Microbial Genomics - Current Issue

The marine cyanobacterium Synechococcus sp. PCC 7002 (Syn7002) is a model organism that lacks the gene cluster required for vitamin B12 biosynthesis, necessitating cooperative interactions with other microbes. In this study, we established a synthetic microbial consortium by co-culturing Syn7002 with a bloom-forming Microcystis community, followed by purification, and subsequently investigated the interactions between Syn7002 and the associated microbial community. Electron microscopy revealed numerous rod-shaped bacteria clustered around Syn7002 cells, indicating close spatial associations between species. Metagenomic analysis showed that the early-stage community consisted mainly of Syn7002, Mesorhizobium sp. TaiHu (MesTH) and Pseudomonas sp. TaiHu (PseTH), although the abundance of PseTH declined after community stabilization. Investigation of vitamin B12 regulation between MesTH and Syn7002 through metatranscriptomic analysis revealed upregulation of nitrogen metabolism-related genes in the microbial community. Transcriptomic data further indicated that vitamin B12 biosynthesis and transport genes were significantly upregulated in MesTH. Combined with vitamin B12-positive control experiments, these results confirm potential vitamin B12 complementarity between the two strains. The results further suggest that MesTH promotes the growth of Syn7002 in the community by providing the small amount of vitamin B12 needed for its growth. These findings provide new insights into vitamin-mediated microbial interactions and reveal additional transcriptional features of the synthetic community.

Recent studies have highlighted the critical roles of the microbiota in faeces, vagina and colostrum in reproductive success and piglet development. Understanding the structural and functional dynamics of these microbial communities is essential for optimizing the health and productivity of high-yielding (HY) sows. This study aimed to characterize the structural and functional features of these microbial communities in HY sows (litter size>10 piglets) vs. low-yielding (LY) sows (≤10 piglets) and to explore their associations with sow performance and piglet health. Fifteen Yorkshire sows from each group were selected, and fresh faecal, vaginal mucus and colostrum samples were collected post-parturition. Microbial composition was analysed using 16S rRNA gene amplicon sequencing, and functional potential was predicted via PICRUSt2. Results showed that HY sows exhibited higher alpha diversity in vaginal and colostrum microbiota and greater community stability (higher neutral community model R 2 values) compared to LY sows. In faeces, HY sows were enriched with Terrisporobacter and Romboutsia, while depleted in Ruminococcus_torques_group. In the vagina, Campylobacter and Peptoniphilus were increased, whereas Eubacterium_nodatum_group decreased. In colostrum, Lactobacillus, Bifidobacterium and Romboutsia were enriched, with reduced Peptostreptococcus, indicating a more beneficial profile for neonatal health. Functional predictions revealed distinct metabolic profiles: HY faecal microbiota upregulated cysteine/methionine metabolism and porphyrin and chlorophyll metabolism; vaginal microbiota enhanced oxidative phosphorylation and thiamine metabolism; colostrum microbiota showed enrichment in monobactam and novobiocin biosynthesis, which is associated with antimicrobial activity and stress response. These findings demonstrate that HY sows harbour a more stable and functionally advantageous microbiome across multiple biological niches, which may contribute to superior reproductive performance and improved offspring health. The results provide a foundation for developing microbiome-targeted strategies to enhance productivity and welfare in commercial pig production.

Background . Helicobacter pylori infection is a major risk factor for gastric cancer (GC), especially in East Asia. However, the mechanisms through which bacterial strain heterogeneity contributes to GC risk remain poorly understood. This study aims to elucidate the roles of specific virulence factors, antibiotic resistance profiles and genetic variations in H. pylori in GC development.

Methods. We integrated host clinical data with phenotypic and genomic analyses of 31 clinical H. pylori isolates. Genomic analysis was performed to determine phylogenetic lineage and virulence markers. Antibiotic susceptibility and biofilm-forming ability of the clinical isolates were also assessed, and a genome-wide association study (GWAS) was employed to identify genetic polymorphisms linked to GC risk.

Results. Among the isolates, 93.5 % of isolates belonged to the East Asian lineage and carried high-risk virulence markers (cagA EPIYA-ABD, vacA s1m1). However, multidrug resistance was observed in 64.5 % of isolates, with high resistance rates to metronidazole (71.0%) and levofloxacin (48.4%) exceeding global averages. Strong biofilm-forming strains were significantly associated with tetracycline resistance compared to weak biofilm-forming strains. Additionally, GWAS identified five SNPs significantly associated with GC risk, with variants in hemC, babB and C694_RS04850 being enriched in high-risk strains.

Conclusions. This study demonstrates the critical impact of H. pylori strain diversity in GC development, emphasizing the necessity for region-specific surveillance and innovative therapeutic strategies.

Background  . Streptococcus pneumoniae is a major human pathogen responsible for invasive pneumococcal diseases (IPDs). We utilized whole-genome sequencing to assess the impact of pneumococcal conjugate vaccines (PCVs) on the pneumococcal population causing IPD in Lebanon.

Methods. S. pneumoniae isolates collected between 2003 and 2025 (n=273) were sequenced and included in the study, which was divided into three periods. Private-PCV7 (2003–2009) and Private-PCV13 (2010–2015) correspond to the periods when the PCV7 and PCV13 vaccines were available only in the private healthcare sector, respectively. EPI-PCV13 (2016–2025) represents the period following PCV13 incorporation into the Expanded Program on Immunization (EPI). The Global Pneumococcal Sequencing (GPS) genome analysis pipeline was used to infer serotypes, genetic lineages, pilus locus and antimicrobial resistance (AMR) for 19 antibiotics. Phylogeny was constructed based on SNPs across the pneumococcal genome.

Results. A total of 58 GPS clusters (GPSCs) expressing 40 serotypes were identified. Overall, serotypes 3, 14 and 19F were the most prevalent serotypes, while GPSC6, GPSC12 and GPSC1 were the most predominant pneumococcal lineages. We detected a significant increase in non-vaccine types (NVTs) after PCV7 and PCV13 introduction. In contrast, PCV7 serotypes declined significantly over the three study periods. Collectively, PCV7 serotypes were associated with significantly higher mortality (31.1%) compared to NVT (15.9%). Moreover, IPD-associated mortality was significantly higher among older adult patients (33.3%) compared to children aged ≤5 years (12.1%). Non-susceptibility to penicillin was the most prevalent resistance (62.1%), and multidrug resistance (MDR; non-susceptibility to at least three antibiotics) was identified in 36.4% of the isolates. MDR was primarily driven by GPSC1, GPSC9, GPSC6 and GPSC10. A significant decline in MDR and AMR against seven antibiotics was observed in the EPI-PCV13 period compared to previous study periods.

Conclusions. Genomic surveillance is robust for tracking current NVT and identifying lineages that may influence future IPD trends in Lebanon. Given the high mortality rate detected in older adult IPD patients, implementing a routine immunization programme in this population may be beneficial.