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Microorganisms
Volume 10
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Microorganisms, Volume 10, Issue 4 (April 2022) – 166 articles

Cover Story (view full-size image): The prevalence of chronic wounds is increasing globally. Most chronic wounds harbor bacterial biofilms that are extremely hard to eradicate and are thought to have numerous survival strategies, resulting in long-term infections. Much of our knowledge around biofilm persistence derives from in vitro and animal models. While the knowledge obtained from such experiments is highly valuable, its direct translation to the human clinical setting should be undertaken with caution. In this review, we highlight knowledge obtained from human clinical samples in different aspects of biofilm survival strategies. We strive to clarify the limitations of the current knowledge regarding this specific topic, without ignoring important in vitro and in vivo observations. View this paper
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16 pages, 2608 KiB  
Article
Microbial Community Composition and Activity in Saline Soils of Coastal Agro–Ecosystems
by Yang Dong, Jianwei Zhang, Ruirui Chen, Linghao Zhong, Xiangui Lin and Youzhi Feng
Microorganisms 2022, 10(4), 835; https://doi.org/10.3390/microorganisms10040835 - 18 Apr 2022
Cited by 17 | Viewed by 3030
Abstract
Soil salinity is a serious problem for agriculture in coastal regions. Nevertheless, the effects of soil salinity on microbial community composition and their metabolic activities are far from clear. To improve such understanding, we studied microbial diversity, community composition, and potential metabolic activity [...] Read more.
Soil salinity is a serious problem for agriculture in coastal regions. Nevertheless, the effects of soil salinity on microbial community composition and their metabolic activities are far from clear. To improve such understanding, we studied microbial diversity, community composition, and potential metabolic activity of agricultural soils covering non–, mild–, and severe–salinity. The results showed that salinity had no significant effect on bacterial richness; however, it was the major driver of a shift in bacterial community composition and it significantly reduced microbial activity. Abundant and diverse of microbial communities were detected in the severe–salinity soils with an enriched population of salt–tolerant species. Co–occurrence network analysis revealed stronger dependencies between species associated with severe salinity soils. Results of microcalorimetric technology indicated that, after glucose amendment, there was no significant difference in microbial potential activity among soils with the three salinity levels. Although the salt prolonged the lag time of microbial communities, the activated microorganisms had a higher growth rate. In conclusion, salinity shapes soil microbial community composition and reduces microbial activity. An addition of labile organic amendments can greatly alleviate salt restrictions on microbial activity, which provides new insight for enhancing microbial ecological functions in salt–affected soils. Full article
(This article belongs to the Special Issue Advances in Soil Microbiome)
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16 pages, 2252 KiB  
Article
Multilayer Regulation of Neisseria meningitidis NHBA at Physiologically Relevant Temperatures
by Sara Borghi, Ana Antunes, Andreas F. Haag, Marco Spinsanti, Tarcisio Brignoli, Enea Ndoni, Vincenzo Scarlato and Isabel Delany
Microorganisms 2022, 10(4), 834; https://doi.org/10.3390/microorganisms10040834 - 18 Apr 2022
Cited by 2 | Viewed by 2556
Abstract
Neisseria meningitidis colonizes the nasopharynx of humans, and pathogenic strains can disseminate into the bloodstream, causing septicemia and meningitis. NHBA is a surface-exposed lipoprotein expressed by all N. meningitidis strains in different isoforms. Diverse roles have been reported for NHBA in [...] Read more.
Neisseria meningitidis colonizes the nasopharynx of humans, and pathogenic strains can disseminate into the bloodstream, causing septicemia and meningitis. NHBA is a surface-exposed lipoprotein expressed by all N. meningitidis strains in different isoforms. Diverse roles have been reported for NHBA in heparin-mediated serum resistance, biofilm formation, and adherence to host tissues. We determined that temperature controls the expression of NHBA in all strains tested, with increased levels at 30–32 °C compared to 37 °C. Higher NHBA expression at lower temperatures was measurable both at mRNA and protein levels, resulting in higher surface exposure. Detailed molecular analysis indicated that multiple molecular mechanisms are responsible for the thermoregulated NHBA expression. The comparison of mRNA steady-state levels and half-lives at 30 °C and 37 °C demonstrated an increased mRNA stability/translatability at lower temperatures. Protein stability was also impacted, resulting in higher NHBA stability at lower temperatures. Ultimately, increased NHBA expression resulted in higher susceptibility to complement-mediated killing. We propose that NHBA regulation in response to temperature downshift might be physiologically relevant during transmission and the initial step(s) of interaction within the host nasopharynx. Together these data describe the importance of NHBA both as a virulence factor and as a vaccine antigen during neisserial colonization and invasion. Full article
(This article belongs to the Special Issue Regulation of Gene Expression in Response to Environmental Changes in Bacterial Pathogens)
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15 pages, 1560 KiB  
Article
Antibiotic Resistance and Molecular Profiling of the Clinical Isolates of Staphylococcus aureus Causing Bovine Mastitis from India
by Umarani Brahma, Akash Suresh, Shweta Murthy, Vasundhra Bhandari and Paresh Sharma
Microorganisms 2022, 10(4), 833; https://doi.org/10.3390/microorganisms10040833 - 18 Apr 2022
Cited by 17 | Viewed by 3265
Abstract
Staphylococcus aureus is an opportunistic bacterium known to cause severe infections in humans and animals. It is one of the major bacteria causing subclinical and clinical mastitis, leading to significant economic losses in livestock industry. In this study, we have isolated and characterized [...] Read more.
Staphylococcus aureus is an opportunistic bacterium known to cause severe infections in humans and animals. It is one of the major bacteria causing subclinical and clinical mastitis, leading to significant economic losses in livestock industry. In this study, we have isolated and characterized 80 S. aureus clinical isolates from mastitis-infected animals. The analysis of antimicrobial susceptibility, molecular typing, biofilm production and genetic determinants was performed to understand molecular and phenotypic features of the prevalent pathogen. Our antibiotic susceptibility assays showed the majority (57.5%) of isolates to be multidrug-resistant (MDR), 38.75% resistant and 3.75% sensitive. We found 25% isolates to be methicillin-resistant S. aureus (MRSA) based on oxacillin susceptibility assays. In the MRSA group, maximum isolates (95%) were MDR compared to 45% in MSSA. Multilocus sequence typing (MLST) revealed 15 different STs; ST-97 was the most common ST, followed by ST-2459, ST-1, ST-9 and ST-72. The agr typing showed agr-I as the most common type, followed by type II and III. Most isolates developed biofilms, which ranged in intensity from strong to weak. The presence or absence of lukS, a virulence-related gene, was found to have a substantial relationship with the biofilm phenotype. However, no significant association was found between biofilm formation and antimicrobial resistance or other virulence genes. We also found four MRSA isolates that were mecA negative based on molecular assays. Our findings reveal the prevalence of multidrug-resistant S. aureus clinical isolates in India that are biofilm positive and have critical genetic factors for disease pathogenesis causing bovine mastitis. This study emphasizes the need for the comprehensive surveillance of S. aureus and other mastitis-causing pathogens to control the disease effectively. Full article
(This article belongs to the Topic Veterinary Infectious Diseases)
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11 pages, 702 KiB  
Article
Assessing Tick-Borne Disease Risk and Surveillance: Toward a Multi-Modal Approach to Diagnostic Positioning and Prediction
by Chris Brooks, Connie L. McNeely, Sarah P. Maxwell and Kevin C. Thomas
Microorganisms 2022, 10(4), 832; https://doi.org/10.3390/microorganisms10040832 - 18 Apr 2022
Cited by 5 | Viewed by 2719
Abstract
The true extent of tick-borne disease (TBD) incidence and risk among humans is largely unknown, posing significant public health challenges. This study offers an exploratory analysis of a multimodal dataset and is part of a larger ongoing project to determine if entomological data, [...] Read more.
The true extent of tick-borne disease (TBD) incidence and risk among humans is largely unknown, posing significant public health challenges. This study offers an exploratory analysis of a multimodal dataset and is part of a larger ongoing project to determine if entomological data, canine serological reports, self-reported human tick bite encounters (TBEs), and/or associated TBD diagnoses can serve as proxies for human disease risk. Focusing on the United States (U.S.), it characterizes self-reported TBD diagnoses (specifically, anaplasmosis, ehrlichiosis, and Lyme disease), co-infections, and their frequency and distribution across U.S. counties in relation to the presence of other factors related to TBD risk. Survey data was used to construct a list of TBEs localizable to individual U.S. counties. National data regarding these counties—namely the presence of official Lyme Disease (LD) case reports from the Centers for Disease Control and Prevention, as well as the tick vectors I. scapularis and I. pacificus within a given county—were then linked with survey-reported TBEs, tabulated by diagnosis (including co-infections), to determine the distribution of county-level endpoints across diagnostic categories. In addition, data on the presence of positive serological diagnostic tests conducted in canines were considered due to their potential utility as a proxy for TBD and TBE risk. The final dataset contained 249 TBEs localized to a total of 144 counties across 30 states. Diagnostic categories included respondents with LD (n = 70) and those with anaplasmosis and ehrlichiosis diagnoses and co-infections (n < 20 per diagnostic category). TBEs also were indicated by respondents who did not report TBD diagnoses, with some indicating uncertainty. The distribution of respondent-reported TBEs varied between canine TBDs, with LD-positive respondents reporting noticeably larger proportions of TBEs in counties with canine LD and smaller proportions in counties with canine anaplasmosis, compared to respondents without an LD diagnosis; a notional logistic regression suggests these differences may be significant (canine LD: Odds Ratio [OR] = 6.04, p = 0.026) (canine anaplasmosis: OR = 0.50, p = 0.095). These results suggest that certain widely available diagnostic TBD data in animals (in this case, domesticated dogs) may be sensitive to differences in human TBD risk factors and thus may have utility as proxies in future research. In the absence of an available standardized, unified, and national TBD database, such proxies, along with relevant surveys and reports, may provide a much-needed working solution for scientists and clinicians studying TBDs. Full article
(This article belongs to the Special Issue Epidemiology, Surveillance and Prevention of Tick-Borne Diseases)
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14 pages, 3133 KiB  
Article
Classification of Environmental Strains from Order to Genus Levels Using Lipid and Protein MALDI-ToF Fingerprintings and Chemotaxonomic Network Analysis
by Marceau Levasseur, Téo Hebra, Nicolas Elie, Vincent Guérineau, David Touboul and Véronique Eparvier
Microorganisms 2022, 10(4), 831; https://doi.org/10.3390/microorganisms10040831 - 17 Apr 2022
Cited by 5 | Viewed by 2684
Abstract
During the last two decades, MALDI-ToF mass spectrometry has become an efficient and widely-used tool for identifying clinical isolates. However, its use for classification and identification of environmental microorganisms remains limited by the lack of reference spectra in current databases. In addition, the [...] Read more.
During the last two decades, MALDI-ToF mass spectrometry has become an efficient and widely-used tool for identifying clinical isolates. However, its use for classification and identification of environmental microorganisms remains limited by the lack of reference spectra in current databases. In addition, the interpretation of the classical dendrogram-based data representation is more difficult when the quantity of taxa or chemotaxa is larger, which implies problems of reproducibility between users. Here, we propose a workflow including a concurrent standardized protein and lipid extraction protocol as well as an analysis methodology using the reliable spectra comparison algorithm available in MetGem software. We first validated our method by comparing protein fingerprints of highly pathogenic bacteria from the Robert Koch Institute (RKI) open database and then implemented protein fingerprints of environmental isolates from French Guiana. We then applied our workflow for the classification of a set of protein and lipid fingerprints from environmental microorganisms and compared our results to classical genetic identifications using 16S and ITS region sequencing for bacteria and fungi, respectively. We demonstrated that our protocol allowed general classification at the order and genus level for bacteria whereas only the Botryosphaeriales order can be finely classified for fungi. Full article
(This article belongs to the Section Systems Microbiology)
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12 pages, 1792 KiB  
Article
Optimization of Bacillus amyloliquefaciens BLB369 Culture Medium by Response Surface Methodology for Low Cost Production of Antifungal Activity
by Imen Zalila-Kolsi, Sameh Kessentini, Slim Tounsi and Kaïs Jamoussi
Microorganisms 2022, 10(4), 830; https://doi.org/10.3390/microorganisms10040830 - 16 Apr 2022
Cited by 10 | Viewed by 2940
Abstract
Bacillus amyloliquefaciens BLB369 is an important plant growth-promoting bacterium, which produces antifungal compounds. A statistics-based experimental design was used to optimize a liquid culture medium using inexpensive substrates for increasing its antifungal activity. A Plackett–Burman design was first applied to elucidate medium components [...] Read more.
Bacillus amyloliquefaciens BLB369 is an important plant growth-promoting bacterium, which produces antifungal compounds. A statistics-based experimental design was used to optimize a liquid culture medium using inexpensive substrates for increasing its antifungal activity. A Plackett–Burman design was first applied to elucidate medium components having significant effects on antifungal production. Then the steepest ascent method was employed to approach the experimental design space, followed by an application of central composite design. Three factors were retained (candy waste, peptone, and sodium chloride), and polynomial and original trigonometric models fitted the antifungal activity. The trigonometric model ensured a better fit. The contour and surface plots showed concentric increasing levels pointing out an optimized activity. Hence, the polynomial and trigonometric models showed a maximal antifungal activity of 251.9 (AU/mL) and 255.5 (AU/mL) for (19.17, 19.88, 3.75) (g/L) and (19.61, 20, 3.7) (g/L) of candy waste, peptone, and NaCl, respectively. This study provides a potential strategy for improving the fermentation of B. amyloliquefaciens BLB369 in low-cost media for large-scale industrial production. Full article
(This article belongs to the Special Issue Biofertilizer Microorganism in Agriculture)
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19 pages, 3777 KiB  
Article
Influence of Different Vegetation Types on Soil Physicochemical Parameters and Fungal Communities
by Xin Sui, Xiannan Zeng, Mengsha Li, Xiaohong Weng, Beat Frey, Libin Yang and Maihe Li
Microorganisms 2022, 10(4), 829; https://doi.org/10.3390/microorganisms10040829 - 16 Apr 2022
Cited by 21 | Viewed by 2869
Abstract
This study assessed the effects of Betula dahurica (BD), Betula platyphylla (BP), Larix gmelinii (LG), Quercus mongolica (QM), and a mixed conifer–broadleaf forest composed of LG and QM (LGQM) on the soil physicochemical parameters and community structure of fungi in the Zhongyangzhan Black-billed [...] Read more.
This study assessed the effects of Betula dahurica (BD), Betula platyphylla (BP), Larix gmelinii (LG), Quercus mongolica (QM), and a mixed conifer–broadleaf forest composed of LG and QM (LGQM) on the soil physicochemical parameters and community structure of fungi in the Zhongyangzhan Black-billed Capercaillie Nature Reserve. Fungal community structures were characterized via ITS rRNA sequencing. The effects of soil parameters on the community structure of soil fungi were assessed by Pearson correlation analysis and redundancy analysis (RDA). LGQM exhibited lower C/N, available nitrogen (AN), total phosphorus (TP), and available phosphorus (AP) compared with the QM broadleaf forest. The fungal Shannon and Simpson diversity indices were highest in BP, whereas LG exhibited the highest ACE index. The Basidiomycota, Ascomycota, Mortierellomycota, and Mucoromycota fungal phyla were dominant across all vegetation types. Each of the different vegetation types studied herein exhibited a unique fungal community structure. The RDA results indicated that fungal community structures were primarily shaped by the total N, available N, and available P of soil. Our findings thus indicated that forests restored with different species of trees may exhibit variations in soil quality and characteristics despite sharing the same climate. Furthermore, broadleaved and coniferous forests exhibited a unique fungal community diversity and composition. Full article
(This article belongs to the Topic Fungal Diversity)
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16 pages, 1996 KiB  
Article
Marker-Free Genome Engineering in Amycolatopsis Using the pSAM2 Site-Specific Recombination System
by Luísa D. F. Santos, Laëtitia Caraty-Philippe, Emmanuelle Darbon and Jean-Luc Pernodet
Microorganisms 2022, 10(4), 828; https://doi.org/10.3390/microorganisms10040828 - 16 Apr 2022
Cited by 3 | Viewed by 2737
Abstract
Actinobacteria of the genus Amycolatopsis are important for antibiotic production and other valuable biotechnological applications such as bioconversion or bioremediation. Despite their importance, tools and methods for their genetic manipulation are less developed than in other actinobacteria such as Streptomyces. We report [...] Read more.
Actinobacteria of the genus Amycolatopsis are important for antibiotic production and other valuable biotechnological applications such as bioconversion or bioremediation. Despite their importance, tools and methods for their genetic manipulation are less developed than in other actinobacteria such as Streptomyces. We report here the use of the pSAM2 site-specific recombination system to delete antibiotic resistance cassettes used in gene replacement experiments or to create large genomic deletions. For this purpose, we constructed a shuttle vector, replicating in Escherichia coli and Amycolatopsis, expressing the integrase and the excisionase from the Streptomyces integrative and conjugative element pSAM2. These proteins are sufficient for site-specific recombination between the attachment sites attL and attR. We also constructed two plasmids, replicative in E. coli but not in Amycolatopsis, for the integration of the attL and attR sites on each side of a large region targeted for deletion. We exemplified the use of these tools in Amycolatopsis mediterranei by obtaining with high efficiency a marker-free deletion of one single gene in the rifamycin biosynthetic gene cluster or of the entire 90-kb cluster. These robust and simple tools enrich the toolbox for genome engineering in Amycolatopsis. Full article
(This article belongs to the Special Issue Current Prokaryotic Genome Engineering)
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11 pages, 1249 KiB  
Article
Enterococcus casseliflavus KB1733 Isolated from a Traditional Japanese Pickle Induces Interferon-Lambda Production in Human Intestinal Epithelial Cells
by Shohei Satomi, Daichi Kokubu, Takuro Inoue, Masaya Sugiyama, Masashi Mizokami, Shigenori Suzuki and Kazumoto Murata
Microorganisms 2022, 10(4), 827; https://doi.org/10.3390/microorganisms10040827 - 15 Apr 2022
Cited by 2 | Viewed by 3610
Abstract
The association between lactic acid bacteria (LAB) and their immunostimulatory effects has attracted considerable attention; however, it remains unclear whether LAB can induce interferon-lambdas (IFN-λs) in human epithelial cells under conditions that do not mimic infection. In this study, we first employed a [...] Read more.
The association between lactic acid bacteria (LAB) and their immunostimulatory effects has attracted considerable attention; however, it remains unclear whether LAB can induce interferon-lambdas (IFN-λs) in human epithelial cells under conditions that do not mimic infection. In this study, we first employed a reporter assay to screen for a potential strain capable of inducing IFN-λ3 among 135 LAB strains derived from traditional Japanese pickles. Next, we assessed the strain’s ability to induce the expression of IFN-λ genes and interferon-stimulated genes (ISGs), and to produce IFN-λs. As a result, we screened and isolated Enterococcus casseliflavus KB1733 (KB1733) as a potential strain capable of inducing IFN-λ3 expression. Furthermore, we clarified that KB1733 induced the expression of IFN-λ genes and ISGs related to antiviral functions, and that KB1733 induced IFN-λ1 and -λ3 expression in a dose-dependent manner up to 10 μg/mL. In addition, KB1733 significantly increased IFN-λ1 production compared to Enterococcus casseliflavus JCM8723T, which belongs to the same genera and species as KB1733. In conclusion, we isolated a unique LAB strain from traditional Japanese pickles that is capable of stimulating IFN-λ production, although further study is needed to investigate how KB1733 protects against viruses in mice and humans. Full article
(This article belongs to the Special Issue Food Fermented with Lactic Acid Bacteria and Its Immune-Related Applications)
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18 pages, 1228 KiB  
Review
The Impacts of Lactiplantibacillus plantarum on the Functional Properties of Fermented Foods: A Review of Current Knowledge
by Birsen Yilmaz, Sneh Punia Bangar, Noemi Echegaray, Shweta Suri, Igor Tomasevic, Jose Manuel Lorenzo, Ebru Melekoglu, João Miguel Rocha and Fatih Ozogul
Microorganisms 2022, 10(4), 826; https://doi.org/10.3390/microorganisms10040826 - 15 Apr 2022
Cited by 70 | Viewed by 9548
Abstract
One of the most varied species of lactic acid bacteria is Lactiplantibacillus plantarum (Lb. plantarum), formerly known as Lactobacillus plantarum. It is one of the most common species of bacteria found in foods, probiotics, dairy products, and beverages. Studies related [...] Read more.
One of the most varied species of lactic acid bacteria is Lactiplantibacillus plantarum (Lb. plantarum), formerly known as Lactobacillus plantarum. It is one of the most common species of bacteria found in foods, probiotics, dairy products, and beverages. Studies related to genomic mapping and gene locations of Lb. plantarum have shown the novel findings of its new strains along with their non-pathogenic or non-antibiotic resistance genes. Safe strains obtained with new technologies are a pioneer in the development of new probiotics and starter cultures for the food industry. However, the safety of Lb. plantarum strains and their bacteriocins should also be confirmed with in vivo studies before being employed as food additives. Many of the Lb. plantarum strains and their bacteriocins are generally safe in terms of antibiotic resistance genes. Thus, they provide a great opportunity for improving the nutritional composition, shelf life, antioxidant activity, flavour properties and antimicrobial activities in the food industry. Moreover, since some Lb. plantarum strains have the ability to reduce undesirable compounds such as aflatoxins, they have potential use in maintaining food safety and preventing food spoilage. This review emphasizes the impacts of Lb. plantarum strains on fermented foods, along with novel approaches to their genomic mapping and safety aspects. Full article
(This article belongs to the Special Issue Screening and Characterization of the Diversity of Food Microorganisms and Their Metabolites 2022)
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2 pages, 184 KiB  
Correction
Correction: Alhamami et al. First Emergence of Resistance to Macrolides and Tetracycline Identified in Mannheimia haemolytica and Pasteurella multocida Isolates from Beef Feedlots in Australia. Microorganisms 2021, 9, 1322
by Tamara Alhamami, Piklu Roy Chowdhury, Nancy Gomes, Mandi Carr, Tania Veltman, Manouchehr Khazandi, Joanne Mollinger, Ania T. Deutscher, Conny Turni, Layla Mahdi, Henrietta Venter, Sam Abraham, Steven P. Djordjevic and Darren J. Trott
Microorganisms 2022, 10(4), 825; https://doi.org/10.3390/microorganisms10040825 - 15 Apr 2022
Cited by 1 | Viewed by 1578
Abstract
The authors wish to make the following corrections to this paper [...] Full article
(This article belongs to the Special Issue Breaking the Code of Antibiotic Resistance)
17 pages, 1431 KiB  
Article
Red Blood Cell BCL-xL Is Required for Plasmodium falciparum Survival: Insights into Host-Directed Malaria Therapies
by Coralie Boulet, Ghizal Siddiqui, Taylah L. Gaynor, Christian Doerig, Darren J. Creek and Teresa G. Carvalho
Microorganisms 2022, 10(4), 824; https://doi.org/10.3390/microorganisms10040824 - 15 Apr 2022
Cited by 4 | Viewed by 3024
Abstract
The development of antimalarial drug resistance is an ongoing problem threatening progress towards the elimination of malaria, and antimalarial treatments are urgently needed for drug-resistant malaria infections. Host-directed therapies (HDT) represent an attractive strategy for the development of new antimalarials with untapped targets [...] Read more.
The development of antimalarial drug resistance is an ongoing problem threatening progress towards the elimination of malaria, and antimalarial treatments are urgently needed for drug-resistant malaria infections. Host-directed therapies (HDT) represent an attractive strategy for the development of new antimalarials with untapped targets and low propensity for resistance. In addition, drug repurposing in the context of HDT can lead to a substantial decrease in the time and resources required to develop novel antimalarials. Host BCL-xL is a target in anti-cancer therapy and is essential for the development of numerous intracellular pathogens. We hypothesised that red blood cell (RBC) BCL-xL is essential for Plasmodium development and tested this hypothesis using six BCL-xL inhibitors, including one FDA-approved compound. All BCL-xL inhibitors tested impaired proliferation of Plasmodium falciparum 3D7 parasites in vitro at low micromolar or sub-micromolar concentrations. Western blot analysis of infected cell fractions and immunofluorescence microscopy assays revealed that host BCL-xL is relocated from the RBC cytoplasm to the vicinity of the parasite upon infection. Further, immunoprecipitation of BCL-xL coupled with mass spectrometry analysis identified that BCL-xL forms unique molecular complexes with human μ-calpain in uninfected RBCs, and with human SHOC2 in infected RBCs. These results provide interesting perspectives for the development of host-directed antimalarial therapies and drug repurposing efforts. Full article
(This article belongs to the Special Issue Exploring Host-Pathogen Interactions – Host-Directed Therapies)
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14 pages, 1667 KiB  
Article
Effects of Rhizobia Isolated from Coffee Fields in the High Jungle Peruvian Region, Tested on Phaseolus vulgaris L. var. Red Kidney
by Jesus Lirio-Paredes, Katty Ogata-Gutiérrez and Doris Zúñiga-Dávila
Microorganisms 2022, 10(4), 823; https://doi.org/10.3390/microorganisms10040823 - 15 Apr 2022
Cited by 2 | Viewed by 2412
Abstract
Soils in the high jungle region of Peru continuously face erosion due to heavy rain, which leads to significant nutrient losses. Leguminous plants may provide a sustainable solution to this problem due to their ability to fix atmospheric nitrogen with the help of [...] Read more.
Soils in the high jungle region of Peru continuously face erosion due to heavy rain, which leads to significant nutrient losses. Leguminous plants may provide a sustainable solution to this problem due to their ability to fix atmospheric nitrogen with the help of symbiotic rhizospheric microbes that reside in their root nodules and help restore soil fertility. The aim of this study was to isolate native rhizobial strains that can form functional nodules in red kidney beans to help improve their growth, development, and yield in field conditions. Rhizobium strains were isolated from soil samples collected from coffee fields using bean plants as trap hosts. The strain RZC12 was selected because it showed good root nodule promotion and a number of PGPR (plant-growth-promoting rhizobacteria) attributes. In the field, bean plants inoculated with the strain RZC12 and co-cultivated with coffee plants produced approximately 21 nodules per plant, whereas control plants produced an average of 1 nodule each. The inoculation with RZC12 significantly increased plant length (72.7%), number of leaves (58.8%), fresh shoot weight (85.5%), dry shoot weight (78%), fresh root weight (85.7%), and dry root weight (82.5%), compared with the control. The dry pod weight produced by the plants inoculated with RZC12 was 3.8 g, whereas the control plants produced 2.36 g of pods. In conclusion, RZC12 is a promising strain that can be used in field conditions to improve the overall productivity of red kidney beans. Full article
(This article belongs to the Special Issue Biofertilizer Microorganism in Agriculture)
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21 pages, 2982 KiB  
Article
Potential Applications of Essential Oils for Environmental Sanitization and Antimicrobial Treatment of Intensive Livestock Infections
by Melinda Mariotti, Giulia Lombardini, Silvia Rizzo, Donatella Scarafile, Monica Modesto, Eleonora Truzzi, Stefania Benvenuti, Alberto Elmi, Martina Bertocchi, Laura Fiorentini, Lorenzo Gambi, Maurizio Scozzoli and Paola Mattarelli
Microorganisms 2022, 10(4), 822; https://doi.org/10.3390/microorganisms10040822 - 15 Apr 2022
Cited by 14 | Viewed by 3044
Abstract
The extensive use of antibiotics has contributed to the current antibiotic resistance crisis. Livestock infections of Salmonella spp, Clostridium spp. and E. coli antimicrobial-resistant bacteria represent a public threat to human and animal health. To reduce the incidence of these zoonoses, essential oils [...] Read more.
The extensive use of antibiotics has contributed to the current antibiotic resistance crisis. Livestock infections of Salmonella spp, Clostridium spp. and E. coli antimicrobial-resistant bacteria represent a public threat to human and animal health. To reduce the incidence of these zoonoses, essential oils (EOs) could be effective antibiotic alternatives. This study aims at identifying EOs safe for use, effective both in complementary therapy and in the environmental sanitization of intensive farming. Natural products were chemo-characterized by gas chromatography. Three S. Typhimurium, three C. perfringens and four E. coli strains isolated from poultry and swine farms were used to assess the antimicrobial properties of nine EOs and a modified GR-OLI (mGR-OLI). The toxicity of the most effective ones (Cinnamomum zeylanicum, Cz; Origanum vulgare, Ov) was also evaluated on porcine spermatozoa and Galleria mellonella larvae. Cz, Ov and mGR-OLI showed the strongest antimicrobial activity; their volatile components were also able to significantly inhibit the growth of tested strains. In vitro, Ov toxicity was slightly lower than Cz, while it showed no toxicity on G. mellonella larvae. In conclusion, the study confirms the importance of evaluating natural products to consolidate the idea of safe EO applications in reducing and preventing intensive livestock infections. Full article
(This article belongs to the Special Issue Antimicrobial Activity of Essential Oils and Hydrolates)
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19 pages, 3275 KiB  
Article
Diffusional Interactions among Marine Phytoplankton and Bacterioplankton: Modelling H2O2 as a Case Study
by Naaman M. Omar, Ondřej Prášil, J. Scott P. McCain and Douglas A. Campbell
Microorganisms 2022, 10(4), 821; https://doi.org/10.3390/microorganisms10040821 - 15 Apr 2022
Cited by 5 | Viewed by 2511
Abstract
Marine phytoplankton vary widely in size across taxa, and in cell suspension densities across habitats and growth states. Cell suspension density and total biovolume determine the bulk influence of a phytoplankton community upon its environment. Cell suspension density also determines the intercellular spacings [...] Read more.
Marine phytoplankton vary widely in size across taxa, and in cell suspension densities across habitats and growth states. Cell suspension density and total biovolume determine the bulk influence of a phytoplankton community upon its environment. Cell suspension density also determines the intercellular spacings separating phytoplankton cells from each other, or from co-occurring bacterioplankton. Intercellular spacing then determines the mean diffusion paths for exchanges of solutes among co-occurring cells. Marine phytoplankton and bacterioplankton both produce and scavenge reactive oxygen species (ROS), to maintain intracellular ROS homeostasis to support their cellular processes, while limiting damaging reactions. Among ROS, hydrogen peroxide (H2O2) has relatively low reactivity, long intracellular and extracellular lifetimes, and readily crosses cell membranes. Our objective was to quantify how cells can influence other cells via diffusional interactions, using H2O2 as a case study. To visualize and constrain potentials for cell-to-cell exchanges of H2O2, we simulated the decrease of [H2O2] outwards from representative phytoplankton taxa maintaining internal [H2O2] above representative seawater [H2O2]. [H2O2] gradients outwards from static cell surfaces were dominated by volumetric dilution, with only a negligible influence from decay. The simulated [H2O2] fell to background [H2O2] within ~3.1 µm from a Prochlorococcus cell surface, but extended outwards 90 µm from a diatom cell surface. More rapid decays of other, less stable ROS, would lower these threshold distances. Bacterioplankton lowered simulated local [H2O2] below background only out to 1.2 µm from the surface of a static cell, even though bacterioplankton collectively act to influence seawater ROS. These small diffusional spheres around cells mean that direct cell-to-cell exchange of H2O2 is unlikely in oligotrophic habits with widely spaced, small cells; moderate in eutrophic habits with shorter cell-to-cell spacing; but extensive within phytoplankton colonies. Full article
(This article belongs to the Special Issue Phytoplankton-Bacteria Interactions 2.0)
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9 pages, 963 KiB  
Article
Microbiological Survey of 47 Permanent Makeup Inks Available in the United States
by Sunghyun Yoon, Sandeep Kondakala, Seong Won Nho, Mi Sun Moon, Mei Chiung J. Huang, Goran Periz, Ohgew Kweon and Seongjae Kim
Microorganisms 2022, 10(4), 820; https://doi.org/10.3390/microorganisms10040820 - 15 Apr 2022
Cited by 4 | Viewed by 3072
Abstract
In two previous surveys, the U.S. Food and Drug Administration (FDA) identified microbial contamination in 53 of 112 (47%) unopened tattoo inks and tattoo-ink-related products (e.g., diluents) from 15 manufacturers in the U.S. In this study, we primarily focused our microbiological survey on [...] Read more.
In two previous surveys, the U.S. Food and Drug Administration (FDA) identified microbial contamination in 53 of 112 (47%) unopened tattoo inks and tattoo-ink-related products (e.g., diluents) from 15 manufacturers in the U.S. In this study, we primarily focused our microbiological survey on permanent makeup (PMU) inks. We conducted a survey of 47 unopened PMU inks from nine manufacturers and a comparative species-centric co-occurrence network (SCN) analysis using the survey results. Aerobic plate count and enrichment culture methods using the FDA’s Bacteriological Analytical Manual (BAM) Chapter 23 revealed that 9 (19%) inks out of 47, from five manufacturers, were contaminated with microorganisms. The level of microbial contamination was less than 250 CFU/g in eight inks and 980 CFU/g in one ink. We identified 26 bacteria that belong to nine genera and 21 species, including some clinically relevant species, such as Alloiococcus otitis, Dermacoccus nishinomiyaensis, Kocuria rosea, and Pasteurella canis. Among the identified microorganisms, the SCN analysis revealed dominance and a strong co-occurrence relation of spore-forming extreme environment survivors, Bacillus spp., with close phylogenetic/phenotypic relationships. These results provide practical insights into the possible microbial contamination factors and positive selection pressure of PMU inks. Full article
(This article belongs to the Special Issue Detection, Genophenotypic Characterization, and Antimicrobial Resistance of Microbial Contaminants)
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22 pages, 5152 KiB  
Article
Discovery of Chlorophyll d: Isolation and Characterization of a Far-Red Cyanobacterium from the Original Site of Manning and Strain (1943) at Moss Beach, California
by Nancy Y. Kiang, Wesley D. Swingley, Dikshyant Gautam, Jared T. Broddrick, Daniel J. Repeta, John F. Stolz, Robert E. Blankenship, Benjamin M. Wolf, Angela M. Detweiler, Kathy Ann Miller, Jacob J. Schladweiler, Ron Lindeman and Mary N. Parenteau
Microorganisms 2022, 10(4), 819; https://doi.org/10.3390/microorganisms10040819 - 14 Apr 2022
Cited by 4 | Viewed by 3906
Abstract
We have isolated a chlorophyll-d-containing cyanobacterium from the intertidal field site at Moss Beach, on the coast of Central California, USA, where Manning and Strain (1943) originally discovered this far-red chlorophyll. Here, we present the cyanobacterium’s environmental description, culturing procedure, pigment [...] Read more.
We have isolated a chlorophyll-d-containing cyanobacterium from the intertidal field site at Moss Beach, on the coast of Central California, USA, where Manning and Strain (1943) originally discovered this far-red chlorophyll. Here, we present the cyanobacterium’s environmental description, culturing procedure, pigment composition, ultrastructure, and full genome sequence. Among cultures of far-red cyanobacteria obtained from red algae from the same site, this strain was an epiphyte on a brown macroalgae. Its Qyin vivo absorbance peak is centered at 704–705 nm, the shortest wavelength observed thus far among the various known Acaryochloris strains. Its Chl a/Chl d ratio was 0.01, with Chl d accounting for 99% of the total Chl d and Chl a mass. TEM imagery indicates the absence of phycobilisomes, corroborated by both pigment spectra and genome analysis. The Moss Beach strain codes for only a single set of genes for producing allophycocyanin. Genomic sequencing yielded a 7.25 Mbp circular chromosome and 10 circular plasmids ranging from 16 kbp to 394 kbp. We have determined that this strain shares high similarity with strain S15, an epiphyte of red algae, while its distinct gene complement and ecological niche suggest that this strain could be the closest known relative to the original Chl d source of Manning and Strain (1943). The Moss Beach strain is designated Acaryochloris sp. (marina) strain Moss Beach. Full article
(This article belongs to the Special Issue Phototrophic Bacteria)
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18 pages, 3769 KiB  
Review
Where the Little Ones Play the Main Role—Picophytoplankton Predominance in the Soda and Hypersaline Lakes of the Carpathian Basin
by Boglárka Somogyi, Tamás Felföldi, Emil Boros, Attila Szabó and Lajos Vörös
Microorganisms 2022, 10(4), 818; https://doi.org/10.3390/microorganisms10040818 - 14 Apr 2022
Cited by 8 | Viewed by 2596
Abstract
The extreme environmental conditions of the diverse saline inland waters (soda lakes and pans, hypersaline lakes and ponds) of the Carpathian Basin are an advantage for picophytoplankton. The abundance of picophytoplankton in these waters can be up to several orders of magnitude higher [...] Read more.
The extreme environmental conditions of the diverse saline inland waters (soda lakes and pans, hypersaline lakes and ponds) of the Carpathian Basin are an advantage for picophytoplankton. The abundance of picophytoplankton in these waters can be up to several orders of magnitude higher than that in freshwater shallow lakes, but differences are also found within different saline water types: higher picophytoplankton abundances were observed in hypersaline lakes compared to humic soda lakes, and their highest numbers were detected in turbid soda lakes. Moreover, their contribution to phytoplankton biomass is higher than that in shallow freshwater lakes with similar trophic states. Based on long-term data, their ratio within the phytoplankton increased with turbidity in the case of turbid soda lakes, while, in hypersaline lakes, their proportion increased with salinity. Picocyanobacteria were only detected with high abundance (>106–107 cells/mL) in turbid soda lakes, while picoeukaryotes occurred in high numbers in both turbid and hypersaline lakes. Despite the extreme conditions of the lakes, the diversity of picophytoplankton is remarkable, with the dominance of non-marine Synechococcus/Cyanobium, Choricystis, Chloroparva and uncultured trebouxiophycean green algae in the soda lakes, and marine Synechococcus and Picochlorum in the hypersaline lakes. Full article
(This article belongs to the Special Issue Ecology, Diversity and Distribution of Pico-Sized Algae)
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17 pages, 26310 KiB  
Article
Responses of Soil Microbial Communities and Networks to Precipitation Change in a Typical Steppe Ecosystem of the Loess Plateau
by Yutao Wang, Yingzhong Xie, Hongbin Ma, Yi Zhang, Juan Zhang, Hao Zhang, Xu Luo and Jianping Li
Microorganisms 2022, 10(4), 817; https://doi.org/10.3390/microorganisms10040817 - 14 Apr 2022
Cited by 10 | Viewed by 2956
Abstract
The response of microbial communities to changes in precipitation can regulate the nutrition cycling of terrestrial ecosystems, but the effect on the structure and interaction of microbial communities and the relationship with environmental factors in arid and semiarid areas are unclear. Here, a [...] Read more.
The response of microbial communities to changes in precipitation can regulate the nutrition cycling of terrestrial ecosystems, but the effect on the structure and interaction of microbial communities and the relationship with environmental factors in arid and semiarid areas are unclear. Here, a field simulation experiment using three precipitation gradients, 50% of normal precipitation (P50), normal precipitation (P100) and 150% of normal precipitation (P150), was carried out in the typical grassland of the Loess Plateau. We applied high-throughput sequencing and network analysis to explore the effect of precipitation changes to soil microbial communities. The results indicated that the structural composition of the microbial community responded to precipitation treatments dramatically. The Top 50 microbials were divided into resource-limited, drought-tolerant and sensitive groups based on their response to altered precipitation. The network of bacteria was more complex and stronger than fungi. Bacterial networks were less stable but more adaptable under drought than fungal. Increasing precipitation promoted the complication and firmness of fungi networks. These findings are crucial for revealing the effects of climate change on soil microbial communities in arid-land and elsewhere and can provide valuable guidance for ecological restoration and response to climate change of the Loess Plateau. Full article
(This article belongs to the Section Environmental Microbiology)
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18 pages, 4685 KiB  
Article
Temporal and Spatial Patterns of Sediment Microbial Communities and Driving Environment Variables in a Shallow Temperate Mountain River
by Wang Tian, Huayong Zhang, Yuhao Guo, Zhongyu Wang and Tousheng Huang
Microorganisms 2022, 10(4), 816; https://doi.org/10.3390/microorganisms10040816 - 14 Apr 2022
Cited by 12 | Viewed by 2848
Abstract
Microbial communities in sediment play an important role in the circulation of nutrients in aquatic ecosystems. In this study, the main environmental factors and sediment microbial communities were investigated bimonthly from August 2018 to June 2020 at River Taizicheng, a shallow temperate mountain [...] Read more.
Microbial communities in sediment play an important role in the circulation of nutrients in aquatic ecosystems. In this study, the main environmental factors and sediment microbial communities were investigated bimonthly from August 2018 to June 2020 at River Taizicheng, a shallow temperate mountain river at the core area of the 2022 Winter Olympics. Microbial community structure was analyzed using 16S rRNA genes (bacteria 16S V3 + V4 and archaea 16S V4 + V5) and high-throughput sequencing technologies. Structure equation model (SEM) and canonical correspondence analysis (CCA) were used to explore the driving environmental factors of the microbial community. Our results showed that the diversity indices of the microbial community were positively influenced by sediment nutrients but negatively affected by water nutrients. Bacteroidetes and Proteobacteria were the most dominant phyla. The best-fitted SEM model indicated that environmental variables not only affected community abundance directly, but also indirectly through influencing their diversity. Flavobacterium, Arenimonas and Terrimonas were the dominant genera as a result of enriched nutrients. The microbial community had high spatial–temporal autocorrelation. CCA showed that DO, WT and various forms of phosphorus were the main variables affecting the temporal and spatial patterns of the microbial community in the river. The results will be helpful in understanding the driving factors of microbial communities in temperate monsoon areas. Full article
(This article belongs to the Section Environmental Microbiology)
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20 pages, 2725 KiB  
Article
Sheep Infection Trials with ‘Phase-Locked’ Vpma Expression Variants of Mycoplasma agalactiae—Towards Elucidating the Role of a Multigene Family Encoding Variable Surface Lipoproteins in Infection and Disease
by Rohini Chopra-Dewasthaly, Andreas Dagn, Christian Lohinger, René Brunthaler, Martina Flöck, Munkhtsetseg Kargl, Shrilakshmi Hegde, Joachim Spergser and Renate Rosengarten
Microorganisms 2022, 10(4), 815; https://doi.org/10.3390/microorganisms10040815 - 14 Apr 2022
Cited by 1 | Viewed by 2092
Abstract
The significance of large multigene families causing high-frequency surface variations in mycoplasmas is not well-understood. Previously, VpmaY and VpmaU clonal variants of the Vpma family of lipoproteins of M. agalactiae were compared via experimental sheep infections using the two corresponding ‘Phase-Locked Mutants’. However, [...] Read more.
The significance of large multigene families causing high-frequency surface variations in mycoplasmas is not well-understood. Previously, VpmaY and VpmaU clonal variants of the Vpma family of lipoproteins of M. agalactiae were compared via experimental sheep infections using the two corresponding ‘Phase-Locked Mutants’. However, nothing is known about the infectivity of the remaining four Vpma expression variants VpmaX, VpmaW, VpmaZ and VpmaV as they were never evaluated in vivo. Here, in vivo infection and disease progression of all six Vpma expressers constituting the Vpma family of type strain PG2 were compared using the corresponding xer1-disrupted PLMs expressing single well-characterized Vpmas. Each of the six PLMs were separately evaluated using the intramammary sheep infection model along with the control phase-variable wildtype strain PG2. Thorough bacteriological, pathological and clinical examinations were performed, including assessment of milk quality, quantity and somatic cell counts. Altogether, the results indicated that the inability to vary the Vpma expression phase does not hamper the initiation of infection leading to mastitis for all six PLMs, except for PLMU, which showed a defect in host colonization and multiplication for the first 24 h p.i. and pathological/bacteriological analysis indicated a higher potential for systemic spread for PLMV and PLMX. This is the first study in which all isogenic expression variants of a large mycoplasma multigene family are tested in the natural host. Full article
(This article belongs to the Special Issue Mycoplasma Pathogenicity, Persistence and Virulence)
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9 pages, 1721 KiB  
Article
Epidemiology of Non-O157 Shiga Toxin-Producing Escherichia coli in the Province of Alberta, Canada, from 2018 to 2021
by Heather Glassman, Christina Ferrato and Linda Chui
Microorganisms 2022, 10(4), 814; https://doi.org/10.3390/microorganisms10040814 - 14 Apr 2022
Cited by 8 | Viewed by 2561
Abstract
Non-O157 serogroups contribute significantly to the burden of disease caused by Shiga toxin-producing Escherichia coli (STEC) and have been underrecognized by traditional detection algorithms. We described the epidemiology of non-O157 STEC in Alberta, Canada for the period of 2018 to 2021. All non-O157 [...] Read more.
Non-O157 serogroups contribute significantly to the burden of disease caused by Shiga toxin-producing Escherichia coli (STEC) and have been underrecognized by traditional detection algorithms. We described the epidemiology of non-O157 STEC in Alberta, Canada for the period of 2018 to 2021. All non-O157 STEC isolated from clinical samples were submitted for serotyping and qPCR targeting the stx1 and stx2 genes. A total of 729 isolates were identified. Increased detection occurred over the summer months, peaking in July. Patients 18 years and younger made up 42.4% of cases, with 31.1% in those 0–9 years of age. There was a slight female predominance (399/729, 54.7%) A total of 50 different serogroups were detected; the most common were O26 (30.3%), O103 (15.9%), O111 (12.8%), O121 (11.0%), O118 (3.3%) and O71 (2.9%). These six serogroups made up 76.2% of all isolates. In total, 567 (77.8%) were positive for stx1, 114 (15.6%) were positive for stx2 and 48 (6.6%) were positive for both stx1 and stx2. A wide variety of non-O157 serogroups have been detected in Alberta, with the most frequent serogroups differing from other locations. These results highlight the need for further characterization of their virulence factors and clinical impact. Full article
(This article belongs to the Special Issue Know Your Enemy: Improved Understanding, Detection, Control, and Therapy for Shiga Toxin-Producing Escherichia coli Infection)
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29 pages, 3265 KiB  
Review
The Retrospective on Atypical Brucella Species Leads to Novel Definitions
by Alessandra Occhialini, Dirk Hofreuter, Christoph-Martin Ufermann, Sascha Al Dahouk and Stephan Köhler
Microorganisms 2022, 10(4), 813; https://doi.org/10.3390/microorganisms10040813 - 14 Apr 2022
Cited by 21 | Viewed by 5077
Abstract
The genus Brucella currently comprises twelve species of facultative intracellular bacteria with variable zoonotic potential. Six of them have been considered as classical, causing brucellosis in terrestrial mammalian hosts, with two species originated from marine mammals. In the past fifteen years, field research [...] Read more.
The genus Brucella currently comprises twelve species of facultative intracellular bacteria with variable zoonotic potential. Six of them have been considered as classical, causing brucellosis in terrestrial mammalian hosts, with two species originated from marine mammals. In the past fifteen years, field research as well as improved pathogen detection and typing have allowed the identification of four new species, namely Brucella microti, Brucella inopinata, Brucella papionis, Brucella vulpis, and of numerous strains, isolated from a wide range of hosts, including for the first time cold-blooded animals. While their genome sequences are still highly similar to those of classical strains, some of them are characterized by atypical phenotypes such as higher growth rate, increased resistance to acid stress, motility, and lethality in the murine infection model. In our review, we provide an overview of state-of-the-art knowledge about these novel Brucella sp., with emphasis on their phylogenetic positions in the genus, their metabolic characteristics, acid stress resistance mechanisms, and their behavior in well-established in cellulo and in vivo infection models. Comparison of phylogenetic classification and phenotypical properties between classical and novel Brucella species and strains finally lead us to propose a more adapted terminology, distinguishing between core and non-core, and typical versus atypical brucellae, respectively. Full article
(This article belongs to the Special Issue Emerging Themes in Brucella and Brucellosis)
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10 pages, 423 KiB  
Article
Evaluation of Antimicrobial Resistance in Salmonella Strains Isolated from Food, Animal and Human Samples between 2017 and 2021 in Southern Italy
by Alessandra Alessiani, Elisa Goffredo, Maria Mancini, Gilda Occhiochiuso, Simona Faleo, Antonella Didonna, Rita Fischetto, Federica Suglia, Danila De Vito, Antonella Stallone, Luigi D’Attoli and Adelia Donatiello
Microorganisms 2022, 10(4), 812; https://doi.org/10.3390/microorganisms10040812 - 13 Apr 2022
Cited by 13 | Viewed by 2735
Abstract
Salmonella enterica is one of the most common causes of foodborne infection in the world, and the most common one in Italy. Italy collaborates with the other EU member states to survey the antimicrobial resistance of Salmonella on a large scale. This study [...] Read more.
Salmonella enterica is one of the most common causes of foodborne infection in the world, and the most common one in Italy. Italy collaborates with the other EU member states to survey the antimicrobial resistance of Salmonella on a large scale. This study on the situation in Apulia and Basilicata provides a more focused point of view on the territory, and anticipates the data reported in future Italian reports. Antimicrobial resistance was detected using the MIC detection method, with EUVSEC® plates, on the strains collected between 2017 and 2021. The results of serotyping showed that Salmonella Infantis is the serovar that has increased the most over time in veterinary samples, while Salmonella Tyhimurium and its monophasic variant are the most isolated in human samples. The results of the antimicrobial resistance study comply with European data, showing high resistance to quinolones, tetracyclines, ampicillin and trimethoprim, and low resistance to colistin and cephems. The significant exception was that all strains were resistant to sulphametoxazole. The presence of MDRs, which was 85% in veterinary and 77.4% in human strains, often included critically important antibiotics, which is a sign that more study and action is needed to manage the use of antibiotics. Full article
(This article belongs to the Section Antimicrobial Agents and Resistance)
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15 pages, 2153 KiB  
Article
Evaluating Methods of Preserving Aquatic Invertebrates for Microbiome Analysis
by Stephanie N. Vaughn and Colin R. Jackson
Microorganisms 2022, 10(4), 811; https://doi.org/10.3390/microorganisms10040811 - 13 Apr 2022
Cited by 3 | Viewed by 2576
Abstract
Research on the microbiomes of animals has increased substantially within the past decades. More recently, microbial analyses of aquatic invertebrates have become of increased interest. The storage method used while collecting aquatic invertebrates has not been standardized throughout the scientific community, and the [...] Read more.
Research on the microbiomes of animals has increased substantially within the past decades. More recently, microbial analyses of aquatic invertebrates have become of increased interest. The storage method used while collecting aquatic invertebrates has not been standardized throughout the scientific community, and the effects of common storage methods on the microbial composition of the organism is unknown. Using crayfish and dragonfly nymphs collected from a natural pond and crayfish maintained in an aquarium, the effects of two common storage methods, preserving in 95% ethanol and freezing at −20 °C, on the invertebrate bacterial microbiome was evaluated. We found that the bacterial community was conserved for two sample types (gut and exoskeleton) of field-collected crayfish stored either in ethanol or frozen, as was the gut microbiome of aquarium crayfish. However, there were significant differences between the bacterial communities found on the exoskeleton of aquarium crayfish stored in ethanol compared to those that were frozen. Dragonfly nymphs showed significant differences in gut microbial composition between species, but the microbiome was conserved between storage methods. These results demonstrate that preserving field-collected specimens of aquatic invertebrates in 95% ethanol is likely to be a simple and effective sample preservation method for subsequent gut microbiome analysis but is less reliable for the external microbiome. Full article
(This article belongs to the Special Issue Gut Microorganisms of Aquatic Animals 2.0)
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20 pages, 1294 KiB  
Review
The Human Mycobiome in Chronic Respiratory Diseases: Current Situation and Future Perspectives
by Juan de Dios Caballero, Rafael Cantón, Manuel Ponce-Alonso, Marta María García-Clemente, Elia Gómez G. de la Pedrosa, José Luis López-Campos, Luis Máiz, Rosa del Campo and Miguel Ángel Martínez-García
Microorganisms 2022, 10(4), 810; https://doi.org/10.3390/microorganisms10040810 - 13 Apr 2022
Cited by 13 | Viewed by 3902
Abstract
Microbes play an important role in the pathogenesis of chronic lung diseases, such as chronic obstructive pulmonary disease, cystic fibrosis, non-cystic fibrosis bronchiectasis, and asthma. While the role of bacterial pathogens has been extensively studied, the contribution of fungal species to the pathogenesis [...] Read more.
Microbes play an important role in the pathogenesis of chronic lung diseases, such as chronic obstructive pulmonary disease, cystic fibrosis, non-cystic fibrosis bronchiectasis, and asthma. While the role of bacterial pathogens has been extensively studied, the contribution of fungal species to the pathogenesis of chronic lung diseases is much less understood. The recent introduction of next-generation sequencing techniques has revealed the existence of complex microbial lung communities in healthy individuals and patients with chronic respiratory disorders, with fungi being an important part of these communities’ structure (mycobiome). There is growing evidence that the components of the lung mycobiome influence the clinical course of chronic respiratory diseases, not only by direct pathogenesis but also by interacting with bacterial species and with the host’s physiology. In this article, we review the current knowledge on the role of fungi in chronic respiratory diseases, which was obtained by conventional culture and next-generation sequencing, highlighting the limitations of both techniques and exploring future research areas. Full article
(This article belongs to the Special Issue Human Pathogenic Fungi: Host-Pathogen Interactions and Virulence)
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18 pages, 3782 KiB  
Article
Bacillus subtilis Inoculation Improves Nutrient Uptake and Physiological Activity in Sugarcane under Drought Stress
by Mariley de Cássia da Fonseca, João William Bossolani, Sirlene Lopes de Oliveira, Luiz Gustavo Moretti, José Roberto Portugal, Daniele Scudeletti, Elisa Fidêncio de Oliveira and Carlos Alexandre Costa Crusciol
Microorganisms 2022, 10(4), 809; https://doi.org/10.3390/microorganisms10040809 - 13 Apr 2022
Cited by 33 | Viewed by 4224
Abstract
Sugarcane (Saccharum spp.) is one of the most important crops in the world. Throughout the sugarcane’s growth stages, periods of drought are common, causing detrimental effects on plant growth. Therefore, the search for strategies for minimizing the impact of drought on sugarcane [...] Read more.
Sugarcane (Saccharum spp.) is one of the most important crops in the world. Throughout the sugarcane’s growth stages, periods of drought are common, causing detrimental effects on plant growth. Therefore, the search for strategies for minimizing the impact of drought on sugarcane development is of great interest. Plant growth-promoting bacteria hold the potential for improving tolerance to drought in agricultural systems. Thus, the present study aimed to evaluate whether inoculation with Bacillus subtilis can reduce the negative effects of drought on the nutritional, physiological, and morphological characteristics of sugarcane plants. For this, sugarcane was cultivated in a greenhouse, under controlled conditions of water and temperature, with the aid of four treatments: without and with inoculation of B. subtilis, in normal conditions of water availability, and in conditions of water restriction (2 × 2 factorial), with four replications. In treatments with inoculation, the pre-emerged seedlings were immersed in a B. subtilis solution and transplanted into experimental pots. Our results showed that inoculation with B. subtilis improved plant nutrition and chlorophyll concentrations. As a result, the gas exchange parameters (especially net photosynthetic rate and water use efficiency) were also improved, even under drought conditions. In addition, stress parameters (antioxidant metabolism activity) were reduced in inoculated plants. The sum of these beneficial effects resulted in increased root growth, tillering, stalk weight, and higher sucrose concentration in the stalks. Full article
(This article belongs to the Section Plant Microbe Interactions)
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16 pages, 816 KiB  
Article
High Genetic Diversity and Antimicrobial Resistance in Escherichia coli Highlight Arapaima gigas (Pisces: Arapaimidae) as a Reservoir of Quinolone-Resistant Strains in Brazilian Amazon Rivers
by Luciana Sampaio Lima, Aldo Aparecido Proietti-Junior, Yan Corrêa Rodrigues, Marcelo Cleyton da Silva Vieira, Luana Nepomuceno Gondim Costa Lima, Cintya de Oliveira Souza, Verônica Dias Gonçalves, Marcelo de Oliveira Lima, Dália dos Prazeres Rodrigues and Karla Valéria Batista Lima
Microorganisms 2022, 10(4), 808; https://doi.org/10.3390/microorganisms10040808 - 13 Apr 2022
Cited by 6 | Viewed by 3170
Abstract
The increasing prevalence of multi-drug resistant (MDR) Escherichia coli in distinct ecological niches, comprising water sources and food-producing animals, such as fish species, has been widely reported. In the present study, quinolone-resistant E. coli isolates from Arapirama gigas, a major fish species [...] Read more.
The increasing prevalence of multi-drug resistant (MDR) Escherichia coli in distinct ecological niches, comprising water sources and food-producing animals, such as fish species, has been widely reported. In the present study, quinolone-resistant E. coli isolates from Arapirama gigas, a major fish species in the Brazilian Amazon rivers and fish farms, were characterized regarding their antimicrobial susceptibility, virulence, and genetic diversity. A total of forty (40) specimens of A. gigas, including 20 farmed and 20 wild fish, were included. Thirty-four quinolone-resistant E. coli isolates were phenotypically tested by broth microdilution, while resistance and virulence genes were detected by PCR. Molecular epidemiology and genetic relatedness were analyzed by MLST and PFGE typing. The majority of isolates were classified as MDR and detected harboring blaCTX-M, qnrA and qnrB genes. Enterotoxigenic E. coli pathotype (ETEC) isolates were presented in low prevalence among farmed animals. MLST and PFGE genotyping revealed a wide genetic background, including the detection of internationally spread clones. The obtained data point out A. gigas as a reservoir in Brazilian Amazon aquatic ecosystems and warns of the interference of AMR strains in wildlife and environmental matrices. Full article
(This article belongs to the Special Issue Farm Animal and Wildlife Zoonotic Microorganisms)
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21 pages, 3769 KiB  
Article
Spread of West Nile Virus and Usutu Virus in the German Bird Population, 2019–2020
by Ute Ziegler, Felicitas Bergmann, Dominik Fischer, Kerstin Müller, Cora M. Holicki, Balal Sadeghi, Michael Sieg, Markus Keller, Rebekka Schwehn, Maximilian Reuschel, Luisa Fischer, Oliver Krone, Monika Rinder, Karolin Schütte, Volker Schmidt, Martin Eiden, Christine Fast, Anne Günther, Anja Globig, Franz J. Conraths, Christoph Staubach, Florian Brandes, Michael Lierz, Rüdiger Korbel, Thomas W. Vahlenkamp and Martin H. Groschupadd Show full author list remove Hide full author list
Microorganisms 2022, 10(4), 807; https://doi.org/10.3390/microorganisms10040807 - 12 Apr 2022
Cited by 28 | Viewed by 4725
Abstract
West Nile virus (WNV) and Usutu virus (USUV) are important flaviviruses circulating in Germany. While USUV was first reported more than 10 years ago, WNV has only reached the country in 2018. Wild birds are important amplifying hosts for both viruses. Therefore, we [...] Read more.
West Nile virus (WNV) and Usutu virus (USUV) are important flaviviruses circulating in Germany. While USUV was first reported more than 10 years ago, WNV has only reached the country in 2018. Wild birds are important amplifying hosts for both viruses. Therefore, we have been monitoring the bird population in different regions of Germany by a previously established network for many years. This report summarizes the results of molecular and/or serological methods of 2345 blood samples from birds of 22 different orders and over 2900 bird carcasses from 2019 and 2020. USUV RNA circulation was found in different regions of Germany, with emphasis on USUV lineages Europe 3 and Africa 3. Increased evidence of USUV lineage Europe 2 was detected in eastern Germany. WNV RNA was found only in birds from the eastern part of the country. The seroprevalence for USUV was between 3.11% and 7.20% in all three regions investigated, whereas the WNV seroprevalence spanned from 14.77% to 16.15% in eastern Germany, with a noticeable tendency for a westward and southward expansion in both years. Thus, wild bird monitoring for WNV and USUV can serve as an early warning system for a human exposure risk. Full article
(This article belongs to the Special Issue Arboviruses)
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11 pages, 961 KiB  
Article
A New Early Predictor of Fatal Outcome for COVID-19 in an Italian Emergency Department: The Modified Quick-SOFA
by Matteo Guarino, Benedetta Perna, Francesca Remelli, Francesca Cuoghi, Alice Eleonora Cesaro, Michele Domenico Spampinato, Martina Maritati, Carlo Contini and Roberto De Giorgio
Microorganisms 2022, 10(4), 806; https://doi.org/10.3390/microorganisms10040806 - 12 Apr 2022
Cited by 6 | Viewed by 2291
Abstract
Background: Since 2019, the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is causing a rapidly spreading pandemic. The present study aims to compare a modified quick SOFA (MqSOFA) score with the NEWS-2 score to predict in-hospital mortality (IHM), 30-days mortality and recovery [...] Read more.
Background: Since 2019, the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is causing a rapidly spreading pandemic. The present study aims to compare a modified quick SOFA (MqSOFA) score with the NEWS-2 score to predict in-hospital mortality (IHM), 30-days mortality and recovery setting. Methods: All patients admitted from March to October 2020 to the Emergency Department of St. Anna Hospital, Ferrara, Italy with clinically suspected SARS-CoV-2 infection were retrospectively included in this single-centre study and evaluated with the MqSOFA and NEWS-2 scores. Statistical and logistic regression analyses were applied to our database. Results: A total of 3359 individual records were retrieved. Among them, 2716 patients were excluded because of a negative nasopharyngeal swab and 206 for lacking data; thus, 437 patients were eligible. The data showed that the MqSOFA and NEWS-2 scores equally predicted IHM (p < 0.001) and 30-days mortality (p < 0.001). Higher incidences of coronary artery disease, congestive heart failure, cerebrovascular accidents, dementia, chronic kidney disease and cancer were found in the deceased vs. survived group. Conclusions: In this study we confirmed that the MqSOFA score was non-inferior to the NEWS-2 score in predicting IHM and 30-days mortality. Furthermore, the MqSOFA score was easier to use than NEWS-2 and is more suitable for emergency settings. Neither the NEWS-2 nor the MqSOFA scores were able to predict the recovery setting. Full article
(This article belongs to the Special Issue Advances in SARS-CoV-2 Infection)
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