Moringa oleifera, known for its nutritional and therapeutic properties, exhibits a complex relationship with its rhizospheric soil microbiome. This study aimed to elucidate the microbiome's structural composition, molecular functions, and its role in plant growth by integrating Clusters of Orthologous Genes (COG) analysis with enzymatic functions previously identified through KEGG, CAZy, and CARD databases. Metagenomic sequencing and bioinformatics analysis were performed from the rhizospheric soil microbiome of M. oleifera collected from the Mecca district in Saudi Arabia. The analysis revealed a role for the rhizospheric microbiome in energy production, storage, and regulation, with glucose serving as a crucial precursor for NADH synthesis and subsequent ATP production via oxidative phosphorylation. Key orthologous genes (OGs) implicated in this process include NuoD, NuoH, NuoM, NuoN, NuoL, atpA, QcrB/PetB, and AccC. Additionally, OGs involved in ATP hydrolysis, such as ClpP, EntF, YopO, and AtoC, were identified. Taxonomic analysis highlighted Actinobacteria and Proteobacteria as the predominant phyla, with enriched genera including Blastococcus, Nocardioides, Streptomyces, Microvirga, Sphingomonas, and Massilia, correlating with specific OGs involved in ATP hydrolysis. This study provides insights into the molecular mechanisms underpinning plant–microbe interactions and highlights the multifaceted roles of ATP-dependent processes in the rhizosphere. Further research is recommended to explore the potential applications of these findings in sustainable agriculture and ecosystem management.

Groundwater microbial communities exhibit pronounced vertical and spatial structuring driven by physicochemical gradients. Here, we investigated microbial assemblages across surface and subsurface layers of three groundwater wells distributed along a 1.26 km transect in the Wadi Awja aquifer system (Jeddah, Saudi Arabia) using high-throughput 16S rRNA gene amplicon sequencing. Across all samples, Pseudomonadota (Proteobacteria) dominated community composition, accounting for ~50–65% of surface assemblages and increasing to ~90% in deeper strata, indicating strong vertical selection. This depth-associated enrichment coincided with reduced community evenness and the prevalence of metabolically versatile, facultatively anaerobic taxa. Although Actinomycetota, Bacteroidota, and Planctomycetota contributed substantially to overall diversity, their relative abundances declined with depth, reinforcing the dominance of Proteobacteria under suboxic conditions. Notably, members of Enterobacteriaceae, particularly Escherichia spp., were consistently enriched in deeper layers, coinciding with simplified community structures. Collectively, these results demonstrate that groundwater microbial communities undergo sharp redox-associated ecological transitions over short spatial scales, emphasizing the role of localized hydrogeochemical heterogeneity in shaping subsurface microbial assemblages.

The core anaerobic component of the human microbiome plays a critical role in preserving the overall structure and function of the microbiome. However, how these core strains interact with each other and with other gut microbes is largely unknown. We employed a modified culturomics approach to selectively culture these core genera from the human gut and provided a snapshot into their ecological interactions, clinically relevant resistome, and whole genome sequence (WGS)-based insights into their observed phenotypes. This strategy successfully isolated representatives of the targeted 21 core genera, with some isolates reported for the first time. Cross-interactions and resistome-based profiling revealed important insights. Out of the 440 interaction assessments, a significant proportion exhibited either cooperative or competitive effects on other core genera. Interestingly, Bacteroides thetaiotaomicron displayed dual roles, inhibiting potential pathogens while enhancing the growth of beneficial probiotic strains. Moreover, resistome profiling revealed variable resistance and susceptibility toward various antibiotics. WGS analysis revealed the ability of the selected organism to produce metabolites consistent with the observed phenotype. Our unique culturomics approach successfully isolated key anaerobic genera and revealed their complex interdependencies and clinically relevant resistance. Furthermore, our approach lays the foundation for exploring larger-scale microbial community dynamics in terms of interdependencies and for assessing how clinically significant antibiotics impact the key microbiome, something that may be important when making therapy decisions. In summary, our research improves our knowledge of the interactions present among core gut microorganisms and hints at possible mechanisms responsible for sustaining gut microbial homeostasis and rehabilitation. IMPORTANCE: This study presents a unique strategy for the targeted isolation and characterization of key interaction dynamics as well as the resistome of core anaerobic bacteria in the healthy human gut. By utilizing this targeted single, optimized core anaerobe-specific growth medium approach, we were able to culture a major proportion of the core anaerobic gut species, where some of those were cultured for the first time. Through the combinatorial approach of cross-interaction, antimicrobial resistance profiling, and whole genome sequencing (WGS) resolved functional insights, we uncovered interesting insights into interdependencies and competition among these core strains as well as their ecological flexibilities. Moreover, we observed that some strains, such as Bacteroides thetaiotaomicron and Bifidobacterium angulatum, are capable of either inhibiting or promoting the growth of certain strains, depending on the pairing. Such findings go against the traditional binary view of microbes as being purely commensal or pathogenic and suggest that microbial behavior is highly context-dependent. Furthermore, WGS analysis provided useful insights into the potential genomic basis of the observed phenotype. Taken together, our findings provide valuable data and enhance our current understanding of how core anaerobes interact with each other, survive, and adapt within the gut environment. Moreover, our work also lays the critical basis for a more rational design of synthetic microbial communities as well as precision-based microbiome aimed at targeted gut health rehabilitation, both with accuracy and sensitivity.

Mosquito-borne diseases pose significant public health challenges, necessitating inno-vative and sustainable control measures. This study evaluates the larvicidal potential of six extremophile Bacillus species against Aedes aegypti larvae, focusing on dose-response relationships, resistance trends, and genetic diversity. Regression analy-sis revealed a significant positive correlation between concentration and larval mortal-ity across species, with B. sonorensis and B. paramycoides demonstrating superior po-tency at lower concentrations (LC₅₀: 19.72 ppm and 23.41 ppm, respectively). Probit analysis confirmed that B. sonorensis is the most effective larvicide, achieving high mortality rates with minimal concentrations. In contrast, B. licheniformis and B. ster-coris exhibited limited efficacy, requiring significantly higher doses to achieve compa-rable results. Resistance analysis highlighted an inverse relationship between toxicity index and resistance ratio, with B. sonorensis maintaining high efficacy even in re-sistant mosquito populations (Resistance Ratio: 1). Furthermore, phylogenetic analysis based on 16S rRNA gene sequences revealed distinct evolutionary relationships among species, with B. rugosus and B. tequilensis clustering closely, suggesting functional similarities. The genetic divergence of B. licheniformis aligns with its lower larvicidal performance. Overall, this study underscores the potential of B. sonorensis and B. paramycoides as robust candidates for mosquito control programs, particularly in re-sistance-prone environments. The findings provide valuable insights into optimizing microbial larvicides by tailoring species-specific application strategies and leveraging genetic diversity within the Bacillus genus.

Abutilon fruticosum is an ecologically and pharmacologically important wild Malvaceae species whose rhizospheric microbiome remains poorly resolved at the level of orthologous-group (OG) genes. Shotgun metagenomic sequencing and eggNOG/COG-based annotation were used to compare rhizosphere and bulk-soil microbiomes, quantify OG repertoires, and infer in silico functional modules. Principal coordinate and Bray-Curtis analyses of COG categories revealed clear functional segregation between rhizosphere and bulk communities, with the rhizosphere enriched in high-abundance OGs linked to energy metabolism, nutrient transport, stress response, and secondary metabolism. Computational ranking identified a cohort of highly recurrent OGs, predominantly associated with Actinobacteria and Proteobacteria but also with Streptophyta, that dominate the predicted functional landscape and are markedly more abundant in silico in rhizospheric soil. Using eggNOG/COG assignments, ten interacting putative functional modules were delineated in silico, encompassing NADH-quinone oxidoreductase-centered bioenergetics, ABC-type nitrogen and sulfur acquisition, fatty-acid and propionate catabolism, sulfur scavenging and detoxification, cell-envelope and biofilm formation, multidrug efflux, DNA maintenance, environmental sensing and transcriptional regulation, specialized competition/protection, and mobile genetic elements. Conceptual, hypothesis-generating frameworks integrating selected modules posit that rhizosphere dominance could arise from the coordinated coupling of ATP/proton motive force (PMF) generation with high-affinity nutrient uptake, sulfur and carbonyl detoxification, iron-sequestering and antioxidant secondary metabolism, and stress-responsive multidrug efflux, based on our analyses. These predictions suggest that specific OG cohorts act as keystone energetic, metabolic, and defense hubs in the A. fruticosum rhizosphere and provide testable hypotheses for future experimental work linking module-level functions to root colonization, stress tolerance, and plant performance. (249 words).