Iranian Journal of Microbiology

Microbiome and thyroid diseases: future precision studies of the gut-thyroid axis to facilitate the adjuvant treatment

2026-04-26T18:43:08+0430

Background and Objectives: The gut microbiome is a key determinant of overall health, impacting numerous bodily functions, such as those of the endocrine glands. The effect of the microbiota on thyroid function has become a matter of interest, more so since the revelation of the possible link between intestinal disease and autoimmune thyroid disorders (AITDs). This review aims to provide an in-depth insight into the possible link between gut microbiota and thyroid diseases and metabolism of thyroid hormones.
Materials and Methods: A set of online sources including, PubMed, Scopus, Google Scholar and CENTRAL were comprehensively searched to find the studies relevant to the topic of the review. Only reports in English were included in this review.
Results: It has been proposed that damage to the intestinal barrier is a key element in the passage of antigens from the lumen into the bloodstream and their subsequent contact with the immune system. In addition to AITDs, dysbiosis has been shown to be linked with thyroid cancers, in which higher counts of certain bacteria associated with inflammation and carcinogenesis have been identified.
Conclusion: The majority of the available literature is focused on the differences in the microbial strain composition in individuals with thyroid disorders compared to that of healthy controls. Nonetheless, the current body of evidence has implied on possible role gut microbiome in the development of thyroid diseases.

Gut microbiome signatures associated with iron-deficiency anemia in young adults

2026-04-26T18:43:08+0430

Background and Objectives: Iron is vital for both the body of the host and the metabolism of microbes. Pathogenic Enterobacteria need iron to grow and cause disease, but many good gut bacteria, like lactobacilli, do not require as much iron. Changes in the amount of iron available in the gut may therefore affect the makeup of the gut microbiome. Iron-deficiency anemia (IDA) represents the most prevalent nutritional disorder globally, concerning about 1.24 billion, mostly women and young people in low- and middle-income countries. This cross-sectional study looked at the link between iron-deficiency anemia and the makeup of the gut microbiome in young adults aged 18 to 30.
Materials and Methods: We looked at hematological and iron status parameters as well as gut microbiota profiling using 16S rRNA gene sequencing. Differences in microbial diversity, taxonomic composition, and the relative abundance of bacteria that make short-chain fatty acids between people with IDA and healthy controls were investigated.
Results: The results show that iron-deficiency anemia is linked to different gut microbiome signatures. This suggests that there may be connections between iron levels and the structure of microbial communities.
Conclusion: These results show how important it is to study the gut microbiome to understand iron-deficiency anemia. They also show how important it is to do long-term, interventional studies to figure out how these associations work and what they mean for health.

Impact of co-amoxiclav–induced gut microbiota modulation on seizure frequency in children with drug-resistant epilepsy

2026-04-26T18:43:09+0430

Background and Objectives: Epilepsy is one of the most common neurological disorders; despite advances in antiepileptic medications, approximately 15-30% of patients continue to experience drug‑resistant seizures. The ketogenic diet has emerged as an effective non-pharmacological treatment for these individuals. Recent studies suggest that changes in gut microbiota may play a role in the diet's ability to reduce seizures. Given this information, our study aimed to investigate the short-term modulation of gut microbiota through antibiotics influences seizure frequency in children with drug-resistant epilepsy.
Materials and Methods: In this open-label clinical trial, 20 children with drug-resistant epilepsy were enrolled in 2020 at a tertiary pediatric clinic in Sari, Iran. Participants received oral co-amoxiclav (amoxicillin-clavulanate) at a dose of 40 mg/kg per day for five consecutive days. Seizure frequency was monitored before and after the antibiotic intervention. Stool samples were collected at baseline and immediately following treatment, and quantitative real-time PCR was performed to assess all bacterial load as well as the relative abundance of the major gut bacterial groups, Firmicutes and Bacteroides.
Results: The short-term course of co-amoxiclav significantly altered the gut microbiota composition, with a notable reduction in Bacteroidetes and a significant increase in all bacterial gene copies, while the abundance of Firmicutes remained largely unchanged. However, there was no statistically significant change in seizure frequency during the 12-week follow-up period.
Conclusion: Although short-term co-amoxiclav treatment modified the gut microbiota, it did not lead to a meaningful reduction in seizure frequency in children with drug-resistant epilepsy. These findings underscore the complexity of the gut-brain axis and suggest that simple, short-term antibiotic interventions may not be sufficient to influence seizure outcomes. Future studies should involve larger, multicenter cohorts, longer treatment durations, and more comprehensive analyses of microbiota profiles.

Impact pattern of heavy metals on gut microbiota in the polluted city of Tehran

2026-04-26T23:36:06+0430

Background and Objectives: This article focuses on the effects of six heavy metals on gut microbiota, which plays a key role in human health. Gut microbiota plays a key role in metabolism, immunity, and maintaining homeostasis. Heavy metals can affect microbiota composition and function, with health consequences. Consuming large amounts of heavy metals may have harmful impacts, including alteration in microbial composition and bacterial population changes.
Materials and Methods: Six heavy metals—cadmium, chromium (toxic metals), copper, zinc, iron, and selenium (beneficial trace elements)—were detected in peripheral blood, serum, or urine, while feces were used for 16S rRNA sequencing. Serum samples from 100 volunteers from Tehran (polluted area) and Firoozkooh (clean city) were collected. Subjects were analyzed for the presence of Escherichia coli, Bacteroides fragilis, Bifidobacterium longum, Lactobacillus acidophilus, Clostridium clostridioforme, Faecalibacterium prausnitzii and Akkermansia muciniphila to evaluate correlations between metals and microbial composition using biochemical, microbial, and molecular methods.
Results: Escherichia coli and Bifidobacterium longum levels in polluted areas were not significantly different from those in unpolluted areas. Bacteroides fragilis in polluted areas was significantly higher compared to non-polluted locations. Clostridium, Akkermansia, Faecalibacterium, and Lactobacillus acidophilus were significantly lower in polluted areas, amounting to less than half the levels in clean areas. Heavy metal concentrations showed no gender differences in either location.
Conclusion: Some heavy metals change intestinal microbiota composition and metabolic profiles, potentially resulting in metabolic diseases and environmental risks.

The effects of Salmonella enterica cell extract on the gene expression of bleomycin hydrolase, puromycin-sensitive aminopeptidase, and thimet oligopeptidase in human colorectal adenocarcinoma cells

2026-04-26T18:43:09+0430

Background and Objectives: Salmonella enterica survival depends on evading CD8+ T-cell recognition, a process governed by the MHC Class I antigen presentation pathway. The cytosolic aminopeptidases—bleomycin hydrolase (BH), puromycin-sensitive aminopeptidase (PSA), and thimet oligopeptidase (TOP)—are critical "final trimmers" that generate the precise peptide epitopes required for MHC Class I loading. This study investigated whether S. enterica cell extract modulates the transcriptional expression of these key enzymes in HT-29 cells, potentially revealing a mechanism of immune evasion mediated by bacterial structural components.
Materials and Methods: Human colorectal adenocarcinoma HT-29 cells were treated with varying concentrations of S. enterica extract. The gene expression levels of BH, PSA, and TOP were quantified using qRT-PCR at multiple time points (6, 12, 24, 48, and 72 hours) post-treatment. Data were statistically analyzed to evaluate significant modulations relative to untreated controls.
Results: The transcriptional response to S. enterica extract was highly selective, with TOP demonstrating the most robust and rapid induction. Significant upregulation of TOP occurred as early as 6 hours post-treatment and reached its maximum induction at 48 hours. Conversely, BH levels remained largely indistinguishable from untreated controls. PSA expression showed no statistically significant alterations relative to the control group throughout the study. These findings suggest that S. enterica components preferentially target the "terminator" peptidase TOP to potentially disrupt the MHC Class I antigen presentation pathway.
Conclusion: S. enterica cell extract significantly and selectively alters the expression of TOP, a critical cytosolic peptidase involved in the final stages of antigen processing. This targeted modulation likely serves as a mechanism for immune evasion by facilitating the destruction of immunogenic epitopes, thereby rendering infected cells less visible to the adaptive immune system.

Identification of plasmid-mediated quinolone resistance genes in Helicobacter pylori isolates from gastrointestinal patients

2026-04-26T18:43:09+0430

Background and Objectives: The expanding antibiotic resistance of Helicobacter pylori isolates is a critical concern for global health. This research aimed to evaluate the prevalence of PMQR genes, including qnrA1-6, qnrB4, qnrB1, qnrS, qepA, and aac(6´)Ib-cr, among H. pylori strains isolated from patients at Qazvin Hospital.
Materials and Methods: In this study, 212 patients with gastrointestinal diseases who were referred to Qazvin Hospital underwent endoscopy, and gastric biopsies were collected. H. pylori isolates were confirmed by biochemical and molecular tests. PCR was performed to detect the virulence genes babA2 and sabA. Subsequently, the presence of the PMQR genes qnrA1-6, qnrB4, qnrS, qnrB1, qepA, and aac(6')Ib-cr were molecularly identified.
Results: 149 (70%) of isolates were phenotypically and molecularly confirmed as H. pylori isolates. Of the 149 isolates, 102 isolates (68.45%) with babA2 and 120 isolates (80.53%) with sabA genes were identified. frequencies of the genes qnrA1-6, qnrB4, qnrB1, and qepA were 8 (5.36%), 4 (2.68%), 12 (8.05%), and 13 (8.72%), respectively. Notably, qnrS and aac(6´)Ib-cr genes were not detected in isolates.
Conclusion: The findings of this study confirm that regular monitoring of antibiotic resistance genes is essential to prevent the further spread of PMQR resistance genes and to optimize clinical decision-making.

Molecular characterization of plasmid-mediated quinolone resistance genes in clinical isolates of Pseudomonas aeruginosa from Al-Muthanna Province, Iraq

2026-04-26T18:43:09+0430

Background and Objectives: Fluoroquinolones represent a class of antibiotics commonly used to manage Pseudomonas aeruginosa infections. The appearance of fluoroquinolone resistance in P. aeruginosa represents a critical challenge to healthcare systems.
Materials and Methods: Between January and December 2024, 650 clinical specimens were collected from Al-Hussein Teaching Hospital and Al-Rumaitha Hospital in Al-Muthanna, Iraq. P. aeruginosa was identified by conventional biochemical assays and confirmed with the Vitek 2® system. Susceptibility testing was performed by disk diffusion. PCR was conducted to detect plasmid-mediated quinolone resistance determinants, namely qnrA, qnrB, qnrD, qnrS, aac(6′)-Ib-cr, and qepA.
Results: Among the 650 specimens analyzed, 374 (57.54%) were positive for bacterial culture, with P. aeruginosa representing 40.10% (150/374) of the identified isolates. Among these, 39 (26%) exhibited resistance to at least one fluoroquinolone used. The most frequently detected gene was qnrB (67.65%), followed by qnrD (61.76%), qnrS (55.88%), aac(6')-Ib-cr (47.00%), and qepA (41.17%), while qnrA and qnrC were not detected in any isolate.
Conclusion: The fluoroquinolone resistance and widespread occurrence in isolates of P. aeruginosa from Al-Muthanna Province pose a challenge to infection management, as mobile genetic elements facilitate the rapid dissemination of resistance and limit available therapeutic options, emphasizing the necessity for genetic monitoring and effective antibiotic management.

Molecular evaluation of colistin resistance in Klebsiella pneumoniae strains isolated from patients in hospitals of Qom province

2026-04-26T18:43:09+0430

Background and Objectives: Colistin is considered as one of the last antibiotic choices for addressing infections resulting from multidrug-resistant Klebsiella pneumoniae. Nevertheless, the rising resistance to colistin is emerging as a growing threat to public health. The aim of the present study was to explore the molecular mechanisms underlying resistance to colistin in a clinical isolate of K. pneumoniae.
Materials and Methods: Colistin resistance was confirmed through antimicrobial susceptibility testing, and the sequence type was identified using Multilocus sequence typing (MLST). The molecular mechanism of colistin resistance was investigated by sequence analysis of resistance-associated loci, including mgrB, pmrAB, phoPQ, crrAB, and PCR detection of plasmid-mediated mcr genes.
Results: Among the studied 38 clinical K. pneumoniae isolates, one strain was colistin-resistant, which belonged to sequence type ST377. PCR results showed that the colistin resistance genes carried by plasmid (mcr-1 to mcr-4) were not present. While gene sequencing revealed wild-type pmrAB and phoPQ, the mgrB and crrA genes were found to be disrupted by insertion of IS elements in the promoter (position-45) and coding regions (position +365/+366), respectively. Moreover, a Q296L amino acid substitution was detected in CrrB.
Conclusion: This study demonstrates that resistance to colistin in the K. pneumoniae ST377 isolate was mainly mediated by inactivation of MgrB and CrrA without the involvement of mcr plasmid genes or pmrAB or phoPQ genetic alterations. To our knowledge, no previous study has reported insertion sequence-mediated disruption of the crrA coding region in K. pneumoniae. The results highlighted the complexity of chromosomal resistance mechanisms and the importance of molecular surveillance in managing colistin-resistant infections.

Molecular profiling of methicillin‑resistant Staphylococcus aureus isolated from healthy pet dogs and their owners in western Iran

2026-04-26T18:43:12+0430

Background and Objectives: Growing apprehension surrounds methicillin-resistant Staphylococcus aureus (MRSA) strains. The objective of this investigation was to molecularly profile MRSA strains recovered from asymptomatic companion dogs and their human caretakers in Kermanshah, located in western Iran, marking the inaugural research of its kind within the country.
Materials and Methods: During a six-month period, specimens were obtained from the oral cavities and nasal passages of 200 clinically normal pet dogs, as well as their owners. MRSA isolates were identified, DNA was extracted, and characterized via staphylococcal cassette chromosome mec (SCCmec), accessory gene regulator (agr), and staphylococcal protein A (spa) typing, plus detection of mecA and Panton-Valentine leukocidin (PVL) genes.
Results: Eighteen MRSA isolates were identified (12 from dogs, six from owners). All carried mecA. Most had SCCmec type III. Human isolates included one agr II and two agr IV; no dog isolates were agr-positive. Isolates belonged to four spa types: t690 (dogs) and t325, t037, t030 (owners). PVL genes were absent. Isolates from dogs and owners showed type diversity.
Conclusion: This study reveals MRSA epidemiology in healthy dogs and owners in Iran, with low colonization rates. Continuous monitoring is essential to track MRSA circulation, as colonization raises infection risk.

HEV prevalence, risk factors and outcomes in a tertiary care hospital of Uttar Pradesh: a retrospective observational study

2026-04-26T18:43:12+0430

Background and Objectives: Acute hepatitis is characterized by inflammation of the liver parenchyma or hepatocellular injury, leading to impaired liver function. Hepatitis E virus (HEV) is a major cause of acute viral hepatitis in Asia, including India. This study aimed to investigate the various etiologies of viral hepatitis and analyse the demographic profile and clinical outcomes of HEV infection.
Materials and Methods: This retrospective observational study was conducted at the VRDL, Department of Microbiology, JNMCH, Aligarh, and included 1,168 patients presenting with deranged liver function tests and clinical signs of hepatitis between August 2022 and March 2024. Serum samples were tested for HAV (IgM), HBV (HBsAg), HCV (IgM and IgG), and HEV (IgM) using ELISA (Dia Pro, Italy). HEV IgM-positive patients were followed up using a predesigned proforma to assess clinical outcomes and their association with demographic factors.
Results: Out of 1,168 samples screened for viral hepatitis markers, 753 (64%) tested positive for Hepatitis A, B, C, or E. HAV was the most common (554 cases, 73.5%), followed by HEV (125 cases, 16.6%). These HEV IgM positive samples were further subjected to RT-PCR, and 34 were positive and 91 negative among them. Most HEV-positive cases were aged 16-30 years, with a mean age of 19.3 ± 12.1 years. A history of consuming unfiltered water was reported in 78% of HEV cases. The highest number of HEV cases were from Jeevangarh (21.6%) and Jamalpur (14.4%), followed by Dodhpur (8.8%) and Nagla Mohalla (8%). Fever (96%) was the most common symptom, followed by jaundice (86%) and abdominal pain (84%). Key risk factors included residing in rural or semi-urban areas, use of public toilets, and overcrowding. Among the 125 HEV IgM-positive patients, only two fatalities were reported; the remaining recovered within 3 to 6 months.
Conclusion: HEV is a major cause of acute hepatitis in our region, with sporadic cases year-round and outbreaks peaking during the monsoon and post-monsoon seasons. Most cases originated from areas with poor sanitation and hygiene.

Synthesis and characterization of silica nano particles-based imprinted polymers for detection of herpes simplex virus type 1 in human plasma

2026-04-26T18:43:12+0430

Background and Objectives: Molecularly imprinted polymers (MIPs) are polymers designed to selectively recognize specific molecules or related compounds. They are created using template molecules, which are later removed, leaving behind cavities tailored to the template's structure. This study aimed to synthesize MIPs for detecting HSV-1 suspended in Human plasma.
Materials and Methods: For synthesizing Silica Nanoparticles and virus-imprinted particles, the Stöber and Sol-gel methods were employed to detect HSV-1 in human plasma. Moreover, ultra-sonication for washing and removal of HSV-1 from VIP, and FESEM were used to determine the shape, size, and characteristics of the synthesized particles. Additionally, DLS was used to confirm the size of particles. MTT assay was employed for cell viability, and TCID50/ml was used for measuring infectious viral titer. Real-time PCR as a molecular assay for virus genome quantification was applied.
Results: The average size of gold-coated freeze-dried SNPs and VIPs was analyzed by FESEM, and the results were 332 and 390 nm, respectively. DLS results showed an average size of 362, 521, and 648 nm for SNPs, VIPs, and NIPs. The VIP cavity size was 156 nm, which was specific for HSV-1. The Real-time PCR confirmed the removal of HSV-1.
Conclusion: The imprinted particles could specifically bind to HSV-1.

Contamination and antibiotic resistance profile of Cronobacter sakazakii isolated from raw milk and infant formula

2026-04-26T18:43:12+0430

Background and Objectives: Cronobacter sakazakii is an opportunistic pathogen associated with severe fatal infections. This study aimed to investigate the contamination of raw milk delivered to a powdered milk factory and the produced powdered milk, with C. sakazakii, and also the antibiotic resistance patterns of the isolates.
Materials and Methods: During 2024, 120 raw milk and 60 powdered milk samples were collected from one of the milk powder processing plants in Shahrekord city. A peptone water medium supplemented with nutrients, followed by Cronobacter Selective Broth, was used as the enrichment medium. Chromogenic Cronobacter Isolation (CCI) agar was used to isolate the suspicious colonies. Biochemical tests were performed on the isolates. The PCR test was performed to confirm the molecular identity of the isolates. The antibiogram test was performed using the disk diffusion method on Mueller-Hinton agar.
Results: A total of 14 suspected C. sakazakii colonies were isolated from the raw milk. However, the PCR test confirmed that only 2 isolates (1.67%) were C. sakazakii. Also, the results revealed that none of the powdered milk samples were contaminated with C. sakazakii. The antibiogram test showed that the isolated C. sakazakii were resistant to erythromycin, ampicillin, amoxicillin, cephalexin, and tetracycline antibiotics.
Conclusion: According to the results, some raw milk is contaminated with C. sakazakii, which is resistant to certain common antibiotics. However, contamination with this bacterium was not observed in the powdered milk samples. Given the importance of C. sakazakii in infant health, further studies should be conducted on other powdered milk and infant food supplements produced in Iran to ensure their safety.

Bioactive okra mucilage films with Aloysia citrodora extract: a natural approach to fish preservation under refrigeration

2026-04-26T18:43:12+0430

Background and Objectives: This study investigated the extraction of okra mucilage and its application in developing bioactive films enriched with Aloysia citrodora extract for food packaging. The effects of microwave-assisted extraction and UV treatment on film properties and preservation performance were evaluated.
Materials and Methods: Okra mucilage was extracted using conventional solvent and microwave-assisted methods. The phenolic profile of A. citrodora extract was analyzed by HPLC-DAD. Films containing up to 2% extract were prepared and subjected to UV treatment. Mechanical properties, thickness, water vapor permeability (WVP), antioxidant capacity (TPC and DPPH), antimicrobial activity, and preservation efficacy were assessed in refrigerated fish fillets.
Results: Microwave extraction slightly improved mucilage yield (8.7 vs. 8.3 g/100 g). Luteolin-7-O-diglucuronide and verbascoside were the dominant phenolics. UV-treated films with 2% extract showed higher tensile strength (45.71 MPa) and lower WVP (4.36 g mm/m² day kPa) compared to the controls. Antioxidant activity and antimicrobial inhibition against foodborne pathogens were significantly enhanced. Treated films delayed Pseudomonas aeruginosa growth in fish fillets.
Conclusion: Combining microwave extraction and UV treatment improved film functionality, highlighting their potential as natural active packaging materials.