Microorganisms

8 pages, 1031 KiB

Open AccessBrief Report

Quantification and Comparison of Different Biofilm Components from Methicillin-Susceptible Staphylococcus aureus Treated with Tranexamic Acid Using an In Vitro Model

by Marta Díaz-Navarro, Antonio Benjumea, Andrés Visedo, Patricia Muñoz, Javier Vaquero, Francisco Chana and María Guembe

Microorganisms 2025, 13(8), 1874; https://doi.org/10.3390/microorganisms13081874 - 11 Aug 2025

Abstract

As we previously demonstrated that tranexamic acid (TXA), an antifibrinolytic, showed an antibacterial effect alone and in combination with vancomycin and gentamicin, we now wanted to analyze its own efficacy using new, different fluorescent staining reagents that target different components of the biofilm [...] Read more.

As we previously demonstrated that tranexamic acid (TXA), an antifibrinolytic, showed an antibacterial effect alone and in combination with vancomycin and gentamicin, we now wanted to analyze its own efficacy using new, different fluorescent staining reagents that target different components of the biofilm matrix and compare which one quantifies biofilm reduction better. A 10⁸ cfu/mL suspension of the Staphylococcus aureus (ATCC29213) strain was placed into the wells of a 24-multiwell plate covered with glass slides coated with 10% poly-L-lysine under agitation for 24 h at 37 °C. After 3 washes with PBS, wells were treated with either TXA 10 mg/mL or sterile water and incubated for 24 h at 37 °C. After three washes with PBS, the density area of the following biofilm components was calculated using confocal laser scanning microscopy: extracellular proteins (Sypro Ruby), α-extracellular polysaccharides (ConA-Alexa fluor 633), α or β-extracellular polysaccharides (GS-II-Alexa fluor 488), bacterial DNA (PI), and eDNA (TOTO^®-1). We observed a statistically significant reduction in the occupied area by all components of the S. aureus biofilm (p < 0.001) after TXA 10 mg/mL treatment, compared to the positive control. All biofilm components’ reduction percentages reached ≥90.0%. We demonstrated that TXA reduced both bacteria and extracellular matrix components of S. aureus biofilm by using five different stain reagents, with all being equally valid for quantification. Full article

(This article belongs to the Collection Device-Related Infections and Bacterial Biofilms)

► Show Figures

Figure 1

25 pages, 1839 KiB

Open AccessReview

Burkholderia Phages and Control of Burkholderia-Associated Human, Animal, and Plant Diseases

by Bingjie Wang, Jiayi Zhang, Lei Chen, Munazza Ijaz, Ji’an Bi, Chenhao Li, Daixing Dong, Yanxin Wang, Bin Li, Jinyan Luo and Qianli An

Microorganisms 2025, 13(8), 1873; https://doi.org/10.3390/microorganisms13081873 - 11 Aug 2025

Abstract

Gram-negative Burkholderia bacteria are known for causing diseases in humans, animals, and plants, and high intrinsic resistance to antibiotics. Phage therapy is a promising alternative to control multidrug-resistant bacterial pathogens. Here, we present an overview of Burkholderia phage characteristics, host specificity, genomic classification, [...] Read more.

Gram-negative Burkholderia bacteria are known for causing diseases in humans, animals, and plants, and high intrinsic resistance to antibiotics. Phage therapy is a promising alternative to control multidrug-resistant bacterial pathogens. Here, we present an overview of Burkholderia phage characteristics, host specificity, genomic classification, and therapeutic potentials across medical, veterinary, and agricultural systems. We evaluate the efficacy and limitations of current phage candidates, the biological and environmental barriers of phage applications, and the phage cocktail strategy. We highlight the innovations on the development of targeted phage delivery systems and the transition from the exploration of clinical phage therapy to plant disease management, advocating integrated disease control strategies. Full article

(This article belongs to the Special Issue Phage–Bacteria Interplay: Phage Biology and Phage Therapy)

► Show Figures

Figure 1

12 pages, 439 KiB

Open AccessArticle

A Single-Center Retrospective Study on Early Treatment for COVID-19 in Solid Organ Transplant Recipients During the Omicron Era: Outcomes and SARS-CoV-2 Viral Kinetics

by Eugenia Milozzi, Elisa Biliotti, Alessandro Caioli, Valentina Mazzotta, Laura Loiacono, Silvia Meschi, Alessia Rianda, Andrea Antinori, Fabrizio Maggi and Gianpiero D’Offizi

Microorganisms 2025, 13(8), 1872; https://doi.org/10.3390/microorganisms13081872 - 11 Aug 2025

Abstract

Solid organ transplant recipients (SOTRs) are at high risk of severe coronavirus disease 2019 (COVID-19), therefore early treatment of mild infections is crucial to prevent increased morbidity and mortality. The effectiveness of early treatment in SOTRs has yet to be fully characterized due [...] Read more.

Solid organ transplant recipients (SOTRs) are at high risk of severe coronavirus disease 2019 (COVID-19), therefore early treatment of mild infections is crucial to prevent increased morbidity and mortality. The effectiveness of early treatment in SOTRs has yet to be fully characterized due to the emergence of new SARS-CoV-2 variants and to COVID-19 vaccination implementation. The aim of this single-center retrospective study is to evaluate the outcomes, safety and impact on SARS-CoV-2 viral load kinetics of COVID-19 early treatment in SOTRs. The study includes 80 SOTRs with a laboratory-confirmed diagnosis of symptomatic SARS-CoV-2 infection enrolled between January and October 2022 and treated with either monoclonal antibodies or antivirals. All patients received COVID-19 vaccination and 68.8% of them showed detectable levels of anti-spike (S) antibodies. The occurrence of clinical events (hospitalization, intensive care unit admission, or death) was assessed within 30 days after treatment initiation. The quantification of SARS-CoV-2 viral load were performed at baseline and at day-7. The rate of hospitalization was 2.5% [0.3–9%] and no deaths occurred. All patients completed treatment with no serious adverse events. Median viral load decrease was 0.48 [0.26–0.69] log₂ cycle threshold (ct) values, with no significant differences between SOTRs treated with monoclonal antibodies and those treated with antivirals. Viral load decrease was significantly associated with positive anti-s serology at baseline (

β

= 0.196, p = 0.01), number of days between symptom onset and treatment (

β

= 0.05, p = 0.03) and the number of comorbidities (

β

= −0.05, p = 0.03). We provide evidence of real-world effectiveness of early therapy in SOTRs infected with SARS-CoV-2 and demonstrate the relevant role of humoral response to vaccination in enhancing early viral load decay during treatment. Full article

(This article belongs to the Topic Advances in Vaccines and Antimicrobial Therapy—2nd Edition)

► Show Figures

Figure 1

14 pages, 493 KiB

Open AccessReview

Recent Changes in the Epidemiology of Group A Streptococcus Infections: Observations and Implications

by Susanna Esposito, Marco Masetti, Carolina Calanca, Nicolò Canducci, Sonia Rasmi, Alessandra Fradusco and Nicola Principi

Microorganisms 2025, 13(8), 1871; https://doi.org/10.3390/microorganisms13081871 - 11 Aug 2025

Abstract

Streptococcus pyogenes (Group A Streptococcus, GAS) is a major human pathogen capable of causing infections ranging from mild pharyngitis and impetigo to severe invasive diseases such as bacteremia, necrotizing fasciitis, and streptococcal toxic shock syndrome (STSS). Historically, the incidence of GAS infections [...] Read more.

Streptococcus pyogenes (Group A Streptococcus, GAS) is a major human pathogen capable of causing infections ranging from mild pharyngitis and impetigo to severe invasive diseases such as bacteremia, necrotizing fasciitis, and streptococcal toxic shock syndrome (STSS). Historically, the incidence of GAS infections declined during the early antibiotic era but began rising again from the early 2000s, driven partly by the emergence of hyper-virulent strains such as emm1 and emm12. From 2005 onward, significant increases in GAS infections were reported globally, accompanied by rising antibiotic resistance, particularly to macrolides and tetracyclines. During the COVID-19 pandemic, widespread public health measures led to a sharp decline in GAS infections, including invasive cases, but this trend reversed dramatically in late 2022 and 2023, with surges exceeding pre-pandemic levels, notably in children. Recent data implicate factors such as “immunity debt,” viral co-infections, and the spread of virulent clones like M1UK. Looking forward, continued surveillance of GAS epidemiology, virulence factors, and resistance patterns is critical. Moreover, the emergence of GAS isolates with reduced susceptibility to beta-lactams underscores the need for vigilance despite the absence of fully resistant strains. The development of an effective vaccine remains an urgent priority to reduce GAS disease burden and prevent severe outcomes. Future research should focus on vaccine development, molecular mechanisms of virulence, and strategies to curb antimicrobial resistance. Full article

(This article belongs to the Special Issue Current Challenges in Infectious Diseases Post COVID-19 Pandemic)

► Show Figures

Figure 1

17 pages, 7998 KiB

Open AccessArticle

The Effect of Apple and Pear Cultivars on In Vitro Fermentation with Human Faecal Microbiota

by Anna M. E. Hoogeveen, Christine A. Butts, Caroline C. Kim, Carel M. H. Jobsis, Shanthi G. Parkar, Halina M. Stoklosinski, Kevin H. Sutton, Patricia Davis, Duncan I. Hedderley, Jason Johnston and Pramod K. Gopal

Microorganisms 2025, 13(8), 1870; https://doi.org/10.3390/microorganisms13081870 - 11 Aug 2025

Abstract

Apples and pears are among the most popular and frequently consumed fruits worldwide. The polyphenol and dietary fibre components of these fruits are known to influence the gut microbiota and the subsequent human health outcomes. This study investigated the effects of New Zealand [...] Read more.

Apples and pears are among the most popular and frequently consumed fruits worldwide. The polyphenol and dietary fibre components of these fruits are known to influence the gut microbiota and the subsequent human health outcomes. This study investigated the effects of New Zealand grown apples and pears with differing polyphenol contents on the structure and function of the human gut microbiota. Five apple and two pear cultivars underwent in vitro human digestion and microbial fermentation. Samples taken at 0 and 18 h were analysed for changes in pH, microbial composition, and organic acid production. The change in pH after faecal fermentation was influenced by the type of fruit (apple or pear), with lower pH being observed in the apples. Significant apple or pear cultivar effects were observed for the gut microbiome and organic acid production. The apple cultivar ‘Golden Hornet’ produced the least butyrate and the greatest microbial alpha diversity, while the pear ‘PremP009’ showed greater butyrate production with increases in a butyrogenic species (Acidaminococcus intestini). Further studies are needed to investigate the effect of cultivar and type of fruit on nutrient absorption and microbial fermentation and the impact of these on human health. Full article

(This article belongs to the Collection Feature Papers in Gut Microbiota Research)

► Show Figures

Figure 1

3 pages, 126 KiB

Open AccessEditorial

Combating Antimicrobial Resistance: Innovations and Strategies

by Vasiliki Koumaki

Microorganisms 2025, 13(8), 1869; https://doi.org/10.3390/microorganisms13081869 - 11 Aug 2025

Abstract

Antimicrobial resistance (AMR) is an increasingly prevalent global health problem that undermines the efficacy of critical antimicrobial agents, including antibiotics, antivirals, antifungals, and antiprotozoals [...] Full article

(This article belongs to the Special Issue Combating Antimicrobial Resistance: Innovations and Strategies)

18 pages, 7947 KiB

Open AccessArticle

Physiological Insights into Enhanced Epsilon-Poly-l-Lysine Production Induced by Extract Supplement from Heterogeneous Streptomyces Strain

by Siyu Tong, Chen Zhang, Zhanyang Zhang, Huawei Zeng, Bingyue Xin, Mingtao Zhao, Deyin Zhao, Xin Zeng and Fei Zhang

Microorganisms 2025, 13(8), 1868; https://doi.org/10.3390/microorganisms13081868 - 10 Aug 2025

Abstract

Epsilon-poly-l-lysine (ε-PL) is a potent antimicrobial agent, but strategies to enhance its biosynthesis remain limited due to insufficient understanding of its physiological regulation. This study explores the interaction between Streptomyces albulus and heterogeneous microbial extracts, with a focus on actinomycete-derived signals. [...] Read more.

Epsilon-poly-l-lysine (ε-PL) is a potent antimicrobial agent, but strategies to enhance its biosynthesis remain limited due to insufficient understanding of its physiological regulation. This study explores the interaction between Streptomyces albulus and heterogeneous microbial extracts, with a focus on actinomycete-derived signals. The S. gilvosporeus extract induces the highest ε-PL production (3.4 g/L), exceeding the control by 2.6-fold and outperforming B. cinerea by 1.8-fold. Multi-omics analyses combined with morphological and biochemical profiling reveal that the induced state is characterized by intensified central carbon flux, enhanced lipid turnover, elevated respiratory activity, and cofactor regeneration, alongside suppression of competing secondary pathways. Morphological alterations, including denser mycelial aggregation and compact colony structures, accompany these metabolic shifts. Compared to B. cinerea, S. gilvosporeus elicits more pronounced stress adaptation and metabolic reprogramming in S. albulus. These findings suggest that interspecies interactions can activate intrinsic aggression resistance mechanisms, thereby driving ε-PL biosynthesis through a previously unrecognized physiological route. Full article

(This article belongs to the Special Issue Microbial Manufacture of Natural Products)

► Show Figures

Figure 1

12 pages, 1115 KiB

Open AccessArticle

Widespread Presence of SPX and Its Potential Role as a Phosphorus Nutrient Regulator in Dinoflagellates

by Jiashun Li, Jingtian Wang, Xiaoyu Wang, Kaidian Zhang and Senjie Lin

Microorganisms 2025, 13(8), 1867; https://doi.org/10.3390/microorganisms13081867 - 10 Aug 2025

Abstract

SPX domain-containing proteins (SPXc) are crucial for regulating phosphorus (P) homeostasis in plants. Recently, the SPX gene was identified in the diatom model Phaeodactylum tricornutum and shown to serve as a negative regulator of P acquisition. Whether SPXc occurs in dinoflagellates is unclear. [...] Read more.

SPX domain-containing proteins (SPXc) are crucial for regulating phosphorus (P) homeostasis in plants. Recently, the SPX gene was identified in the diatom model Phaeodactylum tricornutum and shown to serve as a negative regulator of P acquisition. Whether SPXc occurs in dinoflagellates is unclear. Here, we report the presence and potential functions of genes encoding SPXc in dinoflagellates (dino-SPXc). Four classes of SPXc were identified in dinoflagellates, including the three known classes—the stand-alone SPX, SPX-EXS, and SPX-VTC—and SPX-other, with SPX and SPX-EXS being dominant. Using the TARA Oceans database, we investigated the taxonomic and geographic distributions of dino-SPXc and found variations in dino-SPXc expression among size classes of dinoflagellates. The harmful algal bloom-causative species Prorocentrum shikokuense possesses all four classes of SPXc proteins, showing a fluctuating expression pattern under different nutrient conditions and during different phases of the cell cycle and algal bloom. In addition, the SPXc genes in Symbiodiniaceae respond not only to P stress but also to thermal variations. These results are consistent with a role of dino-SPXc in maintaining P homeostasis in dinoflagellates and suggest the importance of SPX-related genes in enabling dinoflagellates to sustain population growth in nutrient-variable oceans, warranting further research. Full article

(This article belongs to the Section Environmental Microbiology)

► Show Figures

Figure 1

21 pages, 4149 KiB

Open AccessArticle

Genomic Characterization of Marine Staphylococcus shinii Strain SC-M1C: Potential Genetic Adaptations and Ecological Role

by Manar El Samak, Hasnaa Lotfy, Abdelrahman M. Sedeek, Yehia S. Mohamed and Samar M. Solyman

Microorganisms 2025, 13(8), 1866; https://doi.org/10.3390/microorganisms13081866 - 9 Aug 2025

Abstract

Staphylococcus shinii (S. shinii) is a coagulase-negative species primarily associated with the degradation of organic matter, contributing to nutrient cycling in natural environments. This species has been mainly studied in clinical and terrestrial contexts, with no previous reports of its presence [...] Read more.

Staphylococcus shinii (S. shinii) is a coagulase-negative species primarily associated with the degradation of organic matter, contributing to nutrient cycling in natural environments. This species has been mainly studied in clinical and terrestrial contexts, with no previous reports of its presence in marine environments. In this study, we report the first isolation of S. shinii from a marine habitat. The strain SC-M1C was isolated from the Red Sea sponge Negombata magnifica. Whole-genome sequencing confirmed its taxonomic identity as S. shinii. The genome uncovers potential adaptive characteristics that facilitate survival in marine ecosystems, comprising genes associated with osmoregulation, nutrient acquisition, stress response, and resistance to heavy metals. Moreover, multiple genomic islands and plasmids were identified, suggesting a potential role in horizontal gene transfer and environmental adaptability. The presence of biosynthetic gene clusters linked to non-ribosomal peptides, siderophores, and terpene production indicates potential for biochemical versatility beyond traditional metabolic expectations. This study presents the first genomic insights into S. shinii in a marine context, highlighting its ecological significance and adaptive mechanisms in a high-salinity environment. These findings expand our understanding of staphylococcal ecology beyond terrestrial and clinical origins and provide a foundation for exploring the role of S. shinii in marine microbial interactions and environmental resilience. Full article

(This article belongs to the Section Environmental Microbiology)

► Show Figures

Figure 1

12 pages, 2639 KiB

Open AccessArticle

BST-2 Promotes N Protein Degradation and Inhibits Viral Replication Through the MARCHF8/NDP52 Autophagy Pathway

by Chenchen Zhao, Yan Qin, Haixin Huang, Yuying Li, Xinyu Zhang, Lin Zhou, Lulu Xie, Yimin Zhou, Yanqing Hu, Wei Chen, Tian Lan and Wen-Chao Sun

Microorganisms 2025, 13(8), 1865; https://doi.org/10.3390/microorganisms13081865 - 9 Aug 2025

Abstract

Swine acute diarrhea syndrome coronavirus (SADS-CoV) is a recently discovered enteric coronavirus that has caused considerable economic losses in the pig industry. SADS-CoV was first reported in 2017 in Guangdong Province, China, and subsequently in Fujian, Guangxi, Henan and Jiangxi Provinces. Bone marrow [...] Read more.

Swine acute diarrhea syndrome coronavirus (SADS-CoV) is a recently discovered enteric coronavirus that has caused considerable economic losses in the pig industry. SADS-CoV was first reported in 2017 in Guangdong Province, China, and subsequently in Fujian, Guangxi, Henan and Jiangxi Provinces. Bone marrow stromal cell antigen 2 (BST-2), also known as tetherin, acts as an antiviral protein to limit the release of a wide range of enveloped viruses. However, the relationship between BST-2 and SADS-CoV has rarely been studied. Here, we showed that endogenous BST-2 expression is downregulated by SADS-CoV infection in Vero-E6 and ST cells by 2- to 3-fold. The overexpression of BST-2 inhibited SADS-CoV replication, whereas the knockdown of the BST-2 gene in Vero cells restored SADS-CoV replication. Further study revealed that BST-2 targets the SADS-CoV nucleocapsid protein (N) and decreases N protein expression, and that the BST-2 transmembrane (TM) domain is essential for this activity. Moreover, the degradation of the SADS-CoV N protein promoted by BST-2 is mediated by the membrane-associated ring-CH-type finger 8 (MARCHF8)/calcium binding and coiled-coil domain 2 (NDP52) autophagosome pathway. Overall, we found that BST-2 suppresses viral proliferation by inducing the breakdown of the SADS-CoV N protein via the MARCHF8/NDP52 pathway. Full article

(This article belongs to the Special Issue Veterinary Microbiology and Immunology)

► Show Figures

Figure 1

14 pages, 9053 KiB

Open AccessArticle

Response of Chaetomium sp. to Nitrogen Input and Its Potential Role in Rhizosphere Enrichment of Lycium barbarum

by Ru Wan, Hezhen Wang, Xiaojie Liang, Xuan Zhou, Yajun Wang, Yehan Tian, Zhigang Shi and Yuekun Li

Microorganisms 2025, 13(8), 1864; https://doi.org/10.3390/microorganisms13081864 - 9 Aug 2025

Abstract

Lycium barbarum L. (goji berry), a traditional Chinese medicinal plant, depends heavily on nitrogen input to maintain productivity. Nitrogen application also profoundly influences rhizosphere microbial dynamics, which are critical for soil health and plant performance. This study aimed to investigate how the rhizosphere [...] Read more.

Lycium barbarum L. (goji berry), a traditional Chinese medicinal plant, depends heavily on nitrogen input to maintain productivity. Nitrogen application also profoundly influences rhizosphere microbial dynamics, which are critical for soil health and plant performance. This study aimed to investigate how the rhizosphere fungal community responds to nitrogen input and explore the potential role of beneficial fungi (e.g., Chaetomium) in goji berry rhizosphere enrichment. A field experiment with four nitrogen levels (0, 53.82, 67.62, and 80.73 g·N m⁻²·year⁻¹, designated as N0, N1, N2, and N3) was conducted to analyze the fungal community structure in the rhizosphere of goji berry using ITS rRNA gene amplicon sequencing. The results showed that nitrogen input significantly altered the rhizosphere fungal community composition and diversity. Redundancy analysis (RDA) and Mantel tests indicated that soil electrical conductivity, total phosphorus, available phosphorus, and nitrate nitrogen were key environmental factors driving the fungal communities’ shifts. Notably, specific fungal genera, including Chaetomium, Cladosporium, Gibberella, Fusarium, Pyxidiophora, Acaulium, and Lophotrichus, exhibited differential enrichment across nitrogen levels. In particular, Chaetomium was significantly enriched under the conventional nitrogen treatment (N2), a strain of Chaetomium sp. LC101 was successfully isolated from the goji berry rhizosphere, and its functional roles were verified via pot experiments. Inoculation with Chaetomium sp. LC101 significantly promoted goji berry growth, with the most pronounced effects observed under N0 treatments, root fresh weight, root vitality, and leaf chlorophyll content increased by up to 55.10%, 15.69%, and 43.27%, respectively, compared to non-inoculated controls. Additionally, Chaetomium sp. LC101 regulated rhizosphere nitrogen transformation by enhancing urease, nitrite reductase, and polyphenol oxidase activities while inhibiting nitrate reductase activity. These findings demonstrate that Chaetomium responds sensitively to nitrogen input, with enrichment under moderate nitrogen levels, and acts as a beneficial rhizosphere fungus by promoting plant growth and regulating nitrogen cycling. This study provides novel insights for nitrogen management in the goji berry industry, where synergistic regulation via “nitrogen reduction combined with microbial inoculation” can reduce nitrogen loss, improve yield and quality through functional fungi, and contribute to ecological sustainability. Full article

(This article belongs to the Section Plant Microbe Interactions)

► Show Figures

Figure 1

13 pages, 2351 KiB

Open AccessArticle

Desulfitobacterium elongatum sp. nov. NIT-TF6 Isolated from Trichloroethene-Dechlorinating Culture with Formate

by Udaratta Bhattacharjee, Ryuya Tomita, Li Xie and Naoko Yoshida

Microorganisms 2025, 13(8), 1863; https://doi.org/10.3390/microorganisms13081863 - 9 Aug 2025

Abstract

A strictly anaerobic bacterium denoted as strain NIT-TF6 of the genus Desulfitobacterium was isolated from a trichloroethene-dechlorinating culture with formate. Cells were straight rods of 1.6–6 µm long and 0.25–0.5 µm in diameter and used H₂, lactate, pyruvate, and malate as [...] Read more.

A strictly anaerobic bacterium denoted as strain NIT-TF6 of the genus Desulfitobacterium was isolated from a trichloroethene-dechlorinating culture with formate. Cells were straight rods of 1.6–6 µm long and 0.25–0.5 µm in diameter and used H₂, lactate, pyruvate, and malate as electron donors and thiosulfate and Fe (III)-citrate as electron acceptors. The genome of strain NIT-TF6 was 4.8 Mbp in size and included nine 16S rRNA genes. Phylogenetic analysis based on 16S rRNA sequences showed that NIT-TF6 shared the highest sequence similarity (96.39%) with Desulfitobacterium hafniense DCB-2ᵀ, forming an independent clade in the phylogenetic tree. Digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) values between strain NIT-TF6 and other Desulfitobacterium species ranged from 15.9 to 16.9% and from 71.68 to 72.51%, respectively. These are well below the thresholds for species delineation. A distinguishing feature of strain NIT-TF6 was its possession of both L-lactate dehydrogenase (L-LDH) and D-lactate dehydrogenase (D-LDH), in contrast to other Desulfitobacterium strains that exclusively express D-LDH. Based on the dDDH and ANI results, combined with physiological, phylogenetic, morphological, biochemical, genomic, and metabolic iron-related characteristics, strain NIT-TF6 has been proposed as a novel species within the genus Desulfitobacterium. The name Desulfitobacterium elongatum sp. nov. has been proposed for this strain, with NIT-TF6ᵀ designated as the type strain. Full article

(This article belongs to the Section Environmental Microbiology)

► Show Figures

Figure 1

13 pages, 1279 KiB

Open AccessArticle

Variabilities in N2 and E Gene Concentrations in a SARS-CoV-2 Wastewater Multiplex Assay

by Ashley Green, Aiswarya Rani Pappu, Melanie Oakes, Suzanne Sandmeyer, Matthew Hileman and Sunny Jiang

Microorganisms 2025, 13(8), 1862; https://doi.org/10.3390/microorganisms13081862 - 9 Aug 2025

Abstract

Wastewater can serve as both a source of pathogens that pose risks to human health and a valuable resource for tracking and predicting disease prevalence through wastewater-based surveillance (WBS). In WBS for SARS-CoV-2, both nucleocapsid-specific (N1 and N2) and the envelope (E) genes [...] Read more.

Wastewater can serve as both a source of pathogens that pose risks to human health and a valuable resource for tracking and predicting disease prevalence through wastewater-based surveillance (WBS). In WBS for SARS-CoV-2, both nucleocapsid-specific (N1 and N2) and the envelope (E) genes are common targets for primer design, but ambiguity remains regarding differences in results depending on the gene target chosen. This study investigated how and why two SARS-CoV-2 gene targets (N2 and E) varied when analyzed in a multiplex RT-ddPCR assay for a COVID-19 wastewater monitoring study. From December 2021 to June 2022, over 700 raw wastewater samples were collected from thirteen manholes in the University of California, Irvine sewer system. Murine hepatitis virus (MHV) was used as a matrix recovery and process control in the triplex RT-ddPCR assay. Water quality tests (TSS, COD, pH, turbidity and NH₃-N) were performed on all samples. Analyses showed that in over 10% of samples, the E gene concentration exceeded N2 by more than one order of magnitude. To evaluate matrix effects on amplification efficiency for N2 and E genes, multiple regression analysis was performed to explore whether water quality variables and MHV recovery efficiency could predict variance in gene concentrations, but no clear relationship was identified. However, viral recovery, as indicated by MHV recovery efficiency, was negatively impacted in samples with higher TSS and COD, suggesting PCR inhibition. These findings contribute to methodological standardization efforts in WBS and emphasize the importance of primer selection for large-scale monitoring. Full article

(This article belongs to the Special Issue Water Microorganisms Associated with Human Health, 2nd Edition)

45 pages, 3481 KiB

Open AccessReview

Why Are Long-Read Sequencing Methods Revolutionizing Microbiome Analysis?

by Adriana González, Asier Fullaondo and Adrian Odriozola

Microorganisms 2025, 13(8), 1861; https://doi.org/10.3390/microorganisms13081861 - 9 Aug 2025

Abstract

Most of the knowledge available on the composition and functionality of microbial communities in different ecosystems comes from short-read sequencing methods. It implies limitations regarding taxonomic resolution, variant detection, and genome assembly contiguity. Long-read sequencing technologies can overcome these limitations, transforming the analysis [...] Read more.

Most of the knowledge available on the composition and functionality of microbial communities in different ecosystems comes from short-read sequencing methods. It implies limitations regarding taxonomic resolution, variant detection, and genome assembly contiguity. Long-read sequencing technologies can overcome these limitations, transforming the analysis of microbial community composition and functionality. It is essential to understand the characteristics of each sequencing technology to select the most suitable one for each microbiome study. This review aims to show how long-read sequencing methods have revolutionized microbiome analysis in ecosystems and to provide a practical tool for selecting sequencing methods. To this end, the evolution of sequencing technologies, their advantages and disadvantages for microbiome studies, and the new dimensions enabled by long-read sequencing technologies, such as virome and epigenetic analysis, are described. Moreover, desirable characteristics for microbiome sequencing technologies are proposed, including a visual comparison of available sequencing platforms. Finally, amplicon and metagenomics approaches and the sequencing depth are discussed when using long-read sequencing technologies in microbiome studies. In conclusion, although no single sequencing method currently possesses all the ideal features for microbiome analysis in ecosystems, long-read sequencing technologies represent an advancement in key aspects, including longer read lengths, higher accuracy, shorter runtimes, higher output, more affordable costs, and greater portability. Therefore, more research using long-read sequencing is recommended to strengthen its application in microbiome analysis. Full article

(This article belongs to the Special Issue The Microbiome in Ecosystems)

► Show Figures

Figure 1

24 pages, 8045 KiB

Open AccessArticle

Environmental Factors Drive the Changes of Bacterial Structure and Functional Diversity in Rhizosphere Soil of Hippophae rhamnoides subsp. sinensis Rousi in Arid Regions of Northwest China

by Pei Gao, Guisheng Ye, Siyu Guo, Yuhua Ma, Yongyi Zhang, Sixuan Sun, Lin Guo, Hongyuan San, Wenjie Liu, Qingcuo Ren, Shixia Wang and Renyuan Peng

Microorganisms 2025, 13(8), 1860; https://doi.org/10.3390/microorganisms13081860 - 8 Aug 2025

Abstract

Hippophae rhamnoides subsp. sinensis Rousi has high ecological and medicinal value, and it is an important plant resource unique to the arid regions of Northwest China. Exploring the influence of climate characteristics and soil factors on the composition, diversity, and function of the [...] Read more.

Hippophae rhamnoides subsp. sinensis Rousi has high ecological and medicinal value, and it is an important plant resource unique to the arid regions of Northwest China. Exploring the influence of climate characteristics and soil factors on the composition, diversity, and function of the rhizosphere bacterial community of Chinese seabuckthorn is of great value for developing and popularizing characteristic plant resources in the arid regions of Northwest China. In this study, the rhizosphere soil of 13 Chinese seabuckthorn distribution areas in the northwest of China was taken as the research object, the bacterial community map was constructed based on 16S rRNA gene high-throughput sequencing technology, and the species abundance composition, structural diversity, molecular co-occurrence network, and phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt), as well as the function of rhizosphere soil bacterial community, were systematically studied. Combined with Mantel test and redundancy analysis (RDA), the key habitat factors driving the rhizosphere soil bacterial community structure of Chinese seabuckthorn were explored. The results showed that: (1) The number of amplicon sequence variants (ASVs) in rhizosphere soil bacterial community of Chinese seabuckthorn was the highest in S2(3072) and the S12(3637), and the lowest in the S11(1358) and S13(1996). The rhizosphere soil bacterial community was primarily composed of Proteobacteria, Actinobacteriota, and Acidobacteriota. Except for the S6 and S11 habitats, the dominant bacterial genera were mainly Achromobacter, Acidobacter (RB41), and Sphingomonas. (2) The α and β diversity of rhizosphere soil bacterial communities of Chinese seabuckthorn across 13 distribution areas were significantly different. The number of operational taxonomic units (OTUs), Ace index, and Chao 1 index of soil bacterial community in the S12 distribution area are the highest, and they are the lowest in S11 distribution area, with significant differences. The aggregation of soil bacterial communities in the S5 and S10 distribution areas is the highest, while it is the lowest in the S6 and S11 distribution areas. (3) PICRUSt function classification of soil bacteria showed that Metabolism and Genetic Information Processing functions were the strongest across all distribution areas, with S10 exhibiting higher functional capacity than other areas and S11 showing the weakest. (4) Cluster analysis revealed that soil bacteria across the 13 distribution areas were clustered into two groups, with S10 and S12 distribution areas as one group (Group 1) and the remaining 11 distribution areas as another group (Group 2). (5) Redundancy analysis revealed that pH was the key soil environmental factor driving the rhizosphere soil bacterial community α-diversity of Chinese seabuckthorn, followed by altitude (ALT) and soil water content (SWC). In summary, Chinese seabuckthorn prefers neutral to alkaline soils, and environmental factors play an important role in driving bacterial diversity, community structure, functional profiles, and co-occurrence networks in rhizosphere soil of Chinese seabuckthorn. Full article

(This article belongs to the Special Issue Soil Environment and Microorganisms)

► Show Figures

Figure 1

19 pages, 3705 KiB

Open AccessArticle

Pharmacologic Inhibition of Erythrocyte Ferroportin Expression Exacerbates Plasmodium Infection

by Sareh Zeydabadinejad, Benjamin Frederick Theis, Jun Sung Park, Amira F. Gohara, Matam Vijay-Kumar, Beng San Yeoh and Piu Saha

Microorganisms 2025, 13(8), 1859; https://doi.org/10.3390/microorganisms13081859 - 8 Aug 2025

Abstract

Plasmodium parasites rely on host iron for survival and replication, making host iron availability a critical determinant of malaria pathogenesis. Central to iron homeostasis is the hepcidin–ferroportin regulatory axis, where hepcidin suppresses iron export by inducing ferroportin degradation, thus modulating systemic and cellular [...] Read more.

Plasmodium parasites rely on host iron for survival and replication, making host iron availability a critical determinant of malaria pathogenesis. Central to iron homeostasis is the hepcidin–ferroportin regulatory axis, where hepcidin suppresses iron export by inducing ferroportin degradation, thus modulating systemic and cellular iron availability. In the Plasmodium infection model (P. yoelii), we observed a significant downregulation of hepatic hepcidin expression, accompanied by an increase in hepatic ferroportin expression. On the contrary, RBC-ferroportin protein level was notably suppressed upon P. yoelii infection. Given these findings, we aim to investigate the role of a ferroportin inhibitor in Plasmodium infection. In a P. yoelii mouse model, treatment with an oral ferroportin inhibitor, VIT-2763 (Vamifeport) increased parasitemia, accompanied by increased levels of pro-inflammatory cytokines, erythropoietin, and liver injury markers. In P. yoelii infected mice, VIT-2763 treatment suppressed hepcidin expression and increased ferroportin expression in hepatocytes, while reducing ferroportin protein levels in RBCs. VIT-2763 mediated exacerbation of P. yoelii infection reveals the tissue-specific regulation of ferroportin in hepatocytes and RBCs, underscoring the therapeutic potential of modulating the hepcidin–ferroportin axis as an intervention strategy in malaria. Full article

(This article belongs to the Special Issue Latest Research in Parasitology: Unlocking Mechanisms, Developing Solutions)

► Show Figures

Figure 1

16 pages, 1339 KiB

Open AccessArticle

Efficacy of Lactobacillus rhamnosus and Its Metabolites to Mitigate the Risk of Foodborne Pathogens in Hydroponic Nutrient Solution

by Esther Oginni, Robin Choudhury and Veerachandra Yemmireddy

Microorganisms 2025, 13(8), 1858; https://doi.org/10.3390/microorganisms13081858 - 8 Aug 2025

Abstract

Hydroponic nutrient solution (HNS) has been established as an ideal conduit for pathogen contamination and proliferation. This study evaluated the efficacy of lactic acid bacteria and their metabolites in mitigating the risk of foodborne pathogens in HNS when compared to conventional chemical treatments. [...] Read more.

Hydroponic nutrient solution (HNS) has been established as an ideal conduit for pathogen contamination and proliferation. This study evaluated the efficacy of lactic acid bacteria and their metabolites in mitigating the risk of foodborne pathogens in HNS when compared to conventional chemical treatments. Hoagland’s HNS were prepared according to the manufacturer’s instructions and inoculated with Salmonella Typhimurium, Escherichia coli 0157:H7, and Listeria innocua at 10⁵ CFU/mL cell concentration. These nutrient solutions were subjected to treatment with various concentrations of Lactobacillus rhamnosus live cells, a cell-free extract (CFE) of L. rhamnosus metabolites, sodium hypochlorite and peroxyacetic acid at 22 ± 1 °C for up to 96 h using appropriate controls. The survived cells were enumerated on respective selective media at regular intervals. Additionally, the impact of these treatments on lettuce growth and the physico-chemical properties of HNS, such as pH, electrical conductivity, salinity, total dissolved solids, and % lactic acid content, were determined over 21 days using standard procedures. Both S. Typhimurium and E. coli O157: H7, when in combination with L. rhamnosus, remained stable in HNS over a 96 h period, while L. innocua showed a 3-log reduction. Whereas CFE treatment of HNS showed a significant reduction in Salmonella and E. coli O157: H7 (both undetectable after 96 h; LOD: <1 log CFU/mL). Interestingly, L. innocua levels remained stable after CFE treatment. PAA treatments at 12 mg/L notably reduced Salmonella and L. innocua growth, but not E. coli O157:H7. Lettuce plants in untreated control were significantly taller and heavier compared to those treated with CFE. These findings highlight the potential of biological interventions while emphasizing their limitations in hydroponic systems for pathogen control. Full article

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

► Show Figures

Figure 1

31 pages, 9356 KiB

Open AccessArticle

Integrated Microbiome–Metabolome Analysis and Functional Strain Validation Reveal Key Biochemical Transformations During Pu-erh Tea Pile Fermentation

by Mengkai Hu, Huimin Zhang, Leisa Han, Wenfang Zhang, Xinhui Xing, Yi Wang, Shujian Ou, Yan Liu, Xiangfei Li and Zhenglian Xue

Microorganisms 2025, 13(8), 1857; https://doi.org/10.3390/microorganisms13081857 - 8 Aug 2025

Abstract

Fermentation plays a pivotal role in shaping the flavor and overall quality of Pu-erh tea, a microbially fermented dark tea. Here, we monitored physicochemical properties, chemical constituents, and microbial succession at 15 fermentation time points. Amplicon sequencing identified Staphylococcus, Bacillus, Kocuria [...] Read more.

Fermentation plays a pivotal role in shaping the flavor and overall quality of Pu-erh tea, a microbially fermented dark tea. Here, we monitored physicochemical properties, chemical constituents, and microbial succession at 15 fermentation time points. Amplicon sequencing identified Staphylococcus, Bacillus, Kocuria, Aspergillus, Blastobotrys, Thermomyces, and Rasamsonia as dominant genera, with prokaryotic communities showing greater richness and diversity than eukaryotic ones. Beta diversity and clustering analyses revealed stable microbial structures during late fermentation stages. Non-targeted metabolomics detected 347 metabolites, including 56 significantly differential compounds enriched in caffeine metabolism and unsaturated fatty acid biosynthesis. Fermentation phases exhibited distinct metabolic patterns, with volatile aroma compounds (2-acetyl-1-pyrroline, 2,5-dimethylpyrazine) and health-beneficial fatty acids (linoleic acid, arachidonic acid) accumulating in later stages. OPLS-DA and KEGG PATHWAY analyses confirmed significant shifts in metabolite profiles relevant to flavor and biofunctionality. RDA revealed strong correlations between microbial taxa, environmental parameters, and representative metabolites. To functionally verify microbial contributions, 17 bacterial and 10 fungal strains were isolated. Six representative strains, mainly Bacillus and Aspergillus, exhibited high enzymatic activity on macromolecules, confirming their roles in polysaccharide and protein degradation. This integrative multi-omics investigation provides mechanistic insights into Pu-erh tea fermentation and offers a scientific basis for microbial community optimization in tea processing. Full article

(This article belongs to the Special Issue Resource Utilization of Microorganisms: Fermentation and Biosynthesis)

► Show Figures

Figure 1

19 pages, 2244 KiB

Open AccessArticle

Swift Realisation of Wastewater-Based SARS-CoV-2 Surveillance for Aircraft and Airports: Challenges from Sampling to Variant Detection

by Cristina J. Saravia, Kira Zachmann, Natalie Marquar, Ulrike Braun, Claus Gerhard Bannick, Timo Greiner, Peter Pütz, Susanne Lackner and Shelesh Agrawal

Microorganisms 2025, 13(8), 1856; https://doi.org/10.3390/microorganisms13081856 - 8 Aug 2025

Abstract

International air traffic has contributed to the global spread of SARS-CoV-2 and its variants. In early 2023, wastewater-based epidemiology (WBE) has been implemented at airports as a surveillance tool to detect emerging variants at short notice. This study investigates the feasibility and challenges [...] Read more.

International air traffic has contributed to the global spread of SARS-CoV-2 and its variants. In early 2023, wastewater-based epidemiology (WBE) has been implemented at airports as a surveillance tool to detect emerging variants at short notice. This study investigates the feasibility and challenges of applying WBE at Berlin Brandenburg (BER) Airport, including a rapid implementation of wastewater sampling and analysis under unprecedented circumstances. For this purpose, aircraft and airport wastewater was sampled over 13 weeks. Established sampling and analysis protocols for municipal wastewater treatment plants (WWTPs) had to be adapted to the specific conditions of the airport environment. SARS-CoV-2 RNA was quantified and sequenced, revealing SARS-CoV-2 mutations not previously observed in clinical surveillance data in Germany. Despite the logistical and methodological challenges, the study demonstrates that WBE can serve as an early warning system for pathogen introduction. However, our study also underscores the need for realistic timelines for the establishment and validation of WBE monitoring strategies in new contexts. Investments in the establishment of WBE systems, e.g., infrastructure, protocols, trained personnel, and a network of stakeholders at strategic nodes including airports, can act as an effective tool for pandemic preparedness and global health security. Full article

(This article belongs to the Special Issue Surveillance of SARS-CoV-2 Employing Wastewater)

► Show Figures

Graphical abstract

Journal Description

Microorganisms

Latest Articles

Journal Menu

Journal Browser

Highly Accessed Articles

Latest Books

E-Mail Alert

News

Topics

Conferences

Special Issues

Topical Collections

Further Information

Guidelines

MDPI Initiatives

Follow MDPI