Search Results (248)

Background/Objectives: Coronavirus disease 2019 (COVID-19) is associated with gastrointestinal (GI) symptoms. Small intestinal bacterial overgrowth (SIBO) is emerging as a significant GI sequela post-COVID-19 infection. This study aimed to evaluate the prevalence and incidence of SIBO post-COVID-19 infection across different age groups and to identify associated risk factors in a global cohort. Methods: A retrospective study utilized the TriNetX database and included adult patients (≥18 years) diagnosed with SIBO following COVID-19 infection (1 January 2022–30 May 2024). A propensity score matching (1:1) was used to adjust for demographics and SIBO risk factors. Kaplan–Meier survival analysis assessed the SIBO incidence within 12 months. Results: Among 1,660,092 COVID-19 patients and 42,322,017 controls, SIBO was diagnosed in 353 COVID-19 patients without hydrogen breath tests (BT) and 78 with BT, compared to 3368 controls without BT and 871 with BT. Age-specific analysis demonstrated a clear, progressive increase in the SIBO incidence, becoming distinctly significant by 6 months and highest at 12 months post-infection. The highest risks were noted in ages 60–69 (0.011% vs. 0.004%, OR 2.6, p = 0.0003) and 70–79 (0.011% vs. 0.005%, OR 2.0, p = 0.0004), with younger age groups (30–49 years) also showing significantly increased risks. The medication analysis revealed strong associations with chronic opioid, proton pump inhibitor, and antidiarrheal medication. Conclusions: COVID-19 significantly increased the risk of SIBO, particularly within the first 12 months post-infection, across various age groups and, notably, in association with certain chronic medications. Clinical vigilance and targeted management strategies are recommended to mitigate long-term GI consequences. Full article

Biofilms are a spontaneously formed slimy matrix of extracellular polymeric substances (EPS) enveloping miniature bacterial colonies, which aid in pathogen colonization, shielding the bacteria from antibiotics, as well as imparting them resistance towards the same. Biofilms employ a robust communication mechanism called quorum sensing that serves to keep their population density constant. What is most significant about biofilms is that they contribute to the development of bacterial virulence by providing protection to pathogenic species, allowing them to colonize the host, and also inhibiting the activities of antimicrobials on them. They grow on animate surfaces (such as on teeth and intestinal mucosa, etc.) and inanimate objects (like catheters, contact lenses, pacemakers, endotracheal devices, intrauterine devices, and stents, etc.) alike. It has been reported that as much as 80% of human infections involve biofilms. Serious implications of biofilms include the necessity of greater concentrations of antibiotics to treat common human infections, even contributing to antimicrobial resistance (AMR), since bacteria embedded within biofilms are protected from the action of potential antibiotics. This review explores various contemporary strategies for controlling biofilms, focusing on their modes of action, mechanisms of drug resistance, and innovative approaches to find a solution in this regard. This review interestingly targets the extracellular polymeric matrix as a highly effective strategy to counteract the potential harm of biofilms since it plays a critical role in biofilm formation and significantly contributes to antimicrobial resistance. Full article

Colorectal cancer (CRC) is a multifactorial disease increasingly recognized for its complex interplay with the gut microbiota. The disruption of microbial homeostasis—dysbiosis—has profound implications for intestinal barrier integrity and host immune function. Pathogenic bacterial species such as Fusobacterium nucleatum, Escherichia coli harboring polyketide synthase (pks) island, and enterotoxigenic Bacteroides fragilis are implicated in CRC through mechanisms involving mucosal inflammation, epithelial barrier disruption, and immune evasion. These pathogens promote pro-tumorigenic inflammation, enhance DNA damage, and suppress effective anti-tumor immunity. Conversely, commensal and probiotic bacteria, notably Lactobacillus and Bifidobacterium species, exert protective effects by preserving epithelial barrier function and priming host immune responses. These beneficial microbes can promote the maturation of dendritic cells, stimulate CD8⁺ T cell cytotoxicity, and modulate regulatory T cell populations, thereby enhancing anti-tumor immunity. The dichotomous role of the microbiota underscores its potential as both a biomarker and a therapeutic target in CRC. Recent advances in studies have explored microbiota-modulating strategies—ranging from dietary interventions and prebiotics to fecal microbiota transplantation (FMT) and microbial consortia—as adjuncts to conventional therapies. Moreover, the composition of the gut microbiome has been shown to influence the responses to immunotherapy and chemotherapy, raising the possibility of microbiome-informed precision oncology therapy. This review synthesizes the current findings on the pathogenic and protective roles of bacteria in CRC and evaluates the translational potential of microbiome-based interventions in shaping future therapeutic paradigms. Full article

Emerging evidence highlights the critical role of the gut microbiota in the development and progression of eating disorders (EDs), particularly in women, who are more frequently affected by these conditions. Women with anorexia nervosa, bulimia nervosa, and binge eating disorder exhibit distinct alterations in gut microbiota composition compared to healthy controls. These alterations, collectively termed dysbiosis, involve reduced microbial diversity and shifts in key bacterial populations responsible for regulating metabolism, inflammation, and gut–brain signaling. The gut microbiota is known to influence appetite regulation, mood, and stress responses—factors closely implicated in the pathogenesis of EDs. In women, hormonal fluctuations related to menstruation, pregnancy, and menopause may further modulate gut microbial profiles, potentially compounding vulnerabilities to disordered eating. Moreover, the restrictive eating patterns, purging behaviors, and altered dietary intake often observed in women with EDs exacerbate microbial imbalances, contributing to intestinal permeability, low-grade inflammation, and disturbances in neurotransmitter production. This evolving understanding suggests that microbiota-targeted therapies, such as probiotics, prebiotics, dietary modulation, and fecal microbiota transplantation (FMT), could complement conventional psychological and pharmacological treatments in women with EDs. Furthermore, precision nutrition and personalized microbiome-based interventions tailored to an individual’s microbial and metabolic profile offer promising avenues for improving treatment efficacy, even though these approaches remain exploratory and their clinical applicability has yet to be fully validated. Future research should focus on sex-specific microbial signatures, causal mechanisms, and microbiota-based interventions to enhance personalized treatment for women struggling with eating disorders. Full article

Grazing is a free-range farming model commonly practiced in low-external-input agricultural systems. The widespread use of veterinary antibiotics in livestock farming has led to significant environmental accumulation of antibiotic residues and antibiotic resistance genes (ARGs), posing global health risks. This study investigated the antibiotic residues, bacterial community, ARG profiles, and mobile genetic elements (MGEs) in cattle feces from three provinces in western China (Ningxia, Xinjiang, and Inner Mongolia) under grazing modes. The HPLC-MS detection showed that the concentration of tetracycline antibiotics was the highest in all three provinces. Correlation analysis revealed a significant negative correlation between antibiotic residues and the diversity and population abundance of intestinal microbiota. However, the abundance of ARGs was directly proportional to antibiotic residues. Then, the Sankey analysis revealed that the ARGs in the cattle fecal samples were concentrated in 15 human pathogenic bacteria (HPB) species, with 9 of these species harboring multiple drug resistance genes. Metagenomic sequencing revealed that carbapenemase-resistant genes (bla_KPC and bla_VIM) were also present in considerable abundance, accounting for about 10% of the total ARGs detected in three provinces. Notably, Klebsiella pneumoniae strains carrying bla_CTX-M-55 were detected, which had a possibility of IncFII plasmids harboring transposons and IS19, indicating the risk of horizontal transfer of ARGs. This study significantly advances the understanding of the impact of antibiotic residues on the fecal microbiota composition and ARG profiles in grazing cattle from northwestern China. Furthermore, it provides critical insights for the development of rational antibiotic usage strategies and comprehensive public health risk assessments. Full article

Recent advances highlight the crucial role of the gut microbiota in human health and disease, with dietary components emerging as powerful modulators of microbial communities. This review synthesizes current evidence on the effects of olive-derived bioactive compounds, including polyphenols (e.g., hydroxytyrosol, oleuropein or tyrosol), triterpenes and other phytochemicals on gut microbiota composition and function. These compounds have been shown to enhance beneficial bacterial populations such as Lactobacillus and Bifidobacterium, reduce potentially pathogenic taxa, and promote the production of short-chain fatty acids and other health microbial metabolites, reinforcing intestinal barrier integrity. In vitro, in vivo, and clinical studies also reveal the potential of olive bioactives to ameliorate metabolic, inflammatory, and neurocognitive disorders through gut-microbiota-brain axis modulation. Despite promising results, key challenges remain, including interindividual microbiota variability, lack of standardized intervention protocols, and limited human clinical trials. Addressing these gaps through robust translational research could pave the way for microbiota-targeted, personalized nutritional strategies based on olive-derived compounds. Full article

Utilizing straw feed is an effective strategy to optimize straw resource utilization by incorporating microbial degradation agents to expedite lignocellulose breakdown and enhance feed efficiency. Lignocellulose-degrading species and microbial communities are present in various Earth ecosystems, including the rumen of ruminants, insect digestive tracts, forest soil, and microbial populations in papermaking processes. The rumen of ruminants harbors a diverse range of microbial species, making it a promising source of lignocellulose-degrading microorganisms. Exploring alternative systems like insect intestines and forest soil is essential for future research. Current studies primarily rely on traditional microbial isolation techniques to identify lignocellulose-degrading strains, underscoring the necessity to transition to utilizing microbial culturomics and genome-editing technologies for discovering and manipulating cellulose-degrading microbes. This review provides an overview of lignocellulose-degrading microbial communities from diverse environments, encompassing bacterial and fungal populations. It also delves into the use of metagenomic, metatranscriptomic, and metaproteomic approaches to pinpoint highly efficient cellulase genes, along with the application of genome-editing tools for engineering lignocellulose-degrading microorganisms. The primary objective of this review is to offer insights for further exploration of potential lignocellulose-degrading microbial resources and high-performance cellulase genes to enhance roughage utilization in ruminant rumen ecosystems. Full article

Untreated water bodies are critical ecological niches where environmental conditions can drive the adaptive evolution of bacterial populations, enabling them to acquire new traits such as antibiotic-resistance genes. Escherichia coli is typically a commensal bacterium but can evolve into a pathogenic form, known as Diarrheagenic E. coli, responsible for both intestinal and extraintestinal diseases. This study focuses on the characterization of E. coli isolates from water samples collected from the Matasnillo River and the influence of the Juan Díaz Wastewater Treatment Plant (WWTP). While isolates from the Matasnillo River were classified as commensal, 18% of the isolates from the WWTP belonged to either phylogroups D or B2. Pathotype analysis revealed the presence of Entero-Toxigenic and Entero-Hemorrhagic E. coli in the WWTP. Moreover, Matasnillo River isolates exhibited resistance mainly to the quinolone ciprofloxacin, whereas those from the WWTP influent showed resistance to multiple broad-spectrum antibiotics. Sequencing analysis revealed the prevalence of the transmissible quinolone resistance qnrB19 among the Matasnillo River isolates and mutations conferring resistance to quinolone in gyrA, parC, and parE. These findings highlight the importance of monitoring antibiotic-resistant bacterial contamination in both freshwater and wastewater to mitigate the risk of the spread of resistant pathogens and potential epidemic outbreaks. Full article

Histamine intolerance is a condition that occurs when there is an imbalance between the accumulation and degradation of histamine within the body. Excess histamine is metabolized and then degraded by two enzymes, of which the most abundant is the vesicular diamine oxidase (DAO). An imbalance or a state of dysbiosis of the intestinal microbiota has been observed in patients with histamine intolerance compared to healthy individuals. Studies indicate that the administration of bifidobacteria or lactobacilli alone or in mixtures can alter colonic microbiota populations and metabolic activities. The present study has evaluated the ability of a probiotic bacterial strain to stimulate the release of cellular DAO from an in vitro model of the human intestinal epithelial barrier. The results indicate that, under the experimental conditions used, probiotic strain Lactiplantibacillus plantarum LP115 has a significant stimulatory effect on DAO secretion in adenocarcinoma cell line HT-29. Full article

Intestinal microbiota and the host’s immune system form a symbiotic alliance that sustains normal development and function in the human gut. Changes such as dietary habits among societies in developed countries have led to the development of unbalanced microbial populations in the gut, likely contributing to the dramatic increase in inflammatory diseases in the last few decades. Recent advances in DNA sequencing technologies have tremendously helped to characterize the microbiome associated with disease, both in identifying global alterations and discovering specific biomarkers that potentially contribute to disease pathogenesis, as evidenced by animal studies. Beyond bacterial alterations, non-bacterial components such as fungi, viruses, and microbial metabolites have been implicated in these diseases, influencing immune responses and gut homeostasis. Multi-omics approaches integrating metagenomics, metabolomics, and transcriptomics offer a more comprehensive understanding of the microbiome’s role in disease pathogenesis, paving the way for innovative diagnostic and therapeutic strategies. Unraveling the metagenomic profiles associated with disease may facilitate earlier diagnosis and intervention, as well as the development of more personalized and effective therapeutic strategies. This review synthesizes recent and relevant microbiome research studies aimed at characterizing the microbial signatures associated with inflammatory bowel disease, colorectal cancer, and celiac disease. Full article

ACLF is a severe stage of liver cirrhosis, characterized by multiple organ failure, systemic inflammation, and high short-term mortality. The intestinal microbiota (IM) influences its pathophysiology; however, there are currently no studies in Latin American populations. Therefore, we analyzed IM and its relationships with sepsis, organ failure, and mortality. In parallel, we quantified serum lipopolysaccharides as a marker of bacterial translocation. Fecal samples from 33 patients and 20 healthy controls (HCs) were obtained. The IMs were characterized by 16S-rRNA amplicon sequencing, the metagenomic functional predictive profiles were analyzed by PICRUSt2, and LPS quantification was performed by ELISA. Patients with ACLF showed significant alterations in alpha and beta diversity compared to the HCs. A strong dominance index accurately predicted 28-day and 90-day mortalities. The IMs showed a polarization toward Proteobacteria associated with increased LPS. The LPS correlated with clinical severity, organ dysfunction, and higher pathogenic taxa. The Klebsiella/Faecalibacterium ratio showed good performance in identifying sepsis (AUROC = 0.83). Furthermore, Morganella, Proteus, and Klebsiella were enriched in patients with multiorgan failure. Lactobacillus, Escherichia/Shigella, Veillonella, and Ruminococcus gnavus exhibited potential in predicting 28- and 90-day mortalities. The IM alterations in ACLF may be useful as clinical biomarkers of poor prognosis, primarily for mortality and sepsis. These findings are representative of western Mexico. Full article

Background/Objective. Toxin-producing strains of Clostridioides difficile (C. diff) are the most commonly identified cause of healthcare-associated infection in the elderly. Risk factors include advanced age, hospitalization, prior or concomitant systemic antibacterial therapy, chemotherapy, and gastrointestinal surgery. Patients with unspecified and new-onset diarrhea with ≥3 unformed stools in 24 h are the target population for C. diff infection (CDI) testing. To present data on the risks of laboratory misdiagnosis in managing CDI. Materials. In two general hospitals, we examined 116 clinical stool specimens from hospitalized patients with acute diarrhea suspected of nosocomial or antibiotic-associated diarrhea (AAD) due to C. diff. Enzyme immunoassay (EIA) tests for the detection of C. diff toxins A (cdtA) and B (cdtB) in stool, automated CLIA assay for the detection of C. diff GDH antigen and qualitative determination of cdtA and B in human feces and anaerobic stool culture were applied for CDI laboratory diagnosis. MALDI-TOF (Bruker) was used to identify the presumptive anaerobic bacterial colonies. The following methods were used as confirmatory diagnostics: the LAMP method for the detection of Salmonella spp. and simultaneous detection of C. jejuni and C. coli, an E. coli Typing RT-PCR detection kit (ETEC, EHEC, STEC, EPEC, and EIEC), API 20E and aerobic stool culture methods. Results. A total of 40 toxigenic strains of C. diff were isolated from all 116 tested diarrheal stool samples, of which 38/40 produced toxin B and 2/40 strains were positive for both cdtA and cdtB. Of the stool samples positive for cdtA (6/50) and/or cdtB (44/50) by EIA, 33 were negative for C. diff culture but positive for the following diarrheal agents: Salmonella enterica subsp. arizonae (1/33, LAMP, culture, API 20E); C. jejuni (2/33, LAMP, culture, MALDI TOF); ETEC O142 (1/33), STEC O145 and O138 (2/33, E. coli RT-PCR detection kit, culture); C. perfringens (2/33, anaerobic culture, MALDI TOF); hypermycotic enterotoxigenic K. pneumonia (2/33) and enterotoxigenic P. mirabilis (2/33, culture; PCR encoding LT-toxin). Two of the sixty-six cdtB-positive samples (2/66) showed a similar misdiagnosis when analyzed using the CLIA method. However, the PCR analysis showed that they were cdtB-negative. In contrast, the LAMP method identified a positive result for C. jejuni in one sample, and another was STEC positive (stx1+/stx2+) by RT-PCR. We found an additional discrepancy in the CDI test results: EPEC O86 (RT-PCR eae+) was isolated from a fecal sample positive for GHA enzyme (CLIA) and negative for cdtA and cdtB (CLIA and PCR). However, the culture of C. diff was negative. These findings support the hypothesis that certain human bacterial pathogens that produce enterotoxins other than C. diff, as well as intestinal commensal microorganisms, including Klebsiella sp. and Proteus sp., contribute to false-positive EIA card tests for C. diff toxins A and B, which are the most widely used laboratory tests for CDI. Conclusions. CDI presents a significant challenge to clinical practice in terms of laboratory diagnostic management. It is recommended that toxin-only EIA tests should not be used as the sole diagnostic tool for CDI but should be limited to detecting toxins A and B. Accurate diagnosis of CDI requires a combination of laboratory diagnostic methods on which proper infection management depends. Full article

Background/Objectives: Childhood obesity is a growing global concern linked to metabolic disorders such as nonalcoholic fatty liver disease (NAFLD). Small intestinal bacterial overgrowth (SIBO) may exacerbate these conditions by promoting systemic inflammation and metabolic dysfunction. This review evaluates the prevalence of SIBO in obese children, its association with inflammatory and metabolic markers, and the efficacy of diagnostic and therapeutic strategies. Methods: A systematic search of PubMed, Scopus, and Web of Science (2010–present) was conducted using Boolean operators: (‘small intestinal bacterial overgrowth’ OR ‘SIBO’) AND ‘prevalence’ AND (‘low-grade inflammatory markers’ OR ‘metabolic status’) AND ‘gut microbiome’ AND ‘dysbiosis’ AND ‘obese children’. Results: The data show that SIBO is frequently observed in obese pediatric populations and is associated with gut dysbiosis, impaired nutrient absorption, and reduced production of short-chain fatty acids. These changes contribute to increased intestinal permeability, endotoxemia, and chronic low-grade inflammation. Several microbial taxa have been proposed as biomarkers and therapeutic targets. Diagnostic inconsistencies persist, but treatments such as probiotics, prebiotics, dietary interventions, and selective antibiotics show potential, pending further validation. Conclusions: Early identification and treatment of SIBO with tailored strategies may help reduce metabolic complications and improve outcomes in children with obesity. Full article

Background/Objectives: Small Intestinal Bacterial Overgrowth (SIBO) and Small Intestinal Fungal Overgrowth (SIFO) are distinct yet often overlapping conditions characterized by an abnormal increase in microbial populations within the small intestine. SIBO results from an overgrowth of colonic bacteria, while SIFO is driven by fungal overgrowth, primarily involving Candida species. Both conditions present with nonspecific gastrointestinal (GI) symptoms such as bloating, abdominal pain, diarrhea, and malabsorption, making differentiation between SIBO and SIFO challenging. This review aims to elucidate the underlying mechanisms, risk factors, diagnostic challenges, and management strategies associated with SIBO and SIFO. Methods: A comprehensive review of current literature was conducted, focusing on the pathophysiology, diagnostic modalities, and therapeutic approaches for SIBO and SIFO. Results: SIBO is commonly associated with factors such as reduced gastric acid secretion, impaired gut motility, and structural abnormalities like bowel obstruction and diverticula. It is frequently diagnosed using jejunal aspirates (≥10⁵ colony forming units (CFUs)/mL) or breath tests. In contrast, SIFO is linked to prolonged antibiotic use, immunosuppression, and gut microbiome dysbiosis, with diagnosis relying on fungal cultures from small intestinal aspirates due to the absence of standardized protocols. Conclusion: The clinical overlap and frequent misdiagnosis of SIBO and SIFO highlight the need for improved diagnostic tools and a multidisciplinary approach to management. This review emphasizes the importance of understanding the mechanisms behind SIBO and SIFO, how they relate to other health outcomes, and potential management strategies to optimize patient care and therapeutic outcomes. Full article

COVID-19 has caused millions of deaths globally; however, the characterization of molecular biomarkers of severe disease remains of great scientific importance. The aim of this study was to capture the transcriptional differences of the whole blood gene expression between COVID-19 patients with mild and severe disease, using Next Generation Sequencing technologies, on admission and after 7 days. The genes which were differentially expressed in severe compared to mild patients were used for Gene Ontology (GO) enrichment analysis. Gene expression data were used to estimate the cell abundance of 22 immune cell types via digital cytometry. GO terms related to the response to molecules of bacterial origin, such as intestine-derived lipopolysaccharide (LPS), were enriched, among other dysregulated pathways, which are well described as paramount mechanisms of severe manifestations of COVID-19. The neutrophil population increased in patients with severe disease, whereas the monocyte, CD8⁺ T cell, and activated Natural Killer (NK) cell populations were depleted. These cell population dynamics are also indicative of severe COVID-19 and intestinal bacterial translocation. This study elucidates the molecular basis of severe COVID-19 and highlights intestinal bacterial translocation as a potential driver of severe disease. Full article