International Journal of Molecular Sciences

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Open AccessArticle

Essential Role of LapD in the Absence of Cardiolipins

by Satish Raina, Akshay Maniyeri, Aravind Ayyolath and Gracjana Klein

Int. J. Mol. Sci. 2026, 27(3), 1445; https://doi.org/10.3390/ijms27031445 - 31 Jan 2026

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Abstract

To maintain the integrity of the outer membrane of Gram-negative bacteria, such as Escherichia coli, the levels of two essential components, phospholipids (PL) and lipopolysaccharide (LPS), are tightly regulated, although the underlying molecular mechanisms are unclear. E. coli synthesizes three main [...] Read more.

To maintain the integrity of the outer membrane of Gram-negative bacteria, such as Escherichia coli, the levels of two essential components, phospholipids (PL) and lipopolysaccharide (LPS), are tightly regulated, although the underlying molecular mechanisms are unclear. E. coli synthesizes three main PLs, including essential phosphatidylethanolamine and phosphatidylglycerol and nonessential cardiolipin (CL). We showed that CL synthesis is conditionally essential in ΔlapD bacteria. Using this synthetic lethal phenotype, we isolated suppressors that rescued growth at elevated temperatures. We showed that loss-of-function mutations in cdsA encoding CDP-diglyceride synthetase, and pgsA, which encodes phosphatidylglycerophosphate synthase, bypass this lethality. Such mutations reduce the relative abundance of acidic phospholipids, which are otherwise elevated in Δ(lapD clsA) bacteria, and increase the amounts of cis-vaccenic acid without altering amounts of LpxC mediating the first committed step in LPS biosynthesis. Interestingly, overexpression of genes, including accC and glnB, whose products can inhibit fatty acid/PL synthesis, overcame the lethality of Δ(lapD clsA) bacteria. We demonstrated that PgsA co-purifies with LapB, which regulates LpxC stability and acts as a hub for proteins involved in PL and LPS biosynthesis, including LapD. Overall, our results reveal that LapD is positioned at the regulatory nexus between LPS assembly and fatty acid/PL synthesis. Full article

(This article belongs to the Special Issue 25th Anniversary of IJMS: Updates and Advances in Molecular Microbiology)

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12 pages, 932 KB

Open AccessArticle

Molecular Characterization of Gyrovirus galga 1 in Domestic Dogs in the North of Vietnam Indicates the Presence of Recombination Events

by Giang Huong Thi Tran, Amonpun Rattanasrisomporn, Dao Anh Tran Bui, Hieu Van Dong and Jatuporn Rattanasrisomporn

Int. J. Mol. Sci. 2026, 27(3), 1384; https://doi.org/10.3390/ijms27031384 - 30 Jan 2026

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Abstract

A total of 168 fecal samples were obtained from both diarrheic dogs exhibiting clinical symptoms and clinically healthy individuals across four provinces/cities in Northern Vietnam. Based on a polymerase chain reaction method, the Gyrovirus gala 1 (GyVg1) genome was found in 18 (10.71%) [...] Read more.

A total of 168 fecal samples were obtained from both diarrheic dogs exhibiting clinical symptoms and clinically healthy individuals across four provinces/cities in Northern Vietnam. Based on a polymerase chain reaction method, the Gyrovirus gala 1 (GyVg1) genome was found in 18 (10.71%) of 168 samples. Six representative GyVg1 genomes identified in Vietnam were each 2375 nucleotides long. They shared nucleotide identities of 94.98–98.62%. Whole genome phylogenetic analysis showed that the six obtained GyVg1 strains were grouped into two distinct lineages: GyVg1 I (2/6 strains) and GyVg1 II (4/6 strains). Vietnamese GyVg1 strains were genetically related to Chinese strains. Multiple residue replacements were identified in VP (VP1–VP3) proteins of the Vietnamese GyVg1 strains. A recombination event led to the emergence of the GyVg1/Dog/VNUA-06 recombinant strain. Overall, these observations indicate the presence of GyVg1 viruses in domestic dogs in the North of Vietnam. Full article

(This article belongs to the Special Issue 25th Anniversary of IJMS: Updates and Advances in Molecular Microbiology)

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28 pages, 2857 KB

Open AccessArticle

Further Evidence for the Immunosuppressive Activity of Transmembrane Envelope Protein p15E of Porcine Endogenous Retrovirus

by Joachim Denner, Reinhard Schwinzer, Claudia Pokoyski, Benedikt B. Kaufer, Björn Dierkes, Jinzhao Ban and Lovlesh Lovlesh

Int. J. Mol. Sci. 2026, 27(2), 1094; https://doi.org/10.3390/ijms27021094 - 22 Jan 2026

Cited by 1 | Viewed by 392

Abstract

Retroviruses are immunosuppressive, and there is evidence that a highly conserved immunosuppressive domain (isu domain) in their transmembrane envelope protein contributes to this activity. Studies have shown that inactivated retroviruses, their purified transmembrane envelope proteins, and synthetic peptides corresponding to the isu domain [...] Read more.

Retroviruses are immunosuppressive, and there is evidence that a highly conserved immunosuppressive domain (isu domain) in their transmembrane envelope protein contributes to this activity. Studies have shown that inactivated retroviruses, their purified transmembrane envelope proteins, and synthetic peptides corresponding to the isu domain inhibit mitogen-triggered proliferation of peripheral blood mononuclear cells (PBMCs) and modulate their cytokine and gene expression. This has been demonstrated for human immunodeficiency virus type 1 (HIV-1), as well as for beta- and gammaretroviruses and for both exogenous and endogenous retroviruses, including syncytins. In the case of HIV-1, homopolymers of its isu peptide stimulated an increased release of IL-10, IL-6, and other cytokines from human PBMCs. Up-regulated genes included IL-6, IL-8, and IL-10, as well as MMP-1, TREM-1, and IL-1β. In vivo, in a mouse tumor model, tumor cells that were unable to induce tumors in immunocompetent animals gained the ability to do so when expressing the transmembrane envelope protein or the isu domain of various retroviruses on their surface. Here, we demonstrate that the transmembrane envelope protein p15E of PERV can modulate cytokine expression in human PBMCs. Human 293 cells were transfected with four constructs that express a portion of p15E, including the isu domain, and were cultured in the presence of a selection medium containing hygromycin. The p15E-expressing cells were co-cultured with human PBMCs, leading to the release of IL-6 and IL-10 protein and the modulation of multiple cytokines and other markers, including IL-6, IL-10, IFN-α, TNF-α, MMP1, and SEPP1. Similar, but more pronounced, effects were observed when PERV-producing 293 and pig cells were used in parallel; both expressed higher levels of p15E. Additionally, p15E expression reduced MHC class I expression, and preliminary data indicate that p15E expression could have a protective effect against cellular cytotoxicity. This finding underscores the need for further research to elucidate the dynamics of p15E expression and its immunosuppressive activity. It also contributes to the understanding of the immunosuppressive properties of pathogenic retroviruses. Furthermore, expressing the immunosuppressive p15E of PERV on the surface of a pig xenotransplant may reduce the need for pharmaceutical immunosuppressants. Full article

(This article belongs to the Special Issue 25th Anniversary of IJMS: Updates and Advances in Molecular Microbiology)

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28 pages, 10606 KB

Open AccessArticle

Diversity of Cardinium Endosymbiont Genomes from Plant-Parasitic Nematodes

by Sergey V. Tarlachkov, Alexander Y. Ryss, Yury Y. Ilinsky, Dmitry A. Rodionov, Lydmila I. Evtushenko and Sergei A. Subbotin

Int. J. Mol. Sci. 2026, 27(2), 1038; https://doi.org/10.3390/ijms27021038 - 20 Jan 2026

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Abstract

Cardinium endosymbionts are obligate intracellular bacteria found in a wide range of invertebrate hosts. In this study, we generated ten new Cardinium genomes from plant-parasitic nematodes of the genera Amplimerlinius, Bursaphelenchus, Cactodera, Ditylenchus, Globodera, Meloidoderita, and Rotylenchus [...] Read more.

Cardinium endosymbionts are obligate intracellular bacteria found in a wide range of invertebrate hosts. In this study, we generated ten new Cardinium genomes from plant-parasitic nematodes of the genera Amplimerlinius, Bursaphelenchus, Cactodera, Ditylenchus, Globodera, Meloidoderita, and Rotylenchus, revealing their broad ecological and phylogenetic distribution. Using an expanded set of genes, we clarified the relationship between previously defined Cardinium groups B and F from nematodes, showing that they are closely related and likely share a single evolutionary origin within nematode-associated Cardinium. Among the newly assembled Cardinium genomes obtained in this study, two genomes originating from strains associated with wood-inhabiting Bursaphelenchus species exhibited remarkable genome reduction, with estimated sizes of approximately 695 kb. Functional annotation of Cardinium genomes indicated an absence of or a reduction in several central metabolic pathways, including the biotin biosynthetic pathway. A complete biotin pathway was found only in D. weischeri, and this pathway is only partially encoded in Cactodera sp. The polA gene, which encodes DNA polymerase I, showed partial loss in several Cardinium strains. Phylogenetic and comparative genomic analyses provided strong evidence that several carbohydrate, glycerophospholipid, and biotin metabolism genes in these endosymbionts have been acquired through horizontal gene transfer. Future research that integrates high-quality genome assemblies with functional analyses of host–symbiont interactions will be essential to elucidate how metabolic dependency, genome reduction, and horizontal gene transfer collectively shape the evolution and ecological diversification of Cardinium across nematode hosts. Full article

(This article belongs to the Special Issue 25th Anniversary of IJMS: Updates and Advances in Molecular Microbiology)

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29 pages, 4331 KB

Open AccessArticle

Postbiotics Combination Synergises the Antiproliferative Effects of Doxorubicin in Gastric Cancer Cells: A Cellular and Molecular Deep Dive

by Radwa A. Eladwy, Mohamed Fares, Muhammad A. Alsherbiny, Dennis Chang, Chun-Guang Li and Deep Jyoti Bhuyan

Int. J. Mol. Sci. 2026, 27(1), 362; https://doi.org/10.3390/ijms27010362 - 29 Dec 2025

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Abstract

Short-chain fatty acids (SCFAs) acetate, propionate, and butyrate are microbial metabolites with recognised roles in gut and immune homeostasis, but their therapeutic relevance in gastric cancer, particularly in combination with chemotherapeutics, remains unclear. This study investigated the antiproliferative synergy between a combined SCFA [...] Read more.

Short-chain fatty acids (SCFAs) acetate, propionate, and butyrate are microbial metabolites with recognised roles in gut and immune homeostasis, but their therapeutic relevance in gastric cancer, particularly in combination with chemotherapeutics, remains unclear. This study investigated the antiproliferative synergy between a combined SCFA mixture (APB) and doxorubicin (Dox) in AGS gastric adenocarcinoma cells using integrated cellular, molecular, and proteomic approaches. APB and Dox each inhibited cell proliferation, with IC₅₀ values of 568.33 ± 82.56 μg/mL and 0.22 ± 0.04 μg/mL, respectively, and their combination (3000 + 0.27 μg/mL) enhanced cytotoxicity, achieving 103.46% inhibition and reducing the APB IC₅₀ to 512.80 ± 18.37 μg/mL. Combination index values confirmed synergistic interactions (CI₅₀ = 0.61; CI₉₅ = 0.13). APB+Dox significantly increased apoptosis (94.83%) with minimal necrosis (4.64%) and induced strong ROS generation comparable to APB alone, while Dox showed limited oxidative effects. Proteomic profiling revealed downregulation of ribosomal proteins and cell cycle regulators in Dox and APB+Dox groups, with the combination further enhancing apoptosis-related pathways and stress responses. Overall, these findings indicate that SCFA-based interventions, exemplified by APB+Dox, may offer a low-toxicity strategy to potentiate chemotherapy efficacy in gastric cancer through apoptosis induction, redox disruption, and attenuation of drug resistance. Full article

(This article belongs to the Special Issue 25th Anniversary of IJMS: Updates and Advances in Molecular Microbiology)

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28 pages, 4688 KB

Open AccessArticle

The Importance of Humic Acids in Shaping the Resistance of Soil Microorganisms and the Tolerance of Zea mays to Excess Cadmium in Soil

by Agata Borowik, Jadwiga Wyszkowska, Magdalena Zaborowska and Jan Kucharski

Int. J. Mol. Sci. 2025, 26(24), 12175; https://doi.org/10.3390/ijms262412175 - 18 Dec 2025

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Abstract

Contamination with cadmium (Cd²⁺) poses a severe threat to the soil environment due to its toxic effect on bacteria, being of key importance to soil fertility and plant health. The present study aimed to evaluate the effect of a humic preparation, [...] Read more.

Contamination with cadmium (Cd²⁺) poses a severe threat to the soil environment due to its toxic effect on bacteria, being of key importance to soil fertility and plant health. The present study aimed to evaluate the effect of a humic preparation, Humus Active (HA), on the structure, diversity, and functional potential of soil bacteria under conditions of cadmium stress during Zea mays cultivation. A model study was conducted to analyze the response of bacteria to soil contamination with 60 mg Cd kg⁻¹ under conditions of soil fertilization with humic acid at doses of 2 g (HA2) and 4 g (HA4) kg⁻¹ of soil. Microbiological analyses were carried out with both culture and non-culture (16S rRNA gene amplicon sequencing method) methods. Bacteria function prediction was also performed using FAPROTAX software. The study results demonstrated that Cd caused a 92% reduction in Zea mays biomass and a significant decrease (by 52%) in the abundance of organotrophic bacteria. The NGS analysis showed that it also reduced the population of the Neobacillus bacteria in the soil (by 50%), simultaneously causing an over twofold increase in the population of the Nocardioides genus bacteria. The application of HA (particularly in the HA4 dose) substantially mitigated Cd phytotoxicity. In the Cd-contaminated soil, HA4 stimulated the growth of culturable actinobacteria. The soil bacteria community was predominated by chemoheterotrophic bacteria and the nitrogen cycle bacteria, driven by tolerant, Cd²⁺-resistant bacteria from the following genera: Bacillus, Nocardioides, and Arthrobacter. The study results enable concluding that even though Humus Active does not restore the original microbiome structure, it promotes the development of a new stress-resistant bacterial community exhibiting high bioremediating potential, thereby directly translating into improved plant condition. Subsequently, humic acids provide an innovative approach that not only extends knowledge about the mechanisms behind bacterial resistance but also enables developing practical methods for diminishing cadmium mobility in the soil. Full article

(This article belongs to the Special Issue 25th Anniversary of IJMS: Updates and Advances in Molecular Microbiology)

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16 pages, 1472 KB

Open AccessArticle

Innovative Colorimetric Neutral Red-Based Loop-Mediated Isothermal Amplification (NR-LAMP) Assay: Transforming Rapid and Affordable Feline Leukemia Virus Detection

by Witsanu Rapichai, Piyamat Khamsingnok, Anyalak Wachirachaikarn, Thawee Laodim, Hieu Van Dong, Nianrawan Meecharoen, Siriluk Ratanabunyong, Thanawat Khaoiam, Supansa Tuanthap, Amonpun Rattanasrisomporn, Selapoom Pairor, Kiattawee Choowongkomon, Natthasit Tansakul, Peter A. Lieberzeit and Jatuporn Rattanasrisomporn

Int. J. Mol. Sci. 2025, 26(24), 11793; https://doi.org/10.3390/ijms262411793 - 5 Dec 2025

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Abstract

Feline leukemia virus (FeLV) is a retrovirus that globally affects both domestic and wild cats, leading to the development of leukemia, lymphoma, and immunosuppression. However, it is important to note that the daily antigen test may yield false negative results. In this study, [...] Read more.

Feline leukemia virus (FeLV) is a retrovirus that globally affects both domestic and wild cats, leading to the development of leukemia, lymphoma, and immunosuppression. However, it is important to note that the daily antigen test may yield false negative results. In this study, we successfully developed the first colorimetric loop-mediated isothermal amplification (LAMP) associated with neutral red (NR-LAMP) for the detection of FeLV. The NR-LAMP assay exhibited high sensitivity and efficiency compared to the routine polymerase chain reaction (PCR) reference method. To ensure specificity, a novel LAMP primer set was custom-designed based on the pol gene of multiple FeLV strains, which resulted in no cross-amplification with other feline viruses. Under the optimized isothermal amplification conditions at 61 °C for 40 min, the NR-LAMP assay achieved a detection limit of 10⁰ copies/µL. Using a blind clinical test involving 98 samples, the NR-LAMP assay demonstrated perfect agreement with the reference PCR method, providing a sensitivity of 97.3% and a specificity of 100%. This proposed NR-LAMP assay surpasses other related approaches in terms of sensitivity, efficiency, and cost-effectiveness. Consequently, the colorimetric NR-LAMP reaction serves as a robust and convenient diagnostic tool for the inspection of FeLV, offering an alternative molecular method for future clinical applications and commercial utilization. Full article

(This article belongs to the Special Issue 25th Anniversary of IJMS: Updates and Advances in Molecular Microbiology)

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10 pages, 3609 KB

Open AccessArticle

Cooperativity in Escherichia coli L-Threonine Dehydrogenase and Its Inhibition by an Antibacterial N-Pyridylpyrazolone Derivative

by Ana Obaha, Nika Mikulič Vernik, Karmen Mlinar, Marcel Tušek, Milena Stojkovska Docevska, Nejc Petek, Jurij Svete and Marko Novinec

Int. J. Mol. Sci. 2025, 26(23), 11751; https://doi.org/10.3390/ijms262311751 - 4 Dec 2025

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Abstract

Antibiotic resistance is an increasing concern in modern healthcare. Therefore, it is important to identify novel antimicrobial agents and new molecular targets for such compounds. Here, we describe the identification of an N-pyridylpyrazolone derivative, 4-(2-aminoethyl)-2-(pyridin-2-yl)-1,2-dihydro-3H-pyrazol-3-one dihydrochloride (compound 1), which [...] Read more.

Antibiotic resistance is an increasing concern in modern healthcare. Therefore, it is important to identify novel antimicrobial agents and new molecular targets for such compounds. Here, we describe the identification of an N-pyridylpyrazolone derivative, 4-(2-aminoethyl)-2-(pyridin-2-yl)-1,2-dihydro-3H-pyrazol-3-one dihydrochloride (compound 1), which is effective against Gram-positive and Gram-negative bacteria and inhibits the enzymatic activity of Escherichia coli L-threonine dehydrogenase (TDH). To characterize its interaction with compound 1, TDH was overexpressed in E. coli. The recombinant enzyme was shown to exist in dilute solution in equilibrium between dimeric and tetrameric forms, with a K_d value for the dimer/tetramer transition of 3 ± 1 nM, and to bind L-threonine cooperatively with a Hill coefficient of 1.4. Compound 1 acted as a partial mixed inhibitor of TDH with an EC₅₀ value of 47 ± 16 µM and did not affect the equilibrium between oligomeric states. Altogether, these findings identify compound 1 as a promising starting point for the development of novel antibiotics and as a tool compound for studying the functional properties of TDH. Full article

(This article belongs to the Special Issue 25th Anniversary of IJMS: Updates and Advances in Molecular Microbiology)

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12 pages, 2012 KB

Open AccessArticle

Fullerene Gallium Phosphonate Shows Antimycobacterial Effect Against Mycobacterium avium

by Sonyeol Yoon, Kayvan Sasaninia, Iffat Hasnin Era, Sanya Dhama, Aishvaryaa Shree Mohan, Ami Patel, Lannhi Nguyen, Arshavir Karapetyan, Cristian Sy, Nickolas Yedgarian, Nezam Newman, Xiaoning Bi, Michel Baudry, Peter R. Yang and Vishwanath Venketaraman

Int. J. Mol. Sci. 2025, 26(20), 9998; https://doi.org/10.3390/ijms26209998 - 14 Oct 2025

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Abstract

Mycobacterium avium complex (MAC) infections present significant therapeutic challenges due to their inherent antibiotic resistance, demanding innovative treatment approaches. This study investigated the antimicrobial and antioxidant potential of a novel compound, Fullerene Gallium Phosphonate (FGP), and compared its effects against a previously tested [...] Read more.

Mycobacterium avium complex (MAC) infections present significant therapeutic challenges due to their inherent antibiotic resistance, demanding innovative treatment approaches. This study investigated the antimicrobial and antioxidant potential of a novel compound, Fullerene Gallium Phosphonate (FGP), and compared its effects against a previously tested similar compound, Fullerene Disodium Phosphonate (FDSP). Results of experiments using MAC cultures and infected THP-1 macrophages treated with varying FGP and FDSP concentrations (1, 10, 100 µg/mL) revealed that FGP demonstrated greater efficacy than FDSP in reducing M. avium colony-forming units (CFU), achieving a nearly 3-fold reduction by day 8, compared to a 2-fold decrease with FDSP. In infected macrophages, FGP significantly decreased bacterial load at 1 and 10 µg/mL (p < 0.01). FGP also lowered oxidative stress, reflected by a significant reduction in malondialdehyde (MDA) levels on day 4 (p < 0.05) and decreased IL-6 (2-fold) and TNF-α levels (3-fold) by day 8, indicating both antimicrobial and anti-inflammatory effects. However, FGP paradoxically increased MAC burden at its highest concentration and showed no significant difference in efficacy of different concentrations. These findings suggest that FGP may serve as a promising candidate for antimycobacterial therapy with dual antibacterial and antioxidant effects. Further research is crucial to fully elucidate its mechanism of action and find the optimal therapeutic window. Full article

(This article belongs to the Special Issue 25th Anniversary of IJMS: Updates and Advances in Molecular Microbiology)

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17 pages, 1507 KB

Open AccessArticle

Navigating the Fitness Landscape: Host Density, Epistasis, and Clonal Interference Drive Divergent Evolutionary Pathways in Phage Qβ

by Mara Laguna-Castro, Pilar Somovilla, Víctor López-Muñoz, Luis F. Pacios and Ester Lázaro

Int. J. Mol. Sci. 2025, 26(18), 9020; https://doi.org/10.3390/ijms26189020 - 16 Sep 2025

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Abstract

Understanding how ecological factors shape viral evolution is essential for predicting adaptation in RNA viruses. In this study, we investigated the evolutionary dynamics of bacteriophage Qβ under varying host densities, focusing on two nonsynonymous mutations—A1930G and C2011A—located in the A1 protein. Using experimental [...] Read more.

Understanding how ecological factors shape viral evolution is essential for predicting adaptation in RNA viruses. In this study, we investigated the evolutionary dynamics of bacteriophage Qβ under varying host densities, focusing on two nonsynonymous mutations—A1930G and C2011A—located in the A1 protein. Using experimental evolution, phenotypic assays, and competition experiments, we found that C2011A is consistently selected at low bacterial densities, enhancing viral entry but reducing burst size. In contrast, A1930G is fixed at high densities, despite similar phenotypic effects, suggesting its advantage arises from interactions with additional mutations. Clonal analysis revealed that compensatory or beneficial mutations modulate the fitness of A1930G, enabling its fixation. The absence of both mutations in the same genome points to negative epistasis, confirmed by the poor performance of the double mutant generated by site-directed mutagenesis. Sequencing of intermediate transfers showed early emergence of A1930G, but its fixation was prevented by clonal interference with C2011A. These findings highlight how host availability, fitness trade-offs, epistasis, and competition among variants shape the adaptive landscape of RNA viruses. Full article

(This article belongs to the Special Issue 25th Anniversary of IJMS: Updates and Advances in Molecular Microbiology)

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14 pages, 269 KB

Open AccessArticle

Porcine Lymphotropic Herpesvirus (PLHV) Was Not Transmitted During Transplantation of Genetically Modified Pig Hearts into Baboons

by Hina Jhelum, Martin Bender, Bruno Reichart, Jan-Michael Abicht, Matthias Längin, Benedikt B. Kaufer and Joachim Denner

Int. J. Mol. Sci. 2025, 26(15), 7378; https://doi.org/10.3390/ijms26157378 - 30 Jul 2025

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Abstract

Porcine lymphotropic herpesviruses -1, -2, and -3 (PLHV-1, PLHV-2, and PLHV-3) are gammaherpesviruses that are widespread in pigs. These viruses are closely related to the human pathogens Epstein–Barr virus (EBV) and Kaposi sarcoma-associated herpesvirus (KSHV), both of which are known to cause severe [...] Read more.

Porcine lymphotropic herpesviruses -1, -2, and -3 (PLHV-1, PLHV-2, and PLHV-3) are gammaherpesviruses that are widespread in pigs. These viruses are closely related to the human pathogens Epstein–Barr virus (EBV) and Kaposi sarcoma-associated herpesvirus (KSHV), both of which are known to cause severe diseases in humans. To date, however, no definitive association has been established between PLHVs and any disease in pigs. With the growing interest in xenotransplantation as a means to address the shortage of human organs for transplantation, the safety of using pig-derived cells, tissues, and organs is under intense investigation. In preclinical trials involving pig-to-nonhuman primate xenotransplantation, another porcine herpesvirus—porcine cytomegalovirus, a porcine roseolovirus (PCMV/PRV)—was shown to be transmissible and significantly reduced the survival time of the xenotransplants. In the present study, we examined donor pigs and their respective baboon recipients, all of which were part of preclinical pig heart xenotransplantation studies, for the presence of PLHV. PLHV-1, PLHV-2, and PLHV-3 were detected in nearly all donor pigs; however, no evidence of PLHV transmission to the baboon recipients was observed. Full article

(This article belongs to the Special Issue 25th Anniversary of IJMS: Updates and Advances in Molecular Microbiology)

31 pages, 2679 KB

Open AccessArticle

Gut Microbial Postbiotics as Potential Therapeutics for Lymphoma: Proteomics Insights of the Synergistic Effects of Nisin and Urolithin B Against Human Lymphoma Cells

by Ahmad K. Al-Khazaleh, Muhammad A. Alsherbiny, Gerald Münch, Dennis Chang and Deep Jyoti Bhuyan

Int. J. Mol. Sci. 2025, 26(14), 6829; https://doi.org/10.3390/ijms26146829 - 16 Jul 2025

Cited by 2 | Viewed by 1860

Abstract

Lymphoma continues to pose a significant global health burden, highlighting the urgent need for novel therapeutic strategies. Recent advances in microbiome research have identified gut-microbiota-derived metabolites, or postbiotics, as promising candidates in cancer therapy. This study investigates the antiproliferative and mechanistic effects of [...] Read more.

Lymphoma continues to pose a significant global health burden, highlighting the urgent need for novel therapeutic strategies. Recent advances in microbiome research have identified gut-microbiota-derived metabolites, or postbiotics, as promising candidates in cancer therapy. This study investigates the antiproliferative and mechanistic effects of two postbiotics, Nisin (N) and Urolithin B (UB), individually and in combination, against the human lymphoma cell line HKB-11. Moreover, this study evaluated cytotoxic efficacy and underlying molecular pathways using a comprehensive experimental approach, including the Alamar Blue assay, combination index (CI) analysis, flow cytometry, reactive oxygen species (ROS) quantification, and bottom-up proteomics. N and UB displayed notable antiproliferative effects, with IC₅₀ values of 1467 µM and 87.56 µM, respectively. Importantly, their combination at a 4:6 ratio demonstrated strong synergy (CI = 0.09 at IC₉₅), significantly enhancing apoptosis (p ≤ 0.0001) and modulating oxidative stress. Proteomic profiling revealed significant regulation of key proteins related to lipid metabolism, mitochondrial function, cell cycle control, and apoptosis, including upregulation of COX6C (Log₂FC = 2.07) and downregulation of CDK4 (Log₂FC = −1.26). These findings provide mechanistic insights and underscore the translational potential of postbiotics in lymphoma treatment. Further preclinical and clinical investigations are warranted to explore their role in therapeutic regimens. Full article

(This article belongs to the Special Issue 25th Anniversary of IJMS: Updates and Advances in Molecular Microbiology)

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Review

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27 pages, 3544 KB

Open AccessReview

Systematic Review: Long-Read Sequencing in Algal Studies

by Kakima Kastuganova, Alyamdar Askerov, Attila Szabó and Natasha S. Barteneva

Int. J. Mol. Sci. 2026, 27(5), 2415; https://doi.org/10.3390/ijms27052415 - 5 Mar 2026

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Abstract

Long-read sequencing (LRS) has transformed life science research by introducing third-generation sequencing (TGS) platforms applicable across various research fields, including environmental sciences. In the past decade, LRS platforms have been utilized to extensively study algal systems by improving genomic approaches such as metabarcoding, [...] Read more.

Long-read sequencing (LRS) has transformed life science research by introducing third-generation sequencing (TGS) platforms applicable across various research fields, including environmental sciences. In the past decade, LRS platforms have been utilized to extensively study algal systems by improving genomic approaches such as metabarcoding, chromosome-level genome and pangenome assemblies, as well as providing new insights into algae-associated microbiomes and host–symbiont interactions. This review aims to discuss recent advancements in LRS in algal research. To achieve this aim, a systematic review was conducted according to the PRISMA 2020 guidelines and across three electronic databases (Web of Science, Scopus, and Google Scholar), with additional citation searching for relevant studies in four key algal research areas: metabarcoding, genomics, pangenomics, and host–symbionts interactions. Following the inclusion and exclusion criteria, only 51 studies were selected for this review. Throughout the review, we summarize the challenges of short-read sequencing (SRS) and discuss how LRS platforms address these challenges in algal studies. Furthermore, we discuss the future of LRS and explore how artificial intelligence (AI) can advance research on algal biology and ecology. Full article

(This article belongs to the Special Issue 25th Anniversary of IJMS: Updates and Advances in Molecular Microbiology)

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18 pages, 1110 KB

Open AccessReview

Gut Microbiome and Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS): Insights into Disease Mechanisms

by Ralitsa Nikolova, Deyan Donchev, Katya Vaseva and Ivan N. Ivanov

Int. J. Mol. Sci. 2026, 27(1), 425; https://doi.org/10.3390/ijms27010425 - 31 Dec 2025

Cited by 1 | Viewed by 1940

Abstract

Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS) is a disabling clinical condition, whose hallmark characteristic is post-exertional malaise (PEM). It can affect many organs and systems, leading to severe impairment of patients’ quality of life. Although numerous post-infectious, immunological, neurological, metabolic, and endocrine alterations have [...] Read more.

Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS) is a disabling clinical condition, whose hallmark characteristic is post-exertional malaise (PEM). It can affect many organs and systems, leading to severe impairment of patients’ quality of life. Although numerous post-infectious, immunological, neurological, metabolic, and endocrine alterations have been documented, neither a definitive diagnostic marker nor approved treatments are available. The etiology and pathophysiology remain incompletely understood; however, emerging evidence suggests that the gut microbiome plays a role in immune responses and the development of ME/CFS. It is hypothesized that specific disturbances in gut microbiome composition, known as dysbiosis, may compromise the integrity of the intestinal barrier. This consequently leads to translocation of microbial components, which further triggers an immune response and systemic inflammation complicating the clinical presentation of ME/CFS. Furthermore, in terms of the so-called gut–brain axis, microbiome changes may lead to distinct neurocognitive impairments observed in ME/CFS patients. This review offers the readers a broad perspective on the topic on ME/CFS, with a particular emphasis on the interplay between the gut microbiome and disease mechanisms. Last but not least, recent data on potential treatment strategies for intestinal dysbiosis in ME/CFS patients have been included. Full article

(This article belongs to the Special Issue 25th Anniversary of IJMS: Updates and Advances in Molecular Microbiology)

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35 pages, 2746 KB

Open AccessReview

Advances in Biotechnological GABA Production: Exploring Microbial Diversity, Novel Food Substrates, and Emerging Market Opportunities

by Fabian Hernandez-Tenorio, Mateo Mejía-Rúa, Luz Deisy Marín-Palacio, Bernadette Klotz-Ceberio, David Orrego and Catalina Giraldo-Estrada

Int. J. Mol. Sci. 2026, 27(1), 306; https://doi.org/10.3390/ijms27010306 - 27 Dec 2025

Viewed by 1524

Abstract

Gamma-aminobutyric acid (GABA) is a non-protein amino acid distributed in nature by different types of organisms and microorganisms. GABA has been widely studied for its different physiological functions and industrial applications. Its production is mainly carried out through fermentation processes using lactic acid [...] Read more.

Gamma-aminobutyric acid (GABA) is a non-protein amino acid distributed in nature by different types of organisms and microorganisms. GABA has been widely studied for its different physiological functions and industrial applications. Its production is mainly carried out through fermentation processes using lactic acid bacteria (LAB), which are of particular interest because they are safe and possess high glutamate decarboxylase enzyme activity. However, GABA production can vary among different LAB species and is affected by culture conditions. Therefore, strain development and selection, as well as optimization of fermentation parameters, are essential to increase GABA yields and meet the needs of industrial demand. This review quantitatively analyzes recent advances in fermentative GABA production, showing a sustained increase in publications and a predominance of chromatography-based quantification methods (approximately 68%), mainly using pre-column derivatization. Optimized fermentation strategies, supported by statistical and artificial intelligence models, have achieved GABA concentrations of up to 90 mM. In parallel, in silico genomic and metabolic analyses revealed the widespread distribution of key GABA biosynthesis and transport genes among LAB, supporting their selection and engineering. Overall, the integration of advanced analytical methods, bioinformatics-guided strain selection, and computational process optimization emerges as a key strategy to enhance GABA productivity and support future industrial-scale applications. Full article

(This article belongs to the Special Issue 25th Anniversary of IJMS: Updates and Advances in Molecular Microbiology)

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Open AccessReview

siRNA Therapeutics for the Treatment of Hereditary Diseases and Other Conditions: A Review

by Alexei Shevelev, Natalia Pozdniakova, Evgenii Generalov and Olga Tarasova

Int. J. Mol. Sci. 2025, 26(17), 8651; https://doi.org/10.3390/ijms26178651 - 5 Sep 2025

Cited by 2 | Viewed by 5288

Abstract

RNA-based drugs hold significant potential, offering promising new treatments for a wide range of diseases, especially those with a genetic basis. By leveraging RNA interference (RNAi) and other RNA-mediated mechanisms, these therapies can precisely modulate gene expression and address the root causes of [...] Read more.

RNA-based drugs hold significant potential, offering promising new treatments for a wide range of diseases, especially those with a genetic basis. By leveraging RNA interference (RNAi) and other RNA-mediated mechanisms, these therapies can precisely modulate gene expression and address the root causes of genetic defects. RNA-based drugs hold significant potential for treating a range of diseases. However, the transition of these therapies from laboratory research to clinical applications has encountered hurdles. This review explores the composition and outcomes of clinical trials for various modified short RNA drugs. We detail their mechanisms of action, delivery systems—with a focus on lipid nanoparticles and N-acetylgalactosamine (GalNAc) conjugates—and clinical efficacy in treating conditions such as transthyretin (TTR) amyloidosis. Our analysis reveals that while several RNAi-based drugs have achieved clinical approval, a critical unmet need remains: advanced delivery systems capable of precisely targeting diverse tissues, particularly outside the liver. We also underscore the importance of rigorous target validation utilising sophisticated bioinformatics tools and in vitro/in vivo assays to minimise off-target effects and ensure robust therapeutic efficacy. This review proposes a novel framework for optimising RNA drug development, emphasising the crucial interplay between delivery strategies, target specificity, and understanding disease-specific target biology. Full article

(This article belongs to the Special Issue 25th Anniversary of IJMS: Updates and Advances in Molecular Microbiology)

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