, Morganella morganii, Proteus mirabilis, Proteus vulgaris, Providencia rettgeri, and Providencia stuartii. Unreported drug resistance genes and drug-resistant bacteria in Central China were identified in 2023. In the transmission path of drug resistance genes, the transmission path from aquaculture wastewater to human drinking water sources cannot be ignored. For the sake of human health and ecological balance, the treatment of aquaculture wastewater needs to be further strengthened, and the effective blocking of drug resistance gene transmission needs to be considered. Full article
(This article belongs to the Special Issue Advances in Antibiotic and Drug-Resistance Mechanisms)
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12 pages, 918 KiB  
Article
Mold Odor from Wood Treated with Chlorophenols despite Mold Growth That Can Only Be Seen Using a Microscope
by Johnny C. Lorentzen, Olle Ekberg, Maria Alm, Folke Björk, Lars-Erik Harderup and Gunnar Johanson
Microorganisms 2024, 12(2), 395; https://doi.org/10.3390/microorganisms12020395 - 16 Feb 2024
Viewed by 666
Abstract
We previously reported that indoor odorous chloroanisoles (CAs) are still being emitted due to microbial methylation of hazardous chlorophenols (CPs) present in legacy wood preservatives. Meanwhile, Swedish researchers reported that this malodor, described since the early 1970s, is caused by hazardous mold. Here, [...] Read more.
We previously reported that indoor odorous chloroanisoles (CAs) are still being emitted due to microbial methylation of hazardous chlorophenols (CPs) present in legacy wood preservatives. Meanwhile, Swedish researchers reported that this malodor, described since the early 1970s, is caused by hazardous mold. Here, we examined to what extent CP-treated wood contains mold and if mold correlates with perceived odor. We found no studies in PubMed or Web of Science addressing this question. Further, we investigated two schools built in the 1960s with odor originating from crawlspaces. No visible mold was evident in the crawlspaces or on the surfaces of treated wood samples. Using a microscope, varying amounts of mold growth were detected on the samples, all containing both CP(s) and CA(s). Some samples smelled, and the odor correlated with the amount of mold growth. We conclude that superficial microscopic mold on treated wood suffices produced the odor. Further, we argue that CPs rather than mold could explain the health effects reported in epidemiological studies that use mold odor as an indicator of hazardous exposure. Full article
(This article belongs to the Special Issue The Urban Microbiome)
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17 pages, 5616 KiB  
Case Report
Visceral Leishmaniasis in Immunocompetent Hosts in Brescia: A Case Series and Analysis of Cytokine Cascade
by Alice Mulè, Verena Crosato, Douglas Byron Kuhns, Luisa Lorenzi, Claudia Chirico, Giovanni Maifredi, Luigi D. Notarangelo, Francesco Castelli and Lina R. Tomasoni
Microorganisms 2024, 12(2), 394; https://doi.org/10.3390/microorganisms12020394 - 16 Feb 2024
Viewed by 675
Abstract
Visceral leishmaniasis (VL) is a parasitic zoonosis caused by Leishmania spp. that usually manifests itself in immunocompromised subjects. It is a rare and neglected disease, and it is not endemic in the province of Brescia (Italy). Three cases of human VL occurred in [...] Read more.
Visceral leishmaniasis (VL) is a parasitic zoonosis caused by Leishmania spp. that usually manifests itself in immunocompromised subjects. It is a rare and neglected disease, and it is not endemic in the province of Brescia (Italy). Three cases of human VL occurred in Brescia from October to December 2021 in immunocompetent patients. We evaluated the patients looking for signs of underlying immunodeficiencies and conducted further epidemiological evaluations in the province of Brescia without success. An analysis of the sera levels of the main cytokines involved in the immune response to VL was performed. All patients presented a significant augmentation of CXCL-10, CCL-4, and IL-6. The patients tested during the acute phase showed an elevation of IL-1α, IL-5, IL-10, and IL-12, while in the recovery phase, higher levels of TNF-α and IL-7 were detected. Altogether, a predominant activation of the T-helper-2 pathway emerged during the acute phase of the parasite infection, while the cytokines associated with the T-helper-1 pathway were less represented. This imbalanced immune response to the parasite infection might play a crucial role in the development of VL in immunocompetent patients. Full article
(This article belongs to the Special Issue Research on Leishmania and Leishmaniasis)
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16 pages, 7378 KiB  
Article
Reduced Pseudomonas aeruginosa Cell Size Observed on Planktonic Cultures Grown in the International Space Station
by Katherinne Herrera-Jordan, Pamela Pennington and Luis Zea
Microorganisms 2024, 12(2), 393; https://doi.org/10.3390/microorganisms12020393 - 16 Feb 2024
Viewed by 929
Abstract
Bacterial growth and behavior have been studied in microgravity in the past, but little focus has been directed to cell size despite its impact on a myriad of processes, including biofilm formation, which is impactful regarding crew health. To interrogate this characteristic, supernatant [...] Read more.
Bacterial growth and behavior have been studied in microgravity in the past, but little focus has been directed to cell size despite its impact on a myriad of processes, including biofilm formation, which is impactful regarding crew health. To interrogate this characteristic, supernatant aliquots of P. aeruginosa cultured on different materials and media on board the International Space Station (ISS) as part of the Space Biofilms Project were analyzed. For that experiment, P. aeruginosa was grown in microgravity—with matching Earth controls—in modified artificial urine medium (mAUMg-high Pi) or LB Lennox supplemented with KNO3, and its formation of biofilms on six different materials was assessed. After one, two, and three days of incubation, the ISS crew terminated subsets of the experiment by fixation in paraformaldehyde, and aliquots of the supernatant were used for the planktonic cell size study presented here. The measurements were obtained post-flight through the use of phase contrast microscopy under oil immersion, a Moticam 10+ digital camera, and the FIJI image analysis program. Statistical comparisons were conducted to identify which treatments caused significant differences in cell dimensions using the Kruskal–Wallis and Dunn tests. There were statistically significant differences as a function of material present in the culture in both LBK and mAUMg-high Pi. Along with this, the data were also grouped by gravitational condition, media, and days of incubation. Comparison of planktonic cells cultured in microgravity showed reduced cell length (from 4% to 10% depending on the material) and diameter (from 1% to 10% depending on the material) with respect to their matching Earth controls, with the caveat that the cultures may have been at different points in their growth curve at a given time. In conclusion, smaller cells were observed on the cultures grown in microgravity, and cell size changed as a function of incubation time and the material upon which the culture grew. We describe these changes here and possible implications for human space travel in terms of crew health and potential applications. Full article
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17 pages, 5946 KiB  
Article
Cross-Phosphorylation between AgrC Histidine Kinase and the Noncognate Response Regulator Lmo1172 in Listeria monocytogenes under Benzalkonium Chloride Stress
by Tao Yu, Xiaojie Jiang, Xiaobo Xu, Ping Xu, Shuxing Qiu, Junlei Yin, David P. Hamilton and Xiaobing Jiang
Microorganisms 2024, 12(2), 392; https://doi.org/10.3390/microorganisms12020392 - 16 Feb 2024
Viewed by 545
Abstract
Benzalkonium chloride (BC) is widely used for disinfection in the food industry. However, Listeria monocytogenes strains with resistance to BC have been reported recently. In L. monocytogenes, the Agr communication system consists of a membrane-bound peptidase AgrB, a precursor peptide AgrD, a [...] Read more.
Benzalkonium chloride (BC) is widely used for disinfection in the food industry. However, Listeria monocytogenes strains with resistance to BC have been reported recently. In L. monocytogenes, the Agr communication system consists of a membrane-bound peptidase AgrB, a precursor peptide AgrD, a histidine kinase (HK) AgrC, and a response regulator (RR) AgrA. Our previous study showed that the agr genes are significantly upregulated by BC adaptation. This study aimed to investigate the role of the Agr system in BC resistance in L. monocytogenes. Our results showed that the Agr system was involved in BC resistance. However, a direct interaction between BC and AgrC was not observed, nor between BC and AgrA. These results indicated that BC could induce the Agr system via an indirect action. Both AgrBD and AgrC were required for growth under BC stress. Nevertheless, when exposed to BC, the gene deletion mutant ∆agrA strain exhibited better growth performance than its parental strain. The RR Lmo1172 played a role in BC resistance in the ∆agrA strain, suggesting that Lmo1172 may be an alternative to AgrA in the phosphotransfer pathway. Phosphorylation of Lmo1172 by AgrC was observed in vitro. The cognate HK Lmo1173 of Lmo1172 was not involved in BC stress, regardless of whether it was as the wild-type or the ∆agrA mutant strain. Our evidence suggests that the HK AgrC cross-phosphorylates its noncognate RR Lmo1172 to cope with BC stress when the cognate RR AgrA is absent. In vivo, further studies will be required to detect phosphotransfer of AgrC/AgrA and AgrC/Lmo1172. Full article
(This article belongs to the Special Issue Food Microorganisms and Genomics)
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28 pages, 1703 KiB  
Article
The Complete Genome of a Novel Typical Species Thiocapsa bogorovii and Analysis of Its Central Metabolic Pathways
by Ekaterina Petushkova, Makhmadyusuf Khasimov, Ekaterina Mayorova, Yanina Delegan, Ekaterina Frantsuzova, Alexander Bogun, Elena Galkina and Anatoly Tsygankov
Microorganisms 2024, 12(2), 391; https://doi.org/10.3390/microorganisms12020391 - 15 Feb 2024
Viewed by 723
Abstract
The purple sulfur bacterium Thiocapsa roseopersicina BBS is interesting from both fundamental and practical points of view. It possesses a thermostable HydSL hydrogenase, which is involved in the reaction of reversible hydrogen activation and a unique reaction of sulfur reduction to hydrogen sulfide. [...] Read more.
The purple sulfur bacterium Thiocapsa roseopersicina BBS is interesting from both fundamental and practical points of view. It possesses a thermostable HydSL hydrogenase, which is involved in the reaction of reversible hydrogen activation and a unique reaction of sulfur reduction to hydrogen sulfide. It is a very promising enzyme for enzymatic hydrogenase electrodes. There are speculations that HydSL hydrogenase of purple bacteria is closely related to sulfur metabolism, but confirmation is required. For that, the full genome sequence is necessary. Here, we sequenced and assembled the complete genome of this bacterium. The analysis of the obtained whole genome, through an integrative approach that comprised estimating the Average Nucleotide Identity (ANI) and digital DNA-DNA hybridization (DDH) parameters, allowed for validation of the systematic position of T. roseopersicina as T. bogorovii BBS. For the first time, we have assembled the whole genome of this typical strain of a new bacterial species and carried out its functional description against another purple sulfur bacterium: Allochromatium vinosum DSM 180T. We refined the automatic annotation of the whole genome of the bacteria T. bogorovii BBS and localized the genomic positions of several studied genes, including those involved in sulfur metabolism and genes encoding the enzymes required for the TCA and glyoxylate cycles and other central metabolic pathways. Eleven additional genes coding proteins involved in pigment biosynthesis was found. Full article
(This article belongs to the Section Systems Microbiology)
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12 pages, 6769 KiB  
Communication
Metagenomic Analysis of Antarctic Ocean near the King Sejong Station Reveals the Diversity of Carotenoid Biosynthetic Genes
by Woo Yeon Cho and Pyung Cheon Lee
Microorganisms 2024, 12(2), 390; https://doi.org/10.3390/microorganisms12020390 - 15 Feb 2024
Cited by 1 | Viewed by 633
Abstract
Carotenoids, biotechnologically significant pigments, play crucial biological roles in marine microorganisms. While various environments have been explored to understand the diversity of carotenoids and their biosynthesis, the Antarctic Ocean remains relatively under-investigated. This study conducted a metagenomic analysis of seawater from two depths [...] Read more.
Carotenoids, biotechnologically significant pigments, play crucial biological roles in marine microorganisms. While various environments have been explored to understand the diversity of carotenoids and their biosynthesis, the Antarctic Ocean remains relatively under-investigated. This study conducted a metagenomic analysis of seawater from two depths (16 and 25 m) near the King Sejong Station in the Antarctic Ocean. The analysis revealed a rich genetic diversity underlying C40 (astaxanthin, myxol, okenone, spheroidene, and spirilloxanthin), C30 (diaponeurosporene, diapolycopene, and staphyloxanthin), and C50 (C.p. 450) carotenoid biosynthesis in marine microorganisms, with notable differential gene abundances between depth locations. Exploring carotenoid pathway genes offers the potential for discovering diverse carotenoid structures of biotechnological value and better understanding their roles in individual microorganisms and broader ecosystems. Full article
(This article belongs to the Special Issue New Insights into the Diversity and Characterization of Extremophiles)
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