Ahmed A. Shibl

Background/Objectives: Wastewater-based antimicrobial resistance (AMR) surveillance typically relies on treatment plant influent as a single integrated matrix, obscuring source-specific signals. In arid settings where treated effluent is reused, understanding how resistomes and virulomes are structured across wastewater compartments is essential for One Health monitoring. Methods: Shotgun metagenomic sequencing was applied to 57 wastewater samples collected in Dubai, United Arab Emirates, between October 2024 and January 2025. Samples represented nine community sewer nodes, two tertiary-care hospital outflows, and influent and effluent from two wastewater treatment plants (WWTP). Datasets were used for taxonomic, resistome, and virulome profiling. Alpha diversity was compared using Wilcoxon rank-sum tests, beta-diversity differences were assessed using permutational multivariate analysis of variance, and source-associated AMR genes were identified using linear discriminant analysis effect size analysis. Results: A total of 1470 bacterial species, 822 antimicrobial resistance genes (ARGs), and 1554 virulence factor genes were identified. Bacterial diversity was significantly lower in WWTP effluent than in other compartments. Hospital wastewater was enriched for class D β-lactamases, including multiple bla_OXA variants, whereas community wastewater and WWTP influent shared dominant macrolide and aminoglycoside resistance genes including msr(E), mph(E), strB and aadA1. Despite marked reductions in bacterial diversity after treatment, no significant difference in ARG diversity was observed between WWTP influent and WWTP effluent (p = 0.558), with resistance genes such as bla_VEB, msr(E), mph(E) detected in the latter. Virulome profiles shifted from fimbrial gene dominance in untreated sources toward biofilm- and persistence-associated genes in WWTP effluent. ARG alpha diversity varied over time, whereas taxonomic and virulome diversity remained stable. Conclusions: Community and influent wastewater capture population-level AMR carriage, hospital outflows concentrate clinically relevant resistance determinants, and WWTP effluent retains resistance markers despite microbial biomass reduction. Compartment-resolved metagenomic surveillance provides a practical One Health framework for identifying high-value monitoring points.

Background: Wastewater systems provide an integrated One Health perspective on antimicrobial resistance but remain uneven globally, with limited data from rapidly urbanizing and highly connected regions such as the Arabian Gulf. Methods: An eight-month prospective study was conducted in Dubai, United Arab Emirates, with monthly sampling from nine community and two hospital nodes and two wastewater treatment plants (WWTP). Samples were analysed using high-throughput quantitative PCR (HT-qPCR; Resistomap, Finland) with a 72-target One Health gene panel. Results: Across the 120 samples analyzed, the number of detected gene targets ranged from 26 to 68 genes, with the highest diversity in hospital wastewater and the lowest in WWTP effluent. Pathogen-associated markers were detected in all sources, with enterococci, Escherichia coli, and Klebsiella pneumoniae predominant. Hospital wastewater showed broader pathogen-associated gene markers, including those linked to Acinetobacter baumannii and Pseudomonas aeruginosa. Antibiotic resistance genes (ARGs) associated with macrolide–lincosamide–streptogramin B, tetracycline, and aminoglycoside resistance were widespread. Community and influent samples were dominated by msrE, tet(M), and aminoglycoside resistance genes, whereas hospital wastewater showed the highest ARG burden, including enrichment of aac(6′)-Ib, qnrS2, bla_GES, bla_TEM, bla_KPC-2, and bla_IMP-1. Several ARGs, including mcr-1, persisted in WWTP effluent. Mobile genetic elements (MGEs) were ubiquitous, with integron-associated markers prominent in WWTP effluent. ARG–MGE network analysis demonstrated extensive co-occurrence, with MGEs as central hubs linking multiple ARGs. Conclusions: Wastewater captures distinct resistome profiles across urban compartments, supporting its role for AMR surveillance. The persistence of ARGs and MGEs in WWTP effluent highlights the potential for environmental dissemination, through reuse of treated wastewater.

Wastewater-based surveillance (WBS) is valuable for monitoring antimicrobial resistance (AMR). Staphylococci are key targets, as wastewater can facilitate gene transfer and resistance emergence. Data on WBS for population-level AMR in the Arabian-Gulf remain limited. This study assessed Staphylococcus diversity and resistance in Dubai wastewater. Samples were collected over eight months from nine community sites, two hospital nodes, and two wastewater treatment plants (WWTPs) and were analysed by culture-based method. Ninety-six Staphylococcus isolates were recovered from community, hospital, and WWTP influent, with no growth in effluent. Most isolates (n/N = 88/96) were coagulase-negative Staphylococcus (CoNS), spanning 15 species, dominated by S. saprophyticus, S. cohnii and S. sciuri. The only coagulase-positive Staphylococcus was S. aureus (n = 8) and the only species detected across all wastewater sources. Resistance was highest to benzylpenicillin (88%) and fusidic acid (82%), whereas all isolates remained susceptible to glycopeptides, tigecycline, and linezolid. Fusidic acid resistance was higher in community-wastewater isolates, whereas β-lactam resistance predominated in hospital-wastewater isolates. Sixty percent of CoNS were multidrug-resistant; methicillin resistance occurred in 37.5% of CoNS and 50% of S. aureus. Wastewater is a reservoir of diverse multidrug-resistant staphylococci, underscoring One Health relevance reflecting the potential for circulation between humans, animals, and the shared environment. WBS can support population-level AMR monitoring to inform public health and veterinary interventions.

Obesity is a major global health challenge and a leading risk factor for cardiometabolic disorders. The global surge in obesity, driven by industrialization and the widespread consumption of low-fiber, ultra-processed food, highlights an urgent need for deeper biological insights. While the gut microbiome has been studied in the context of obesity, the contribution of the oral microbiome—the second largest microbial ecosystem in the human body–remains largely underexplored. Here, we report findings from a deeply-phenotyped prospective-cohort of 628 Emirati adults, leveraging amplicon sequencing of mouthwash samples and multi-omics profiling and functional and metabolic activity analysis of 97 obese individuals and 95 matched controls, making this the most comprehensive multi-omics analysis of the oral microbiome. We identified significant differences in oral microbial diversity, composition, functional pathways, and metabolic profiles between obese and non-obese groups. Integrated multi-omics analysis of the 192 matched metagenomes and metabolome samples uncovered significant metabolic reprogramming and altered energy regulation in obesity. Specifically, the oral microbiome of obese participants were enriched for the proinflammatory Streptococcus parasanguinis and Actinomyces oris, and the lactate-producing Oribacterium sinus. Many microbial pathways involved in dietary carbohydrate metabolism, histidine degradation, as well as the production of obesogenic biomolecules were also enriched in obese participants; however, B-vitamin and heme production pathways were depleted. Consequently, metabolites resulting from these pathways such as lactate, histidine derivatives, choline, uridine, and uracil were elevated in obesity. These consistent microbiome-metabolite shifts were strongly associated with prominent obesity-associated cardiometabolic markers, including serum triglycerides and alkaline phosphatases, establishing a robust link between oral microbiome and obesity. These findings provide the most comprehensive insights into how disrupted microbial-metabolic cross-talk in the oral cavity may contribute to obesity and related cardiometabolic disease risk, underscoring the potential of targeting of oral microbiome-host interactions as a novel avenue for obesity prevention and intervention.

Background Lifestyle plays an important role in shaping the gut microbiome. However, its contributions to the oral microbiome remains less clear, due to the confounding effects of geography and methodology in investigations of populations studied to date. Furthermore, while the oral microbiome seems to differ between foraging and industrialized populations, we lack insight into whether transitions to and away from agrarian lifestyles shape the oral microbiota. Given the growing interest in so-called ‘vanishing microbiomes’ potentially being a risk factor for increased disease prevalence in industrialized populations, it is important that we distinguish lifestyle from geography in the study of microbiomes across populations. Results Here, we investigate salivary microbiomes of 63 Nepali individuals representing a spectrum of lifestyles: foraging, subsistence farming (individuals that transitioned from foraging to farming within the last 50 years), agriculturalists (individuals that have transitioned to farming for at least 300 years), and industrialists (expatriates that immigrated to the United States within the last 20 years). We characterize the role of lifestyle in microbial diversity, identify microbes that differ between lifestyles, and pinpoint specific lifestyle factors that may be contributing to differences in the microbiomes across populations. Contrary to prevailing views, when geography is controlled for, oral microbiome alpha diversity does not differ significantly across lifestyles. Microbiome composition, however, follows the gradient of lifestyles from foraging through agrarianism to industrialism, supporting the notion that lifestyle indeed plays a role in the oral microbiome. Relative abundances of several individual taxa, including Streptobacillus and an unclassified Porphyromonadaceae genus, also mirror lifestyle. Finally, we identify specific lifestyle factors associated with microbiome composition across the gradient of lifestyles, including smoking and grain source. Conclusion Our findings demonstrate that by controlling for geography, we can isolate an important role for lifestyle in determining oral microbiome composition. In doing so, we highlight the potential contributions of several lifestyle factors, underlining the importance of carefully examining the oral microbiome across lifestyles to improve our understanding of global microbiomes.

Photosynthetic eukaryotes, such as microalgae and plants, foster fundamentally important relationships with their microbiome based on the reciprocal exchange of chemical currencies. Among these, the dicarboxylate metabolite azelaic acid (Aze) appears to play an important, but heterogeneous, role in modulating these microbiomes, as it is used as a carbon source for some heterotrophs but is toxic to others. However, the ability of Aze to promote or inhibit growth, as well as its uptake and assimilation mechanisms into bacterial cells are mostly unknown. Here, we use transcriptomics, transcriptional factor coexpression networks, uptake experiments, and metabolomics to unravel the uptake, catabolism, and toxicity of Aze on two microalgal-associated bacteria, Phycobacter and Alteromonas, whose growth is promoted or inhibited by Aze, respectively. We identify the first putative Aze transporter in bacteria, a ‘C₄-TRAP transporter’, and show that Aze is assimilated through fatty acid degradation, with further catabolism occurring through the glyoxylate and butanoate metabolism pathways when used as a carbon source. Phycobacter took up Aze at an initial uptake rate of 3.8×10^–9 nmol/cell/hr and utilized it as a carbon source in concentrations ranging from 10 μM to 1 mM, suggesting a broad range of acclimation to Aze availability. For growth-impeded bacteria, we infer that Aze inhibits the ribosome and/or protein synthesis and that a suite of efflux pumps is utilized to shuttle Aze outside the cytoplasm. We demonstrate that seawater amended with Aze becomes enriched in bacterial families that can catabolize Aze, which appears to be a different mechanism from that in soil, where modulation by the host plant is required. This study enhances our understanding of carbon cycling in the oceans and how microscale chemical interactions can structure marine microbial populations. In addition, our findings unravel the role of a key chemical currency in the modulation of eukaryote-microbiome interactions across diverse ecosystems.

Photosynthetic eukaryotes, such as microalgae and plants, foster fundamentally important relationships with their microbiome based on the reciprocal exchange of chemical currencies. Among these, the dicarboxylate metabolite azelaic acid (Aze) appears to play an important, but heterogeneous, role in modulating these microbiomes, as it is used as a carbon source for some heterotrophs but is toxic to others. However, the ability of Aze to promote or inhibit growth, as well as its uptake and assimilation mechanisms into bacterial cells are mostly unknown. Here, we use transcriptomics, transcriptional factor coexpression networks, uptake experiments, and metabolomics to unravel the uptake, catabolism and toxicity of Aze on two microalgal-associated bacteria, Phycobacter and Alteromonas, whose growth is promoted or inhibited by Aze, respectively. We identify the first putative Aze transporter in bacteria, a ‘C4-TRAP transporter’, and show that Aze is assimilated through fatty acid degradation, with further catabolism occurring through the glyoxylate and butanoate metabolism pathways when used as a carbon source. Phycobacter took up Aze at an initial uptake rate of 3.8×10-9 nmol cell-1 hr-1 and utilized it as a carbon source in concentrations ranging from 10 μM-1 mM, suggesting a broad range of acclimation to Aze availability. For inhibited bacteria, we infer that Aze inhibits the ribosome and/or protein synthesis and that a suite of efflux pumps is utilized to shuttle Aze outside the cytoplasm. We demonstrate that seawater amended with Aze becomes enriched in bacterial families that can catabolise Aze, which appears to be a different mechanism from that in soil, where modulation by the host plant is required. This study enhances our understanding of carbon cycling in the oceans and how microscale chemical interactions can structure marine microbial populations. In addition, our findings unravel the role of a key chemical currency in the modulation of eukaryote-microbiome interactions across diverse ecosystems.

Prochlorococcus play a crucial role in the ocean's biogeochemical cycling, but it remains controversial how they will respond to global warming. Here we assessed the response to temperature (22–30°C) of the growth dynamics and gene expression profiles of a Red Sea Prochlorococcus strain (RSP50) in a non‐axenic culture. Both the specific growth rate (0.55–0.80 day ⁻¹ ) and cell size (0.04–0.07 μm ³ ) of Prochlorococcus increased significantly with temperature. The primary production released extracellularly ranged from 20% to 34%, with humic‐like fluorescent compounds increasing up to fivefold as Prochlorococcus reached its maximum abundance. At 30°C, genes involved in carbon fixation such as CsoS2 and CsoS3 and photosynthetic electron transport including PTOX were downregulated, suggesting a cellular homeostasis and energy saving mechanism response. In contrast, PTOX was found upregulated at 22°C and 24°C. Similar results were found for transaldolase, related to carbon metabolism, and citrate synthase, an important enzyme in the TCA cycle. Our data suggest that in spite of the currently warm temperatures of the Red Sea, Prochlorococcus can modulate its gene expression profiles to permit growth at temperatures lower than its optimum temperature (28°C) but is unable to cope with temperatures exceeding 30°C.

The gut microbiome is increasingly being appreciated as a master regulator of animal health. However, most avian gut microbiome studies have focused on birds of economic importance while the gut microbiomes of raptors remain underexplored. Here we examine the gut microbiota of 29 samples from four Falco species including hybrid birds— raptors of historic importance —in the context of avian evolution by sequencing the 16S rDNA V4 region. Our results reveal that evolutionary histories and diet are significantly associated with avian gut microbiota in general, whereas diet plays a major role in shaping the falcon gut microbiota. Multiple analyses revealed that gut microbial diversity, composition, and abundance of key diet-discriminating bacterial genera in the falcon gut closely resemble those of carnivorous raptors rather than those of their closest phylogenetic relatives. Furthermore, the falcon microbiota is dominated by Firmicutes and consists of Salmonella at appreciable levels. Salmonella presence may potentially alter the functional capacity of the falcon gut microbiota as its abundance is associated with depletion of multiple predicted metabolic pathways involved in protein mass buildup, muscle maintenance, and enrichment of antimicrobial compound degradation, thus increasing the pathogenic potential of the falcon gut and presents a potential risk to human health. Author Summary in Arabic:

Photosynthetic eukaryotes, such as microalgae and plants, foster fundamentally important relationships with their microbiome based on the reciprocal exchange of chemical currencies. Among these, the dicarboxylate metabolite azelaic acid (Aze) appears to play an important, but heterogeneous, role in modulating these microbiomes, as it is used as a carbon source for some heterotrophs but is toxic to others. However, the ability of Aze to promote or inhibit growth, as well as its uptake and assimilation mechanisms into bacterial cells are mostly unknown. Here, we use transcriptomics, transcriptional factor coexpression networks, uptake experiments, and metabolomics to unravel the uptake, catabolism and toxicity of Aze on two microalgal-associated bacteria, Phycobacter and Alteromonas , whose growth is promoted or inhibited by Aze, respectively. We identify the first putative Aze transporter in bacteria, a ‘C ₄ -TRAP transporter’, and show that Aze is assimilated through fatty acid degradation, with further catabolism occurring through the glyoxylate and butanoate metabolism pathways when used as a carbon source. Phycobacter took up Aze at an initial uptake rate of 3.8×10 ^-9 nmol cell ^-1 hr ^-1 and utilized it as a carbon source in concentrations ranging from 10 μM ^-1 mM, suggesting a broad range of acclimation to Aze availability. For inhibited bacteria, we infer that Aze inhibits the ribosome and/or protein synthesis and that a suite of efflux pumps is utilized to shuttle Aze outside the cytoplasm. We demonstrate that seawater amended with Aze becomes enriched in bacterial families that can catabolise Aze, which appears to be a different mechanism from that in soil, where modulation by the host plant is required. This study enhances our understanding of carbon cycling in the oceans and how microscale chemical interactions can structure marine microbial populations. In addition, our findings unravel the role of a key chemical currency in the modulation of eukaryote-microbiome interactions across diverse ecosystems.