Microorganisms

24 pages, 1704 KiB

Open AccessArticle

In Vitro Antioxidant and Antibacterial Activities of Ethyl Acetate Extracts of Ziziphus lotus Leaves and Five Associated Endophytic Fungi

by Amel Ghazi-Yaker, Bart Kraak, Jos Houbraken, El-hafid Nabti, Cristina Cruz, Noria Saadoun and Karim Houali

Microorganisms 2024, 12(12), 2671; https://doi.org/10.3390/microorganisms12122671 - 23 Dec 2024

Viewed by 650

Abstract

The exploration of new pharmacological compounds from endophytic fungi offers infinite possibilities. The aim of this study was to evaluate the antibacterial and antioxidant activities of extracts from the leaves of Ziziphus lotus and five of its endophytic fungi and investigate the chemical [...] Read more.

The exploration of new pharmacological compounds from endophytic fungi offers infinite possibilities. The aim of this study was to evaluate the antibacterial and antioxidant activities of extracts from the leaves of Ziziphus lotus and five of its endophytic fungi and investigate the chemical diversity of the secondary metabolites produced. Isolated, purified, and molecularly identified endophytes and plant leaves were subjected to ethyl acetate extraction. The antibacterial potential of the extracts was assessed by the disc diffusion method against five bacterial strains: Staphylococcus aureus ATCC 25923; Staphylococcus aureus MU50; Enterococcus faecalis WDCM00009; Escherichia coli ATCC 25922; and Pseudomonas aeruginosa ATCC 27853. DPPH and reducing power tests were performed to assess antioxidant potential. GC–MS analysis was used to identify volatile compounds in extracts. Fungal endophytes were identified as Aspergillus cavernicola, Aspergillus persii, Alternaria alternata, Cladosporium asperlatum, and Fusarium incarnatum–equiseti complex, with respective accession numbers DTO 412-G6, DTO 412-I5, DTO 413-E7, DTO 412-G4, and DTO 414-I2. GC–MS analysis revealed a large number of bioactive compounds. All extracts showed antibacterial activity against at least two of the bacteria tested, and most showed antioxidant activity. The Aspergillus cavernicola extract stood out for its higher phenolic content and higher antioxidant and antibacterial activities in all tests. Full article

(This article belongs to the Special Issue Endophytic Fungus as Producers of New and/or Bioactive Substances)

► Show Figures

Figure 1

29 pages, 7062 KiB

Open AccessArticle

Gram Negative Biofilms: Structural and Functional Responses to Destruction by Antibiotic-Loaded Mixed Polymeric Micelles

by Tsvetozara Damyanova, Rumena Stancheva, Milena N. Leseva, Petya A. Dimitrova, Tsvetelina Paunova-Krasteva, Dayana Borisova, Katya Kamenova, Petar D. Petrov, Ralitsa Veleva, Ivelina Zhivkova, Tanya Topouzova-Hristova, Emi Haladjova and Stoyanka Stoitsova

Microorganisms 2024, 12(12), 2670; https://doi.org/10.3390/microorganisms12122670 - 23 Dec 2024

Viewed by 547

Abstract

Biofilms are a well-known multifactorial virulence factor with a pivotal role in chronic bacterial infections. Their pathogenicity is determined by the combination of strain-specific mechanisms of virulence and the biofilm extracellular matrix (ECM) protecting the bacteria from the host immune defense and the [...] Read more.

Biofilms are a well-known multifactorial virulence factor with a pivotal role in chronic bacterial infections. Their pathogenicity is determined by the combination of strain-specific mechanisms of virulence and the biofilm extracellular matrix (ECM) protecting the bacteria from the host immune defense and the action of antibacterials. The successful antibiofilm agents should combine antibacterial activity and good biocompatibility with the capacity to penetrate through the ECM. The objective of the study is the elaboration of biofilm-ECM-destructive drug delivery systems: mixed polymeric micelles (MPMs) based on a cationic poly(2-(dimethylamino)ethyl methacrylate)-b-poly(ε-caprolactone)-b-poly(2-(dimethylamino)ethyl methacrylate) (PDMAEMA₃₅-b-PCL₇₀-b-PDMAEMA₃₅) and a non-ionic poly(ethylene oxide)-b-poly(propylene oxide)-b-poly(ethylene oxide) (PEO₁₀₀-b-PPO₆₅-b-PEO₁₀₀) triblock copolymers, loaded with ciprofloxacin or azithromycin. The MPMs were applied on 24 h pre-formed biofilms of Escherichia coli and Pseudomonas aeruginosa (laboratory strains and clinical isolates). The results showed that the MPMs were able to destruct the biofilms, and the viability experiments supported drug delivery. The biofilm response to the MPMs loaded with the two antibiotics revealed two distinct patterns of action. These were registered on the level of both bacterial cell-structural alterations (demonstrated by scanning electron microscopy) and the interaction with host tissues (ex vivo biofilm infection model on skin samples with tests on nitric oxide and interleukin (IL)-17A production). Full article

(This article belongs to the Special Issue Contemporary Perspectives on Bacterial Virulence Factors)

► Show Figures

Figure 1

26 pages, 1262 KiB

Open AccessReview

Campylobacter jejuni/coli Infection: Is It Still a Concern?

by Piero Veronese and Icilio Dodi

Microorganisms 2024, 12(12), 2669; https://doi.org/10.3390/microorganisms12122669 - 23 Dec 2024

Viewed by 483

Abstract

Campylobacteriosis is a leading cause of infectious diarrhea and foodborne illness worldwide. Campylobacter infection is primarily transmitted through the consumption of contaminated food, especially uncooked meat, or untreated water; contact with infected animals or contaminated environments; poultry is the primary reservoir and source [...] Read more.

Campylobacteriosis is a leading cause of infectious diarrhea and foodborne illness worldwide. Campylobacter infection is primarily transmitted through the consumption of contaminated food, especially uncooked meat, or untreated water; contact with infected animals or contaminated environments; poultry is the primary reservoir and source of human transmission. The clinical spectrum of Campylobacter jejuni/coli infection can be classified into two distinct categories: gastrointestinal and extraintestinal manifestations. Late complications are reactive arthritis, Guillain–Barré syndrome, and Miller Fisher syndrome. In the pediatric population, the 0–4 age group has the highest incidence of campylobacteriosis. Regarding the use of specific antimicrobial therapy, international guidelines agree in recommending it for severe intestinal infections. Host factors, including malnutrition, immunodeficiency, and malignancy, can also influence the decision to treat. The Centers for Disease Control and Prevention (CDC) has identified antibiotic resistance in Campylobacter as a ‘significant public health threat’ due to increasing resistance to FQs or macrolides. Although numerous vaccines have been proposed in recent years to reduce the intestinal colonization of poultry, none have shown sufficient efficacy to provide a definitive solution. Full article

(This article belongs to the Special Issue Epidemiology, Prevention and Control of Foodborne Microbial Pathogens)

► Show Figures

Figure 1

Figure 1
Transmission, environmental reservoirs, and risk factors for human Campylobacteriosis. As a zoonotic disease, poultry is the primary reservoir for Campylobacter. In non-endemic regions, consuming raw or undercooked poultry meat and direct contact with animals are the primary risk factors. However, in endemic areas, environmental contamination, including water sources, along with poultry contact, increased meat consumption, and inadequate hygienic practices contribute to the widespread persistence of the bacterium. Full article ">Figure 2
Campylobacter jejuni/coli virulence factors. The main pathogenic factors of Campylobacter have been categorized into four broad groups in this image: motility and chemotaxis, adhesion and translocation, invasion and evasion of the host immune system, and survival and biofilm formation. The flagellar apparatus, encoded by the FlgA gene, is the factor that confers motility to the bacterium, counteracting peristaltic movements. Additionally, it is involved in the secretion of effector molecules (Campylobacter invasion antigens, Cia), in the evasion of TLR5-mediated immunity, and in the biofilm formation. CiaB, CiaC, and CiaD facilitate bacterial uptake by and invasion of host cells. The type 3 secretion system (T3SS), a key virulence factor in many Gram-negative pathogens, is primarily responsible for the secretion of Cia effectors. Despite T4SS presence in Campylobacter remaining unclear, T6SS plays a clear role in host invasion, mediating both invasion and adhesion to colon cells. During invasion, Campylobacter jejuni cytolethal distending toxin (Cj-CDT). Capsular polysaccharide (CPS) and Campylobacter-containing vacuoles (CCVs) act as an immune shield, allowing the bacterium to persist within the host. Full article ">Figure 3
Clinical manifestations and late complications of Campylobacter infection. While uncommon, bacteremia is a key factor in the systemic spread of the bacteria following intestinal infection, leading to potential complications in distant organs. Molecular mimicry underlies the pathogenesis of late complications. Full article ">

22 pages, 5914 KiB

Open AccessArticle

The Effect of Oral Care Product Ingredients on Oral Pathogenic Bacteria Transcriptomics Through RNA-Seq

by Ping Hu, Sancai Xie, Baochen Shi, Cheryl S. Tansky, Benjamin Circello, Paul A. Sagel, Eva Schneiderman and Aaron R. Biesbrock

Microorganisms 2024, 12(12), 2668; https://doi.org/10.3390/microorganisms12122668 - 23 Dec 2024

Viewed by 562

Abstract

Various ingredients are utilized to inhibit the growth of harmful bacteria associated with cavities, gum disease, and bad breath. However, the precise mechanisms by which these ingredients affect the oral microbiome have not been fully understood at the molecular level. To elucidate the [...] Read more.

Various ingredients are utilized to inhibit the growth of harmful bacteria associated with cavities, gum disease, and bad breath. However, the precise mechanisms by which these ingredients affect the oral microbiome have not been fully understood at the molecular level. To elucidate the molecular mechanisms, a high-throughput bacterial transcriptomics study was conducted, and the gene expression profiles of six common oral bacteria, including two Gram-positive bacteria (Actinomyces viscosus, Streptococcus mutans) and four Gram-negative bacteria (Porphyromonas gingivalis, Tannerella forsythia, Fusobacterium nucleatum, and Prevotella pallens), were analyzed. The bacteria were exposed to nine common ingredients in toothpaste and mouthwash at different concentrations (stannous fluoride, stannous chloride, arginine bicarbonate, cetylpyridinium chloride, sodium monofluorophosphate, sodium fluoride, potassium nitrate, zinc phosphate, and hydrogen peroxide). Across 78 ingredient–microorganism pairs with 360 treatment–control combinations, significant and reproducible ingredient-based transcriptional response profiles were observed, providing valuable insights into the effects of these ingredients on the oral microbiome at the molecular level. This research shows that oral care product ingredients applied at biologically relevant concentrations manifest differential effects on the transcriptomics of bacterial genes in a variety of oral periodontal pathogenic bacteria. Stannous fluoride, stannous chloride, and cetylpyridinium chloride showed the most robust efficacy in inhibiting the growth or gene expression of various bacteria and pathogenic pathways. Combining multiple ingredients targeting different mechanisms might be more efficient than single ingredients in complex oral microbiomes. Full article

(This article belongs to the Special Issue Oral Microbiomes and One Health Approach)

► Show Figures

Figure 1

13 pages, 3058 KiB

Open AccessArticle

Characteristics of the Stool, Blood and Skin Microbiome in Rosacea Patients

by Marie Isolde Joura, Antal Jobbágy, Zsuzsanna A. Dunai, Nóra Makra, András Bánvölgyi, Norbert Kiss, Miklós Sárdy, Sarolta Eszter Sándor, Péter Holló and Eszter Ostorházi

Microorganisms 2024, 12(12), 2667; https://doi.org/10.3390/microorganisms12122667 - 23 Dec 2024

Viewed by 476

Abstract

Several research groups have confirmed that in the pathogenesis of the chronic inflammatory skin disorder rosacea, the composition of the skin and fecal microbiome of affected patients differs from that of healthy individuals. We studied the stool, blood and skin microbiomes of rosacea [...] Read more.

Several research groups have confirmed that in the pathogenesis of the chronic inflammatory skin disorder rosacea, the composition of the skin and fecal microbiome of affected patients differs from that of healthy individuals. We studied the stool, blood and skin microbiomes of rosacea and control patients using 16S rRNA sequencing. Our goals were to determine 1. whether the microbiome characteristics of rosacea patients differ from that of healthy individuals, 2. whether the change experienced on the skin can be confirmed by alterations in the stool microbiome through the mediation of the blood and 3. whether the metabolic activity of the changed skin, blood or fecal microbiome can play a role in the pathogenesis of rosacea. The rosacea skin microbiome differed significantly from the healthy skin microbiome in both alpha and beta diversity, as well as in the abundance of the genera. Only a few genera abundances differed significantly in stool and blood samples. The most significant representatives of the rosacea skin microbiome, Staphylococcus, Cutibacterium, Corynebacterium and Neisseria, cannot be derived from the feces or blood. The metabolic pathways associated with healthy fecal microbiome contributed to the production of anti-inflammatory short-chain fatty acids. While the increased production of adenosylcobalamin, L-isoleucine and thiazole by the microbiome of healthy skin appeared to have a protective effect, the excessive heme and H₂S production experienced in rosacea skin likely contribute to the deterioration of the pathology. Full article

(This article belongs to the Special Issue Human Skin Microbiota, 2nd Edition)

► Show Figures

Figure 1

Figure 1
Principal component analysis (A) and heatmap (B) of bacterial abundance of stool, blood and skin samples of the rosacea patients and control healthy volunteers. Full article ">Figure 2
Comparison of Chao1 alpha diversity (A) or Bray–Curtis beta diversity (B) of stool, blood and skin samples from the rosacea patients and control patients. Full article ">Figure 3
The genus relative abundance in the composition of the skin microbiome of rosacea patients and control individuals, aggregated by cohort (A) and individual data (B) by stacked bar representation. Full article ">Figure 4
Abundance distribution of Bacteroides, Faecalibacterium, Blautia, Prevotella, Ruminococcus and Subdoligranulum genera among the different sample types. Full article ">Figure 5
LEfSe bar chart; visual representation of discriminative features of genera abundances among the control and rosacea blood and stool samples (A), and discriminative biochemical pathways in stool samples (B). LDA is the linear discriminant analysis score. Full article ">Figure 6
LefSe analysis of metabolic pathways of the rosacea and control skin microbiome. LDA is the linear discriminant analysis score. Full article ">

14 pages, 1014 KiB

Open AccessArticle

Haemophilus influenzae Invasive Infections in Children in Vaccine Era: Phenotypic and Genotypic Characterization Tunis, Tunisia

by Yasmine Chelbi, Khaoula Meftah, Ala-Eddine Deghmane, Samar Mhimdi, Firas Aloui, Aida Bouafsoun, Eva Hong, Khaled Menif, Khadija Boussetta, Monia Khemiri, Samir Boukthir, Mehdi Trifa, Said Jlidi, Riadh Jouini, Zohra Fitouri, Mohamed-Nabil Nessib, Muhamed-Kheir Taha and Hanen Smaoui

Microorganisms 2024, 12(12), 2666; https://doi.org/10.3390/microorganisms12122666 - 23 Dec 2024

Viewed by 649

Abstract

The changing epidemiological profile of invasive Haemophilus influenzae infections (IIHi) is noted in the post-vaccination era. The aim of this study was to characterize phenotypically and genotypically invasive Haemophilus influenzae (Hi) isolates detected in Tunisian pediatric patients. A retrospective study was conducted in [...] Read more.

The changing epidemiological profile of invasive Haemophilus influenzae infections (IIHi) is noted in the post-vaccination era. The aim of this study was to characterize phenotypically and genotypically invasive Haemophilus influenzae (Hi) isolates detected in Tunisian pediatric patients. A retrospective study was conducted in the microbiology laboratory of the Children’s Hospital of Tunis over ten years (2013–2023). All IIHi cases were included. Molecular identification and serotyping were conducted through qPCR. Molecular typing and analysis of resistance genes were extracted from whole genome sequencing data. Fifty-three IIHi cases were collected. Children under five years old were the most affected (81%). Non-typable isolates (NTHi) were predominant (79%) followed by serotype b (17%) and serotype a (4%). Genetic diversity was observed, essentially among NTHi isolates. Resistance of Hi isolates to ampicillin, amoxicillin–clavulanic acid and cefotaxime (CTX) were 42%, 20% and 4%, respectively. Thirteen isolates (29%) produced a beta-lactamase and 14 carried the blaTEM-1 gene (kappa = 0.95). For non-enzymatic resistance, group 3 (n = 12) showed resistance to ampicillin. Groupe 4 (n = 9, NTHi) showed discordances with resistance to CTX. The emergence of resistance to CTX is concerning. Continuous surveillance through molecular tools in conjunction with phenotypic and clinical data is necessary to ensure better management of these infections. Full article

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

► Show Figures

Figure 1

15 pages, 4536 KiB

Open AccessArticle

Transcriptome Analysis of the Harmful Dinoflagellate Heterocapsa bohaiensis Under Varied Nutrient Stress Conditions

by Peng Peng, Fangxin Han, Xue Gong, Xiangyuan Guo, Ying Su, Yiwen Zhang and Jingjing Zhan

Microorganisms 2024, 12(12), 2665; https://doi.org/10.3390/microorganisms12122665 - 22 Dec 2024

Viewed by 864

Abstract

The increasing prevalence of harmful algal blooms (HABs) driven by eutrophication, particularly in China’s nearshore waters, is a growing concern. Dinoflagellate Heterocapsa bohaiensis blooms have caused significant ecological and economic damage, as well as mass mortality, in cultivated species. Nutrients are one of [...] Read more.

The increasing prevalence of harmful algal blooms (HABs) driven by eutrophication, particularly in China’s nearshore waters, is a growing concern. Dinoflagellate Heterocapsa bohaiensis blooms have caused significant ecological and economic damage, as well as mass mortality, in cultivated species. Nutrients are one of the primary inducers of H. bohaiensis blooms. However, the transcriptomic studies of H. bohaiensis remain sparse, and its metabolic pathways are unknown. This study analyzed the transcriptome of H. bohaiensis under varying nutrient conditions (nitrogen at 128, 512, and 880 μM; phosphate at 8, 6, and 32 μM), focusing on differential gene expression. The results indicated that deviations in nutrient conditions (higher or lower N:P ratios) led to a higher number of differentially expressed genes compared to the control (N:P ratios = 27.5), thereby underscoring their pivotal role in growth. Gene Ontology (GO) enrichment analyses showed that nutrient limitation upregulated the biosynthesis and catabolism processes while downregulating the cell cycle and division functions. The Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that, under nitrogen limitation, the proteasome pathways were upregulated, while photosynthesis and carbon fixation were downregulated; under phosphorus limitation, the proteasome pathways were upregulated and nitrogen metabolism was downregulated. These findings suggest that H. bohaiensis adapts to nutrient stress by adjusting its metabolic processes. Full article

(This article belongs to the Special Issue Research on Biology of Dinoflagellates)

► Show Figures

Figure 1

Figure 1
(a) Gene Ontology (GO) assignment and (b) KEGG assignment of assembled unigenes of H. bohaiensis. Full article ">Figure 2
Differential genetic volcanoes of H. bohaiensis under different nitrogen concentration conditions ((A) LNP vs. NP; (B) LLNP vs. NP). Full article ">Figure 3
GO enrichment of differential genes under nitrogen-limited conditions in H. bohaiensis: (A) upregulated; (B) downregulated. Full article ">Figure 4
Differential genetic volcanoes of H. bohaiensis under different phosphorus concentration conditions ((A) HNP vs. NP; (B) HHNP vs. NP). Full article ">Figure 5
GO enrichment of differential genes under phosphorus-limited conditions in H. bohaiensis ((A) upregulated; (B) downregulated). Full article ">Figure 6
Different nitrogen (LLNP) and phosphorus (HHNP) conditions on photosynthesis enrichment pathway of H. bohaiensis. The red and green squares in the figure represent gene expression that is either up- or downregulated. The yellow squares represent gene expression that exhibits both up- and downregulation. Full article ">Figure 7
Different nitrogen (LLNP) and phosphorus (HHNP) conditions on carbon fixation in photosynthetic organism enrichment pathway of H. bohaiensis. The red and green squares in the figure represent gene expression that is either up- or downregulated. The yellow squares represent gene expression that exhibits both up- and downregulation. Full article ">Figure 8
Different nitrogen (LLNP) and phosphorus (HHNP) conditions on proteasome enrichment pathway of H. bohaiensis. The red squares in the figure represent gene expression that is upregulated. The yellow squares represent gene expression that exhibits both up- and downregulation. Full article ">Figure 9
Different nitrogen (LLNP) and phosphorus (HHNP) conditions on nitrogen metabolism enrichment pathway of H. bohaiensis. The red and green squares in the figure represent gene expression that is either up- or downregulated. The yellow squares represent gene expression that exhibits both up- and downregulation. Full article ">

19 pages, 1244 KiB

Open AccessArticle

Phytochemical Analysis and Antimicrobial Activity of Terminalia bellirica (Gaertn.) Roxb. and Terminalia chebula Retz. Fruit Extracts Against Gastrointestinal Pathogens: Enhancing Antibiotic Efficacy

by Gagan Tiwana, Ian Edwin Cock and Matthew James Cheesman

Microorganisms 2024, 12(12), 2664; https://doi.org/10.3390/microorganisms12122664 - 22 Dec 2024

Viewed by 751

Abstract

Terminalia bellirica (Gaertn) Roxb. and Terminalia chebula Retz. are significant botanicals in ancient Ayurvedic medicine. They are renowned for their therapeutic properties, notably in addressing gastrointestinal (GI) diseases. These plants have undergone thorough examination related to their antibacterial, anti-inflammatory, and antioxidant properties, which [...] Read more.

Terminalia bellirica (Gaertn) Roxb. and Terminalia chebula Retz. are significant botanicals in ancient Ayurvedic medicine. They are renowned for their therapeutic properties, notably in addressing gastrointestinal (GI) diseases. These plants have undergone thorough examination related to their antibacterial, anti-inflammatory, and antioxidant properties, which make them highly efficient natural treatments for controlling gastrointestinal infections. The current research demonstrated the antibacterial efficacy of fruit extracts of Terminalia bellirica and Terminalia chebula against Bacillus cereus, Shigella sonnei, Shigella flexneri, and Salmonella typhimurium. We performed disc diffusion and liquid microdilution experiments to evaluate the antibacterial efficacy. All extracts of Terminalia bellirica and Terminalia chebula showed good antibacterial effects against B. cereus and S. flexneri. The minimum inhibitory concentration (MIC) values ranged from 94 µg/mL to 556 µg/mL. The methanolic extracts from both plants also showed noteworthy antibacterial activity against S. sonnei and S. typhimurium, with MIC values of 755 µg/mL for both. Fractional inhibitory concentration studies revealed additive interactions between some conventional antibiotics and the plant extracts when used concurrently. Liquid chromatography–mass spectrometry (LC-MS) analyses revealed that the T. bellirica and T. chebula extracts contained various tannins including methyl gallate, propyl gallate, gallic acid, and ellagic acid. Lethality assays conducted using Artemia franciscana Kellogg nauplii indicated that all the plant extracts are non-toxic. The antibacterial properties and absence of toxicity in T. bellirica and T. chebula fruit extracts indicate their potential for antibiotic development, warranting additional mechanistic and phytochemical studies. Full article

(This article belongs to the Special Issue Plant Extracts and Antimicrobials, Second Edition)

► Show Figures

Figure 1

Figure 1
Antimicrobial activity of T. bellirica and T. chebula fruit extracts in the disc diffusion assays against (A) B. cereus, (B) S. flexneri, (C) S. sonnei, (D) S. typhimurium. TB-AQ = T. bellirica aqueous (50.2 mg/mL); TB-MeOH = T. bellirica methanolic (48.3 mg/mL); TB-EtOAc = T. bellirica ethyl acetate (4.9 mg/mL). TCh-AQ = T. chebula aqueous (35.6 mg/mL); TCh-MeOH = T. chebula methanol (48.3 mg/mL); TCh-EtOAc = T. chebula ethyl acetate (4.9 mg/mL). Negative controls = 1% DMSO and blank = sterile water. Reference antibiotics: PEN G = penicillin G (10 IU), ERY = erythromycin (10 µg), TET = tetracycline (30 µg), CHL = chloramphenicol (30 µg), CIP = ciprofloxacin (1 µg), POL B = polymyxin B (300IU), OXA = oxacillin (1 µg), AMX = amoxycillin (10 µL of 0.01 mg/mL stock solution), GEN = gentamicin (10 µg), VAN = vancomycin (30 µg), AUG = Augmentin® (15 µg), CEF = cefoxitin (30 µg). Horizontal red lines on the y-axis at 6 mm indicate the disc diameter used in the assay. Mean values (±SEM) are reported from three independent studies. p-values < 0.05 are represented with a single asterisk symbol (*), while p-values < 0.01 are represented with a double asterisk symbol (**). Full article ">Figure 2
Structures of noteworthy compounds identified in the fruit extracts of T. bellirica and T. chebula. Methyl gallate (A), propyl gallate (B), gallic acid (C), ellagic acid (D), hamamelitannin (E), pyrogallol (F), quercetin (G), 6-galloylglucose (H), gallic acid 3-O-(6-galloylglucoside) (I), 1,2,6-trigalloyl-β-D-glucopyranose (J), 1,3,6-tri-O-galloyl-β-D-glucose (K), 1,6-bis-O-(3,4,5-trihydroxybenzoyl) hexopyranose (L), chebulic acid (M), and chebuloside II (N). Structures were prepared using Chemsketch Version 2024. Full article ">

17 pages, 4623 KiB

Open AccessArticle

Development of a TaqMan qPCR for the Simultaneous Detection of the TuMV and BBWV2 Viruses Responsible for the Viral Disease in Pseudostellaria heterophylla

by Li Gu, Chensi Liu, Shuting Yao, Jiaxin Wu, Lianghong Wang, Jing Mu, Yankun Wang, Jianming Wang, Zhongyi Zhang and Mingjie Li

Microorganisms 2024, 12(12), 2663; https://doi.org/10.3390/microorganisms12122663 - 22 Dec 2024

Viewed by 467

Abstract

Pseudostellaria heterophylla (Miq.) Pax, a highly valued Chinese medicinal plant, is experiencing a notable decline in yield and quality due to viral diseases, particularly caused those by TuMV and BBWV2. Currently, the absence of a quantitative detection method for these viruses in P. [...] Read more.

Pseudostellaria heterophylla (Miq.) Pax, a highly valued Chinese medicinal plant, is experiencing a notable decline in yield and quality due to viral diseases, particularly caused those by TuMV and BBWV2. Currently, the absence of a quantitative detection method for these viruses in P. heterophylla impedes the accurate diagnosis. The development of an accurate quantitative detection method is thus essential for effectively managing viral diseases in this plant. In this study, singleplex and duplex TaqMan qPCR were developed for the detection of the two viruses, based on two viral cloning vectors. Concurrently, the levels of both viruses were examined in the main produced regions of P. heterophylla. Furthermore, the levels of BBWV2 were examined during its infection of P. heterophylla. The optimal singleplex qPCR employed 0.1 μM of hydrolysis probe and 0.1 μM of primer for TuMV, while 0.2 μM of hydrolysis probe and 0.1 μM of primer were utilised for BBWV2. In contrast, the duplex qPCR employed the use of 0.1 μM of the upstream/downstream primer from each primer pair, with 0.2 μM of the respective hydrolysis probes. The 95% limit of detection (LOD) for singleplex qPCR was 734 copies for TuMV and 20 copies for BBWV2, while the 95% LOD for duplex qPCR was 945 copies for TuMV and 47 copies for BBWV2. Furthermore, the intra- and inter-assay coefficients of variation were found to be less than 1.2% for both singleplex and duplex qPCR. Of the P. heterophylla sampled 60 sites, 96% were found to be infected by one of two viruses. The levels of BBWV2 in N. benthamiana and P. heterophylla demonstrated an initial increase, followed by a subsequent decrease. The TaqMan qPCR methods provide a technical foundation for the monitoring of virus infections in P. heterophylla. Full article

(This article belongs to the Section Virology)

► Show Figures

Figure 1

Figure 1
The construction process of the P. heterophylla BBWV2 cloning vector and infectious cloning vector. The RNA1 and RNA2 genomes from the BBWV2 virus were transferred into the pSMART (Lucigen)-E cloning vector, respectively (A). Subsequently, the RNA1 and RNA2 genomes of the BBWV2 virus in the pSMART-E vector were further transferred into the pCB301 expression vector, thereby forming the BBWV2 infectious clone vector (B,C). Full article ">Figure 2
The evaluation for the initial detection range of singleplex (A,B) and duplex (C,D) TaqMan qPCR by using virus standard plasmid with a range of 105 to 100 copies/μL. Full article ">Figure 3
The standard curve of singleplex and duplex TaqMan qPCR. The standard curve for TaqMan qPCR, used for the singleplex (A) and duplex detection (B) of the BBWV2 or TuMV virus, was identified using the concentrations of virus standard plasmid ranging from 109 to 103. The linear equations between Cq values and virus concentration were obtained by utilising the qPCR Cq values of two viruses as the independent variable (y) and the corresponding plasmid concentration (Log x) as the dependent variable. Full article ">Figure 4
The symptoms of the viral disease of P. heterophylla for partial samples from the main cultivation region of P. heterophylla. The figure illustrates the infection levels of the TuMV and BBWV2 viruses, as determined via duplex TaqMan qPCR. Detailed infection level data across the various samples can be found in <a href="#app1-microorganisms-12-02663" class="html-app">Table S4</a>, which provides a summary of the infection levels in P. heterophylla at 60 sampling sites. It should be noted that the present study has only identified P. heterophylla TuMV and BBWV2. However, P. heterophylla has previously been shown to harbour a variety of viruses and their subtypes. Consequently, the virus symptoms displayed in the figure may not wholly be attributable to the presence of these two viruses. It is more probable that the observed disease results from a combination of multiple viral infections. Full article ">Figure 5
The phenotypic characteristics and BBWV2 levels of N. benthamiana following infection with BBWV2 infectious clones. The external characteristics N. benthamiana following infection with BBWV2 infectious clones were observed (A). The presence of the BBWV2 infectious clone in N. benthamiana was determined through the use of PCR methods (B). The singleplex qPCR was employed to detect BBWV2 levels during its process of infecting N. benthamiana (C). Full article ">Figure 6
The phenotypic characteristics and BBWV2 levels of P. heterophylla following the infection with BBWV2 infections clones. The phenotypic characteristics of P. heterophylla at varying stages after injection with BBWV2 infectious clones were observed (A). BBWV2 levels in the leaves and roots of these P. heterophylla were identified through singleplex TaqMan qPCR for BBWV2 detection (B,C). Full article ">

18 pages, 7731 KiB

Open AccessArticle

Identification, Characterization, and Ultrastructure Analysis of the Phenol-Degrading Rhodococcus erythropolis 7Ba and Its Viable but Nonculturable Forms

by Valentina N. Polivtseva, Anton N. Zvonarev, Olesya I. Sazonova, Yanina A. Delegan, Yulia N. Kocharovskaya, Alexander G. Bogun and Nataliya E. Suzina

Microorganisms 2024, 12(12), 2662; https://doi.org/10.3390/microorganisms12122662 - 22 Dec 2024

Viewed by 538

Abstract

Phenol and its chlorinated derivatives are introduced into the environment with wastewater effluents from various industries, becoming toxic pollutants. Phenol-degrading bacteria are important objects of research; among them, representatives of the genus Rhodoccocus are often highlighted as promising. Strain 7Ba was isolated by [...] Read more.

Phenol and its chlorinated derivatives are introduced into the environment with wastewater effluents from various industries, becoming toxic pollutants. Phenol-degrading bacteria are important objects of research; among them, representatives of the genus Rhodoccocus are often highlighted as promising. Strain 7Ba was isolated by enrichment culture. A new isolate was characterized using culturing, biochemistry, high-throughput sequencing, microscopy (including electron microscopy), and functional genome analysis. Rhodococcus erythropolis strain 7Ba is able to grow on phenol and chlorophenols without losing its properties during long-term storage. It was shown that strain 7Ba is able to form viable but nonculturable (VBNC) forms during long-term storage under nutrient limitation, preserving both cell viability and the ability to degrade phenols. The ultrastructural organization of the vegetative forms of cells and VBNC forms was characterized. The following distinctive features were found: modifications (thickening) of cell membranes, cell size reduction, nucleoid condensation. Functional analysis of the genome showed the presence of genes for the degradation of alkanes, and two branches of the β-ketoadipate pathway for the degradation of aromatic compounds. Also, the genome of strain 7Ba contains several copies of Rpf (resuscitation promoting factor) genes, a resuscitation factor of resting bacterial forms. The new isolate strain 7Ba is a promising biotechnological agent that can not only utilize toxic aromatic compounds but also remain viable during long-term storage. For this reason, its further application as an agent for bioremediation can be successful under changing conditions of climate and given the deficiency of nutrient compounds in nature. Minor biostimulation will allow the strain to recover its metabolic activity and effectively degrade pollution. Full article

(This article belongs to the Section Environmental Microbiology)

► Show Figures

Figure 1

Figure 1
Growth of strain 7Ba on phenol: (a) vegetative cells 7Ba from the reseeded culture, phenol 0.5 g/L, (b) vegetative cells 7Ba from the reseeded culture, phenol 1 g/L, (c) 7Ba(24) cells (vegetative cells of strain 7Ba after dormancy at 24 °C), phenol 0.5 g/L, (d) 7Ba(24) cells (vegetative cells of strain 7Ba after dormancy at 24 °C), phenol 1 g/L, (e) 7Ba(24) cells (vegetative cells of strain 7Ba after dormancy at 24 °C), phenol up to 2 g/L. Full article ">Figure 2
Degradation level of phenol by 7Ba and 7Ba (24). Values are mean ± SD of triplicate sets, * p-value ≤ 0.05 and ** p-value = less than 0.001 represent the significant difference between variants. Full article ">Figure 3
Cell morphology of strain 7Ba: (a) vegetative cells 7Ba from the reseeded culture grown on LB medium for 48 h, (b) VBNC cells of the 7Ba(4), (c) VBNC cells of the 7Ba(24). Phase-contrast microscopy. Scale bar—10 μm. Full article ">Figure 4
Ultrastructural organization of cells of strain 7Ba: (a) vegetative cells 7Ba from the reseeded culture, (b) VBNC cells of 7Ba(4), (c) VBNC 7Ba(24), (d) VBNC 7Ba(24) after 3.5 years of storage. Transmission electron microscopy. Designations: CM—cytoplasm membrane, CW—cell wall, Inc—inclusions, M—murein, MlOL—“membrane-like limiting outer layer”, Mls—myeline-like structures, N—nucleoid, IM—inner space between cytoplasm membrane and peptidoglycan layer. Full article ">Figure 5
Cells of strain 7Ba stained with Live/Dead dye. (a) vegetative cells 7Ba from the reseeded culture, (b) VBNC cells of the 7Ba(24) after 3.5 years of storage. Cells that are green in color are live cells, dead cells are red in color. Fluorescence microscopy. Full article ">Figure 6
Phylogenetic tree showing the position of strain 7Ba within the genus Rhodococcus. The genomes of only type strains were used in the construction of the tree. The strain under study is labeled in red. Full article ">Figure 7
Genomic fingerprint of strain Rhodococcus sp. 7Ba with primers BoxA1R and (GTG)5. The figure demonstrates changes in the genome by the presence of Box A1R (circles) and (GTG)5 (index line) sequence amplification products for different samples. M—GeneRuler 1 kb Plus DNA Ladder, 1—vegetative cells of the 7Ba(4) (vegetative cells of strain 7Ba after dormancy at 4 °C), 2—VBNC cells of the 7Ba(24), 3—vegetative cells of the 7Ba(24) (vegetative cells of strain 7Ba after dormancy at 24 °C), 4—vegetative cells of the 7Ba routinely reseed into laboratory culture. Full article ">

12 pages, 577 KiB

Open AccessArticle

Correlation of Geographic Variables with the Incidence Rate of Dengue Fever in Mexico: A 38-Year Study

by Porfirio Felipe Hernández Bautista, David Alejandro Cabrera Gaytán, Alfonso Vallejos Parás, Olga María Alejo Martínez, Lumumba Arriaga Nieto, Brenda Leticia Rocha Reyes, Carmen Alicia Ruíz Valdez, Leticia Jaimes Betancourt, Gabriel Valle Alvarado, Yadira Pérez Andrade and Alejandro Moctezuma Paz

Microorganisms 2024, 12(12), 2661; https://doi.org/10.3390/microorganisms12122661 - 22 Dec 2024

Viewed by 520

Abstract

Background: Dengue is a viral disease transmitted by the mosquitoes Aedes, which is characterized by fever, myalgia and arthralgia. In some cases, it can be fatal. For many years, dengue fever has been endemic to Mexico; however, few studies have investigated the [...] Read more.

Background: Dengue is a viral disease transmitted by the mosquitoes Aedes, which is characterized by fever, myalgia and arthralgia. In some cases, it can be fatal. For many years, dengue fever has been endemic to Mexico; however, few studies have investigated the historical and current extents of dengue fever at the national level or considered the effects of variables such as temperature, precipitation and elevation on its occurrence. Methods: An ecological study was carried out to compare the incidence rates of different types of dengue fever per hundred thousand inhabitants with temperature, precipitation and elevation between 1985 and 2023 in Mexico. The sources of information were the public records of the Ministry of Health and the National Meteorological Service. Multiple linear regression analysis was performed with Pearson and Spearman correlation coefficients at an alpha of <0.05. Results: The global linear regression presented an R² of 0.68 between the mean temperature and the cases of haemorrhagic dengue/severe/with warning signs. The degree of rainfall was not strongly correlated with the incidence rate, except in the eastern part of the country, where average temperature was also strongly correlated with the incidence rate. Nonsevere/classic dengue was most common from 1501 to 2000 m elevation, whereas severe forms of the disease were more prevalent at elevations greater than 2000 m. Full article

(This article belongs to the Special Issue Climate Change and Emerging Arboviruses)

► Show Figures

Figure 1

9 pages, 273 KiB

Open AccessCase Report

Trypanosoma cruzi DNA Identification in Breast Milk from Mexican Women with Chagas Disease

by María del Pilar Crisóstomo-Vázquez, Griselda Rodríguez-Martínez, Verónica Jiménez-Rojas, Leticia Eligio-García, Alfonso Reyes-López, María Hernández-Ramírez, Francisco Hernández-Juárez, José Luis Romero-Zamora, Silvia Guadalupe Vivanco-Tellez, Fortino Solorzano-Santos, Victor M. Luna-Pineda and Guillermina Campos-Valdez

Microorganisms 2024, 12(12), 2660; https://doi.org/10.3390/microorganisms12122660 - 21 Dec 2024

Viewed by 761

Abstract

(1) Background: Chagas disease is a public health problem affecting nearly 2 million women of reproductive age in Latin America. From these, 4–8% can transmit the infection to the foetus through the vertical route, whereas horizontal transmission through milk during breastfeeding remains controversial. [...] Read more.

(1) Background: Chagas disease is a public health problem affecting nearly 2 million women of reproductive age in Latin America. From these, 4–8% can transmit the infection to the foetus through the vertical route, whereas horizontal transmission through milk during breastfeeding remains controversial. Therefore, the presence of Trypanosoma cruzi (T. cruzi) DNA in the milk of women seropositive for Chagas disease was analysed to determine whether a relationship with the infection of their children can exist. (2) Methods: 260 pairs (mother–child) from four hospitals located in rural areas endemic to T. cruzi (state of Oaxaca) were studied. The presence of anti-T. cruzi antibodies in the serum of lactating women were determined by ELISA, whereas parasitic DNA in either breast milk or newborn’s blood was identified by PCR; (3) Results: The seroprevalence of infection in lactating women was 5.76%, and the frequency of infection detected by PCR in breast milk was 1.92%, while the frequency of infection in the blood of newborns was 1.92%. Pochutla-Oaxaca presented the highest number of positive cases in both breast milk and blood. The only risk factor found was the presence of the vector in the geographical area analysed, favouring the parasite’s transmission. Overall, the results suggest a probable transmission of T. cruzi, although whether it was through breastfeeding or through the blood during delivery could not be determined. (4) Conclusions: T. cruzi DNA was identified in lactating women’s milk and newborn blood, which is probable evidence of transmission through breastfeeding; nevertheless, future studies must be performed to confirm the presence of the parasite, alive or dead. Full article

(This article belongs to the Special Issue Parasitic Infection and Host Immunity, 2nd Edition)

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 - 21 Dec 2024

Viewed by 583

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)

► Show Figures

Figure 1

18 pages, 4133 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 - 21 Dec 2024

Viewed by 484

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)

► Show Figures

Figure 1

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 - 21 Dec 2024

Viewed by 480

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)

► Show Figures

Figure 1

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 - 21 Dec 2024

Viewed by 645

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)

► Show Figures

Figure 1

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 - 21 Dec 2024

Viewed by 710

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)

► Show Figures

Figure 1

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 - 21 Dec 2024

Viewed by 700

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)

► Show Figures

Figure 1

18 pages, 1578 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 - 20 Dec 2024

Viewed by 519

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)

► Show Figures

Figure 1

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 - 20 Dec 2024

Viewed by 472

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)

► Show Figures

Figure 1

Figure 1
(a) The heterotrophic nitrification and (b) aerobic denitrification performances of the nine preliminarily selected strains within 48 h. The letters above the columns are used to show the significant difference (p < 0.05). Full article ">Figure 2
(a) A scanning electron micrograph of DGFC5, (b) the Gram staining results, and (c) the neighbor-joining phylogenetic tree of DGFC5 and its related bacteria. The number of bootstrap replications is 1000 and the bootstrap values are indicated at the branch nodes. The scale bar represents a 0.1% sequence divergence. Full article ">Figure 3
Nitrogen removal and growth characteristics of DGFC5 under 5% salinity conditions. (a) Nitrogen source corresponding to ammonium, (b) nitrogen source corresponding to nitrite, (c) nitrogen source corresponding to nitrate, and (d) ammonium, nitrite, and nitrate as mixed nitrogen sources. Full article ">Figure 4
(a) A genetic map of DGFC5, (b) a nitrogen metabolism pathway map, (c) the KEGG pathway analysis, and (d) a schematic diagram of the nitrogen removal process. The green boxes indicate the genes present in the nitrogen metabolism pathway, and the numbers inside are the EC numbers of the key enzymes. Full article ">Figure 5
(a,b) The influences of different carbon sources, (c,d) C/N ratios, (e,f) rotation speeds, (g,h) temperatures, and (i,j) pH values on the heterotrophic nitrification performance of DGFC5 at 5% salinity. The values are the mean ± SD (error bars) of three replicates. Full article ">

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

Viewed by 505

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)

► Show Figures

Figure 1

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

Viewed by 732

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)

► Show Figures

Figure 1

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

Viewed by 1018

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)

► Show Figures

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

Viewed by 674

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)

► Show Figures

Figure 1

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

Viewed by 523

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)

► Show Figures

Figure 1

Figure 1
Experimental grouping of broiler chickens. This figure illustrates the randomized allocation of 240 Arbor Acres (AA) broiler chicks into four treatment groups, with each group containing six replicates of 10 chicks each. The dosing levels of M. chinensis extract for each group were based on established experimental protocols. The design ensures a balanced distribution of subjects to examine the effects on growth performance, serum biochemistry, antioxidant capacity, immune function, and gut microbiota over a 42-day period. Full article ">Figure 2
Effects of M. chinensis extract on antioxidant activity in serum and liver of white feather broilers: (A) total antioxidant capacity (T-AOC) in the liver; (B) glutathione peroxidase (GSH-PX) activity in the liver; (C) superoxide dismutase (SOD) activity in the liver; (D) catalase (CAT) activity in the liver; (E) malondialdehyde (MDA) levels in the liver; (F) glutathione peroxidase (GSH-PX) activity in the serum; (G) malondialdehyde (MDA) levels in the serum; (H) nitric oxide (NO) levels in the serum. * p < 0.05, ** p < 0.01, *** p < 0.001. Full article ">Figure 3
Effects of M. chinensis extract on the immune performance of white feather broilers: (A) serum IgA levels; (B) serum IgM levels; (C) serum IgG levels; (D) serum IL-4 levels; (E) serum IL-10 levels; (F) serum IFN-γ levels * p < 0.05, ** p < 0.01, *** p < 0.001, **** p < 0.0001. Full article ">Figure 4
Effects of MCE on intestinal tight junction protein gene expression in white feather broilers: (A) ZO-1 expression in the duodenum; (B) Claudin-1 expression in the duodenum; (C) Occludin expression in the duodenum; (D) ZO-1 expression in the cecum; (E) Claudin-1 expression in the cecum. * p < 0.05, ** p < 0.01. Full article ">Figure 5
Effects of MCE on short-chain fatty acid production in intestinal contents of white feather broilers: (A) acetic acid in the large intestine; (B) propionic acid in the large intestine; (C) butyric acid in the large intestine; (D) valeric acid in the large intestine; (E) acetic acid in the small intestine; (F) propionic acid in the small intestine. * p < 0.05, ** p < 0.01. Full article ">Figure 6
Microbial composition analysis of intestinal contents: (A) gate level composition analysis of colonic contents; (B) gate level composition analysis of small intestine contents; (C) analysis of the genus level composition of the contents of the large intestine; (D) analysis of genus level composition of small intestine contents. Full article ">Figure 7
Effects of dietary MCE on OTU counts in the intestinal microbiota of broilers: (A) OTU count changes in large intestinal contents; (B) OTU count changes in small intestinal contents. Full article ">Figure 8
Effects of dietary MCE on alpha diversity of intestinal microbiota in broilers: (A) Chao index for large intestinal contents; (B) coverage index for large intestinal contents; (C) Simpson index for large intestinal contents; (D) Sobs index for large intestinal contents; (E) Chao index for small intestinal contents; (F) coverage index for small intestinal contents; (G) Simpson index for small intestinal contents; (H) Sobs index for small intestinal contents. * p < 0.05, ** p < 0.01, *** p < 0.001. Full article ">Figure 9
Principal component analysis of intestinal microbiota at the genus level in broilers supplemented with MCE: (A) PCA plot of large intestinal microbiota; (B) PCoA plot of large intestinal microbiota; (C) PCA plot of small intestinal microbiota; (D) PCoA plot of small intestinal microbiota. Full article ">Figure 10
Differential analysis of intestinal microbiota at the genus level in broilers supplemented with MCE: (A) bar chart of the large intestinal microbial community composition; (B) inter-group differential analysis of large intestinal microbiota; (C) bar chart of the small intestinal microbial community composition; (D) inter-group differential analysis of small intestinal microbiota. * p < 0.05, ** p < 0.01. Full article ">Figure 11
Correlation analysis between short-chain fatty acids and microbiota in the large intestine. This figure presents the Spearman correlation analysis between short-chain fatty acids (SCFAs) and the microbial genera in the large intestine. * p < 0.05, ** p < 0.01. Full article ">

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

Viewed by 481

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)

► Show Figures

Figure 1

Figure 1
Vegetable cultivation area sampling map (white dots are greenhouse locations). Full article ">Figure 2
Clustering by phylogenetic group, MLST type and serotype to analyze the status of resistance genes carried by intestinal colonized ESBL-Ec isolates (red is carrying the resistance gene; blue is not carrying the resistance gene). Full article ">Figure 3
Different subtypes of CTX-M resistance gene skeletons (red arrows are CTX-M resistance genes, blue arrows are mobile genetic elements, yellow arrows are other resistance genes, and orange arrows are other genes): (a) gene skeleton of blaCTX-M-65; (b) gene skeleton of blaCTX-M-14; (c) gene skeleton of blaCTX-M-55; (d) gene skeleton of blaCTX-M-3; (e) gene skeleton of blaCTX-M-15; (f) gene skeleton of blaCTX-M-27. Full article ">Figure 4
Phylogenetic clusters, MLST typing and serotype correlation analysis of intestinal colonized ESBL-Ec (right side is labeled as carrying the virulence gene). Full article ">Figure 5
PFGE fingerprints of different samples of ESBL-Ec isolates within the vegetable cultivation area. Full article ">Figure 6
Transmission patterns of ESBL-Ec in vegetable cultivation environments identified based on PFGE analysis (F: cultivator feces; R: river water; D: river sediment). Full article ">Figure 7
SNP phylogenetic analysis of ESBL-Ec isolates from different times and sources with farmer gut-colonized ESBL-Ec in Shandong Province, October 2012–March 2024 (labels outside the phylogenetic tree are labeled for strains (SNP < 10) for time, source, ST type, serotype, and resistance genes). Full article ">

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

Viewed by 672

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)

► Show Figures

Figure 1

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

Viewed by 742

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)

► Show Figures

Figure 1

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

Viewed by 458

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)

► Show Figures

Figure 1

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

Viewed by 502

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)

► Show Figures

Figure 1

Journal Menu

Journal Browser

Microorganisms, Volume 12, Issue 12 (December 2024) – 290 articles

Further Information

Guidelines

MDPI Initiatives

Follow MDPI