Abstract Microbiome research has identified many highly valuable associations between microbial communities and factors such as diet, antibiotics use, lifestyle, inflammation, infection and chronic disease. However, many findings remain difficult to translate into clinical practice because they are only association-based and vulnerable to confounding. Many studies also often lack reproducibility. Comparisons between “dysbiotic” and “healthy” microbiome states can be misleading because microbiome profiles are shaped by factors such as diet, medication, geography, host genetics, demographics, disease severity and reverse causation. Moreover, there remains no universally accepted definition or consensus regarding what constitutes a ‘’healthy’’ microbiota. What in one individual may be considered a healthy mix of species may not necessarily serve another individual whose diet and lifestyle is completely different. The microbiome research must move beyond descriptive profiling toward clinically actionable and mechanistically informed study designs. The key barriers include small cohort sizes, inconsistent sample collection and treatment, differences in sequencing methods, constantly evolving bioinformatic pipelines, limited availability of raw data, and differences between OTU- and ASV-based analyses. To support a large-scale population studies and meta-analysis a transparent reporting along with shared analytical workflows are essential for progress in this field. Microbiome signatures should not only be reproducible, biologically plausible and modifiable but also linked to the treatment decisions or improved outcomes. This requires longitudinal modelling, external validation, mechanistic studies, and eventually interventional or pragmatic trials. The need for standardisation and reproducibility in microbiome research is widely recognised. This paper builds on that foundation by proposing an actionability-focused framework for designing translational microbiome studies. Using Type 2 Diabetes treatment as a worked example demonstrates that microbiome features should be evaluated not only for their statistical associations, but also for the additional predictive value they provide beyond established clinical variables.
Abstract Pathogenic Shiga toxin-producing Escherichia coli (STEC) are a major public health concern and a key issue for the agri-food sector. However, their isolation remains challenging because STEC lack distinctive biochemical characteristics that clearly differentiate them from other Escherichia coli. This study evaluated the performance of nine commonly used agar media for STEC isolation using three types of samples: pure cultures, experimentally spiked food matrices, and naturally contaminated foods. Two isolation approaches were compared: direct streaking and immuno-separation followed by plating. In pure cultures, five media (TBX, SMAC, Rainbow®AgarO157, CHROMID®EHEC Agar, and IDEA™ STEC with or without cefixime-tellurite) achieved complete recovery, whereas CT-CHROMID®EHEC, CT-SMAC and CHROMagarTMSTEC agar inhibited the growth of several strains, particularly those sensitive to tellurite. In food matrices, immunomagnetic separation resulted in high and comparable detection rates across media (80–95%; n = 16/20–19/20). In contrast, direct streaking showed highly variable recovery depending on the medium (29–100%; n = 7/20–20/20). These results demonstrate that combining selective and non-selective media improves STEC detection. Immuno separation enhances recovery of key serogroups, while IDEA STEC enables additional differentiation through halo formation. The observed variability in toxin production suggests that environmental and physiological factors influence STEC detection.
Abstract Selective antimicrobial susceptibility supports antimicrobial stewardship strategy but may have limitations in high-resistance prevalence settings. We report a community-acquired infection of necrotic metastatic inguinal lymphadenopathy caused by two mcr-producing Escherichia coli isolates, including one blaOXA-48 producer. Initial selective susceptibility testing delayed recognition of clinically relevant resistance. This case highlights the risk of silent community dissemination of high-priority resistance determinants. It underscores the need for context-adapted susceptibility reporting to balance antimicrobial stewardship and resistance surveillance.
Abstract The efficacy of antimicrobial therapy against Shiga toxin-producing Escherichia coli (STEC) infections has been a matter of global debate. In Japan, fosfomycin is often prescribed for pediatric patients to prevent life-threatening sequelae. Recently, E. coli strains harboring plasmid-mediated fosfomycin-resistant genes (fos genes) have been disseminated worldwide, yet the prevalence of these genes among STEC remains unclear. This study aimed to determine the prevalence of fosfomycin resistance among STEC strains isolated from humans, as well as to analyze the molecular characteristics of a conjugative plasmid carrying a fos gene in a STEC strain. Two fosfomycin-resistant STEC O26:H11 strains were identified among 206 STECs by the disk diffusion method. The primary fos gene, fosA3, was identified on an IncF2:A-:B- plasmid in one strain. This plasmid could be transferred to recipients, and the frequency of transfer was higher for STEC O26 recipients compared to STEC O157 recipients. Sequence-based comparative analysis of the plasmid suggested horizontal transfer of fosA3 gene among diverse bacterial strains, with insertion sequences playing a pivotal role in its mobilization. These findings suggest the possibility of fosA3 gene disseminating among diverse STEC strains and emphasize the importance of monitoring fosfomycin resistance and characterizing resistance plasmids in STEC strains.
Abstract White grub (Holotrichia serrata F.) is a destructive soil-dwelling pest causing severe yield losses in several agricultural and horticultural crops. Owing to its subterranean habit, chemical control is often ineffective, necessitating sustainable biological alternatives. This study investigated the distribution of coleopteran-active cry genes among indigenous Bacillus thuringiensis strains and evaluated their insecticidal activity against H. serrata. A total of 100 indigenous B. thuringiensis strains isolated from the Western Ghats of India were screened using gene-specific PCR for 12 coleopteran-active cry genes. The most prevalent genes were cry7 (66%), cry26 (65%), cry1b (64%), and cry34 (63%), whereas cry8 and cry9 occurred in fewer than 10% of the isolates. Preliminary bioassays at 380 µg mL⁻¹ identified 20 strains causing > 50% larval mortality. Concentration-dependent bioassays showed that strain NBAIR Bt68 was the most virulent, causing 73% mortality with an LC₅₀ of 149.95 µg mL⁻¹. Highly toxic strains consistently possessed the cry7–cry26–cry34–cry35 gene combination, whereas the total number of cry genes did not correlate with high insecticidal activity. Molecular profiling combined with bioassay evaluation identified indigenous B. thuringiensis strains with promising biocontrol potential and provides insights into the association between cry gene combinations and insecticidal activity against H. serrata.
