Background/Aim. Post-traumatic stress disorder (PTSD) is a significant challenge in military medicine, increasingly linked to the systemic and gut-microbiome dysregulation. This study aimed to characterize the gut microbiome of Ukrainian military personnel with PTSD, identify a reproducible core microbiome, and inform a microbiome-based risk-stratification model and personalized probiotic strain selection. Methods. Gut microbiota profiling was performed in n = 41 male Ukrainian military personnel with PTSD (DSM-5-TR), comprising two platform-based cohorts: Cohort 1 (n = 18, Illumina MiSeq, 16S rRNA V3–V4) and Cohort 2 (n = 23, Oxford Nanopore MinION, full-length 16S rRNA; HAC v4.3.0, Q ≥ 10). No non-PTSD comparator group was included in this analysis; findings are a descriptive characterization within a larger ongoing project (n = 300) that also includes combat-exposed non-PTSD, IDP and healthy-control arms, to be reported separately. Core taxa were defined as present in ≥ 75% of samples at >0.1% relative abundance; co-occurrence networks used SparCC (1,000 bootstraps, |r| ≥ 0.3, pseudo-P < 0.05, BH-FDR < 0.05). Candidate probiotic strains were selected using the literature-established criteria (antagonism to pathobionts, acid resistance, organic acid production), corroborated by preliminary in vitro screening. Results. Across both cohorts, a reproducible core microbiome dominated by Bacillota (Faecalibacterium prausnitzii, F. duncaniae) and Bacteroidota (Segatella copri) was identified despite pronounced inter-individual heterogeneity (a single taxon often exceeded 40—60% relative abundance per patient). PCA showed clear separation by sequencing platform (PC1), indicating a technical batch effect; alpha-diversity comparisons were therefore exploratory (Wilcoxon test), and beta-diversity centroids differed by platform (PERMANOVA, 999 permutations). Network analysis identified Faecalibacterium duncaniae as a central hub, positively linked to Marseillibacter massiliensis and Waltera intestinalis and negatively to Blautia fibrosolvens. Based on antagonism, acid resistance and organic-acid production, candidate strains (Lactiplantibacillus plantarum A, L. plantarum IBM B-7413, L. bulgaricus A22, Lacticaseibacillus rhamnosus S25) were selected for a personalized probiotic prototype, DefendX. A preliminary Microbiome-Based Risk Score integrating these features was formulated; its predictive performance (sensitivity, specificity, AUC) is currently being validated in the extended cohort. Conclusions. In the absence of a matched comparator, these findings characterize a reproducible, platform-independent core gut microbiome in PTSD rather than confirm PTSD-specific dysbiosis. The Microbiome-Based Risk Score and the DefendX probiotic remain an in vitro/in silico-stage laboratory prototype; their diagnostic and therapeutic potential for military medicine requires validation in larger, controlled studies before clinical application can be considered. Grants. Ministry of Education and Science of Ukraine, project No. 0124U004303 (2024—2026).