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Host–Microbe Interactions in Health and Disease

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A special issue of Microbiology Research (ISSN 2036-7481).

Deadline for manuscript submissions: 31 May 2026 | Viewed by 10080

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Dr. Josué Juárez

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Departamento de Física, Universidad de Sonora, Hermosillo 83000, Mexico
Interests: nanotechnology applications in biomedicine fields; development of biomaterials; physicochemical properties of biomacromolecules; protein aggregation; biomolecules adsorption at interfaces
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Dr. Pablo Mendez-Pfeiffer

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Departamento de Ciencias Químico Biológicas y Agropecuarias, Universidad de Sonora, Caborca CP 83600, Mexico
Interests: bacteria; antimicrobial therapy; nanotechnology; drug delivery systems; host-microbe interactions

Dr. Manuel Ballesteros-Monrreal

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Departamento de Ciencias Químico Biológicas y Agropecuarias, Universidad de Sonora, Caborca CP 83600, Mexico
Interests: Escherichia coli; epidemiology; host-microbe interactions; antibacterial therapy

Special Issue Information

Dear Colleagues,

Understanding the complex interplay between hosts and microbes is essential for unraveling the mechanisms underlying health and disease. This Special Issue explores the multifaceted interactions between the human host and its resident or invading microbial communities, including bacteria, viruses, fungi, and parasites. From mutualistic relationships that support immune development and metabolic balance to pathogenic interactions driving chronic inflammation, infection, and systemic disease, this collection highlights recent advances in microbiology, immunology, and systems biology.

Contributions cover diverse topics such as the role of the microbiota in modulating immune responses, mechanisms of microbial pathogenesis, host genetic and epigenetic factors influencing susceptibility to infection, and emerging insights into microbial dysbiosis in diseases such as cancer, metabolic syndrome, and autoimmune disorders. This Special Issue also addresses novel therapeutic strategies, including microbiome-targeted interventions, probiotics, phage therapy, and antimicrobial resistance management.

By integrating basic and translational research, this Special Issue aims to provide a comprehensive perspective on how host–microbe interactions shape health outcomes. It is intended for researchers, clinicians, and public health experts interested in the latest developments in microbial ecology, infection biology, and personalized medicine approaches for disease prevention and treatment.

Dr. Josué Juárez
Guest Editor

Dr. Pablo Mendez-Pfeiffer
Dr. Manuel Ballesteros-Monrreal
Guest Editor Assistants

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Keywords

host–microbe interactions
microbiota
microbial pathogenesis
immune response
antimicrobial resistance
gut microbiome
host response
dysbiosis
antimicrobial therapy

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Published Papers (9 papers)

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Research

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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

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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 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 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 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

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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 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 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

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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 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 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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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

Viewed by 897

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 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

Viewed by 647

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 (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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