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15 pages, 1230 KB

Open AccessArticle

A Cross-Sectional Study on the Association Between Hepatocellular Carcinoma and Gut Microbiota in Chronic Hepatitis B Virus Infection

by Yusuke Tanaka, Daiki Miki, C. Nelson Hayes, Yusuke Johira, Ryoichi Miura, Hatsue Fujino, Atsushi Ono, Eisuke Murakami, Tomokazu Kawaoka, Masataka Tsuge and Shiro Oka

Microbiol. Res. 2026, 17(7), 120; https://doi.org/10.3390/microbiolres17070120 - 23 Jun 2026

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Abstract

There have been reports of an association between the gut microbiota and the development of chronic liver disease, fibrosis, and carcinogenesis; however, it is not yet possible to reach a definite conclusion. In this cross-sectional study, we examined the association between the presence [...] Read more.

There have been reports of an association between the gut microbiota and the development of chronic liver disease, fibrosis, and carcinogenesis; however, it is not yet possible to reach a definite conclusion. In this cross-sectional study, we examined the association between the presence or absence of hepatocellular carcinoma (HCC) and the gut microbiota in patients with chronic hepatitis B virus (HBV) infection. The study subjects consisted of 62 consecutive HBV patients admitted to our hospital who provided informed consent to participate in the study. We performed 16S rRNA analysis using DNA extracted from fecal pellets. The sequencing depth per sample was 80,000 to 90,000 reads. We calculated the proportion of each bacterial genus so that the total for each sample added up to 100%. The male-to-female ratio was 49/13, the median age was 67 years, and 46 of the patients had HCC. Twenty microbial phyla spanning 41 classes, 79 orders, 163 families, and 431 genera were identified. Receiver operating characteristic (ROC) analysis was performed on the identified bacterial taxa, from the level of phylum down to genus, to assess their ability to distinguish between patients with and without HCC. Several bacteria with an area under the curve (AUC) > 0.65 were identified as follows: TM7 phylum TM7-3 class (AUC = 0.700); Firmicutes phylum Clostridiales class Lachnobacterium genus, Dialister genus, Ruminococcus genus, and Roseburia genus (AUC = 0.670, 0.668, 0.667, and 0.660, respectively); and Firmicutes phylum Erysipelotrichi class (AUC = 0.656). Combining three of these taxa resulted in high discriminative power (p = 0.000585) with a sensitivity and specificity of 0.761 and 0.750, respectively. A similar trend was observed in the subgroup analysis based on liver reserve capacity. Even after adjusting for factors related to liver reserve capacity in the multivariate analysis, an association between these bacterial genera and HCC was confirmed. Our results suggest that gut microbiota may be associated with the prevalence of HCC in HBV patients. Full article

(This article belongs to the Special Issue Host–Microbe Interactions in Health and Disease)

15 pages, 1051 KB

Open AccessArticle

Association of HHV-6 Reactivation with NLRP3 Inflammasome Activation in Chemotherapy-Treated Iraqi Cancer Patients: A Cross-Sectional Study

by Nadia Habeeb Sarhan, Maroua Gdoura-Ben Amor, Saif Jabbar Yasir and Radhouane Gdoura

Microbiol. Res. 2026, 17(5), 98; https://doi.org/10.3390/microbiolres17050098 - 19 May 2026

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Abstract

Human herpesvirus 6 (HHV-6) typically remains latent but can reactivate during immunosuppression caused by chemotherapy, potentially driving immune dysregulation. The NLRP3 inflammasome is a critical innate immune complex mediating pro-inflammatory signaling implicated in tumor progression and treatment toxicity. This study investigated the association [...] Read more.

Human herpesvirus 6 (HHV-6) typically remains latent but can reactivate during immunosuppression caused by chemotherapy, potentially driving immune dysregulation. The NLRP3 inflammasome is a critical innate immune complex mediating pro-inflammatory signaling implicated in tumor progression and treatment toxicity. This study investigated the association between HHV-6 antigenemia and NLRP3 inflammasome activation in 193 chemotherapy-treated cancer patients at the Oncology Hospital in Al-Najaf, Iraq. Serological markers for HHV-6 IgG, IgM, and circulating viral antigen, along with serum NLRP3 levels, were quantified using ELISA. Active HHV-6 antigenemia was observed in over half the cohort, with 56.5% positive for IgM and 42.5% exhibiting antigenemia. Elevated serum NLRP3 levels were detected in 65.8% of patients and correlated significantly with HHV-6 antigen presence, particularly in hematological and genitourinary cancers. Viral antigenemia and inflammasome activity were more prominent in females and older patients. Host gene analysis revealed Hepcidin (HAMP) polymorphisms and altered expression compared to healthy controls, suggesting links between iron metabolism, viral antigenemia, and inflammasome activity. These findings highlight a potential mechanistic connection between HHV-6 antigenemia and inflammasome-driven inflammation, which may contribute to chemotherapy-associated immune dysregulation. Monitoring HHV-6 antigenemia and NLRP3 activation may offer valuable insight into the inflammatory status of cancer patients undergoing chemotherapy. Full article

(This article belongs to the Special Issue Host–Microbe Interactions in Health and Disease)

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16 pages, 16849 KB

Open AccessArticle

Faecal Microbiota Transplantation in IL-10 Knockout Mice Reverses Increased Susceptibility to Pseudomonas aeruginosa Lung Infection

by Natália Cristina de Melo Santos, Evandro Neves Silva, Leonardo Pereira de Araújo, Carlos Roberto Prudêncio, Rômulo Dias Novaes, Patrícia Paiva Corsetti and Leonardo Augusto de Almeida

Microbiol. Res. 2026, 17(4), 83; https://doi.org/10.3390/microbiolres17040083 - 20 Apr 2026

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Abstract

Differences in the gut microbiota are directly reflected in lung–gut axis crosstalk, which may increase susceptibility to pulmonary infections, such as those caused by the bacterium Pseudomonas aeruginosa. Deficiency of the cytokine IL-10 leads to gut inflammation, and this pro-inflammatory environment is [...] Read more.

Differences in the gut microbiota are directly reflected in lung–gut axis crosstalk, which may increase susceptibility to pulmonary infections, such as those caused by the bacterium Pseudomonas aeruginosa. Deficiency of the cytokine IL-10 leads to gut inflammation, and this pro-inflammatory environment is partly due to changes in the gut microbiota. To better understand the effects of IL-10 deficiency on the gut microbiota, the intestinal microbial composition of IL-10 KO mice was assessed, and an increase in the phyla Bacteroidetes and Proteobacteria and a decrease in the phylum Firmicutes were observed in the faeces compared with the wild-type group (WT). Additionally, IL-10 KO mice had a higher pro-inflammatory immunostimulatory caecal content. Furthermore, it was found that heterologous faecal microbiota transplantation (FMT) between groups reversed this gut imbalance. IL-10 KO mice showed greater susceptibility to acute pulmonary infection by P. aeruginosa, with a higher recovery of viable bacteria in the lung and spleen, greater tissue damage and increased expression of genes encoding pro-inflammatory cytokines in the lungs. This greater susceptibility was reversed after FMT. Taken together, these results demonstrate the role of endogenous IL-10 in the gut microbiota constitution and its importance in the pulmonary immune response against P. aeruginosa infection. Full article

(This article belongs to the Special Issue Host–Microbe Interactions in Health and Disease)

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13 pages, 734 KB

Open AccessArticle

Emerging Resistance in Oral Candida Isolates from Patients with Periodontal Disease

by Claudia Berenice Tinoco-Cabral, Luis Alfonso Muñoz-Miranda, Manuel R. Kirchmayr, Vianeth Martínez-Rodríguez, Miguel Padilla-Rosas, Maricarmen Iñiguez-Moreno, Suchiquil Rangel-Velázquez, Fabiola Berenice Hernández-Reyes, Claudia Lisette Charles-Niño and Cesar Arturo Nava-Valdivia

Microbiol. Res. 2026, 17(4), 80; https://doi.org/10.3390/microbiolres17040080 - 10 Apr 2026

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Abstract

Candida species can shift from commensal organisms to opportunistic pathogens. Both Candida albicans and non-albicans Candida (NAC) species colonize oral biofilms and periodontal pockets, where they may contribute to inflammation and the progression of periodontal disease. This study aimed to determine the [...] Read more.

Candida species can shift from commensal organisms to opportunistic pathogens. Both Candida albicans and non-albicans Candida (NAC) species colonize oral biofilms and periodontal pockets, where they may contribute to inflammation and the progression of periodontal disease. This study aimed to determine the prevalence and antifungal susceptibility profiles of Candida species in individuals with different stages of periodontal disease. A cross-sectional study was conducted in 100 participants whose periodontal status was clinically evaluated. Saliva samples were cultured on chromogenic agar for yeast isolation, species identification was confirmed by MALDI-TOF MS, and antifungal susceptibility to fluconazole, clotrimazole, nystatin, and amphotericin B was assessed. Candida spp. was detected in 35% of participants, where C. albicans was the most prevalent species, followed by Nakaseomyces glabratus (formerly Candida glabrata), Candida parapsilosis, Candida dubliniensis, and Candida tropicalis. Species distribution varied according to periodontal status, with N. glabratus predominating in early periodontitis and C. albicans appeared more frequently in higher severe stages of periodontitis. Susceptibility testing showed resistance of C. albicans to clotrimazole (63.6%) and nystatin (22.7%), whereas amphotericin B and fluconazole remained effective. NAC species, particularly N. glabratus, exhibited resistance to nystatin and variable resistance to clotrimazole but remained susceptible to amphotericin B. These findings underscore the importance of early detection and personalized antifungal strategies for managing periodontal disease complicated by Candida colonization. Full article

(This article belongs to the Special Issue Host–Microbe Interactions in Health and Disease)

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14 pages, 1647 KB

Open AccessArticle

Effect of Pregnancy Gingivitis on Maternal Saliva Microbiota

by Ana K. Rocha-Viggiano, Saray Aranda-Romo, Edgar R. Rocha-Lara, Karla G. López-Macías, Sergio Casas-Flores, Nicolás Gómez-Hernández, Daniel E. Noyola, Cesaré Ovando-Vázquez and Mariana Salgado-Bustamante

Microbiol. Res. 2026, 17(3), 50; https://doi.org/10.3390/microbiolres17030050 - 26 Feb 2026

Cited by 1 | Viewed by 822

Abstract

Pregnant women undergo a myriad of physiological changes, including important hormonal variations. Pregnancy gingivitis is a condition that affects up to 30% to 100% of women, is related to hormonal modifications, and could play an important role in gestational gut colonization and immunological [...] Read more.

Pregnant women undergo a myriad of physiological changes, including important hormonal variations. Pregnancy gingivitis is a condition that affects up to 30% to 100% of women, is related to hormonal modifications, and could play an important role in gestational gut colonization and immunological training of the newborn. Nonetheless, oral health is not always included in routine prenatal care. In this study, we collected saliva samples of pregnant women with and without pregnancy gingivitis and analyzed the oral microbiota through 16S sequencing. In addition, meconium samples from the infants of participating women were analyzed. The oral microbiota of pregnant women with and without pregnancy gingivitis did not show significant differences in diversity. However, significant differences in microbiome composition were observed. Pathway analysis showed that, despite taxonomic similarity, the PG group had activated energy metabolism, bacterial growth, lipid metabolism, and virulence pathways with NOD-like receptor activation, indicating pro-inflammatory microbial activity. In contrast, the NPG group exhibited central metabolism and repair mechanisms, suggesting that PG could affect microbiome function rather than composition. In addition, it appears that the microbiome composition of offspring of mothers with gingivitis also differs from that of offspring from mothers without gingivitis, although the number of available samples did not allow for definite conclusions. As such, a larger cohort and deeper sequencing methods are needed to assess the oral microbiota of pregnant women with and without gingivitis and to explore the possibility of bacterial translocation from the maternal gingiva to the fetal gut. Full article

(This article belongs to the Special Issue Host–Microbe Interactions in Health and Disease)

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9 pages, 12341 KB

Open AccessCommunication

Anomalous Emergence of D614 Reverse Mutations in the Delta and Omicron BA.2 Variants

by Hideki Kakeya and Yoshihisa Matsumoto

Microbiol. Res. 2026, 17(2), 44; https://doi.org/10.3390/microbiolres17020044 - 20 Feb 2026

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Abstract

Background: The spike D614G substitution became globally dominant early in the COVID-19 pandemic, and reversion to ancestral D614 is expected to be rare once D614G is fixed. SARS-CoV-2 sequences lacking D614G detected later raise questions about the origin of these reversions. Methods: We [...] Read more.

Background: The spike D614G substitution became globally dominant early in the COVID-19 pandemic, and reversion to ancestral D614 is expected to be rare once D614G is fixed. SARS-CoV-2 sequences lacking D614G detected later raise questions about the origin of these reversions. Methods: We analyzed spike protein amino-acid sequences from 22 SARS-CoV-2 Variants of Concern (VOCs) deposited in the NCBI GenBank database, screening for sequences carrying ancestral D614 and comparing their distributions across VOCs. Results: D614 reversions (reverse mutations of D614G) were not evenly distributed across VOCs but were strongly enriched in Delta (B.1.617.2) and Omicron BA.2, reaching levels statistically inconsistent with other VOCs. In both lineages, D614-containing sequences showed limited mutational diversity and pronounced geographic clustering within specific U.S. regions. Conclusions: These non-random patterns are difficult to reconcile with spontaneous reverse mutation arising and spreading through typical community transmission and are more consistent with localized reintroduction of an older genetic background. Further investigation is warranted to assess whether laboratory-associated events could be involved. Full article

(This article belongs to the Special Issue Host–Microbe Interactions in Health and Disease)

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16 pages, 1577 KB

Open AccessArticle

Genomic Relationship Between High-Risk Pseudomonas aeruginosa Clone ST244 Serotypes O5 and O12 from Southeastern Brazil

by Kayo Bianco, Thereza Cristina da Costa Vianna, Samara Santanna de Oliveira, Kaylanne Montenegro, Claudia Flores, Ana Paula Alves do Nascimento, Alexander Machado Cardoso and Maysa Mandetta Clementino

Microbiol. Res. 2026, 17(1), 27; https://doi.org/10.3390/microbiolres17010027 - 21 Jan 2026

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Abstract

Pseudomonas aeruginosa is an opportunistic pathogen commonly associated with nosocomial infections and environmental dissemination. Among its high-risk clones, ST244 is notable for its global distribution and distinctive genomic traits. This study reports whole-genome sequencing of ten ST244 isolates from hospitalized patients and wastewater [...] Read more.

Pseudomonas aeruginosa is an opportunistic pathogen commonly associated with nosocomial infections and environmental dissemination. Among its high-risk clones, ST244 is notable for its global distribution and distinctive genomic traits. This study reports whole-genome sequencing of ten ST244 isolates from hospitalized patients and wastewater in a healthcare complex in Southeastern Brazil. Genomic comparisons revealed a highly conserved clonal group, with nine isolates forming a tight monophyletic cluster based on rMLST, SNP phylogeny, and average nucleotide identity (>99.5%). One isolate showed close phylogenetic proximity to strains from Asia and North America, suggesting international dissemination. Serotype analysis revealed both O5 and O12 variants, indicating intra-lineage antigenic diversity. Resistance profiling identified multidrug-resistant phenotypes carrying carbapenemase genes (bla_OXA-494, bla_OXA-396) and diverse insertion sequences (ISPa1, ISPa6, ISPa22, ISPa32, and ISPa37), facilitating horizontal gene transfer. Virulence gene analysis showed conserved elements related to adhesion, iron uptake, secretion systems, and quorum sensing, while the cytotoxin gene exoU was absent. These results highlight clonal persistence, possible intra-hospital transmission, and links to globally circulating ST244 sublineages. Our findings underscore the importance of genomic surveillance to track high-risk P. aeruginosa clones at the clinical–environmental interface. Full article

(This article belongs to the Special Issue Host–Microbe Interactions in Health and Disease)

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10 pages, 223 KB

Open AccessArticle

Antimicrobial Resistance Patterns of Escherichia coli Isolates from Female Urinary Tract Infection Patients in Lebanon: An Age-Specific Analysis

by Samara Hassan, Ghassan Ghssein, Zeina Kassem, Sema Alarab, Jana El Aris and Zeinab Ezzeddine

Microbiol. Res. 2025, 16(11), 240; https://doi.org/10.3390/microbiolres16110240 - 13 Nov 2025

Cited by 4 | Viewed by 3573

Abstract

Urinary tract infections (UTIs) are a global health concern, with over 150 million cases annually, primarily caused by Escherichia coli. Due to anatomical differences, females, especially children and postmenopausal women, are four times more susceptible. Crucially, E. coli has developed widespread antimicrobial [...] Read more.

Urinary tract infections (UTIs) are a global health concern, with over 150 million cases annually, primarily caused by Escherichia coli. Due to anatomical differences, females, especially children and postmenopausal women, are four times more susceptible. Crucially, E. coli has developed widespread antimicrobial resistance (AMR), including resistance to broad-spectrum agents and the emergence of Extended-Spectrum Beta-Lactamase (ESBL)-producing strains. This retrospective study analyzed hospital records from 95 female patients with positive urine cultures at Siblin Governmental Hospital in 2024. Patients were stratified into three age categories: children (≤18 years), adults (18–64 years) and elderly patients (>64 years). Statistical analysis using SPSS focused on descriptive resistance patterns and differences across age groups. Overall, cephalothin (85.7%) and cefaclor (78.49%) exhibited the highest resistance rates. Conversely, tigecycline (97.22%) and ertapenem (91.67%) showed the highest susceptibility. Resistance patterns varied significantly by age. For instance, elderly patients showed high resistance to agents like Augmentin (52.5%) and cefixime (66.1%), while the pediatric group (≤18 years) displayed exceptionally high resistance to cefixime (90.0%). E. coli isolates show high resistance to conventionally used antibiotics, complicating UTI treatment. These findings highlight the need for continuous local surveillance, particularly focusing on third-generation cephalosporins and beta-lactamase production. Ultimately, age is a critical factor that must be considered when determining empirical antibiotic therapy for UTIs. Full article

(This article belongs to the Special Issue Host–Microbe Interactions in Health and Disease)

20 pages, 1488 KB

Open AccessArticle

Vimentin Methylation as a Potential Screening Biomarker for Colorectal Cancer in HIV-Helminth Co-Infected Individuals

by Botle Precious Damane, Shakeel Kader, Mohammed Alaouna, Pragalathan Naidoo, Zodwa Dlamini and Zilungile Lynette Mkhize-Kwitshana

Microbiol. Res. 2025, 16(11), 236; https://doi.org/10.3390/microbiolres16110236 - 11 Nov 2025

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Abstract

Colonoscopy remains the gold standard for colorectal cancer (CRC) screening, but its invasiveness, cost, and limited availability in resource-constrained settings pose major barriers. Stool-based methylated DNA biomarkers, such as vimentin, offer sensitive, non-invasive alternatives. Given the high burden of HIV and helminth co-infections [...] Read more.

Colonoscopy remains the gold standard for colorectal cancer (CRC) screening, but its invasiveness, cost, and limited availability in resource-constrained settings pose major barriers. Stool-based methylated DNA biomarkers, such as vimentin, offer sensitive, non-invasive alternatives. Given the high burden of HIV and helminth co-infections in sub-Saharan Africa and their potential contribution to cancer susceptibility, this study investigated whether stool-derived vimentin methylation could detect early oncogenic changes in these high-risk groups. In this retrospective cross-sectional study, archived stool samples from 62 South African adults were stratified into five groups: uninfected controls, HIV-infected only, helminth-infected only, HIV-helminth co-infected, and CRC-confirmed patients. DNA was extracted, bisulfite-converted, and analyzed for vimentin methylation using a high-resolution melt assay. Fecal occult blood testing (FOBT) was also performed. Vimentin methylation differed significantly across groups (p < 0.0001). CRC cases showed 90% methylation, confirming its role as a CRC biomarker. Interestingly, vimentin methylation frequencies were also observed in HIV-only (92.9%, p < 0.0001 vs. controls), helminth-only (93.3%, p < 0.0001), and HIV-helminth co-infected (77.9%, p < 0.0001) individuals without diagnosed cancer, compared to 10% in controls. Methylation levels in infected groups were not significantly different from CRC patients (all p > 0.05), suggesting infection-induced epigenetic changes of comparable magnitude to malignancy. To support these results, DNMT1–RG108 molecular docking (PDB 4WXX, Maestro 2025-3) demonstrated stable binding (GlideScore −6.285 kcal/mol; ΔG_bind −49.61 kcal/mol) via hydrogen bonding with Glu1266 and Asn1578 and π–π stacking with Phe1145, providing a mechanistic explanation for infection-driven vimentin methylation. No significant differences were found between infected groups. FOBT was positive in 83.3% of CRC cases, with only sporadic positives in infected groups. These findings provide novel evidence that chronic HIV and helminth infections are associated with vimentin promoter methylation at levels indistinguishable from CRC. This supports the hypothesis that persistent infection-driven inflammation promotes early epigenetic reprogramming toward oncogenesis. In high-burden African settings, stool-based methylation assays could serve as early diagnostic tools to identify at-risk individuals long before clinical disease manifests, enabling targeted surveillance and prevention. Full article

(This article belongs to the Special Issue Host–Microbe Interactions in Health and Disease)

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11 pages, 1535 KB

Open AccessArticle

Helicobacter pylori-Associated Infection: A Comprehensive Histopathological Analysis of Gastric Biopsies from Patients of Pakistan

by Obaid Ullah, Hazir Rahman and Salma Ijaz

Microbiol. Res. 2025, 16(11), 232; https://doi.org/10.3390/microbiolres16110232 - 2 Nov 2025

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Abstract

Helicobacter pylori is a gastric pathogen that induces chronic gastritis, which may progress to neutrophilic activity, glandular atrophy, intestinal metaplasia, and gastric carcinoma. The aim of this study was to evaluate H. pylori-induced tissue damage. A total of 602 gastric biopsy samples [...] Read more.

Helicobacter pylori is a gastric pathogen that induces chronic gastritis, which may progress to neutrophilic activity, glandular atrophy, intestinal metaplasia, and gastric carcinoma. The aim of this study was to evaluate H. pylori-induced tissue damage. A total of 602 gastric biopsy samples were collected, categorized, and analyzed using hematoxylin and eosin and Giemsa staining, followed by molecular confirmation through PCR targeting the species-specific 16S rRNA gene. H. pylori density and histopathological features were evaluated and graded according to the updated Sydney classification system. H. pylori was detected in 55% (n = 334) of cases, and the antrum (50.83%, p < 0.00001) was the predominant site. A slightly higher prevalence was observed in females, accounting for 56.9% compared to males at 43.1%, which was attributed to sociocultural exposure differences. Individuals aged 11–40 years accounted for 58.3% (n = 195), highlighting early-age acquisition of infection. H. pylori infection was significantly linked to moderate-to-severe inflammation (63.2%, p < 0.00001) and neutrophilic activity (53.3%, p < 0.00001). Intestinal metaplasia and atrophy were infrequent, present in 0.6% (95% CI, 0.02, p = 0.149) and 0.9% (95% CI, 0.05, p = 0.430) of individuals. H. pylori infection causes chronic inflammation and neutrophilic infiltration of the stomach mucosa. Early identification and histopathological examination are essential in assessing H. pylori-related gastric pathology. Full article

(This article belongs to the Special Issue Host–Microbe Interactions in Health and Disease)

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15 pages, 4268 KB

Open AccessArticle

Metagenomic Insights into the Impact of Nutrition on Human Gut Microbiota and Associated Disease Risk

by Preethi Balasundaram, Kirti Dubli, Rinku Chaudhari, Sarvesh Vettrivelan, Amrita Kaur, Raman Kapoor, Raja Singh, Anmol Kapoor and Minal Borkar Tripathi

Microbiol. Res. 2025, 16(9), 197; https://doi.org/10.3390/microbiolres16090197 - 1 Sep 2025

Cited by 1 | Viewed by 2881

Abstract

Metagenomic investigation of gut microbiome is a comprehensive and rapid technique for the analysis and diagnosis of numerous diseases. The gut microbiome is an intricate ecosystem, coordinated by the interaction of various microbes and the metabolites produced by them, which helps in developing [...] Read more.

Metagenomic investigation of gut microbiome is a comprehensive and rapid technique for the analysis and diagnosis of numerous diseases. The gut microbiome is an intricate ecosystem, coordinated by the interaction of various microbes and the metabolites produced by them, which helps in developing and sustaining immunity and homeostasis. A healthy gut microbiome is driven by different factors, such as nutrition, lifestyle, etc. The current study examines the association of diet to gut microbiome dysbiosis and its role in various disease conditions. Gut microbiome data was collected from 73 patients and tested at BioAro Inc. lab, using shotgun metagenomics through next generation sequencing. It was then analyzed and compared with data from 20 healthy subjects from HMP database. An in-house bioinformatics pipeline (PanOmiQ) and Pathogen Fast Identifier were utilized for secondary analysis, while tertiary analysis was accomplished using R software. Results showed a higher number of opportunistic pathogen microorganisms in the gut microbiome of subjects consuming a meat diet, as compared to those consuming a plant diet. These opportunistic pathogens included Ruminococcus torques (>3.34%), Ruminococcus gnavus (>2.22%), and Clostridium symbiosum (>1.87%). The study also found a higher relative abundance of these pathogens in cancer patients, as compared to healthy subjects. We also observed a highly significant (p < 0.0001) correlation of a meat diet with obesity in comparison to the subjects on a plant diet and the healthy subjects. Our findings suggest that patients following a plant diet have a lower relative abundance of pathogens that are associated with cancer and obesity. These findings provide critical insight into how we can use shotgun metagenomics to study the composition and diversity of the gut microbiome and the effects of a diet on the gut microbiome and its role in metabolic diseases. This is the first report investigating gut microbiota using shotgun metagenomics, correlating with different diseases and diet followed, which might impact the presence of opportunistic pathogens or keystones species. Additionally, it can provide valuable insights to physicians and dietetic practitioners for providing personalized treatment or customizing a diet plan. Full article

(This article belongs to the Special Issue Host–Microbe Interactions in Health and Disease)

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23 pages, 5810 KB

Open AccessArticle

Oral Intake of Klebsiella oxytoca Disrupts Murine Intestinal Bacteriota and Anti-K. oxytoca Compound Baicalin by In Silico and In Vitro Analysis

by Yuming Ma, Xinchi Qin, Yongjie Wang, Lu Xie and Lanming Chen

Microbiol. Res. 2025, 16(8), 189; https://doi.org/10.3390/microbiolres16080189 - 14 Aug 2025

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Abstract

Klebsiella oxytoca originating from shellfish Scapharca subcrenata contains a number of virulence-related genes. In this study, we investigated its pathogenicity using a murine intestinal infection model and predicted its antibacterial compounds and targets via molecular docking analysis. The results revealed that the intake [...] Read more.

Klebsiella oxytoca originating from shellfish Scapharca subcrenata contains a number of virulence-related genes. In this study, we investigated its pathogenicity using a murine intestinal infection model and predicted its antibacterial compounds and targets via molecular docking analysis. The results revealed that the intake of K. oxytoca 8-2-11 strain (10⁹ CFU/day) via oral gavage for 7 days reduced the average body weight of the mice. The bacterium was present in fecal samples but absent from blood, lung, and liver samples from the mice. The intake of K. oxytoca 8-2-11 significantly altered colon bacteriota, with reduced abundance of Firmicutes, Lachnospiraceae, Lactobacillaceae, Lactobacillus, and Lactobacillus murinus, and increased in Bacteroidota, Muribaculaceae, and Alistipes (p < 0.05). Forty-four bioactive compounds in Scutellaria baicalensis and Forsythia suspensa were screened for docking with 117 potential virulence factors (VFs) in K. oxytoca 8-2-11. The compound baicalin displayed higher binding affinity toward these VFs, with the lowest mean binding energy (−8.4 kcal/mol). Baicalin was able to bind to key VFs in biofilm formation and adherence/motility (e.g., Mrks and EcpA) via forming stable hydrogen bonds, π-stacking, and π-cation interaction. In vitro, baicalin inhibited the bacterial growth and biofilm formation. This study establishes the first murine infection model using aquatic animal-derived K. oxytoca, and it provides candidate antibacterial compounds and targets for control of K. oxytoca infections. Full article

(This article belongs to the Special Issue Host–Microbe Interactions in Health and Disease)

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13 pages, 1098 KB

Open AccessArticle

Risk Factors and Seroprevalence of Infection by Corynebacterium pseudotuberculosis in Goats from Espírito Santo State, Southeastern Brazil

by Letícia Pereira Pedrini Vicentini, Thiago Doria Barral, Marcus Alexandre Vaillant Beltrame, Luiz Filippe Simão Soares, Ricardo Wagner Portela and Blima Fux

Microbiol. Res. 2025, 16(8), 185; https://doi.org/10.3390/microbiolres16080185 - 8 Aug 2025

Cited by 1 | Viewed by 3097

Abstract

Corynebacterium pseudotuberculosis is the causative agent of caseous lymphadenitis, a significant infectious disease that affects small ruminants and poses economic challenges to livestock production. This study aimed to assess the seroprevalence of C. pseudotuberculosis in goats from Espírito Santo state, Brazil, and identify [...] Read more.

Corynebacterium pseudotuberculosis is the causative agent of caseous lymphadenitis, a significant infectious disease that affects small ruminants and poses economic challenges to livestock production. This study aimed to assess the seroprevalence of C. pseudotuberculosis in goats from Espírito Santo state, Brazil, and identify risk factors associated with infection by the bacterium. Serum samples from 145 goats were analyzed using an indirect enzyme-linked immunosorbent assay (ELISA). The overall seroprevalence was found to be 34.5%. The risk factors significantly associated with infection included the presence of abscesses and the absence of veterinary assistance on farms. The findings emphasize the need for improved management practices and veterinary oversight to mitigate caseous lymphadenitis transmission. This research provides critical insights into the epidemiology of caseous lymphadenitis in goats from Espírito Santo, informing effective disease control strategies. Full article

(This article belongs to the Special Issue Host–Microbe Interactions in Health and Disease)

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13 pages, 892 KB

Open AccessArticle

Comparative Evaluation of Recombinant Chlamydia abortus and Chlamydia trachomatis Major Outer Membrane Proteins for Diagnosing Human Chlamydial Infection

by Fernando M. Guerra-Infante, María J. de Haro-Cruz, Marcela López-Hurtado, Miguel A. De la Rosa-Ramos, Efrén Díaz-Aparicio and Beatriz Arellano-Reynoso

Microbiol. Res. 2025, 16(7), 159; https://doi.org/10.3390/microbiolres16070159 - 9 Jul 2025

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Abstract

Chlamydia trachomatis infection is a public health problem. Serological tests can determine the disease burden and serve as a biomarker for identifying patients with infertility due to tubal obstruction. However, cross-reactions between chlamydial species have been reported, which causes problems with diagnosis. A [...] Read more.

Chlamydia trachomatis infection is a public health problem. Serological tests can determine the disease burden and serve as a biomarker for identifying patients with infertility due to tubal obstruction. However, cross-reactions between chlamydial species have been reported, which causes problems with diagnosis. A real-time PCR commercial test for the detection of endocervical infection and two ELISAs with the recombinant major outer membrane protein (rMOMP) from C. trachomatis and C. abortus as antigens were used to diagnose both infections. The prevalence of endocervical infection by C. trachomatis was 7.77%, and that of IgG antibodies against C. trachomatis and C. abortus was 31.1% and 10.7%, respectively. The ELISA with C. trachomatis rMOMP showed a sensitivity of 75% and a specificity of 72.5%. The lowest sensitivity (25%) and high specificity (76.8%) were obtained with anti-C. abortus rMOMP ELISAs. A low cross-reactivity of 7% between ELISA tests was observed. Conclusion. The recombinant MOMP ELISA could help identify women who had contact with C. trachomatis or C. abortus and could be a tool to lower the costs of performing molecular testing on all patients attending an infertility clinic. Full article

(This article belongs to the Special Issue Host–Microbe Interactions in Health and Disease)

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22 pages, 1290 KB

Open AccessSystematic Review

Molecular and Proteomic Determinants of Trypanosoma cruzi Adaptation Within Triatomine Vectors: Insights from Current Experimental Models

by Jessy T. Santana, Berenice González-Rete, Elia Torres-Gutiérrez, Juliana Cordeiro Cardoso, Cláudia Moura Melo and Paz M. S. Salazar-Schettino

Microbiol. Res. 2026, 17(5), 92; https://doi.org/10.3390/microbiolres17050092 - 8 May 2026

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Abstract

Trypanosoma cruzi exhibits complex genetic diversity, organized into seven distinct typing units. To complete its life cycle, the parasite must adapt to the digestive tract of various species of triatomine bugs. This systematic review aimed to understand the molecular adaptation mechanisms of T. [...] Read more.

Trypanosoma cruzi exhibits complex genetic diversity, organized into seven distinct typing units. To complete its life cycle, the parasite must adapt to the digestive tract of various species of triatomine bugs. This systematic review aimed to understand the molecular adaptation mechanisms of T. cruzi in relation to different vector species, systematizing knowledge on vector competence. Following PRISMA guidelines, 18 experimental studies (published between 1995 and 2025) were selected from the ScienceDirect, PubMed, Scopus, and Web of Science databases, focusing on the parasite–vector interface and proteomic analyses. There was a predominance of studies conducted in Brazil (66.67%), using the Rhodnius prolixus model (72.22%) and the TcI strain (clone Dm28c). The evolution of methodological approaches reflects a transition from classical techniques, such as SDS-PAGE, to high-throughput omics strategies, including LC-MS/MS and gene editing tools such as CRISPR. The findings were organized into key biological processes, including parasite adhesion mediated by perimicrovillar membrane components, glycoinositolphospholipids (GIPLs), and mucins; the influence of the metabolic and nutritional microenvironment, particularly hemoglobin-derived peptides and glucose availability; and the role of intestinal redox conditions in triggering metacyclogenesis. Overall, the available evidence suggests that T. cruzi adaptation within triatomine vectors is a multifactorial process driven by proteomic reprogramming and post-transcriptional regulation in response to environmental signals within the vector gut. However, this understanding is largely derived from studies based on Rhodnius prolixus and TcI strains, which limits the generalization of these mechanisms across other triatomine species and parasite lineages. Full article

(This article belongs to the Special Issue Host–Microbe Interactions in Health and Disease)

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12 pages, 3527 KB

Open AccessCase Report

Dermatofibrosarcoma Protuberans in a Patient Living with Human Immunodeficiency Virus Infection

by Vincenzo Verdura, Pasquale Bisceglia, Luigi Annacontini, Luigi Cagiano, Francesca Sanguedolce, Martina Miracapillo, Fabrizia Fusco, Sergio Lo Caputo, Francesco Drago, Gaetano Serviddio, Aurelio Portincasa and Giulia Ciccarese

Microbiol. Res. 2026, 17(3), 61; https://doi.org/10.3390/microbiolres17030061 - 19 Mar 2026

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Abstract

Dermatofibrosarcoma protuberans (DFSP) is a rare tumor presenting as a slow-growing, plaque-like or multinodular, brownish lesion on the trunk in adult patients. Diagnosis is established by histological examination and surgical excision is the primary treatment. Typically, DFSP has an indolent course and local [...] Read more.

Dermatofibrosarcoma protuberans (DFSP) is a rare tumor presenting as a slow-growing, plaque-like or multinodular, brownish lesion on the trunk in adult patients. Diagnosis is established by histological examination and surgical excision is the primary treatment. Typically, DFSP has an indolent course and local spread. In the present work, we describe the clinical–histologic features, surgical treatment and follow-up of a case of DFSP in a patient living with HIV infection (PLWH). A 40-year-old man was referred to us with confluent lesions on the left shoulder, present for about 3 years. His medical history was positive for HIV-1 infection, for which he was taking antiretroviral therapy. Microscopic examination showed dermal and hypodermic proliferation of spindle cells in a storiform pattern, confirming the clinical diagnosis of DFSP. A wide excision was performed with 3 cm clinically healthy tissue margins, and the defect was repaired using an artificial bilaminar dermal matrix. The histological examination revealed tumor-free margins, and a split-thickness skin graft was harvested from the same arm. After 10 months, the patient was free from the disease. As observed with other skin cancers, DFSP may have a higher incidence and greater aggressiveness in immunosuppressed than in immunocompetent patients. DFSP has been reported only twice in PLWH. Our case constitutes a third report, adding to the evidence that there may be an over-representation of this cancer in immunosuppressed individuals. Full article

(This article belongs to the Special Issue Host–Microbe Interactions in Health and Disease)

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12 pages, 557 KB

Open AccessCase Report

Pulmonary Cryptococcosis in a Diabetic Patient Without Severe Immunosuppression: Case Report and 25-Year Literature Review

by Suyapa Sosa, María Fernanda Manzanares, Daniel Rivera, Asly Villeda-Barahona, Gustavo Fontecha, Yaxsier de Armas and Bryan Ortiz

Microbiol. Res. 2025, 16(11), 245; https://doi.org/10.3390/microbiolres16110245 - 20 Nov 2025

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Abstract

Pulmonary cryptococcosis is an invasive fungal infection usually linked to severe immunosuppression, particularly HIV/AIDS, but is increasingly reported in immunocompetent hosts, including those with uncontrolled diabetes mellitus (DM). We describe a 51-year-old woman with poorly controlled type 2 DM and no other immunosuppressive [...] Read more.

Pulmonary cryptococcosis is an invasive fungal infection usually linked to severe immunosuppression, particularly HIV/AIDS, but is increasingly reported in immunocompetent hosts, including those with uncontrolled diabetes mellitus (DM). We describe a 51-year-old woman with poorly controlled type 2 DM and no other immunosuppressive conditions who developed pulmonary cryptococcosis. Diagnosis was made by microscopy, India ink, cryptococcal antigen lateral flow assay (CrAg LFA), and ITS sequencing; culture was negative. Despite treatment with deoxycholate amphotericin B and fluconazole, the patient died 36 days after admission. A systematic literature review (2000–2025) identified 40 cases of pulmonary cryptococcosis, with 17.5% occurring in patients whose only comorbidity was DM. Cryptococcus neoformans was the most frequent species. Non-culture-based methods, especially CrAg detection, were widely used, underscoring their value for rapid and sensitive diagnosis. Pulmonary cryptococcosis should be considered in diabetic patients even without classical immunosuppression. Broader use of non-culture-based diagnostic tools may enable earlier intervention, which is particularly relevant in resource-limited settings such as Honduras. Full article

(This article belongs to the Special Issue Host–Microbe Interactions in Health and Disease)

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17 pages, 1230 KB

Open AccessSystematic Review

Association Between Gut Microbiome Alterations and Hypertension-Related Cardiovascular Outcomes: A Systematic Review and Meta-Analysis

by Adina-Cristiana Avram, Maria-Laura Craciun, Ana-Maria Pah, Florina Buleu, Ioana-Georgiana Cotet, Diana-Maria Mateescu, Stela Iurciuc, Simina Crisan, Oana Belei, Anda Gabriela Militaru and Claudiu Avram

Microbiol. Res. 2025, 16(11), 244; https://doi.org/10.3390/microbiolres16110244 - 19 Nov 2025

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Abstract

Hypertension (HTN) remains a major modifiable risk factor for cardiovascular disease (CVD), yet the mechanisms linking environmental and metabolic factors to vascular injury are incompletely understood. Recent evidence implicates gut microbiome dysbiosis and microbial metabolites, particularly short-chain fatty acids (SCFAs) and trimethylamine N-oxide [...] Read more.

Hypertension (HTN) remains a major modifiable risk factor for cardiovascular disease (CVD), yet the mechanisms linking environmental and metabolic factors to vascular injury are incompletely understood. Recent evidence implicates gut microbiome dysbiosis and microbial metabolites, particularly short-chain fatty acids (SCFAs) and trimethylamine N-oxide (TMAO), in the pathogenesis of hypertension and its cardiovascular complications. We systematically searched PubMed, Embase, Cochrane, Web of Science, and Scopus from inception to 1 October 2025 for observational studies evaluating gut microbiome composition or circulating TMAO levels in adults with hypertension or related cardiovascular outcomes. Random-effects meta-analyses were conducted using standardized mean differences (SMD) for alpha diversity indices and hazard ratios (HR) for TMAO-associated major adverse cardiovascular events (MACE). Heterogeneity (I²), publication bias (Egger’s test), and certainty of evidence (GRADE) were assessed according to PRISMA 2020 guidelines (PROSPERO CRD420251162222). A total of 22 studies (n = 24,512 participants) were included, of which 15 were eligible for quantitative synthesis (11 for alpha diversity, 4 for TMAO). Pooled analysis showed significantly lower microbial diversity among hypertensive versus normotensive individuals (SMD = −0.15, 95% CI −0.25 to −0.05; p = 0.004; I² = 35%). Circulating TMAO was associated with increased risk of major adverse cardiovascular events (HR = 1.25, 95% CI 1.10 to 1.42; p < 0.001). Funnel plots were symmetric, and Egger’s test indicated no significant bias (p > 0.3). The certainty of evidence was graded as moderate for microbial diversity and high for TMAO-related outcomes. This meta-analysis provides robust evidence that gut microbiome dysbiosis and elevated TMAO levels are associated with hypertension and heightened cardiovascular risk, supporting the concept of a “gut–vascular axis.” Microbiota-targeted interventions such as high-fiber diets, prebiotics, or TMAO-lowering strategies warrant further investigation as adjunctive tools in precision hypertension management. Full article

(This article belongs to the Special Issue Host–Microbe Interactions in Health and Disease)

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