Journal Description
Microorganisms
Microorganisms
is a scientific, peer-reviewed, open access journal of microbiology, published monthly online by MDPI. The Hellenic Society Mikrobiokosmos (MBK), the Spanish Society for Nitrogen Fixation (SEFIN) and the Society for Microbial Ecology and Disease (SOMED) are affiliated with Microorganisms, and their members receive a discount on the article processing charges.
- Open Access— free for readers, with article processing charges (APC) paid by authors or their institutions.
- High Visibility: indexed within Scopus, SCIE (Web of Science), PubMed, PMC, PubAg, CAPlus / SciFinder, AGRIS, and other databases.
- Journal Rank: JCR - Q2 (Microbiology) / CiteScore - Q1 (Microbiology (medical))
- Rapid Publication: manuscripts are peer-reviewed and a first decision is provided to authors approximately 15.2 days after submission; acceptance to publication is undertaken in 2.9 days (median values for papers published in this journal in the first half of 2025).
- Recognition of Reviewers: reviewers who provide timely, thorough peer-review reports receive vouchers entitling them to a discount on the APC of their next publication in any MDPI journal, in appreciation of the work done.
- Testimonials: See what our editors and authors say about Microorganisms.
- Companion journal for Microorganisms include: Applied Microbiology and Bacteria.
Impact Factor:
4.2 (2024);
5-Year Impact Factor:
4.6 (2024)
Latest Articles
Bioeconomy-Based Approaches for the Microbial Valorization of Citrus Processing Waste
Microorganisms 2025, 13(8), 1891; https://doi.org/10.3390/microorganisms13081891 - 13 Aug 2025
Abstract
The citrus processing industry is an economically important agro-industrial sector worldwide; however, it produces significant amounts of waste annually. The biorefinery concept and the recovery of bio-based materials from agro-industrial residues, including citrus processing waste, are emphasized in the European Green Deal, reflecting
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The citrus processing industry is an economically important agro-industrial sector worldwide; however, it produces significant amounts of waste annually. The biorefinery concept and the recovery of bio-based materials from agro-industrial residues, including citrus processing waste, are emphasized in the European Green Deal, reflecting the EU’s commitment to fostering circularity. Biotreatment of citrus processing waste, including bioconversion into biomethane, biohydrogen, bioethanol and biodiesel, has been applied to valorize biomass for energy recovery. It can also be composted into a valuable soil conditioners and fertilizers, while raw and fermented citrus residues may exhibit phytoprotective activity. Citrus-derived residues can be converted into materials such as nanoparticles with adsorptive capacity for heavy metals and recalcitrant organic pollutants, and materials with antimicrobial properties against various microbial pathogens, or the potential to remove antibiotic-resistance genes (ARGs) from wastewater. Indeed, citrus residues are an ideal source of industrial biomolecules, like pectin, and the recovery of bioactive compounds with added value in food processing industry. Citrus processing waste can also serve as a source for isolating specialized microbial starter cultures or as a substrate for the growth of bioplastic-producing microorganisms. Solid-state fermentation of citrus residues can enhance the production of hydrolytic enzymes, with applications in food and environmental technology, as well as in animal feed. Certain fermented products also exhibit antioxidant properties. Citrus processing waste may be used as alternative feedstuff that potentially improves the oxidative stability and quality of animal products.
Full article
(This article belongs to the Special Issue Earth Systems: Shaped by Microbial Life)
Open AccessArticle
Investigating the Alleviating Effects of Dihydromyricetin on Subclinical Mastitis in Dairy Cows: Insights from Gut Microbiota and Metabolomic Analysis
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Jie Yu, Yingnan Ao, Hongbo Chen, Tinxian Deng, Chenhui Liu, Dingfa Wang, Pingmin Wan, Min Xiang and Lei Cheng
Microorganisms 2025, 13(8), 1890; https://doi.org/10.3390/microorganisms13081890 - 13 Aug 2025
Abstract
Mastitis is a common disease for dairy cows that exerts tremendously detrimental impacts on the productivity of cows and economic viability of pasture. Dihydromyricetin (DMY) is a flavonoid monomeric compound that possesses anti-inflammatory and antioxidant activity. This study aimed at dissecting the effects
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Mastitis is a common disease for dairy cows that exerts tremendously detrimental impacts on the productivity of cows and economic viability of pasture. Dihydromyricetin (DMY) is a flavonoid monomeric compound that possesses anti-inflammatory and antioxidant activity. This study aimed at dissecting the effects of DMY on the lactation performance, blood parameters, gut microbiota, and metabolite profiles of dairy cows with subclinical mastitis (SM). The results showed that dietary supplementation with DMY resulted in a reduction in milk somatic cell count, an increase in serum T-AOC and CAT activity, as well as a decrease in serum MDA content. DMY significantly enhanced the prevalence of Coprococcus and Roseburia and reduced the proportion of Cyanobacteria, Proteobacteria, and Dehalobacterium. The amino acid degradation, antibiotic resistance, and O-antigen building blocks biosynthesis (E. coli) capacity of gut microbes were notably diminished by DMY supplementation in cows with SM. Moreover, fecal and plasma metabolomic analysis revealed that DMY intervention reduced the abundance of pro-inflammatory metabolites including arachidonic acid analogues, ω-6 PUFA, and structural components of bacteria. Nevertheless, the levels of anti-inflammatory and antioxidant metabolites involving secondary bile acids, antioxidant vitamins, specific amino acid analogues, etc. were elevated by DMY administration. Overall, DMY might ameliorate SM via enhancing antioxidant capacity and improving the structure of the hindgut microbial community and metabolite profiles in dairy cows. These findings underscore the potential of DMY as a valuable dietary supplement for the improvement of mammary inflammatory diseases in dairy cows.
Full article
(This article belongs to the Section Gut Microbiota)
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Open AccessProtocol
Automated Platform for the Analysis of Multi-Plate Growth and Reporter Data
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Avichay Nahami, Dor Kain, Yonatan Cohen, Yuval Kolodkin-Gal, Yohanan Assouline, Avihu H. Yona, Ilana Kolodkin-Gal and Yuval Dorfan
Microorganisms 2025, 13(8), 1889; https://doi.org/10.3390/microorganisms13081889 - 13 Aug 2025
Abstract
Researchers traditionally calculate growth rates using the natural logarithm of optical density (OD), with existing script packages facilitating this process. Automatic plate readers, capable of simultaneously measuring OD across 384 cultures, significantly enhance data collection efficiency. Furthermore, these readers also measure luminescence and
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Researchers traditionally calculate growth rates using the natural logarithm of optical density (OD), with existing script packages facilitating this process. Automatic plate readers, capable of simultaneously measuring OD across 384 cultures, significantly enhance data collection efficiency. Furthermore, these readers also measure luminescence and fluorescence, providing valuable insights into gene expression. However, current analysis software often struggle with data generated by robotic systems measuring multiple plates, limiting the integration of growth and reporter analyses. This method paper addresses three key challenges: (a) the incompatibility of robotic multi-plate systems with existing analysis software, (b) the integration of growth and reporter analyses, and (c) the development of user-friendly interfaces for non-programmers. To address these challenges, we offer optimized script packages and a relevant case study on matrix expression in response to antibiotics. Our platform facilitates the efficient and integrated analysis of multi-plate growth and reporter data.
Full article
(This article belongs to the Special Issue Antimicrobial Testing (AMT), Third Edition)
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Open AccessArticle
Alteromonas nitratireducens sp. nov., a Novel Nitrate-Reducing Bacterium Isolated from Marine Sediments, and the Evolution of Nitrate-Reducing Genes in the Genus Alteromonas
by
Ying-Li Chang, Jia-Xi Li, Xing-Chen Wang, Yang Li, Yun-Fei Cao, Xiang-Wen Duan, Cong Sun, Can Chen and Lin Xu
Microorganisms 2025, 13(8), 1888; https://doi.org/10.3390/microorganisms13081888 - 13 Aug 2025
Abstract
Nitrate reduction serves as a pivotal process in the global nitrogen cycle, playing a crucial role in natural ecosystems and industrial applications. Although the genus Alteromonas is not traditionally regarded as a nitrate reducer, several Alteromonas strains have recently been found to be
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Nitrate reduction serves as a pivotal process in the global nitrogen cycle, playing a crucial role in natural ecosystems and industrial applications. Although the genus Alteromonas is not traditionally regarded as a nitrate reducer, several Alteromonas strains have recently been found to be capable of doing so. However, the evolutionary trajectory of this capability remains undiscovered. In this study, 32 bacterial strains were isolated and cultivated from the tidal flat sediment in Hangzhou Bay and classified into the classes Cytophagia (n = 2), Alphaproteobacteria (n = 2), Gammaproteobacteria (n = 17), Flavobacteriia (n = 5), and Bacilli (n = 6). One nitrate-reducing strain, designated as CYL-A6T, was identified by polyphasic taxonomy and proposed as a novel Alteromonas species. Genomic analysis reveals that seven Alteromonas genomes encode the dissimilatory nitrate reduction genes narGHI. Evolutionary analysis showed that these three nitrate-reducing genes were present in the early common ancestor of the genus Alteromonas, while gene loss events occurred in the subsequent evolution. With the loss of nitrate-reducing genes in the ancestry nodes, a wide variety of genes related to energy production and conversion, as well as carbohydrate, nucleotide, coenzyme, and inorganic ion metabolism, were gained in those nodes, which enabled Alteromonas members to utilize diverse substrates for increased energy production. This study enhances the understanding of microbial diversity in marine tidal flat sediments, proposes a novel nitrate-reducing species of the genus Alteromonas, and highlights the ecological diversification and ecological niche breadth in the evolution of the microbial metabolic network.
Full article
(This article belongs to the Special Issue Genomics of Marine and Aquatic Bacteria: A Focus on Novel Taxa, Diversity and Biotechnological Potential, 3rd Edition)
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Open AccessArticle
Structural and Functional Differences in the Gut and Lung Microbiota of Pregnant Pomona Leaf-Nosed Bats
by
Taif Shah, Qi Liu, Guiyuan Yin, Zahir Shah, Huan Li, Jingyi Wang, Binghui Wang and Xueshan Xia
Microorganisms 2025, 13(8), 1887; https://doi.org/10.3390/microorganisms13081887 - 13 Aug 2025
Abstract
Mammals harbor diverse microbial communities across different body sites, which are crucial to physiological functions and host homeostasis. This study aimed to understand the structure and function of gut and lung microbiota of pregnant Pomona leaf-nosed bats using V3-V4 16S rRNA gene sequencing.
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Mammals harbor diverse microbial communities across different body sites, which are crucial to physiological functions and host homeostasis. This study aimed to understand the structure and function of gut and lung microbiota of pregnant Pomona leaf-nosed bats using V3-V4 16S rRNA gene sequencing. Of the 350 bats captured using mist nets in Yunnan, nine pregnant Pomona leaf-nosed bats with similar body sizes were chosen. Gut and lung samples were aseptically collected from each bat following cervical dislocation and placed in sterile cryotubes before microbiota investigation. Microbial taxonomic annotation revealed that the phyla Firmicutes and Actinobacteriota were most abundant in the guts of pregnant bats, whereas Proteobacteria and Bacteroidota were abundant in the lungs. Family-level classification revealed that Bacillaceae, Enterobacteriaceae, and Streptococcaceae were more abundant in the guts, whereas Rhizobiaceae and Burkholderiaceae dominated the lungs. Several opportunistic and potentially pathogenic bacterial genera were present at the two body sites. Bacillus, Cronobacter, and Corynebacterium were abundant in the gut, whereas Bartonella, Burkholderia, and Mycoplasma dominated the lungs. Alpha diversity analysis (using Chao1 and Shannon indices) within sample groups examined read depth and species richness, whereas beta diversity using unweighted and weighted UniFrac distance metrics revealed distinct clustering patterns between the two groups. LEfSe analysis revealed significantly enriched bacterial taxa, indicating distinct microbial clusters within the two body sites. The two Random Forest classifiers (MDA and MDG) evaluated the importance of microbial features in the two groups. Comprehensive functional annotation provided insights into the microbiota roles in metabolic activities, human diseases, signal transduction, etc. This study contributes to our understanding of the microbiota structure and functional potential in pregnant wild bats, which may have implications for host physiology, immunity, and the emergence of diseases.
Full article
(This article belongs to the Special Issue Gut Microbiome in Homeostasis and Disease, 3rd Edition)
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Open AccessArticle
Bacterial Diversity Dynamics in Sandy Loam Soils in Tanzania Under Varying Fertilizer-Derived Uranium Concentrations
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Dennis A. Mwalongo, Jacob B. Lisuma, Nils H. Haneklaus, Ali Maged, Hendrik Brink, Fernando P. Carvalho, Stanisław Wacławek, Nelson Mpumi, Aloyce I. Amasi, Jerome M. Mwimanzi, Furaha M. Chuma, Thomas T. Kivevele and Kelvin M. Mtei
Microorganisms 2025, 13(8), 1886; https://doi.org/10.3390/microorganisms13081886 - 13 Aug 2025
Abstract
The presence of radiotoxic uranium (U) in mineral fertilizers is of global concern. A pilot study was conducted in Tabora (Tanzania) to determine the release of U from three brands of phosphate fertilizers and its impact on soil bacteria. The experiment used three
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The presence of radiotoxic uranium (U) in mineral fertilizers is of global concern. A pilot study was conducted in Tabora (Tanzania) to determine the release of U from three brands of phosphate fertilizers and its impact on soil bacteria. The experiment used three types of fertilizer: Minjingu Powder (MP), Nafaka Plus (NP), a mixed and granulated fertilizer made from Minjingu Phosphate Rock (MPR), and YaraMila Cereal (YC) fertilizer. There was also a control treatment that was not fertilized (NF). Alpha diversity and the R tool were used to analyze bacterial diversity in four samples within an average sequencing depth of 74,466 reads, using metrics like ASVs, Shannon index, and Chao1. The results showed that the number of amplicon sequence variants (ASVs) in the DNA from soil bacteria decreased, specifically to 400 ASVs, in the NP treatment, which was in line with the higher U concentration (3.93 mg kg−1) in the soils. In contrast, the MP fertilizer treatment, associated with a lower U concentration (3.06 mg kg−1) in soils, exhibited an increase in ASVs within the DNA of soil bacteria, reaching 795; the highest ASV value (822) was observed in the NF treatment. Higher amounts of U in the soil plots seemed to have resulted in more types of bacteria, with the Actinobacteriota phylum being the most common in all of the treatments. The NP (3.93 mg kg−3 U concentration) and MP (3.06 mg kg−3 U concentration) treatments were the only ones that showed Halobacteriota and Crenarchaeota phyla. Nonetheless, bacterial diversity may also account for the alterations in soil phosphorus and nitrogen following fertilizer application. The YaraMila Cereal treatment did not seem to be linked to any particular bacterial phylum. This means that in this study it did not have any measurable effect on the soil bacteria species compared to the MP and NP treatments.
Full article
(This article belongs to the Special Issue Advances in Agro-Microbiology)
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Open AccessArticle
Influence of Two Root Media and Three Vermicompost Amendments on Bacterial Communities in a Greenhouse Container Garden Model System
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Sihan Bu, Nikita H. Nel, Alyssa W. Beavers, Kameron Y. Sugino, Katherine Alaimo, John A. Biernbaum and Sarah S. Comstock
Microorganisms 2025, 13(8), 1885; https://doi.org/10.3390/microorganisms13081885 - 13 Aug 2025
Abstract
The aim of this study was to determine the impact of two root media and three vermicompost amendments on the root zone bacterial communities and harvest mass of lettuce grown in a greenhouse container garden model system. Lettuce seeds were planted in seven
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The aim of this study was to determine the impact of two root media and three vermicompost amendments on the root zone bacterial communities and harvest mass of lettuce grown in a greenhouse container garden model system. Lettuce seeds were planted in seven root media/amendment conditions. Lettuce was later harvested, and root media DNA was extracted for 16S rRNA sequencing to determine the composition of, as well as the alpha and beta diversity of, the bacterial communities. Fresh weight, dry weight, and percentage dry weight of lettuce were calculated under each treatment. Results indicate that the peat-lite growth media without any additions had the lowest rhizosphere bacterial alpha diversity compared to the other six growth media. Bacterial communities from containers with peat-lite media were significantly different than those from containers with compost-based media as measured by beta diversity. Moreover, the compost-based medium with vermicompost condition tended to result in a higher percentage dry weight lettuce than lettuce grown under the peat-lite condition. The peat-lite treatment condition had the numerically lowest dry weight (%) and bacterial diversity. Addition of vermicompost amendments had varying impacts on bacterial diversity, bacterial community composition, and harvest mass. Overall, this experiment establishes a protocol which can be applied for further understanding of the impact of root media type and vermicompost amendments on rhizosphere bacterial diversity and harvest mass.
Full article
(This article belongs to the Special Issue Interactions of Mycorrhizal Fungi and Other Soil Microorganisms with Plants)
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Open AccessArticle
Cervico-Vaginal Microbiome Dynamics Across HPV-Driven Lesion Stages in Moroccan Women
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Malika Allali, Khaoula Errafii, Rachid El Fermi, Karima Fichtali, Sanaa El Majjaoui, Adil El Ghanmi, Hicham El Fazazi, Najib Al Idrissi, Bouchra Ghazi, Youssef Bakri, Hassan Ghazal and Salsabil Hamdi
Microorganisms 2025, 13(8), 1884; https://doi.org/10.3390/microorganisms13081884 - 13 Aug 2025
Abstract
Cervical cancer (CC), often caused by persistent high-risk HPV infection, is a major health issue for Moroccan women. This study is the first in Morocco to examine how the cervico-vaginal microbiome differs across HPV-related clinical stages. Using 16S rRNA sequencing, the researchers analyzed
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Cervical cancer (CC), often caused by persistent high-risk HPV infection, is a major health issue for Moroccan women. This study is the first in Morocco to examine how the cervico-vaginal microbiome differs across HPV-related clinical stages. Using 16S rRNA sequencing, the researchers analyzed samples from 247 women—100 healthy controls, 43 hr-HPV+ pre-cancer cases, and 104 post-treatment CC cases. In healthy women, Lactobacillus dominated (70%), but it significantly declined in the pre-cancer group (45%, p < 0.01) and remained low post-treatment (50%). Meanwhile, Pseudomonadota and Actinobacteriota increased in pre-cancer samples (up to 25–30%, p < 0.01). Although the alpha diversity remained stable, the beta diversity differed significantly across stages (p = 0.001), but not by HPV status. Post-treatment samples showed a sharp decline in Bacillota (logFC −5, p < 10−15) and increases in Campylobacterota and Fusobacteriota (logFC +6 to +21, p < 10−16). Functionally, chemo-heterotrophy and fermentation declined, while nitrogen fixation and phototrophy rose in pre-cancer cases. Host factors like late menarche, high parity, STIs, and contraceptive use correlated with specific microbiota shifts.
Full article
(This article belongs to the Section Medical Microbiology)
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Open AccessReview
The Potential Role of Helicobacter pylori-Related Mast Cell Activation in the Progression from Gastroesophageal Reflux to Barrett’s Esophagus and Esophageal Adenocarcinoma
by
Evangelos I. Kazakos, Efthymia Petinaki, Christos Liatsos, Ioannis S. Papanikolaou, Kyriaki Anastasiadou and Jannis Kountouras
Microorganisms 2025, 13(8), 1883; https://doi.org/10.3390/microorganisms13081883 - 12 Aug 2025
Abstract
Helicobacter pylori (Hp), a widespread gastric pathogen, has long been studied for its role in upper gastrointestinal disorders. While its involvement in gastritis, peptic ulcer disease, and gastric cancer is well established, its impact on esophageal diseases remains an area of
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Helicobacter pylori (Hp), a widespread gastric pathogen, has long been studied for its role in upper gastrointestinal disorders. While its involvement in gastritis, peptic ulcer disease, and gastric cancer is well established, its impact on esophageal diseases remains an area of ongoing investigation. Nevertheless, some data indicate that Hp may be involved in the pathogenesis of gastroesophageal reflux disease–Barrett’s esophagus–esophageal adenocarcinoma sequence. Similarly, the Hp-related mast cell activation—an essential immunological event—may also play a crucial role in the progression from gastroesophageal reflux disease to Barrett’s esophagus and esophageal adenocarcinoma. The underlying mechanisms include immune modulation, cytokine cascades, and microbial interactions that collectively shape the esophageal microenvironment. This review provides an in-depth analysis of these pathways, highlighting the potential role of Hp-induced, mast cell-driven inflammation in esophageal disease progression and discussing emerging therapeutic strategies.
Full article
(This article belongs to the Special Issue Helicobacter pylori Infection: Detection and Novel Treatment)
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Open AccessArticle
Sustainable Formulation of Chewing Candies Using Liver Hydrolysates with Antioxidant and Antimicrobial Properties
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Ignė Juknienė, Naga Pavan Kumar Reddy Jonnagiri, Irena Mačionienė, Gintarė Zakarienė, Jūratė Stankevičienė, Ingrida Sinkevičienė, Vitalijs Radenkovs, Vaida Andrulevičiūtė and Gintarė Zaborskienė
Microorganisms 2025, 13(8), 1882; https://doi.org/10.3390/microorganisms13081882 - 12 Aug 2025
Abstract
This study aimed to develop innovative functional gummy candies enriched with protein hydrolysates derived from porcine liver, enhancing their antioxidant and antimicrobial properties. First, the overall consumer acceptability (OA) was assessed to determine the most suitable combination of gummy matrix components. Selected combinations
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This study aimed to develop innovative functional gummy candies enriched with protein hydrolysates derived from porcine liver, enhancing their antioxidant and antimicrobial properties. First, the overall consumer acceptability (OA) was assessed to determine the most suitable combination of gummy matrix components. Selected combinations were then analyzed for antioxidant activity (ABTS•+, DPPH•), antimicrobial effects, microbiological safety, and physicochemical characteristics. The incorporation of liver hydrolysates significantly increased antioxidant capacity. The highest activity was observed in sample GC5Pa24Ag, hydrolyzed with papain for 24 h and formulated with agar, showing ABTS•+ and DPPH• scavenging activities of (67.6 ± 0.98 µmol/g) and (49.14 ± 1.00%), respectively (p ≤ 0.05). Pepsin hydrolyzed samples (GC2Pe3Gl, GC2Pe6Gl, GC2Pe24Gl) exhibited significantly larger inhibition zones against Listeria monocytogenes ATCC 13932, Escherichia coli ATCC 25922, and Salmonella enterica subsp. enterica serovar Typhimurium ATCC 14028 compared to the control (p < 0.05). Among all, GC5Pa24Ag demonstrated the broadest antimicrobial activity, with a 29.0 ± 0.2 mm inhibition zone against all tested pathogens. These findings suggest that porcine liver hydrolysates can be successfully incorporated into confectionery products to create functional gummies with potential health benefits, offering antioxidant protection and antimicrobial effects in a consumer-friendly form.
Full article
(This article belongs to the Special Issue Antimicrobial Testing (AMT), Third Edition)
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Open AccessArticle
Dynamics and Assembly Mechanisms of Bacterial Communities During Larval Development of Macrobrachium rosenbergii: A High-Frequency Sampling Study Based on 16S rRNA Absolute Quantification Sequencing
by
Zhibin Lu, Jingwen Hao, Jilun Meng, Cui Liu, Tiantian Ye, Junjun Yan, Guo Li, Yutong Zheng, Pao Xu and Zhimin Gu
Microorganisms 2025, 13(8), 1881; https://doi.org/10.3390/microorganisms13081881 - 12 Aug 2025
Abstract
This study aimed to elucidate stage-specific dynamics, assembly mechanisms, and functional roles of bacterial communities during Macrobrachium rosenbergii larval development through high-resolution microbiota profiling. A high-frequency sampling strategy (126 samples across 11 zoeal stages and 1 post-larval stage within 21 days) and 16S
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This study aimed to elucidate stage-specific dynamics, assembly mechanisms, and functional roles of bacterial communities during Macrobrachium rosenbergii larval development through high-resolution microbiota profiling. A high-frequency sampling strategy (126 samples across 11 zoeal stages and 1 post-larval stage within 21 days) and 16S rRNA absolute quantification sequencing were employed. Bacterial succession, persistent taxa, and ecological processes were analyzed using abundance-occupancy modeling, neutral community modeling, and PICRUSt2-based functional prediction. Absolute bacterial abundance exhibited a triphasic abundance trajectory. Initial accumulation: Linear increase (Dph 1–5, peak Δlog10 = +1.7). Mid-stage expansion: Peak abundance (log10 = 7.5 copies/g, Dph 7–8). Late-stage remodeling: Secondary peak (log10 = 7.1 copies/g, Dph 19). Eighty dominant amplicon sequence variants (ASVs) (dominant taxa: Herminiimonas, Maritalea, and Enterobacteriaceae) comprised > 95% of the total abundance and coexisted via niche partitioning. Community construction was dominated by ecological drift/dispersal limitation (neutral model R2 = 0.16, p < 0.01). Metabolic pathways (e.g., nutrient metabolism) shifted with dietary transition. “Phylogenetic replacement” underpinned microbiota resilience against environmental perturbations. Optimizing aquaculture environments offers a viable antibiotic-free strategy for microbial management, advancing our understanding of host microbe interactions and ecological niche differentiation in aquatic animals.
Full article
(This article belongs to the Topic Diversity of Insect-Associated Microorganisms)
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Open AccessArticle
Molecular Surveillance of ESBL and Carbapenemase Genes in Gram-Negative Bacterial Pathogens Isolated from Various Clinical Samples Collected from Northern Region of United Arab Emirates
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Premalatha Ragupathi, Vaneezeh Khamisani, Aisha Fadila Sadiq, Mariam Aliyu Mobiddo, Nasir Parwaiz, Sovan Bagchi and Nazeerullah Rahamathullah
Microorganisms 2025, 13(8), 1880; https://doi.org/10.3390/microorganisms13081880 - 12 Aug 2025
Abstract
The aim of this study was to explore the prevalence of ESBL and carbapenemase genes in Gram-negative bacteria isolated from various clinical samples collected from northern regions of UAE. In total 3670 clinical samples were obtained from patients attending various hospitals and clinics
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The aim of this study was to explore the prevalence of ESBL and carbapenemase genes in Gram-negative bacteria isolated from various clinical samples collected from northern regions of UAE. In total 3670 clinical samples were obtained from patients attending various hospitals and clinics in the northern regions of the UAE. All the samples underwent routine bacterial culture examination, and their antibiotic sensitivity patterns mainly on beta-lactam and carbapenem resistance in Gram-negative bacteria. Molecular detection of ESBL and carbapenemase genes (blaCTX-M, blaTEM, blaSHV, blaNDM, blaIMP, and blaOXA-48) was performed on them. A total of 249 MDR Gram-negative bacteria (E. coli, K. pneumoniae, P. aeruginosa, P. mirabilis and A. baumannii) were isolated. The genes blaCTX-M, blaTEM, and blaSHV were detected in all the MDR isolates. Among them, the blaCTX-M was predominant especially in E. coli. The blaNDM and blaIMP were detected in a few K. pneumoniae and A. baumannii. The genes combination blaCTX-M+TEM and blaCTX-M+SHV, blaCTX-M+SHV, blaTEM+SHV, and blaTEM+NDM were detected mostly in K. pneumoniae and E. coli, and few A. baumannii. The gene combination blaCTX-M+TEM+SHV and blaCTX-M+TEM+SHV+IMP were also detected in few E. coli, P. aeruginosa, and A. baumannii. The current findings highlight the importance of molecular detection of ESBL and carbapenemase genes to emphasize monitoring and controlling the development of MDR bacterial pathogens.
Full article
(This article belongs to the Special Issue Evolution and Spread of Drug-Resistant Pathogens)
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Open AccessArticle
Altered Gut Microbiota and Predicted Immune Dysregulation in Early Childhood SARS-CoV-2 Infection
by
Dong Hyun Kim, Byung Ok Kwak and Ky Young Cho
Microorganisms 2025, 13(8), 1879; https://doi.org/10.3390/microorganisms13081879 - 12 Aug 2025
Abstract
The gut microbiome plays a key role in immune regulation. Young children experience rapid microbiome development, yet data on its alteration during severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection remain limited. This study aimed to characterize gut microbiome changes and immune-related pathway
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The gut microbiome plays a key role in immune regulation. Young children experience rapid microbiome development, yet data on its alteration during severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection remain limited. This study aimed to characterize gut microbiome changes and immune-related pathway alterations in young children with coronavirus disease 2019 (COVID-19). Eighteen children under 2 years old with confirmed SARS-CoV-2 infection and seven healthy controls were enrolled between December 2021 and June 2022. Stool samples were analyzed using 16S rRNA gene sequencing. In children with COVID-19, the gut microbiome exhibited an increase in Bacteroidota and Bacillota, whereas Actinomycetota and Pseudomonadota were reduced, with higher abundances of Bifidobacterium, Escherichia, and Streptococcus and lower abundances of Faecalibacterium, Clostridium, and Ruminococcus compared with healthy controls. Children with COVID-19 exhibited reduced alpha diversity, indicating microbial dysbiosis, and significant differences in beta diversity compared with healthy controls. Predictive functional analysis revealed downregulation of key immune-related pathways, such as interleukin-17, NOD-like receptor, and Toll-like signaling, which may impact mucosal immunity and viral clearance in children with COVID-19. SARS-CoV-2 infection in early childhood is associated with gut dysbiosis and the suppression of key immune pathways. These findings highlight the potential long-term impact of early-life microbial disruptions on immune development.
Full article
(This article belongs to the Section Gut Microbiota)
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Open AccessArticle
A Lyophilizable Nanoparticle Anthrax Vaccine Targeting the Loop-Neutralizing Determinant in Protective Antigen from Bacillus anthracis
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Jon Oscherwitz, Kemp Cease, David Milich, Tod Merkel, Thomas Braun, Fen Yu and David C. Whitacre
Microorganisms 2025, 13(8), 1878; https://doi.org/10.3390/microorganisms13081878 - 12 Aug 2025
Abstract
Anthrax remains a formidable bioterrorism threat for which new, optimized and thermostable vaccines are needed. We previously demonstrated that five immunizations of rabbits with a multiple-antigenic-peptide (MAP) vaccine in either Freund’s adjuvant or human-use adjuvants can elicit antibody (Ab) against the loop-neutralizing determinant
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Anthrax remains a formidable bioterrorism threat for which new, optimized and thermostable vaccines are needed. We previously demonstrated that five immunizations of rabbits with a multiple-antigenic-peptide (MAP) vaccine in either Freund’s adjuvant or human-use adjuvants can elicit antibody (Ab) against the loop-neutralizing determinant (LND), a cryptic neutralizing epitope in the 2β2-2β3 loop of protective antigen from Bacillus anthracis (B. anthracis), which mediates complete protection of rabbits from inhalation spore challenge with the B. anthracis Ames strain. To develop a more immunogenic vaccine, we molecularly constructed a virus-like particle (VLP) vaccine, comprising the Woodchuck hepatitis core antigen capsid (WHcAg) displaying 240 copies of the LND epitope on each nanoparticle. Initial studies showed that the LND-VLP was immunogenic in rabbits following two immunizations, and passive transfer of the rabbit sera into A/J mice conferred complete protection from aerosol challenge with B. anthracis. Further optimization of the vaccine revealed that the lyophilized LND-VLP vaccine was capable of eliciting highly protective levels of neutralizing antibody with two immunizations, and in some rabbits, a single immunization, using human-use adjuvants. A lyophilized LND-VLP nanoparticle vaccine may be an effective stand-alone vaccine or may complement PA-based vaccines as a future pre- or post-exposure vaccine for anthrax.
Full article
(This article belongs to the Section Molecular Microbiology and Immunology)
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Open AccessArticle
Key Bacterial Taxa Differences Associated with Polypharmacy in Elderly Patients
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Betti Shahin, Tahniat Nadeem, Tanya Khosla and Guy R. Adami
Microorganisms 2025, 13(8), 1877; https://doi.org/10.3390/microorganisms13081877 - 12 Aug 2025
Abstract
Changes in health, lifestyle, and medication usage significantly impact overall well-being. Aging is associated with an increased need for multiple medications, or polypharmacy. Despite extensive research on how aging and polypharmacy affect the gut microbiome, relatively little is known about their impact on
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Changes in health, lifestyle, and medication usage significantly impact overall well-being. Aging is associated with an increased need for multiple medications, or polypharmacy. Despite extensive research on how aging and polypharmacy affect the gut microbiome, relatively little is known about their impact on the oral microbiome and how shifts there can contribute to oral and systemic disease. An initial group of 55 saliva donors was formed of individuals with stage 3 periodontal disease and well-characterized for dental decay, both factors that contribute strongly to salivary microbiome identity. Relative levels of saliva bacteria were determined by 16S rRNA amplicon sequencing. Multiple variable analysis was performed to determine taxa associated with polypharmacy after correction for dental decay, tobacco use and gender. A second group, all with stage 3 periodontal disease, over 55 years of age and controlled for caries, served as a validation set. Two differences in taxa were validated as associated with polypharmacy in the elderly group. The tooth surface commensal Corynebacterium durum was lower with polypharmacy, and the dental decay-associated Propionibacterium acidifaciens was elevated. Saliva flow rate differences did not appear to be responsible for the differences seen in these taxa. Additionally, taxa associated with caries level and gender were identified. Polypharmacy associated taxa differences are potentially directly affected by medication usage, or the ailments associated with polypharmacy, and they are strong candidates to contribute to disease in the large group of elderly with poor oral health.
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(This article belongs to the Section Medical Microbiology)
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Open AccessReview
Immunomodulation in Respiratory Syncytial Virus Infection: Mechanisms, Therapeutic Targets, and Clinical Implications
by
Vasiliki Epameinondas Georgakopoulou and Vassiliki C. Pitiriga
Microorganisms 2025, 13(8), 1876; https://doi.org/10.3390/microorganisms13081876 - 12 Aug 2025
Abstract
Respiratory syncytial virus (RSV) remains a leading cause of acute lower respiratory tract infections globally, particularly affecting infants, older adults, and immunocompromised individuals. While recent advances in prophylaxis, such as long-acting monoclonal antibodies and maternal immunization, offer promise for prevention, therapeutic options for
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Respiratory syncytial virus (RSV) remains a leading cause of acute lower respiratory tract infections globally, particularly affecting infants, older adults, and immunocompromised individuals. While recent advances in prophylaxis, such as long-acting monoclonal antibodies and maternal immunization, offer promise for prevention, therapeutic options for active infection remain limited. Severe RSV disease is often driven not solely by viral replication but by dysregulated host immune responses, including excessive cytokine production, T helper type 2 (Th2) and T helper type 17 (Th17) cell polarization, and impaired interferon signaling. RSV has evolved sophisticated immune evasion strategies, such as inhibition of dendritic cell maturation, degradation of signal transducer and activator of transcription 2 (STAT2) via nonstructural proteins 1 and 2 (NS1/NS2), and interference with pattern recognition receptor signaling, particularly Toll-like receptors (TLRs) and retinoic acid-inducible gene I (RIG-I)-like receptors. These mechanisms result in attenuated innate immune responses and defective adaptive immunity, contributing to viral persistence, immunopathology, and recurrent infections. Moreover, age-dependent vulnerabilities, such as immune immaturity in infants and immunosenescence in older adults, exacerbate disease severity. Excessive immune activation leads to bronchiolitis, airway remodeling, and long-term sequelae including wheezing and asthma. Emerging immunomodulatory therapies aim to restore immune balance, targeting cytokines (e.g., interleukin-6 [IL-6], interleukin-1 beta [IL-1β]), the Janus kinase–signal transducer and activator of the transcription (JAK-STAT) pathway, or inflammasome activity. Host-directed therapies and direct-acting antivirals are also under investigation. A better understanding of RSV–host immune interactions is critical for optimizing therapeutic strategies and designing effective vaccines. This review synthesizes current knowledge on RSV immunopathogenesis and highlights immunomodulation as a promising frontier for therapeutic intervention.
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(This article belongs to the Special Issue The Microbial Pathogenesis)
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Open AccessArticle
Serrapeptase Eliminates Escherichia coli Biofilms by Targeting Curli Fibers, Lipopolysaccharides, and Phosphate Metabolism
by
Georgios Katsipis, Michalis Aivaliotis and Anastasia A. Pantazaki
Microorganisms 2025, 13(8), 1875; https://doi.org/10.3390/microorganisms13081875 - 11 Aug 2025
Abstract
Escherichia coli biofilms are implicated in the development of persistent infections and increased antibiotic resistance, posing a significant challenge in clinical settings. These biofilms enhance bacterial survival by forming protective extracellular matrices, rendering conventional treatments less effective. Serrapeptase (SPT), a proteolytic enzyme, has
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Escherichia coli biofilms are implicated in the development of persistent infections and increased antibiotic resistance, posing a significant challenge in clinical settings. These biofilms enhance bacterial survival by forming protective extracellular matrices, rendering conventional treatments less effective. Serrapeptase (SPT), a proteolytic enzyme, has emerged as a potential anti-biofilm agent due to its ability to degrade biofilm components and disrupt bacterial adhesion. In this study, we report the inhibitory effect of SPT against E. coli biofilm and its effect on key virulence factors. In vitro assays, including crystal violet staining, optical and fluorescence microscopy, and viability measurements, revealed the dose-dependent inhibition of biofilm formation (IC50 = 14.2 ng/mL), reduced biofilm (−92%, 500 ng/mL) and planktonic viability (−45%, 500 ng/mL), and a marked loss of amyloid curli fibers. SPT treatment also lowered the levels of key virulence factors: cellular and secreted lipopolysaccharides (−76%, 8 ng/mL; −94%, 32 ng/mL), flagellin (−63%, 8 ng/mL), and peptidoglycan (−29%, 125 ng/mL). Mechanistically, SPT induced a phosphate-dysregulating response: secreted alkaline phosphatase activity rose (+70%, 125 ng/mL) while cellular DING/PstS proteins declined (−84%, 64 ng/mL), correlating strongly with biofilm inhibition. In silico docking further suggests direct interactions between SPT and the curli subunits CsgA and CsgB, potentially blocking fiber polymerization. Together, these findings position SPT as a powerful non-antibiotic biofilm disruptor against E. coli, offering a promising strategy to undermine bacterial persistence and resistance by targeting both structural matrix components and metabolic regulatory pathways.
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(This article belongs to the Special Issue Pathogenic Biofilms: Physiology, Molecular Mechanisms and Counter Strategies)
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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
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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.
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(This article belongs to the Collection Device-Related Infections and Bacterial Biofilms)
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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,
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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.
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(This article belongs to the Special Issue Phage–Bacteria Interplay: Phage Biology and Phage Therapy)
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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
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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 ( = 0.196, p = 0.01), number of days between symptom onset and treatment ( = 0.05, p = 0.03) and the number of comorbidities ( = −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.
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(This article belongs to the Topic Advances in Vaccines and Antimicrobial Therapy—2nd Edition)
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