FEMS Microbes

Background: Dental caries is increasingly understood as an ecological biofilm disorder rather than the consequence of a single organism. Although Streptococcus mutans is strongly implicated in cariogenesis, it remains unclear whether caries-associated plaque-community differences persist beyond this organism. Methods: We reanalysed publicly available supragingival-plaque 16S rRNA sequencing data from 88 preschool children with rampant caries (n=44) or who were caries-free (n=44; BioProject PRJNA1141721). Single-end DADA2 processing yielded 25,669 amplicon sequence variants (ASVs), including one ASV confirmed as S. mutans by an eHOMD reference-window procedure. The pre-specified primary analysis compared Bray-Curtis community composition after exclusion of this ASV. Results: Non-S. mutans community composition differed between groups (PERMANOVA pseudo-R2=0.0462, pseudo-F=4.16, P<0.001), without evidence of unequal multivariate dispersion (P=0.796); rarefaction produced a nearly identical result. Shannon diversity did not differ (P=0.486). The confirmed S. mutans ASV was detected in 8/44 rampant-caries and 42/44 caries-free samples and was lower in abundance in rampant caries. Among 758 prevalence-filtered non-S. mutans ASVs, 239 showed conventional FDR-significant differential abundance, with more showing lower than higher bias-corrected abundance in rampant caries (176 versus 63); 239 additional ASVs were classified as structural zeros. Individual ASV findings were sensitive to prevalence filtering. Adjustment for S. mutans abundance attenuated the global caries-group association (marginal pseudo-R2=0.0149, P=0.085) in the presence of strong collinearity. Conclusions: Rampant caries was associated with modest but reproducible plaque-community restructuring after exclusion of a confirmed S. mutans ASV, without a corresponding Shannon-diversity difference. These findings support a community-level ecological interpretation but do not establish statistical independence from S. mutans or a causal role for individual taxa.

Microbial communities in indoor environments are shaped by resource availability and disturbances, yet their growth dynamics and compositional changes remain unclear. Here we combined quantitative colony growth analysis with 16S rRNA gene sequencing to investigate bacterial communities on public restroom surfaces before and after routine cleaning under varied nutrient conditions. Cultivation revealed that nutrient availability strongly influenced bacterial growth and selectively enriched distinct taxa, while cleaning caused limited shifts in overall community structure and diversity. Correlations between growth parameters and diversity indices were weak, indicating that taxon-specific responses to nutrients primarily drive growth outcomes. These findings suggest that resource composition, rather than cleaning disturbance, governs bacterial growth and community assembly in built environments. Integrating culture-based phenotyping with sequencing provides a comprehensive framework to understand microbial dynamics following environmental perturbations.

Abstract The upper respiratory tract (URT) microbiome plays a vital role in respiratory health, with older children (5-14 years old) serving as key reservoirs for the transmission of bacteria to younger individuals (< 5 years old). However, the URT microbiome in this age group remains poorly characterised, particularly in relation to colonisation by the pathobiont Streptococcus pneumoniae. To address this gap, we analysed URT samples collected over eight visits from 134 healthy children aged 5-14 years in The Gambia, using culture-dependent methods to detect S. pneumoniae and culture-independent 16S rRNA sequencing to characterise the microbiome in parallel. 16S rRNA sequencing identified Streptococcus and Prevotella as the dominant microbiome constituents. When integrating longitudinal sampling data, we observed temporal instability with frequent switches in microbiome profiles over time. URT samples colonised with S. pneumoniae were associated with increased abundance of Moraxella, Streptococcus and Haemophilus, whereas non-colonised URT samples were enriched with Granulicatella and Filifactor. S. pneumoniae colonisation was also associated with lower Shannon diversity compared with non-colonised samples. Age and season were the strongest determinants of microbiome composition; increasing age was associated with decreasing prevalence and abundance of taxa including Haemophilus and Moraxella, while gram-positive taxa were predominantly enriched in the dry season. These findings provide new insight into the URT microbiome of older children in The Gambia and highlight Granulicatella and Filifactor as potential contributors to colonisation resistance against S. pneumoniae.

Microbial-mediated plastic degradation has the potential to address the persistent global problems of plastic waste and pollution. Previous work has shown that soils can harbour microbes capable of plastic degradation, but we expect there is a broader diversity of soil microbes capable of metabolizing plastics than identified to date using more traditional cultivation-based screening methods. Here we demonstrate a novel approach to identify putative plastic degrading microbes in soil. We paired in situ, real-time measurements of microbial plastic degradation on conductive sensors with subsequent microbial community profiling of the sensor-associated biofilms exhibiting appreciable degradation. To illustrate the utility of our approach, we focus on microbial degradation of the bioplastic polymer PHBV, poly(3-hydroxybutuyrate-co-3-hydroxyvalerate). We screened a range of soils with the in situ sensors to identify a subset of five soils with high PHBV degradation rates, and confirmed that PHBV degradation was due to microbial activity. We then extracted DNA directly from sensors placed in soils with high measured rates of PHBV degradation and used marker gene sequencing to identify the bacterial and fungal taxa associated with the observed PHBV degradation. We confirmed via in vitro culturing that microbes isolated from the sensors have a demonstrated capacity for PHBV metabolism. Together, these results highlight the benefit and feasibility of using low-cost, in-soil sensors to simultaneously collect real-time data on plastic degradation rates in soil and identify previously unrecognized microbial taxa capable of degrading and metabolizing plastic polymers in situ.

Abstract Background: Soil microbiomes play critical roles in plant health and resilience, yet it is still poorly understood how disruptions in local microbial communities, such as during soil management, impact these ecological functions. In this study, we investigated how compost addition, a widely used soil management practice, and microbiome origin influence microbiome-mediated plant resistance to insects. We combined surveys of working organic farms across New York with controlled laboratory experiments, amplicon sequencing, plant-insect bioassays, and mass spectrometry. Results: Compost use was associated with shifts in the relative abundance of 20 fungal and 2 bacterial genera across ten working farms. However, no consistent changes in bacterial or fungal diversity or community structure in fields with compost were observed across the farms. Under controlled conditions using a common compost source, compost increased rhizosphere microbial diversity and significantly altered rhizosphere community structure, including the relative abundance of 6 fungal and 41 bacterial genera. Despite these substantial community-level changes, compost did not affect populations of green peach aphids (Myzus persicae) on kale (Brassica oleracea). Instead, aphid populations and plant salicylic acid concentrations were more strongly associated with microbiome origin, demonstrating that compost can substantially restructure soil and rhizosphere microbial communities without corresponding changes in microbiome-mediated plant resistance to insects. Conclusions: Our findings demonstrate that microbial diversity and compositional responses to management are not necessarily reliable indicators of all microbiome functions. More broadly, this work highlights the importance of local soil microbiome variation in shaping plant-insect interactions and emphasizes the need to link community-level responses to direct functional measurements when evaluating microbiome responses to agricultural management.

Multiple external factors shape human microbial communities. Beverages represent particularly frequent dietary exposures that may impact oral microbiome composition. We examined associations of coffee, tea, alcohol, sugar-sweetened beverages, artificially-sweetened beverages, and fruit juice consumption with the oral microbiome in three large cohort studies (n=5,598). Beverage consumption was assessed by food frequency questionnaire and categorized as non-consumers and tertiles of intake among consumers, except fruit juice, which was categorized into quartiles. DNA from oral wash specimens was sequenced (16S rRNA, V4 region). Associations with alpha and beta diversity and individual genera were assessed using multivariable linear, logistic, count-based regression models and weighted permutation-based models accounting for multiple comparisons in genus-level analyses. Only alcoholic beverage consumption was associated with all alpha diversity metrics; the highest tertile of alcohol drinking was associated with 10.18 (95% CI: 5.56, 14.80) greater observed amplicon sequence variants vs. non-consumers. All beverages accounted for 4.06% of variability in beta diversity (unweighted UniFrac); in univariable models, alcoholic beverages had the largest R2 among individual beverages (0.86%) and accounted for the majority (25/28, 89.3%) of genus-level associations, mostly with beer and liquor. For example, high alcoholic beverage intake (T3 vs. non-consumers) was associated with 2.25 and 2.17 times the odds of having Megasphaera and Peptostreptococcus, respectively, and 23% lower abundance of Lautropia. Alcoholic beverage consumption was strongly associated with oral microbes, including taxa linked to poor oral health; these findings suggest that alcohol-associated differences in the oral microbiome may have implications for oral and systemic health.

Introduction: Protease activated receptor (PAR2) is a prominent sensor of environmental and microbial proteases and may serve as an important interface between the host epithelium and mucosal microbes. However, whether PAR2 helps shape microbial community structure and function at barrier surfaces remains unclear. To address this, we examined how PAR2 deficiency or activation affects microbial composition and metabolic potential across the gut lumen, airway lumen, and lung tissue in the context of exposure to protease-rich house dust mite allergen (HDM) exposure. Methods: Wild type and PAR2 deficient littermates of both sexes received a single intranasal challenge with phosphate buffered saline, HDM extract, or a selective PAR2 agonist. Microbial communities from feces, bronchoalveolar lavage fluid (BALF), and lung tissue were profiled using 16S rRNA gene sequencing and PICRUSt2 based functional inference to assess compartment specific taxonomic and metabolic responses. Results: Alpha and beta diversity remained stable across all experimental groups, but distinct conditions resulted in compartment specific remodeling of the microbial population. At baseline, PAR2 deficiency altered multiple genera in the gut and lung and shifted predicted pathways linked to amino acid, lipid, and sulfur metabolism. HDM induced broad taxonomic and functional changes in the gut and lung tissue, including shifts in coenzyme A biosynthesis, reductive TCA activity, lysine fermentation, and nucleotide biosynthesis, while producing only limited taxonomic changes in BALF. PAR2 signaling accounted for a substantial portion of HDM driven remodeling, and direct PAR2 activation reproduced many compartment specific effects, including mucin derived sugar degradation in the gut and suppression of nucleotide biosynthesis in the lung. Sex moderately modified microbial and metabolic responses, with males and females exhibiting divergent, condition dependent functional biases across gut and lung. Conclusion: These findings identify PAR2 as a mucosal niche modifying receptor whose activation or loss reshapes microbial composition and metabolic potential along the gut-lung axis.

The role of bioaerosols in the transmission of pathogens and antimicrobial resistance (AMR) is of increasing clinical importance, particularly in settings housing vulnerable populations. Air filtration (e.g. HEPA filtration) and ventilation (e.g. minimum air changes per hour) measures are designed to restrict the airborne transmission of microorganisms. Despite these measures, airborne transmission remains a persistent issue in hospitals, workplaces, aged care, and schools, and is not typically assessed in routine surveillance for infection prevention. Here, we evaluated the efficacy of a high-volume air sampling approach to capture the indoor 'aerobiome', and investigated the potential for bioaerosols to mediate disease and AMR transmission in workplace and hospital settings. Our sampling approach demonstrates the benefits of simple decontamination procedures and personal protective equipment on the ability to distinguish genuine low biomass signals in air samples from blank controls, enabling reliable and sensitive microbial detection down to a limit of 69 bacterial cells/m3 of air. In a workplace bathroom setting, increased airborne biomass was strongly associated with human activity. This diminished significantly after a few hours of no activity, yet persisted in the indoor environment, with viable identical bacterial strains recovered from bioaerosols and bathroom surfaces across months of sampling. Applying our approach in a hospital ward, air samples from occupied patient rooms were not distinguishable from blank controls and contained negligible fungal and bacterial content, with only trace contributions from human occupancy. Our findings indicate that air filtration measures in this ward are effective at minimising airborne risks, but periodic testing of high-risk areas may be valuable in indoor settings with greater human traffic and may contribute key information to outbreak investigations.

RationaleLung cancer is the leading cause of cancer-related death globally, and rising incidence among traditionally low-risk individuals intensifies the need for improved early-detection methods that the lower-airway microbiome may inform. ObjectivesTo evaluate how respiratory tract sampling method shapes inferred microbiome structure, and whether bronchial brushing recovers a microbial community ecologically distinct from BAL and oral rinse. MethodsProspective cohort of 33 participants (8 lung cancer, 25 non-cancer controls) underwent oral rinse, bilateral bronchoalveolar lavage (BAL), and bronchial brushing. Microbiome structure was characterized by small subunit ribosomal rRNA gene amplicon sequence variant (ASV) profiling, with indicator-species analysis and SPIEC-EASI correlation-network mapping used to identify ASVs associated with sample type or cancer status. Measurements and Main ResultsSampling method was the dominant axis of variation. BAL communities closely resembled oral rinse (65 jointly indicative ASVs; none shared with brushing), whereas bronchial brushing yielded a distinct but low-biomass signal. After excluding host-derived sequences, two brush-specific indicator ASVs affiliated with Sphingomonadaceae and an uncultured Steroidobacteraceae were identified that co-localized within a single co-occurrence module. Cancer-status effects were not detectable in this pilot cohort, consistent with limited statistical power. ConclusionsSampling method is the primary determinant of inferred respiratory microbiome structure. Bronchial brushing recovers a distinct but low-biomass signal that is obscured when BAL is used in isolation. However, overlap between this low-biomass signal with host and contaminant sequences indicates that confidently resolving a discrete lower-airway community will require deeper sequencing and dedicated contamination controls. These methodological findings directly inform the design of future cancer-and disease-association studies.

Antimicrobial resistance (AMR) in soils frequently arises from low-level antibiotic presence in agriculture systems where livestock receive antibiotics for disease prevention. Here we assess the influence of oak (Quercus robur) wood biochar (pyrolysis at 7600C) on the microbiome of a parkland soil, after 300 days of incubation, in the presence and absence of the antibiotic sulphamethazine (SMZ). Stable isotope probing coupled to metagenomics was carried out to identify metabolically active microorganisms and quantify antimicrobial resistance gene (ARG) prevalence. Across all treatments, Pseudomonadota and Actinobacteriota dominated (63-78%), with Pseudomonadota enriched in the biologically active heavy water fraction. Gemmatimonadota increased, and Bacillota decreased in heavy fractions, while minor phyla displayed variable shifts. Biochar significantly reduced ARG prevalence in the active heavy water metagenome from 23,485 ARGs in control soils to 10,002 ARGs in biochar-amended soils, while SMZ alone increased to 26,193 ARGs found in their metagenome. Combined biochar and SMZ treatment resulted in lower ARGs (16,890 ARGs) than both control and SMZ-only soils, likely due to a combination of ARG adsorption, antibiotic immobilisation, and microbial community restructuring. These results highlight the potential of biochar as a soil amendment for mitigating the proliferation of AMR in agriculture environments.

Surveillance of SARS-CoV-2 through wastewater proved crucial during the height of the pandemic for estimating community COVID-19 cases and continues to be useful for monitoring this and other pathogens that are a public health burden. Gastrointestinal symptoms of acute COVID-19 have been well characterized, with demonstrated significant effects on the respiratory, oral, and gut microbiomes. With this understanding, we sought to characterize the wastewater microbiome in the context of COVID-19 rates, identify associations with the wastewater SARS-CoV-2 viral loads, and apply modeling to assess the ability of the wastewater microbiome to predict COVID-19 case rate. We observed numerous microbes associated with case rate including genera that are known to be depleted in vivo during SARS-CoV-2 infection such as keystone SCFA-producers such as Blautia, Dorea, and Akkermansia with implicated pathobionts Ruminococcus gnavus group and Ruminococcus torques group that expand. Non-human origin bacteria including Uruburuella and Stenoxybacter were also strongly associated with community case rates. Our predictive models highlighted a combination between bacteria and SARS-CoV-2 gene copies as an effective combination of covariates to estimate present cases, however microbiome covariates alone proved modestly more useful in predicting future case rates. These results highlight the heavy influence of local ecosystem and urbanicity in defining microbial composition of WWTPs. Alterations in the fecal microbiome from acute COVID-19 infection are detectable in wastewater and strongly associated with case rate, even in low-population areas. Our predictive models underscore the utility of the wastewater microbiome in understanding public health burden of COVID-19 and possibly other infectious diseases.

As circular agricultural inputs are increasingly sought, feather hydrolysate (FH), derived from keratin-rich poultry waste, has emerged as a promising fertilizer and biostimulant. However, how FH shapes soil microbiome succession over time, and what functional potential this restructuring carries, remains poorly understood. Here, we used multi-marker high-throughput sequencing of 16S, 18S, and ITS rDNA to track soil microbial communities over 30 days following FH amendment, with sampling at days 0, 1, 4, 14, and 30. FH induced a rapid and reproducible microbial succession characterized by an early decline in alpha diversity and a pronounced day-1 bloom of copiotrophic taxa, as inferred from predicted rrn operon copy-number profiles. This initial response was accompanied by enrichment of bacterial genera previously associated with plant growth-promoting traits, including pathogen suppression, nutrient solubilization, siderophore production, phytohormone synthesis, and ACC deaminase activity. Although these groups gradually declined after the initial peak, several remained at significantly elevated abundances throughout the 30-day experimental period. In parallel, FH-treated soils showed a sustained reduction in the cumulative relative abundance of genera annotated as putative phytopathogens. By integrating temporal community profiling, rrn-based life-strategy inference, and literature-derived functional annotation, we show that FH acts as a strong ecological filter, shifting the soil microbiome toward copiotrophic and putatively plant-beneficial taxa. These findings provide a temporal framework for understanding FH-mediated microbiome restructuring and highlight the need for future studies linking inferred microbial functional potential to measured disease incidence, nutrient fluxes, and plant performance across diverse soil contexts.

Microplastics are pervasive environmental contaminants and are increasingly detected in contexts relevant to human health, yet their effects on antimicrobial resistance, host-pathogen interactions, and infection outcomes remain poorly understood. Here, we show that exposure to polystyrene microplastics alters both antibiotic resistance evolution and pathogenic behavior in Acinetobacter baumannii, a leading cause of multidrug-resistant hospital-acquired infections. Using experimental evolution under antibiotic selection, we demonstrate that microplastic exposure accelerates resistance emergence across multiple antibiotic classes. Although microplastic exposure did not uniformly enhance biofilm formation, it modestly impaired macrophage-mediated bacterial clearance, suggesting broader effects on bacterial adaptation and host interaction. In vivo, microplastic-associated infection resulted in more severe disease, characterized by increased lung tissue damage and reduced survival in a murine model of A. baumannii pneumonia. Together, these findings identify microplastics as ecological modifiers of bacterial adaptation, linking widespread plastic pollution to enhanced antimicrobial resistance and worsened infectious disease outcomes.

The perennial grass Miscanthus x giganteus (miscanthus) offers a sustainable alternative to traditional biomass feedstocks while improving key soil health parameters, including aggregation. Aggregate stability results from dynamic soil-plant-microbe interactions, yet the relative importance of each factor remains an active research question. Building on previous observations that miscanthus alters soil structure to improve water-holding capacity and aggregate stability, we characterized the communities of soil bacteria and arbuscular mycorrhizal fungi (AMF) across three sites in Iowa, USA, comparing miscanthus to annual maize (Zea mays L.) and non-cropped perennial turfgrass (Poa spp.). We examined whether microbiomes co-varied with soil aggregation and, if so, whether plant cover identity or life history categorization better explained the observed patterns. Bacterial and AMF communities varied across sites and plant types, with signals that life history and plant cover identity both mattered. Aggregate stability aligned with a perennial-annual divergence in microbial beta diversity, while finer-scale differences in community composition and network structure were plant-specific. Soils under perennial plants were enriched in microbial groups positively correlated with aggregate stability; we identified 61 bacterial and 8 AMF "architect" taxa for future study. Within- and cross-kingdom co-occurrence network analysis revealed greater complexity under perennial plants: 1.9-fold more network links in miscanthus bacteria-bacteria networks than in maize, and 1.7-fold more in turfgrass AMF-AMF networks. Miscanthus fundamentally shapes microbial interactions, particularly among bacteria, relating to improved soil physical structure. Understanding these soil-plant-microbe feedbacks advances the development of biomass feedstocks with a portfolio of soil health benefits for next-generation biofuels and bioproducts. IMPORTANCEPerennial bioenergy crops can provide the raw material for biofuels and bioproducts while simultaneously improving soil health. Miscanthus x giganteus (miscanthus) efficiently stabilizes soil aggregates, potentially leading to higher water retention and erosion resistance. Understanding the microbial contributions to these outcomes is key to building resilient, sustainable bioenergy systems. This study highlights the connections between communities of soil microbes--bacteria and arbuscular mycorrhizal fungi--across three sites and three plant covers, including miscanthus, maize, and turfgrass. We identify a guild of potential "microbial architects" linked to soil aggregation and show more interconnected microbial networks under the perennial plant covers compared to annual maize. These insights shed light on the interactions between soil biological communities and soil physical and chemical properties. More broadly, the results may inform efforts to harness plant-associated microbiomes for sustainable biomass production.

Excessive application of boron-based fertilizers in agriculture has led to increased boron accumulation in soil, adversely affecting microbial communities and plant species, ultimately contributing to boron-induced desertification. This study presents the first metagenome-based analysis of boron-contaminated agricultural soil in Northern West Bengal, India, providing a comprehensive profile of the soil microbiome under boron stress. Boron-amended and unamended agricultural soil samples were analyzed using metagenomics sequencing approach over 365 days under natural environmental conditions. The results revealed a significant decline in bacterial diversity in boron-amended soil, with Firmicutes emerging as the dominant phylum. Notably, all boron-tolerant bacterial strains belonged to Firmicutes, suggesting that high boron levels impose selective pressure favouring Gram-positive bacteria. The enrichment of metal-resistant and oligotrophic bacterial taxa in boron-amended soil underscores microbial adaptation to boron stress. In addition to microbial community dynamics, we investigated plant succession in boron-enriched soil, offering novel insights into the interplay between above- and below-ground ecosystems. Our findings highlight two key adaptive traits, high boron tolerance and oligotrophic survival strategies, that enable bacterial communities to persist in boron-rich environments. These results enhance our understanding of microbial resilience in chemically stressed soils and have implications for soil health and sustainable agriculture.

Dental caries is a biofilm-mediated disease associated with ecological changes in the oral microbiome. How microbial community organization differs among healthy plaque, caries-associated plaque, and carious dentin remains incompletely defined. We used 16S rRNA gene sequencing to profile paired supragingival plaque and carious dentin samples from patients with caries, together with supragingival plaque from healthy controls. Caries-associated plaque showed higher diversity than healthy plaque, whereas diversity was lower in carious dentin. Ecological ordering placed the three sample types along a health-plaque-dentin continuum. Association-network analysis showed distinct network structures in caries-associated plaque and carious dentin, with the dentin network displaying greater density and lower modularity. By integrating differential-abundance and network-centrality results, we identified taxa associated with the dentin niche. A sparse logistic-regression model using three genera distinguished plaque from dentin in patient-grouped cross-validation (AUROC, 0.780; AUPRC, 0.718). These cross-sectional findings describe niche-associated microbiome organization in dental caries and provide candidate features for future validation in independent, clinically relevant cohorts.

Subgingival biofilms in periodontitis exhibit spatial heterogeneity, yet the organization of microbial communities across periodontal niches remains incompletely defined. Using paired sampling and 16S rRNA gene sequencing, we characterized non-attached and attached subgingival plaque from patients with periodontitis, together with non-attached plaque from periodontally healthy individuals. Across diversity metrics and ordination analyses, non-attached plaque from periodontitis patients occupied positions between healthy-associated and attached-plaque communities. Taxonomically, these communities contained both health-associated commensals and anaerobic genera commonly enriched in periodontitis. Network analysis identified differences in association-network topology among niches, with the non-attached periodontitis network containing more retained associations than the healthy network. These cross-sectional results describe niche-associated patterns of subgingival community composition and association structure. They do not establish temporal progression, direct microbial interactions, or clinical utility.

Stratified benthic deposits offer crucial modern analogs for Precambrian biogeochemical dynamics, yet whether the vertical organization of deep sedimentary columns reflects depositional history, present-day geochemical conditions, or both remains poorly understood, particularly under extreme oligotrophy. Here, we present a depth-resolved exploratory survey of a continuous 34-cm sediment core partitioned into 11 discrete horizons (L1 to L11) from Poza Roja 2, an alkaline, sub-hypersaline pond in the Cuatro Cienegas Basin, Mexico. Integrating physical stratigraphy, organic carbon and nutrient stoichiometry, and 16S rRNA gene metabarcoding, we evaluated down-core microbial community structure alongside acute phosphorus scarcity. Molar C:Po and N:Po ratios exceeded canonical Redfield proportions (106:16:1) in every layer, by up to 48.5-fold and 87.8-fold, respectively, both peaking in layer L4. Unconstrained ordination (PCoA) and hierarchical clustering grouped the layers into three compositional zones: upper (L2-L4), intermediate (L5-L6), and basal (L8-L11), with L1 and L7 occupying transitional positions. Archaea accounted for 31.0% of prokaryotic reads, ranging from 8.3% (L5) to 43.7% (L9), and were dominated by SM1-50 (Thermoplasmatota) and Halobacteriota. The phototrophic heliobacterium Heliorestis peaked in the intermediate zone (47.6% of bacterial reads in L6). Constrained Redundancy Analysis models lacked statistical significance (P >= 0.12), highlighting the exploratory nature of a single core (n = 11). This pilot characterization provides a baseline for understanding deep biogenic archives under severe nutrient limitation.

Chronic kidney disease (CKD)-associated dysbiosis is well described after diagnosis, but whether microbial changes precede clinical recognition is unclear. We integrated insurance claims, fecal and oral 16S rRNA profiles, and clinical laboratory data from companion dogs. Among 140,025 dogs, lower gut microbial diversity was associated with incident CKD after adjustment for age, sex and body size. Prediagnostic samples showed reduced evenness-related diversity, modest community shifts and seven differentially abundant genera. A five-genus score was elevated more than two years before diagnosis, although it was derived and evaluated in the same cohort and was not intended as a predictive model. In a laboratory subset, microbial changes preceded the largest increases in blood urea nitrogen and creatinine. Paired oral-gut samples showed limited exploratory associations between periodontal-associated taxa and the gut score. These findings identify microbial features associated with future claims-defined canine CKD and support independent validation and mechanistic investigation.

Wastewater systems are increasingly recognized as important environmental reservoirs of antimicrobial resistance (AMR), acting as interfaces where resistant bacteria, antimicrobial resistance genes (ARGs), and mobile genetic elements (MGEs) converge and potentially disseminate. Wastewater samples were collected from hospital and community sites, including municipal medical centers, household wastewater outlets, and open drainage systems. Genomic DNA was extracted using the ZymoBIOMICS DNA/RNA Miniprep Kit and sequenced on the Oxford Nanopore Technologies MinION MK1D platform using the Native Barcoding Kit (SQK-NBD114.24, V14). Sequencing data were processed through a custom Snakemake workflow integrating quality control, taxonomic profiling, resistome characterization, mobilome analysis, and genome-resolved metagenomics. A total of 489 unique ARGs conferring resistance to 29 antibiotic classes were identified through metagenomic analysis. The resistome was dominated by genes conferring resistance to {beta}-lactams (including cephalosporins and carbapenems), aminoglycosides, tetracyclines, macrolides, and fluoroquinolones. Clinically important resistance determinants, including blaOXA, blaTEM, blaGES, blaCARB, cfxA, tet, qnr, sul, dfrA, erm, msrE, and aminoglycoside-modifying enzyme genes such as aac(3) and ant(3'') were detected across both hospital and community wastewater samples. Resistance mechanisms were predominantly driven by antibiotic inactivation, followed by efflux and target protection. Several priority bacterial pathogens were detected, including Escherichia coli, Klebsiella pneumoniae, Enterobacter cloacae, Pseudomonas aeruginosa, and Acinetobacter baumannii. Integration/excision elements were the predominant category of MGEs, followed by transfer-associated elements and replication/recombination/repair functions. Plasmid analysis further identified diverse incompatibility groups, predominantly IncP6, IncC, IncF, and IncR replicons, supporting the widespread occurrence of plasmid-mediated horizontal gene transfer in both settings. These findings reveal a substantial burden of clinically relevant ARGs, mobile genetic elements, and potential bacterial pathogens in hospital and community wastewater in Conakry. This study provides the first metagenomic baseline for environmental AMR surveillance in Guinea and highlights the urgent need for integrated One Health strategies to mitigate the environmental dissemination of antimicrobial resistance.