Microorganisms

14 pages, 3946 KiB

Open AccessSystematic Review

White Coats at a Crossroads: Hygiene, Infection Risk, and Patient Trust in Healthcare Attire—An Umbrella Review with Quantitative Synthesis and Stress, Weaknesses, Opportunities, and Threats Analysis

by Christos Tsagkaris, Matthias Rueger, Samuel B. Tschudi and Thomas Dreher

Microorganisms 2024, 12(12), 2659; https://doi.org/10.3390/microorganisms12122659 (registering DOI) - 21 Dec 2024

Abstract

White coats, traditionally symbols of physicians’ hygiene and professionalism, are now scrutinized for potential infection risks during patient interactions. This review investigates whether wearing white coats is linked to microbial contamination, infection transmission, and patient expectations. An umbrella review of peer-reviewed studies and [...] Read more.

White coats, traditionally symbols of physicians’ hygiene and professionalism, are now scrutinized for potential infection risks during patient interactions. This review investigates whether wearing white coats is linked to microbial contamination, infection transmission, and patient expectations. An umbrella review of peer-reviewed studies and guidelines was conducted, with searches in PubMed/Medline and Scopus using terms related to medical attire, infection control, patient perceptions, and discrimination. Ten records were included, and a bibliometric analysis was performed with VOS Viewer. Bias appraisal was conducted using the JBI Bias Assessment Toolset, and a SWOT analysis was developed to support evidence-based decision-making. Findings indicate that white coats may harbor pathogens such as Staphylococcus aureus, Gram-positive cocci, Gram-negative rods, and MRSA. To mitigate contamination risks, it is recommended that physicians roll up coat sleeves during examinations and that the coats receive daily laundering in healthcare settings. However, evidence supporting a coatless policy is yet to be published. Patients tend to expect physicians to wear identifiable attire, like white coats or scrubs for surgeons. Recent research in this field shifts the focus from infection control to the impact of attire on patient trust and physician–patient relationships. Full article

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

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18 pages, 2363 KiB

Open AccessArticle

Differential Immunological Responses of Adult Domestic and Bighorn Sheep to Inoculation with Mycoplasma ovipneumoniae Type Strain Y98

by Sally A. Madsen-Bouterse, David R. Herndon, Paige C. Grossman, Alejandra A. Rivolta, Lindsay M. Fry, Brenda M. Murdoch and Lindsay M. W. Piel

Microorganisms 2024, 12(12), 2658; https://doi.org/10.3390/microorganisms12122658 (registering DOI) - 21 Dec 2024

Abstract

Bighorn sheep (BHS) populations have been reported to experience high levels of morbidity and mortality following infection with Mycoplasma ovipneumoniae. This contrasts with the subclinical presentation in domestic sheep (DS). Understanding this difference requires baseline knowledge of pre- and post-infection immune responses [...] Read more.

Bighorn sheep (BHS) populations have been reported to experience high levels of morbidity and mortality following infection with Mycoplasma ovipneumoniae. This contrasts with the subclinical presentation in domestic sheep (DS). Understanding this difference requires baseline knowledge of pre- and post-infection immune responses of both species. The present study identifies differences in leukocyte phenotypes between adult BHS and DS before and after intranasal inoculation with 1 × 10⁸ Mycoplasma ovipneumoniae. Prior to inoculation, BHS were confirmed to have a higher abundance of leukocyte CD14 and serum concentrations of IL-36RA. In contrast, DS had a higher leukocyte abundance of CD16 in addition to previously observed integrin markers and CD172a, as well as greater serum TNF-α concentrations. Within 15 days of inoculation, BHS displayed signs of mild respiratory disease and M. ovipneumoniae DNA was detected on nasal swabs using a quantitative PCR; meanwhile, DS exhibited few to no clinical signs and had levels of M. ovipneumoniae DNA below the standard curve threshold. Immunologic markers remained relatively consistent pre- and post-inoculation in DS, while BHS demonstrated changes in the peripheral leukocyte expression of CD172a and CD14. Circulating serum IL-36RA decreased and CXCL10 increased within BHS. These findings highlight significant differences in cellular immunity between BHS and DS, raised and housed under similar conditions, prior to and following inoculation with M. ovipneumoniae. Full article

(This article belongs to the Special Issue Advances in Mycoplasma Research)

20 pages, 8907 KiB

Open AccessArticle

Proline Improves Pullulan Biosynthesis Under High Sugar Stress Condition

by Keyi Liu, Junqing Wang, Feng Li, Ruiming Wang, Qingming Zeng, Zhenxing Zhang, Hongwei Liu and Piwu Li

Microorganisms 2024, 12(12), 2657; https://doi.org/10.3390/microorganisms12122657 (registering DOI) - 21 Dec 2024

Abstract

Pullulan is an extracellular polysaccharide produced via the fermentation of Aureobasidium pullulans. However, high sugar concentrations and hyperosmotic stress limit pullulan biosynthesis during the fermentation process. Therefore, we investigated the effects of proline supplementation on A. pullulans growth and pullulan biosynthesis [...] Read more.

Pullulan is an extracellular polysaccharide produced via the fermentation of Aureobasidium pullulans. However, high sugar concentrations and hyperosmotic stress limit pullulan biosynthesis during the fermentation process. Therefore, we investigated the effects of proline supplementation on A. pullulans growth and pullulan biosynthesis under high sugar and hyperosmotic stress using physiological, biochemical, and transcriptomic analyses. High sugar concentrations significantly inhibited A. pullulans growth and pullulan biosynthesis. High sugar and hyperosmotic stress conditions significantly increased intracellular proline content in A. pullulans. However, treatment with proline (400 mg/L proline) significantly increased biomass and pullulan yield by 10.75% and 30.06% (174.8 g/L), respectively, compared with those in the control group. To further investigate the effect of proline on the fermentation process, we performed scanning electron microscopy and examined the activities of key fermentation enzymes. Proline treatment preserved cell integrity and upregulated the activities of key enzymes involved in pullulan biosynthesis. Transcriptome analysis revealed that most differentially expressed genes in the proline group were associated with metabolic pathways, including glycolysis/gluconeogenesis, pyruvate metabolism, and sulfur metabolism. Conclusively, proline supplementation protects A. pullulans against high sugar and hyperosmotic stress, providing a new theoretical basis and strategy for the efficient industrial production of pullulans. Full article

(This article belongs to the Special Issue Advances in Metabolic Engineering of Industrial Microorganisms)

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16 pages, 946 KiB

Open AccessReview

Host Long Noncoding RNAs as Key Players in Mycobacteria–Host Interactions

by Stephen K. Kotey, Xuejuan Tan, Audrey L. Kinser, Lin Liu and Yong Cheng

Microorganisms 2024, 12(12), 2656; https://doi.org/10.3390/microorganisms12122656 (registering DOI) - 21 Dec 2024

Abstract

Mycobacterial infections, caused by various species within the Mycobacterium genus, remain one of the main challenges to global health across the world. Understanding the complex interplay between the host and mycobacterial pathogens is essential for developing effective diagnostic and therapeutic strategies. Host long [...] Read more.

Mycobacterial infections, caused by various species within the Mycobacterium genus, remain one of the main challenges to global health across the world. Understanding the complex interplay between the host and mycobacterial pathogens is essential for developing effective diagnostic and therapeutic strategies. Host long noncoding RNAs (lncRNAs) have emerged as key regulators in cellular response to bacterial infections within host cells. This review provides an overview of the intricate relationship between mycobacterial infections and host lncRNAs in the context of Mycobacterium tuberculosis and non-tuberculous mycobacterium (NTM) infections. Accumulation of evidence indicates that host lncRNAs play a critical role in regulating cellular response to mycobacterial infection within host cells, such as macrophages, the primary host cells for mycobacterial intracellular survival. The expression of specific host lncRNAs has been implicated in the pathogenesis of mycobacterial infections, providing potential targets for the development of novel host-directed therapies and biomarkers for TB diagnosis. In summary, this review aims to highlight the current state of knowledge regarding the involvement of host lncRNAs in mycobacterial infections. It also emphasizes their potential application as novel diagnostic biomarkers and therapeutic targets. Full article

(This article belongs to the Special Issue Editorial Board Members’ Collection Series: Bacterial Infection)

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21 pages, 15157 KiB

Open AccessArticle

Microbial Dynamics: Assessing Skincare Regimens’ Impact on the Facial Skin Microbiome and Skin Health Parameters

by Nicole Wagner, Valerie Diane Valeriano, Samuel Diou-Hirtz, Evelina Björninen, Ulf Åkerström, Lars Engstrand, Ina Schuppe-Koistinen and Johanna Maria Gillbro

Microorganisms 2024, 12(12), 2655; https://doi.org/10.3390/microorganisms12122655 (registering DOI) - 21 Dec 2024

Abstract

The human skin microbiome, a complex ecosystem of microbes, plays a pivotal role in skin health. This study aimed to investigate the impact of two skincare regimens, with preservatives (CSPs) and preservative-free (PFPs), on the skin microbiome in correlation to skin quality. double-blind [...] Read more.

The human skin microbiome, a complex ecosystem of microbes, plays a pivotal role in skin health. This study aimed to investigate the impact of two skincare regimens, with preservatives (CSPs) and preservative-free (PFPs), on the skin microbiome in correlation to skin quality. double-blind randomized cosmetic studywith a split-face design was conducted on 26 female participants. Microbial diversity and abundance were analyzed using 16S rRNA amplicon sequence data and skin quality utilizing the Antera 3D skin camera. We confirmed earlier studies on the identification of major skin microbial taxa at the genus level, including Cutibacterium acnes, Corynebacterium, and Neisseriaceae as a predominant part of the facial skin microbiome. Furthermore, microbiome profile-based subgrouping was employed, which revealed that the cluster, characterized by the Neisseriaceae family as its predominant organism, exhibited significant reduction in folds count, fine lines, and redness after application of PFP compared to CSP. A Spearman correlation analysis highlighted the correlation between changes in specific bacteria and skin quality parameters such as redness, pores, and texture in the context of comparing PFP and CSP. Overall, the PFP treatment demonstrated a greater number of significant correlations between bacterial changes and skin quality compared to the CSP treatment, suggesting a distinct impact of the preservative-free skincare regimen on the skin microbiome and skin quality. Our study provides insights into different microbiome-centered approaches to improve our understanding of the skin microbiome’s interplay with skin quality but also highlights the need for larger, comprehensive research to further understand the microbiome’s role in dermatology. Full article

(This article belongs to the Special Issue Feature Papers in Microbiomes)

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23 pages, 7582 KiB

Open AccessArticle

Endophytic Bacteria from the Desiccation-Tolerant Plant Selaginella lepidophylla and Their Potential as Plant Growth-Promoting Microorganisms

by Maria Guadalupe Castillo-Texta, José Augusto Ramírez-Trujillo, Edgar Dantán-González, Mario Ramírez-Yáñez and Ramón Suárez-Rodríguez

Microorganisms 2024, 12(12), 2654; https://doi.org/10.3390/microorganisms12122654 (registering DOI) - 21 Dec 2024

Abstract

Bacteria associated with plants, whether rhizospheric, epiphytic, or endophytic, play a crucial role in plant productivity and health by promoting growth through complex mechanisms known as plant growth promoters. This study aimed to isolate, characterize, identify, and evaluate the potential of endophytic bacteria [...] Read more.

Bacteria associated with plants, whether rhizospheric, epiphytic, or endophytic, play a crucial role in plant productivity and health by promoting growth through complex mechanisms known as plant growth promoters. This study aimed to isolate, characterize, identify, and evaluate the potential of endophytic bacteria from the resurrection plant Selaginella lepidophylla in enhancing plant growth, using Arabidopsis thaliana ecotype Col. 0 as a model system. Plant growth-promotion parameters were assessed on the bacterial isolates; this assessment included the quantification of indole-3-acetic acid, phosphate solubilization, and biological nitrogen fixation, a trehalose quantification, and the siderophore production from 163 endophytic bacteria isolated from S. lepidophylla. The bacterial genera identified included Agrobacterium, Burkholderia, Curtobacterium, Enterobacter, Erwinia, Pantoea, Pseudomonas, and Rhizobium. The plant growth promotion in A. thaliana was evaluated both in Murashige Skoog medium, agar-water, and direct seed inoculation. The results showed that the bacterial isolates enhanced primary root elongation and lateral root and root hair development, and increased the fresh and dry biomass. Notably, three isolates promoted early flowering in A. thaliana. Based on these findings, we propose the S. lepidophylla bacterial isolates as ideal candidates for promoting growth in other agriculturally important plants. Full article

(This article belongs to the Section Plant Microbe Interactions)

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18 pages, 1176 KiB

Open AccessReview

Respiratory Flora Intervention: A New Strategy for the Prevention and Treatment of Occupationally Related Respiratory Allergy in Healthcare Workers

by Linglin Gao, Xi Chen, Ziyi Jiang, Jie Zhu and Qiang Wang

Microorganisms 2024, 12(12), 2653; https://doi.org/10.3390/microorganisms12122653 (registering DOI) - 20 Dec 2024

Abstract

Occupational allergic respiratory disease in healthcare workers due to occupational exposure has received widespread attention. At the same time, evidence of altered respiratory flora associated with the development of allergy has been found in relevant epidemiologic studies. It is of concern that the [...] Read more.

Occupational allergic respiratory disease in healthcare workers due to occupational exposure has received widespread attention. At the same time, evidence of altered respiratory flora associated with the development of allergy has been found in relevant epidemiologic studies. It is of concern that the composition of nasopharyngeal flora in healthcare workers differs significantly from that of non-healthcare workers due to occupational factors, with a particularly high prevalence of carriage of pathogenic and drug-resistant bacteria. Recent studies have found that interventions with upper respiratory tract probiotics can significantly reduce the incidence of respiratory allergies and infections. We searched PubMed and other databases to describe the burden of allergic respiratory disease and altered respiratory flora in healthcare workers in this narrative review, and we summarize the mechanisms and current state of clinical research on the use of flora interventions to ameliorate respiratory allergy, with the aim of providing a new direction for protecting the respiratory health of healthcare workers. Full article

(This article belongs to the Section Medical Microbiology)

16 pages, 3242 KiB

Open AccessArticle

The Nitrogen Removal Characteristics of a Novel Salt-Tolerant Bacterium, Enterobacter quasihormaechei DGFC5, Isolated from Municipal Sludge

by Bingguo Wang, Huanlong Peng and Wei Liu

Microorganisms 2024, 12(12), 2652; https://doi.org/10.3390/microorganisms12122652 (registering DOI) - 20 Dec 2024

Abstract

A novel bacterial strain, Enterobacter quasihormaechei DGFC5, was isolated from a municipal sewage disposal system. It efficiently removed ammonium, nitrate, and nitrite under conditions of 5% salinity, without intermediate accumulation. Provided with a mixed nitrogen source, DGFC5 showed a higher utilization priority for [...] Read more.

A novel bacterial strain, Enterobacter quasihormaechei DGFC5, was isolated from a municipal sewage disposal system. It efficiently removed ammonium, nitrate, and nitrite under conditions of 5% salinity, without intermediate accumulation. Provided with a mixed nitrogen source, DGFC5 showed a higher utilization priority for NH₄⁺-N. Whole-genome sequencing and nitrogen balance experiments revealed that DGFC5 can simultaneously consume NH₄⁺-N in the liquid phase through assimilation and heterotrophic nitrification, and effectively remove nitrate via aerobic denitrification and dissimilatory reduction reactions. Single-factor experiments were conducted to determine the optimal nitrogen removal conditions, which were as follows: a carbon-to-nitrogen ratio of 15, a shaking speed of 200 rpm, a pH of 7, C₄H₄Na₂O₄ as the carbon source, and a temperature of 30 °C. DGFC5 showed efficient nitrogen purification capabilities under a wide range of environmental conditions, indicating its potential for disposing of nitrogenous wastewater with high salinity. Full article

(This article belongs to the Section Environmental Microbiology)

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13 pages, 561 KiB

Open AccessArticle

Elimination of Methicillin-Resistant Staphylococcus aureus from Mammary Glands of Dairy Cows by an Additional Antibiotic Treatment Prior to Dry Cow Treatment

by Bernd-Alois Tenhagen, Mirka Elisabeth Wörmann, Anja Gretzschel, Mirjam Grobbel, Sven Maurischat and Tobias Lienen

Microorganisms 2024, 12(12), 2651; https://doi.org/10.3390/microorganisms12122651 - 20 Dec 2024

Abstract

Methicillin-resistant Staphylococcus aureus (MRSA) have been isolated from quarter milk samples of dairy cows, raising concerns over transmission to consumers of raw milk. This study investigates whether pre-treatment before dry-off can increase the success rate of dry cow treatment against MRSA. MRSA positive [...] Read more.

Methicillin-resistant Staphylococcus aureus (MRSA) have been isolated from quarter milk samples of dairy cows, raising concerns over transmission to consumers of raw milk. This study investigates whether pre-treatment before dry-off can increase the success rate of dry cow treatment against MRSA. MRSA positive cows were assigned to two treatment groups. Both groups received dry cow treatment with a licensed product. The test group was additionally treated intramammarily with pirlimycin over seven days prior to the dry-off treatment. The use of pirlimycin increased the elimination of MRSA from previously MRSA positive udder quarters significantly (96.0 vs. 53.3%). However, MRSA were still present in noses and udder clefts of cows in MRSA negative quarter milk samples. New infections were observed in some quarters in both groups. Quarters that remained positive carried the same strain as prior to treatment. All MRSA isolates were associated with clonal complex CC398. Resistance to pirlimycin associated with the genes erm(C) or lnu(B) was observed in one isolate each from new infections after calving. Pretreatment supported the elimination of MRSA from the udder but did not eliminate MRSA from other body sites. Using the treatment will not eliminate the bacteria from the herd. Full article

(This article belongs to the Special Issue Bacterial Infections and Antimicrobial Resistance in Animals)

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25 pages, 4800 KiB

Open AccessArticle

Innovative Methodology for Antimicrobial Susceptibility Determination in Mycoplasma Biofilms

by B. Tegner Jacobson, Jessica DeWit-Dibbert, Eli T. Selong, McKenna Quirk, Michael Throolin, Chris Corona, Sobha Sonar, LaShae Zanca, Erika R. Schwarz and Diane Bimczok

Microorganisms 2024, 12(12), 2650; https://doi.org/10.3390/microorganisms12122650 - 20 Dec 2024

Abstract

Mycoplasma spp. are facultative pathogens that contribute to the pathogenesis of multiple bovine diseases, including the bovine respiratory disease complex, and have been shown to form biofilms. Biofilm formation is associated with increased antibiotic resistance in many organisms, but accurate determination of antimicrobial [...] Read more.

Mycoplasma spp. are facultative pathogens that contribute to the pathogenesis of multiple bovine diseases, including the bovine respiratory disease complex, and have been shown to form biofilms. Biofilm formation is associated with increased antibiotic resistance in many organisms, but accurate determination of antimicrobial susceptibility in biofilms is challenging. In Mycoplasma spp., antimicrobial susceptibility is routinely determined using metabolic pH-dependent color change. However, biofilm formation can lead to reduced metabolism, making interpretation of metabolic readouts difficult. Therefore, we developed and optimized a new flow cytometry-based method for antimicrobial susceptibility testing in biofilm-forming Mycoplasma, termed the live/dead antimicrobial susceptibility test (LD-AST). The LD-AST measures the proportion of live bacteria upon exposure to antibiotics, works robustly with both planktonic and biofilm cultures, and enables the determination of the minimum bactericidal concentration (MBC) for a given antibiotic. We used two strains of Mycoplasma bovis (Donetta PG45 and Madison) and two clinical Mycoplasma bovoculi isolates (MVDL1 and MVDL2) to determine the impact of biofilm growth on antimicrobial susceptibility for gentamicin, enrofloxacin, or tetracycline. All Mycoplasma strains were susceptible to all antibiotics when cultured as planktonic cells, with MBCs in the expected range. However, three out of four strains (Donetta PG45, MVDL1, and MVDL2) were completely resistant to all three antibiotics when newly adhered biofilms were analyzed, whereas M. bovis Madison gave variable results. For mature biofilms that were cultured for 4–5 days before antibiotic exposure, results also were variable, with some strains showing an increased resistance with certain antibiotics and a decreased resistance with others. Overall, these results are consistent with earlier reports that biofilms can exhibit increased antimicrobial resistance. Full article

(This article belongs to the Special Issue Detection, Diagnosis, and Host Interactions of Animal Mycoplasmas)

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24 pages, 1561 KiB

Open AccessReview

Association Between Diabetes Mellitus–Tuberculosis and the Generation of Drug Resistance

by Axhell Aleid Cornejo-Báez, Roberto Zenteno-Cuevas and Julieta Luna-Herrera

Microorganisms 2024, 12(12), 2649; https://doi.org/10.3390/microorganisms12122649 - 20 Dec 2024

Abstract

Tuberculosis (TB), caused by Mycobacterium tuberculosis (Mtb), remains one of the leading infectious causes of death globally, with drug resistance presenting a significant challenge to control efforts. The interplay between type 2 diabetes mellitus (T2DM) and TB introduces additional complexity, as [...] Read more.

Tuberculosis (TB), caused by Mycobacterium tuberculosis (Mtb), remains one of the leading infectious causes of death globally, with drug resistance presenting a significant challenge to control efforts. The interplay between type 2 diabetes mellitus (T2DM) and TB introduces additional complexity, as T2DM triples the risk of active TB and exacerbates drug resistance development. This review explores how T2DM-induced metabolic and immune dysregulation fosters the survival of Mtb, promoting persistence and the emergence of multidrug-resistant strains. Mechanisms such as efflux pump activation and the subtherapeutic levels of isoniazid and rifampicin in T2DM patients are highlighted as key contributors to resistance. We discuss the dual syndemics of T2DM–TB, emphasizing the role of glycemic control and innovative therapeutic strategies, including efflux pump inhibitors and host-directed therapies like metformin. This review underscores the need for integrated diagnostic, treatment, and management approaches to address the global impact of T2DM–TB comorbidity and drug resistance. Full article

(This article belongs to the Special Issue Prevention, Treatment and Diagnosis of Tuberculosis, 2nd Edition)

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Graphical abstract

23 pages, 8712 KiB

Open AccessArticle

A Tachyplesin Antimicrobial Peptide from Theraphosidae Spiders with Potent Antifungal Activity Against Cryptococcus neoformans

by Brenda B. Michira, Yi Wang, James Mwangi, Kexin Wang, Demeke Asmamaw, Dawit Adisu Tadese, Jinai Gao, Mehwish Khalid, Qiu-Min Lu, Ren Lai and Juan Li

Microorganisms 2024, 12(12), 2648; https://doi.org/10.3390/microorganisms12122648 - 20 Dec 2024

Abstract

The venoms of Theraphosidae spiders have evolved into diverse natural pharmacopeias through selective pressures. Cryptococcus neoformans is a global health threat that frequently causes life-threatening meningitis and fungemia, particularly in immunocompromised patients. In this study, we identify a novel anti-C. neoformans peptide, [...] Read more.

The venoms of Theraphosidae spiders have evolved into diverse natural pharmacopeias through selective pressures. Cryptococcus neoformans is a global health threat that frequently causes life-threatening meningitis and fungemia, particularly in immunocompromised patients. In this study, we identify a novel anti-C. neoformans peptide, QS18 (QCFKVCFRKRCFTKCSRS), from the venom gland of China’s native spider species Chilobrachys liboensis by utilizing bioinformatic tools. QS18 shares over 50% sequence similarity with tachyplesin peptides, previously identified only in horseshoe crab hemocytes, expanding the known repertoire of the tachyplesin family to terrestrial arachnids. The oxidative folding of QS18 notably enhances its antifungal activity and stability, resulting in a minimum inhibitory concentration of 1.4 µM. The antimicrobial mechanism of QS18 involves cell membrane disruption. QS18 exhibits less than 5% hemolysis in human erythrocytes, indicating microbial selectivity and a favorable safety profile for therapeutic use. Furthermore, mouse model studies highlight QS18’s ability as an antifungal agent with notable anti-inflammatory activity. Our study demonstrates QS18 as both a promising template for spider venom peptide research and a novel candidate for the development of peptide antifungals. Full article

(This article belongs to the Special Issue Advances in Antimicrobial Peptides)

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24 pages, 4556 KiB

Open AccessArticle

Mosla Chinensis Extract Enhances Growth Performance, Antioxidant Capacity, and Intestinal Health in Broilers by Modulating Gut Microbiota

by Wei Wang, Yuyu Wang, Peng Huang, Junjuan Zhou, Guifeng Tan, Jianguo Zeng and Wei Liu

Microorganisms 2024, 12(12), 2647; https://doi.org/10.3390/microorganisms12122647 - 20 Dec 2024

Abstract

This study aimed to evaluate the effects of Mosla chinensis extract (MCE) on broiler intestinal health. A total of 240 1-day-old Arbor Acres (AA) broilers (balanced for sex) were randomly allocated into four treatment groups, each with six replicates of 10 chickens. The [...] Read more.

This study aimed to evaluate the effects of Mosla chinensis extract (MCE) on broiler intestinal health. A total of 240 1-day-old Arbor Acres (AA) broilers (balanced for sex) were randomly allocated into four treatment groups, each with six replicates of 10 chickens. The study comprised a starter phase (days 1–21) and a grower phase (days 22–42). The control group (C) received a basal diet, while the experimental groups were supplemented with low (S1, 500 mg/kg), medium (S2, 1000 mg/kg), and high doses (S3, 2000 mg/kg) of MCE. The results showed that MCE supplementation significantly improved average daily gain in broilers (p < 0.05) and reduced the feed-to-gain ratio in broilers. Additionally, MCE enhanced the anti-inflammatory and antioxidant capacity of broilers. In the duodenum and cecum, MCE significantly upregulated the expression of tight junction proteins Claudin-1, and Occludin, with the high-dose group showing the strongest effect on intestinal barrier protection (p < 0.05). There was no significant difference in ZO-1 in dudenum (p > 0.05). Microbial analysis indicated that MCE supplementation significantly reduced the Chao and Sobs indices in both the small and large intestines (p < 0.05). At the same time, the Coverage index of the small intestine increased, with the high-dose group demonstrating the most pronounced effect. Beta diversity analysis revealed that MCE had a significant modulatory effect on the microbial composition in the large intestine (p < 0.05), with a comparatively smaller impact on the small intestine. Furthermore, MCE supplementation significantly increased the relative abundance of Ruminococcaceae and Alistipes in the large intestine, along with beneficial genera that promote short-chain fatty acid (SCFA) production, thus optimizing the gut microecological environment. Correlation analysis of SCFAs further confirmed a significant association between the enriched microbiota and the production of acetate, propionate, and butyrate (p < 0.05). In conclusion, dietary supplementation with MCE promotes healthy growth and feed intake in broilers and exhibits anti-inflammatory and antioxidant effects. By optimizing gut microbiota composition, enhancing intestinal barrier function, and promoting SCFA production, MCE effectively maintains gut microecological balance, supporting broiler intestinal health. Full article

(This article belongs to the Special Issue Advances in Diet–Host–Gut Microbiome Interactions)

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13 pages, 4837 KiB

Open AccessArticle

Genetic Characterization, Transmission Pattern and Health Risk Analysis of Intestinal Colonization ESBL-Producing Escherichia coli in Vegetable Farming Population

by Fanghui Yao, Qian Zhao, Di Wang and Xuewen Li

Microorganisms 2024, 12(12), 2646; https://doi.org/10.3390/microorganisms12122646 - 20 Dec 2024

Abstract

The surging prevalence rates of ESBL-producing Escherichia coli (ESBL-Ec) pose a serious threat to public health. To date, most research on drug-resistant bacteria and genes has focused on livestock and poultry breeding areas, hospital clinical areas, natural water environments, and wastewater treatment plants. [...] Read more.

The surging prevalence rates of ESBL-producing Escherichia coli (ESBL-Ec) pose a serious threat to public health. To date, most research on drug-resistant bacteria and genes has focused on livestock and poultry breeding areas, hospital clinical areas, natural water environments, and wastewater treatment plants. However, few studies have been conducted on drug-resistant bacteria in vegetable cultivation. In this study, a total of vegetable farmers (n = 59) from six villages were surveyed. Fecal samples were collected from vegetable farmers; we also collected environmental samples, including river water, well water, soil, river sediment, vegetable surface swabs, and fish intestinal tracts. The ESBL-Ec intestinal colonization rate in vegetable farmers was 76.27%. PFGE results indicated two patterns of ESBL-Ec transmission within the vegetable cultivation area: among vegetable farmers, and among river water, river sediments, and vegetable farmers. Based on the phylogenetic analysis, three transmission patterns of ESBL-Ec outside the vegetable cultivation area were inferred: human–human, human–animal–human, and human–animal–environment. Twelve of the isolates carried closely related or identical IncF plasmids carrying bla_CTX-M. Whole genome sequencing (WGS) analysis showed that ST569-B2-O134:H31 and ST38-D-O50:H30 were associated with high disease risk. We assessed the health risks of the farming population and provided a reference basis for public health surveillance and environmental management by monitoring the prevalence and transmission of ESBL-Ec in vegetable areas. Full article

(This article belongs to the Special Issue Antimicrobial Stewardship: Strategies for Optimizing Antimicrobial Use and Combating Resistance)

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13 pages, 872 KiB

Open AccessArticle

Molecular Analysis of Escherichia coli and Correlations Between Phylogroups and Sequence Types from Different Sources

by João Gabriel Material Soncini, Vanessa Lumi Koga, Bruna Fuga, Zuleica Naomi Tano, Gerson Nakazato, Renata Katsuko Takayama Kobayashi, Nilton Lincopan and Eliana Carolina Vespero

Microorganisms 2024, 12(12), 2645; https://doi.org/10.3390/microorganisms12122645 - 20 Dec 2024

Abstract

Escherichia coli is a significant pathogen responsible for infections in both humans and livestock, possessing various virulence mechanisms and antimicrobial resistance that make it even more concerning. In this study, several internationally recognized clones of E. coli were identified, such as ST131, ST38, [...] Read more.

Escherichia coli is a significant pathogen responsible for infections in both humans and livestock, possessing various virulence mechanisms and antimicrobial resistance that make it even more concerning. In this study, several internationally recognized clones of E. coli were identified, such as ST131, ST38, ST648, and ST354, from chicken meat, pork, and human infection samples. Notably, ST131, belonging to phylogroup B2, was the dominant sequence type (ST) in human samples, while ST38, belonging to phylogroup D, was the most prevalent in meat samples. Several antibiotic resistance genes were identified: the gyrA gene mutation was the most prevalent, and CTX-M-55 was the most common extended-spectrum beta-lactamases (ESBLs), with significant differences noted for CTX-M-2 and CTX-M-15. Virulence-associated genes (VAGs) such as gad and iss were frequently found, especially in human isolates. These findings highlight the complex epidemiology of antibiotic-resistant E. coli in community settings and the potential risks associated with commercial meat. Full article

(This article belongs to the Special Issue Antimicrobial Resistance in Enterobacteriaceae and Enterococci)

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13 pages, 783 KiB

Open AccessArticle

Molecular Testing of Zoonotic Bacteria in Cattle, Sheep, and Goat Abortion Cases in Botswana

by Boitumelo M. Modise-Tlotleng, Sununguko W. Mpoloka, Tirumala B. K. Settypalli, Joseph Hyera, Tebogo Kgotlele, Kago Kumile, Mosarwa E. Sechele, Obuile O. Raboloko, Chandapiwa Marobela-Raborokgwe, Gerrit J. Viljoen, Giovanni Cattoli and Charles E. Lamien

Microorganisms 2024, 12(12), 2644; https://doi.org/10.3390/microorganisms12122644 - 20 Dec 2024

Abstract

Abortion is one of the major causes of economic losses in livestock production worldwide. Because several factors can lead to abortion in cattle, sheep and goats, laboratory diagnosis, including the molecular detection of pathogens causing abortion, is often necessary. Bacterial zoonotic diseases such [...] Read more.

Abortion is one of the major causes of economic losses in livestock production worldwide. Because several factors can lead to abortion in cattle, sheep and goats, laboratory diagnosis, including the molecular detection of pathogens causing abortion, is often necessary. Bacterial zoonotic diseases such as brucellosis, coxiellosis, leptospirosis, and listeriosis have been implicated in livestock abortion, but they are under diagnosed and under-reported in most developing countries, including Botswana. This study applied a recently developed multiplex high-resolution melting analysis technique, coupled with singleplex qPCR assays, to investigate abortions in livestock in Botswana, using 152 samples from cattle, sheep, and goat abortion cases. Brucella spp. were the most frequent pathogen detected, with an overall frequency of 21.1%, followed by Coxiella burnetii with 19.1%. Listeria monocytogenes and Leptospira spp. were not detected in any of specimens samples investigated. Mixed infections with Brucella spp. and C. burnetii were observed in 35% specimes examined. There was a good agreement between the multiplex qPCR-HRM and singleplex qPCR for detecting Brucella spp. and C. burnetii. This study is the first report on the syndromic testing of abortion-causing pathogens in Botswana. It shows the importance of molecular methods in the differential diagnosis of abortion-causing diseases in domestic ruminants. Full article

(This article belongs to the Section Veterinary Microbiology)

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15 pages, 694 KiB

Open AccessArticle

Subclinical Mastitis in Small-Holder Dairy Herds of Gansu Province, Northwest China: Prevalence, Bacterial Pathogens, Antimicrobial Susceptibility, and Risk Factor Analysis

by Ling Wang, Shahbaz Ul Haq, Muhammad Shoaib, Jiongjie He, Wenzhu Guo, Xiaojuan Wei and Xiaohong Zheng

Microorganisms 2024, 12(12), 2643; https://doi.org/10.3390/microorganisms12122643 - 20 Dec 2024

Abstract

This cross-sectional study assessed the prevalence, bacterial distribution, antimicrobial susceptibility, and potential risk factors associated with subclinical mastitis (SCM) in small-holder dairy herds in Gansu Province, Northwest China. Forty small-holder cow farms were randomly selected from eight cities/counties in six districts of Gansu [...] Read more.

This cross-sectional study assessed the prevalence, bacterial distribution, antimicrobial susceptibility, and potential risk factors associated with subclinical mastitis (SCM) in small-holder dairy herds in Gansu Province, Northwest China. Forty small-holder cow farms were randomly selected from eight cities/counties in six districts of Gansu Province, and a total of n = 530 lactating cows were included in this study. SCM prevalence was noted at 38.87% and 9.72% at the cow and quarter levels, respectively, based on the California Mastitis Test (CMT). The prevalence of the recovered bacterial species was noted as follows: S. agalactiae (36.02%), S. aureus (19.43%), coagulase-negative staphylococci (CNS) (16.11%), S. dysgalactiae (12.80%), E. coli (9.00%), and S. uberis (6.64%). All isolated bacteria were 100% multi-drug-resistant (MDR) except S. aureus (87.8% MDR). Antimicrobial susceptibility profiles revealed the increased resistance (>85%) of these pathogens to penicillin, streptomycin, trimethoprim–sulfamethoxazole, vancomycin, and erythromycin. However, these pathogens showed increased susceptibility to ampicillin, amoxicillin–sulbactam, ceftazidime, neomycin, kanamycin, spectinomycin, norfloxacin, ciprofloxacin, and doxycycline. The multivariate regression analysis demonstrated that old age, high parity, late lactation, lesions on teats, previous history of clinical mastitis, higher milk yield, and milking training were found to be potential risk factors (p < 0.001) associated with developing SCM in small-holder dairy cows in Gansu Province, China. These findings highlight the need for routine surveillance, antimicrobial stewardship, and effective preventive strategies to mitigate SCM in small-holder dairy production and their possible impacts, i.e., increased antimicrobial resistance and infection, on public health. Full article

(This article belongs to the Special Issue Antimicrobial Testing (AMT), Third Edition)

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14 pages, 4221 KiB

Open AccessArticle

Differences in the Microbial Composition and Function of the Arundo donax Rhizosphere Under Different Cultivation Conditions

by Fan Yang, Miaomiao Liu, Xin Wang, Yuting Hong, Qiuju Yao, Xiaoke Chang, Gongyao Shi, Weiwei Chen, Baoming Tian and Abeer Hegazy

Microorganisms 2024, 12(12), 2642; https://doi.org/10.3390/microorganisms12122642 - 19 Dec 2024

Abstract

Rhizosphere microorganisms play an important role in the health and development of root systems. Investigating the microbial composition of the rhizosphere is central to understanding the inter-root microbial function of Arundo donax under various cultivation conditions. To complement the metagenomic study of the [...] Read more.

Rhizosphere microorganisms play an important role in the health and development of root systems. Investigating the microbial composition of the rhizosphere is central to understanding the inter-root microbial function of Arundo donax under various cultivation conditions. To complement the metagenomic study of the Arundo donax rhizosphere, here, an amplicon-based metagenomic survey of bacteria and fungi was selected as a practical approach to analyzing the abundance, diversity index, and community structure of rhizosphere bacteria and fungi, as well as to study the effects of different cultivation methods on rhizosphere microbial diversity. Next-generation sequencing and QIIME2 analysis were used. The results indicated that microbial community richness, diversity, and evenness of the hydroponic samples were lower than those of soil samples when examining the α diversity indices of bacteria and fungi using Chao1, ACE, and Shannon metrics. In particular, the relative abundances of Proteobacteria, Rhizobiales, and Incertae sedis in hydroponic materials were higher, while Basidiomycota, Ascomycota, and Actinobacteriota dominated the flora in soil materials when comparing the numbers of OTUs and the ACE community richness estimator. Furthermore, the rhizosphere of hydroponic A. donax contained a higher abundance of nitrogen-fixing bacteria and photosynthetic bacteria, which contribute to root formation. Additionally, there was a significant presence of Basidiomycota, Ascomycota, and Actinobacteriota in soil A. donax, which can form hyphae. This reveals that the microbial community composition of the A. donax rhizosphere is significantly different under various cultivation conditions, suggesting that employing two distinct culturing techniques for Arundo donax may alter the microbiome. Furthermore, it provides technical support for the synergistic interaction between Arundo donax and rhizosphere microorganisms so as to better use the relationship between Arundo donax and basic microorganisms to solve the problems of Arundo donax growth and ecological restoration. Full article

(This article belongs to the Section Plant Microbe Interactions)

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16 pages, 7231 KiB

Open AccessArticle

Inhibitory Effects of Sulfur Derivatives on Leishmania tarentolae Cell Viability and Secreted Acid Phosphatase In Vitro

by Henry H. Shang, Zaryna Z. Zelaya, Christopher G. Hamaker and Marjorie A. Jones

Microorganisms 2024, 12(12), 2641; https://doi.org/10.3390/microorganisms12122641 - 19 Dec 2024

Abstract

Sulfonamide drugs were the original class of antibiotics, demonstrating the antibacterial potential of dithiocarbazate and thiosemicarbazone Schiff base derivatives of syringaldehyde and 4-hydroxy-3,5-dimethylbenzaldehyde. We synthesized unique Schiff bases via the condensation of the aldehydes with hydrazine derivatives, which allows for the easy synthesis [...] Read more.

Sulfonamide drugs were the original class of antibiotics, demonstrating the antibacterial potential of dithiocarbazate and thiosemicarbazone Schiff base derivatives of syringaldehyde and 4-hydroxy-3,5-dimethylbenzaldehyde. We synthesized unique Schiff bases via the condensation of the aldehydes with hydrazine derivatives, which allows for the easy synthesis of several related compounds. These Schiff base derivatives were tested for antileishmanial properties against the parasitic protozoan Leishmania tarentolae. The inhibitory properties of these sulfur compounds were tested using a series of cell viability and secreted acid phosphatase (SAP) assays. The results demonstrated that compounds ZZ1-04 and ZZ1-20 had potent inhibitory effects on parasite cell viability and SAP, an enzyme that may play a role in infectivity. These results increase our understanding of the role of sulfur in inhibiting Leishmania, providing more knowledge of the structural activity relationships that may prove critical for their development into possible antileishmanial treatments. Full article

(This article belongs to the Section Public Health Microbiology)

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11 pages, 1426 KiB

Open AccessArticle

Quantification of Viable Salmonella by Propidium Monoazide Real-Time PCR After Long-Term Storage of Peanut Products

by Aline M. von Hertwig, André A. Pereira, Dionisio Pedro Amorim Neto and Maristela S. Nascimento

Microorganisms 2024, 12(12), 2640; https://doi.org/10.3390/microorganisms12122640 (registering DOI) - 19 Dec 2024

Abstract

In this study, the performance of quantitative PCR, combined or not with propidium monoazide (PMA), to recover Salmonella from peanut products after different storage times was evaluated. The samples were inoculated with 5–6 log cfu g⁻¹ of Salmonella Typhimurium ATCC 14028 and [...] Read more.

In this study, the performance of quantitative PCR, combined or not with propidium monoazide (PMA), to recover Salmonella from peanut products after different storage times was evaluated. The samples were inoculated with 5–6 log cfu g⁻¹ of Salmonella Typhimurium ATCC 14028 and stored at 28 °C for up to 540 d. The correlation between the threshold cycle number (Ct) and the colony-forming units (cfu) was obtained by a standard curve, which showed a linear correlation (R² = 0.97). The highest counts were recovered by qPCR (p < 0.05); however, it quantified both viable and non-viable cells. For roasted peanuts, a significant difference (p < 0.05) between qPCR-PMA and the culture method was verified only for samples stored for 30 d, i.e., 2.8 versus 4.0 log cfu g⁻¹. Further, there was no VBNC status in the roasted peanuts, even after long-term exposure to desiccation stress. For peanut-based products, after 540 d, only paçoca showed a significant difference (p < 0.05) among the three methods evaluated. In peanut brittle, qPCR-PMA detected 1.5 log cfu g⁻¹, while, in the culture method, Salmonella was recovered in 1 g. The pathogen was below the detection limit in pé-de-moça either by plate count or qPCR-PMA. Therefore, qPCR-PMA shows potential for use in quantifying Salmonella in peanut products. Full article

(This article belongs to the Special Issue Salmonella Infections: Trends and Updates)

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20 pages, 1382 KiB

Open AccessReview

The Daunomycin: Biosynthesis, Actions, and the Search for New Solutions to Enhance Production

by Baveesh Pudhuvai, Karel Beneš, Vladislav Čurn, Andrea Bohata, Jana Lencova, Radka Vrzalova, Jan Barta and Vladimir Matha

Microorganisms 2024, 12(12), 2639; https://doi.org/10.3390/microorganisms12122639 - 19 Dec 2024

Abstract

Daunorubicin (DNR) is an anthracycline antibiotic originating from soil-dwelling actinobacteria extensively used to treat malignant tumors. Over the decades, extensive attempts were made to enhance the production of anthracyclines by introducing genetic modifications and mutations in combination with media optimization, but the target [...] Read more.

Daunorubicin (DNR) is an anthracycline antibiotic originating from soil-dwelling actinobacteria extensively used to treat malignant tumors. Over the decades, extensive attempts were made to enhance the production of anthracyclines by introducing genetic modifications and mutations in combination with media optimization, but the target production levels remain comparatively low. Developing an appropriate culture medium to maximize the yield of DNR and preventing autotoxicity for the producing organism remains a challenge. Our prospective review sheds light on a method involving perturbation that enhances the precursors to regulate the type II PKS pathway, enhancing cells’ capacity to increase secondary metabolite production. The suggested method also entails the preparation of culture media for the cultivation of Streptomyces sp. and enhanced yield of DNR, as well as making it inactive with iron or its reduced forms following efflux from the producer. The iron or iron–DNR complex is encapsulated by oleic acid or lipid micelle layers in the culture media, finally resulting in the generated inactive DNR and the DNR–iron–oil complex. This idea has the potential to protect the producer organism from autotoxicity and prevent the inhibition of metabolite production. The approach of substituting sugar with oil in culture media has a dual role wherein it promotes Streptomyces growth by utilizing lipids as an energy source and encapsulating the generated DNR–iron complex in the medium. In this review, we discussed aspects like anthracycline producers, biosynthesis pathways, and gene regulation; side effects of DNR; mechanisms for autotoxicity evasion; and culture media components for the enhancement of DNR production in Streptomyces sp. We anticipate that our work will help researchers working with secondary metabolites production and decipher a methodology that would enhance DNR yield and facilitate the extraction of the resulting DNR by lowering costs in large-scale fermentation. Full article

(This article belongs to the Section Microbial Biotechnology)

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12 pages, 1928 KiB

Open AccessArticle

Using Catalytic Models to Interpret Age-Stratified Lyme Borreliosis Seroprevalence Data: Can This Approach Help Provide Insight into the Full Extent of Human Infection Occurring at the Population Level?

by Andrew Vyse and Emily Colby

Microorganisms 2024, 12(12), 2638; https://doi.org/10.3390/microorganisms12122638 - 19 Dec 2024

Abstract

Diagnosis of Lyme borreliosis (LB) is prone to under ascertainment with the true extent of infection unknown. Cross sectional age-stratified population-based serological survey data may provide insight into this issue. Using data from a previously published Dutch seroprevalence study, we describe the application [...] Read more.

Diagnosis of Lyme borreliosis (LB) is prone to under ascertainment with the true extent of infection unknown. Cross sectional age-stratified population-based serological survey data may provide insight into this issue. Using data from a previously published Dutch seroprevalence study, we describe the application of catalytic models to make estimates of the annual extent of LB infection. A common assumption when using catalytic models is that IgG is protective and immunity is lifelong. However, human IgG produced in response to natural LB infection does not protect against subsequent infection and its duration may be limited. Individuals were thus assumed to be continually susceptible to LB infection, with a range of scenarios used that varied the length of time that IgG may remain detectable, from 5 years post-infection to lifelong. The possibility that IgG may remain detectable for longer in adults than in children was also explored. Estimates for the annual number of LB infections occurring in the Dutch population ranged from 163,265 (95%CI 130,150–201,723) when assuming IgG remains detectable for only 5 years post-infection to 26,209 (95%CI 17,159–36,557) when assuming IgG is lifelong. Full article

(This article belongs to the Special Issue Epidemiology of Vector-Borne Diseases (3rd Edition))

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23 pages, 5278 KiB

Open AccessArticle

Comparative Genomics and Biosynthetic Cluster Analysis of Antifungal Secondary Metabolites of Three Strains of Streptomyces albidoflavus Isolated from Rhizospheric Soils

by Adilene Gonzalez-Silva, Magali San Juan-Mendo, Gustavo Delgado-Prudencio, Juan Alfredo Hernández-García, Violeta Larios-Serrato, César Aguilar, Lourdes Villa-Tanaca and César Hernández-Rodríguez

Microorganisms 2024, 12(12), 2637; https://doi.org/10.3390/microorganisms12122637 - 19 Dec 2024

Abstract

Streptomyces is a genus of Gram-positive bacteria with high GC content. It remains attractive for studying and discovering new antibiotics, antifungals, and chemotherapeutics. Streptomyces genomes can contain more than 30 cryptic and expressed biosynthetic gene clusters (BGC) encoding secondary metabolites. In this study, [...] Read more.

Streptomyces is a genus of Gram-positive bacteria with high GC content. It remains attractive for studying and discovering new antibiotics, antifungals, and chemotherapeutics. Streptomyces genomes can contain more than 30 cryptic and expressed biosynthetic gene clusters (BGC) encoding secondary metabolites. In this study, three Streptomyces strains isolated from jungle rhizospheric soil exhibited supernatants that can inhibit sensitive and fluconazole-resistant Candida spp. The genomes of the strains Streptomyces sp. A1, J25, J29 ori2 were sequenced, assembled de novo, and analyzed. The genome assemblies revealed that the size of the genomes was 6.9 Mb, with linear topology and 73.5% GC. A phylogenomic approach identified the strains with high similitudes between 98.5 and 98.7% with Streptomyces albidoflavus SM254 and R-53649 strains, respectively. Pangenomic analysis of eight genomes of S. albidoflavus strains deposited in the Genomes database recognized 4707 core protein orthogroups and 745 abundant accessory and exclusive protein orthogroups, suggesting an open pangenome in this species. The antiSMASH software detected candicidin and surugamide BGC-encoding polyene and octapeptide antifungal secondary metabolites in other S. albidoflavus. CORASON software was used to compare the synteny, and the abundance of genes harbored in the clusters was used. In conclusion, although the three strains belong to the same species, each possesses a distinct genome, as evidenced by the different phenotypes, including antifungal and extracellular enzymatic activities. Full article

(This article belongs to the Special Issue Genomics Approaches in Microbial Ecology)

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10 pages, 2153 KiB

Open AccessCommunication

Antibiotic Susceptibility and Technological Properties of Leuconostoc citreum for Selecting Starter Candidates

by Sumin Lee, Sojeong Heo, Gawon Lee, Yura Moon, Minkyeong Kim, Mi-Sun Kwak and Do-Won Jeong

Microorganisms 2024, 12(12), 2636; https://doi.org/10.3390/microorganisms12122636 - 19 Dec 2024

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Abstract

Antibiotic susceptibilities, hemolytic activities, and technological properties of 46 Leuconostoc citreum isolates from kimchi were evaluated to select starter candidates. All strains were susceptible to clindamycin and erythromycin, while some exhibited resistance to ampicillin, chloramphenicol, gentamicin, streptomycin, and tetracycline; all were resistant to [...] Read more.

Antibiotic susceptibilities, hemolytic activities, and technological properties of 46 Leuconostoc citreum isolates from kimchi were evaluated to select starter candidates. All strains were susceptible to clindamycin and erythromycin, while some exhibited resistance to ampicillin, chloramphenicol, gentamicin, streptomycin, and tetracycline; all were resistant to kanamycin based on the EFSA breakpoint values for Leuconostoc species. PCR analysis did not detect resistance genes for these six antibiotics in any strain. None of the strains demonstrated clear α- or β-hemolytic activity. All strains thrived in a medium supplemented with 6% NaCl, displaying protease activity and acid in media containing 6% and 3% NaCl, respectively. Consequently, five strains, AK5T17, AK5T19, AK10M04, DMLC16, and YK10T20, were identified as starter candidates, with L. citreum strain DMLC16 emerging as the top choice due to its elevated protease and acid production capacities. These findings support the safe application of L. citreum strain DMLC16 as a starter candidate in fermented food production. Full article

(This article belongs to the Special Issue Microorganisms in Functional Foods)

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7 pages, 214 KiB

Open AccessOpinion

Lessons Learned from COVID-19 Pandemic in Combating Antimicrobial Resistance—Experience of Hong Kong, China

by Edmond Siu-Keung Ma, Shuk-Ching Wong, Vincent Chi-Chung Cheng, Hong Chen and Peng Wu

Microorganisms 2024, 12(12), 2635; https://doi.org/10.3390/microorganisms12122635 - 19 Dec 2024

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Abstract

The world has gone through the COVID-19 pandemic and has now returned to normalcy. We reviewed the strategies and public health actions conducted in Hong Kong during the COVID-19 pandemic, and reflected on the lessons learned, which are potentially useful in the fight [...] Read more.

The world has gone through the COVID-19 pandemic and has now returned to normalcy. We reviewed the strategies and public health actions conducted in Hong Kong during the COVID-19 pandemic, and reflected on the lessons learned, which are potentially useful in the fight against antimicrobial resistance (AMR). We recommended extending wastewater surveillance for AMR, apart from SARS-CoV2. We suggested exploring the use of rapid tests in outpatients to aid clinical diagnosis and reduce antibiotic use for viral infections. Stringent infection control measures are crucial to prevent nosocomial transmission of resistant microorganisms, such as vancomycin-resistant enterococci and carbapenemase-producing Enterobacterales in hospitals and in elderly homes. Taking COVID-19 experiences as a reference, transparent data, the prompt dissemination of information, and strategic risk communication should be adopted to maintain sustained behavioral changes in AMR. We also encouraged the adoption of information technology, artificial intelligence, and machine learning in antimicrobial stewardship programs. We also discussed the potential merits and limitations of these strategies. The lessons learned from the COVID-19 pandemic may provide insights into the long battle against AMR. Full article

(This article belongs to the Special Issue Antimicrobial Resistance: Challenges and Innovative Solutions)

13 pages, 1253 KiB

Open AccessArticle

Excessive Extracellular Ammonium Production by a Free-Living Nitrogen-Fixing Soil Clostridium sp. Strain

by Soyeon Park and Jeonghwan Jang

Microorganisms 2024, 12(12), 2634; https://doi.org/10.3390/microorganisms12122634 - 19 Dec 2024

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Abstract

A Gram-positive, rod-shaped, and obligate anaerobic bacterial strain OS1-26 was isolated from apple orchard soil in Iksan, South Korea. Interestingly, strain OS1-26 was observed to possess the functional genes involved in biological nitrogen fixation (BNF), including nifH, which was actively transcribed during [...] Read more.

A Gram-positive, rod-shaped, and obligate anaerobic bacterial strain OS1-26 was isolated from apple orchard soil in Iksan, South Korea. Interestingly, strain OS1-26 was observed to possess the functional genes involved in biological nitrogen fixation (BNF), including nifH, which was actively transcribed during the anaerobic cultivation with excessive production of extracellular NH₄⁺ despite of presence of other fixed N nutrients. The BNF of strain OS1-26 was distinguished from the other well-known Clostridium diazotrophs, such as C. pasteurianum and C. acetobutylicum. The altruistic N-fixing ability of the strain may play a pivotal role in providing N nutrients to the microbial community and plants in the soil ecosystem. The microorganism grew at 25–35 °C (optimum 30–35 °C) and pH 5.0–8.0 (optimum 6.0–8.0) but was not able to grow in the presence of >0.5% NaCl. The major cellular fatty acids of strain OS1-26 were C_16:0, C_14:0, and the summed feature consisted of C_16:1 ω7c and C_16:1 ω6c (35.63%, 25.29%, and 18.84%, respectively). The 16S rRNA phylogeny indicated that strain OS1-26 is a member of the genus Clostridium, and the closest species are C. aciditolerans, C. nitrophenolicum, and C. thailandense, with 16S rRNA sequence similarities such as 99.71%, 98.52%, and 98.45%, respectively. In spite of the high 16S rRNA sequence similarity, strain OS1-26 showed overall genomic relatedness, such as the average nucleotide identity (ANI), and phenotypical features distinctly different from Clostridium aciditolerans. Although the species taxonomy of strain OS1-26 is undetermined within the genus Clostridium based on overall genomic and phenotypic properties, further studies on the soil bacterial strain would enhance our understanding of its taxonomic identity, ecological roles for the terrestrial soil N cycle, and the potential to be developed as a biological N fertilizer. Full article

(This article belongs to the Special Issue Soil Microbiome and Ecological Biogeochemical Cycles)

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22 pages, 4731 KiB

Open AccessArticle

Characterization and Molecular Insights of a Chromium-Reducing Bacterium Bacillus tropicus

by Shanjana Rahman Tuli, Md. Firoz Ali, Tabassum Binte Jamal, Md. Abu Sayem Khan, Nigar Fatima, Irfan Ahmed, Masuma Khatun and Shamima Akhtar Sharmin

Microorganisms 2024, 12(12), 2633; https://doi.org/10.3390/microorganisms12122633 - 19 Dec 2024

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Abstract

Environmental pollution from metal toxicity is a widespread concern. Certain bacteria hold promise for bioremediation via the conversion of toxic chromium compounds into less harmful forms, promoting environmental cleanup. In this study, we report the isolation and detailed characterization of a highly chromium-tolerant [...] Read more.

Environmental pollution from metal toxicity is a widespread concern. Certain bacteria hold promise for bioremediation via the conversion of toxic chromium compounds into less harmful forms, promoting environmental cleanup. In this study, we report the isolation and detailed characterization of a highly chromium-tolerant bacterium, Bacillus tropicus CRB14. The isolate is capable of growing on 5000 mg/L Cr (VI) in an LB (Luria Bertani) agar plate while on 900 mg/L Cr (VI) in LB broth. It shows an 86.57% reduction ability in 96 h of culture. It can also tolerate high levels of As, Cd, Co, Fe, Zn, and Pb. The isolate also shows plant growth-promoting potential as demonstrated by a significant activity of nitrogen fixation, phosphate solubilization, IAA (indole acetic acid), and siderophore production. Whole-genome sequencing revealed that the isolate lacks Cr resistance genes in their plasmids and are located on its chromosome. The presence of the chrA gene points towards Cr(VI) transport, while the absence of ycnD suggests alternative reduction pathways. The genome harbors features like genomic islands and CRISPR-Cas systems, potentially aiding adaptation and defense. Analysis suggests robust metabolic pathways, potentially involved in Cr detoxification. Notably, genes for siderophore and NRP-metallophore production were identified. Whole-genome sequencing data also provides the basis for molecular validation of various genes. Findings from this study highlight the potential application of Bacillus tropicus CRB14 for bioremediation while plant growth promotion can be utilized as an added benefit. Full article

(This article belongs to the Special Issue Biotechnology for Environmental Remediation)

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14 pages, 5046 KiB

Open AccessArticle

Diversity and Composition of the Airborne Fungal Community in Mexico City with a Metagenomic Approach

by Carolina Brunner-Mendoza, María del Carmen Calderón-Ezquerro, César Guerrero-Guerra, Alejandro Sanchez-Flores, Ilse Salinas-Peralta and Conchita Toriello

Microorganisms 2024, 12(12), 2632; https://doi.org/10.3390/microorganisms12122632 - 19 Dec 2024

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Abstract

Airborne fungi are widely distributed in the environment and originate from various sources like soil, plants, decaying organic matter, and even indoor environments. Exposure to airborne fungal spores can cause allergic reactions, asthma, and respiratory infections. Certain fungi can cause serious infections, particularly [...] Read more.

Airborne fungi are widely distributed in the environment and originate from various sources like soil, plants, decaying organic matter, and even indoor environments. Exposure to airborne fungal spores can cause allergic reactions, asthma, and respiratory infections. Certain fungi can cause serious infections, particularly in individuals with weakened immune systems. An aerobiological study was conducted to detect airborne fungi using metagenomics in three areas of Mexico City, each representing different degrees of urbanization, during the dry and rainy seasons of 2017. Seasonality showed a significant role in the composition of airborne fungi. Ascomycota predominated in the three areas sampled during dry and rainy seasons, with the genera Cladosporium and Penicillium presenting the highest relative abundances across seasons. The Agaromycetes showed an increase during the rainy season. Regarding the areas, the north and center sites showed similar meteorological conditions and fungal community composition patterns. According to the Shannon and Simpson indices, the south area showed a greater species diversity during the dry season. These insights into the interactions between urbanization, seasonality, and airborne microbial communities could contribute to more effective urban management, reduced health risks, and the promotion of sustainable development. Full article

(This article belongs to the Special Issue The Urban Microbiome)

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16 pages, 1531 KiB

Open AccessArticle

Mercury-Resistant Bacteria Isolated from an Estuarine Ecosystem with Detoxification Potential

by Marynes Quintero, Sol D. Zuluaga-Valencia, Lady Giselle Ríos-López, Olga Sánchez, Cesar A. Bernal, Niza Sepúlveda and Javier Gómez-León

Microorganisms 2024, 12(12), 2631; https://doi.org/10.3390/microorganisms12122631 - 19 Dec 2024

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Abstract

Mercury pollution is a significant environmental issue, primarily resulting from industrial activities, including gold mining extraction. In this study, 333 microorganisms were tested in increasing mercury concentrations, where 158 bacteria and 14 fungi were able to grow and remain viable at concentrations over [...] Read more.

Mercury pollution is a significant environmental issue, primarily resulting from industrial activities, including gold mining extraction. In this study, 333 microorganisms were tested in increasing mercury concentrations, where 158 bacteria and 14 fungi were able to grow and remain viable at concentrations over 5.0 mg/L of mercuric chloride (II). One of the bacterial strains, Stenotrophomonas sp. INV PRT0231, isolated from the mouth of the San Juan River in the Chocó region in Colombia, showed a high mercury resistance level (MIC₉₀ of 27 ± 9 mg/L), with a removal rate of 86.9%, an absorption rate of 1.2%, and a volatilization rate of 85.7% at pH 6.0 and 30.0 °C. The FTIR analysis showed changes in the functional groups, including fatty acid chains and methyl groups, proteins, and lipopolysaccharides associated with the carboxylate group (COO⁻), suggesting an important role of these biomolecules and their associated functional groups as mechanisms employed by the bacterium for mercury detoxification. Our study contributes to the understanding of the mechanisms of mercury biotransformation in microbial environmental isolates to help develop bioremediation strategies to mitigate mercury pollution caused by anthropogenic activities. Full article

(This article belongs to the Section Environmental Microbiology)

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21 pages, 3321 KiB

Open AccessArticle

Microbiome Structures and Beneficial Bacteria in Soybean Roots Under Field Conditions of Prolonged High Temperatures and Drought Stress

by Sandeep Gouli, Aqsa Majeed, Jinbao Liu, David Moseley, M. Shahid Mukhtar and Jong Hyun Ham

Microorganisms 2024, 12(12), 2630; https://doi.org/10.3390/microorganisms12122630 - 19 Dec 2024

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Abstract

Drought stress has a significant impact on agricultural productivity, affecting key crops such as soybeans, the second most widely cultivated crop in the United States. Endophytic and rhizospheric microbial diversity analyses were conducted with soybean plants cultivated during the 2023 growing season amid [...] Read more.

Drought stress has a significant impact on agricultural productivity, affecting key crops such as soybeans, the second most widely cultivated crop in the United States. Endophytic and rhizospheric microbial diversity analyses were conducted with soybean plants cultivated during the 2023 growing season amid extreme weather conditions of prolonged high temperatures and drought in Louisiana. Specifically, surviving and non-surviving soybean plants were collected from two plots of a Louisiana soybean field severely damaged by extreme heat and drought conditions in 2023. Although no significant difference was observed between surviving and non-surviving plants in microbial diversity of the rhizosphere, obvious differences were found in the structure of the endophytic microbial community in root tissues between the two plant conditions. In particular, the bacterial genera belonging to Proteobacteria, Pseudomonas and Pantoea, were predominant in the surviving root tissues, while the bacterial genus Streptomyces was conspicuously dominant in the non-surviving (dead) root tissues. Co-occurrence patterns and network centrality analyses enabled us to discern the intricate characteristics of operational taxonomic units (OTUs) within endophytic and rhizospheric networks. Additionally, we isolated and identified bacterial strains that enhanced soybean tolerance to drought stresses, which were sourced from soybean plants under a drought field condition. The 16S rDNA sequence analysis revealed that the beneficial bacterial strains belong to the genera Acinetobacter, Pseudomonas, Enterobacter, and Stenotrophomonas. Specific bacterial strains, particularly those identified as Acinetobacter pittii and Pseudomonas sp., significantly enhanced plant growth metrics and reduced drought stress indices in soybean plants through seed treatment. Overall, this study advances our understanding of the soybean-associated microbiome structure under drought stress, paving the way for future research to develop innovative strategies and biological tools for enhancing soybean resilience to drought. Full article

(This article belongs to the Section Plant Microbe Interactions)

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