Characterization Of Microbial Communities Research Articles

Characterisation of microbial communities and quantification of antibiotic resistance genes in Italian wastewater treatment plants using 16S rRNA sequencing and digital PCR

The spread of antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs) in humans, animals and environment is a growing threat to public health. Wastewater treatment plants (WWTPs) are crucial in mitigating the risk of environmental contamination by effectively removing contaminants before discharge. However, the persistence of ARB and ARGs even after treatment is a challenge for the management of water system.To comprehensively assess antimicrobial resistance dynamics, we conducted a one-year monitoring study in three WWTPs in central Italy, both influents and effluents. We used seasonal sampling to analyze microbial communities by 16S rRNA, as well as to determine the prevalence and behaviour of major ARGs (sul1, tetA, blaTEM, blaOXA-48, blaCTX-M-1 group, blaKPC) and the class 1 Integron (int1). Predominant genera included in order: Arcobacter, Acinetobacter, Flavobacterium, Pseudarcobacter, Bacteroides, Aeromonas, Trichococcus, Cloacibacterium, Pseudomonas and Streptococcus. A higher diversity of bacterial communities was observed in the effluents compared to the influents. Within these communities, we also identified bacteria that may be associated with antibiotic resistance and pose a significant threat to human health. The mean concentrations (in gene copies per liter, gc/L) of ARGs and int1 in untreated wastewater (absolute abundance) were as follows: sul1 (4.1 × 109), tetA (5.2 × 108), blaTEM (1.1 × 108), blaOXA-48 (2.1 × 107), blaCTX-M-1 group (1.1 × 107), blaKPC (9.4 × 105), and int1 (5.5 × 109). The mean values in treated effluents showed reductions ranging from one to three log. However, after normalizing to the 16S rRNA gene (relative abundance), it was observed that in 37.5 % (42/112) of measurements, the relative abundance of ARGs increased in effluents compared to influents. Furthermore, correlations were identified between ARGs and bacterial genera including priority pathogens. This study improves our understanding of the dynamics of ARGs and provides insights to develop more effective strategies to reduce their spread, protecting public health and preserving the future efficacy of antibiotics.

Characterization and functional analysis of microbial communities in Bletilla striata

Characterization and functional analysis of microbial communities in Bletilla striata

Modeling Dynamics of Human Gut Microbiota Derived from Gluten Metabolism: Obtention, Maintenance and Characterization of Complex Microbial Communities.

Western diets are rich in gluten-containing products, which are frequently poorly digested. The human large intestine harbors microorganisms able to metabolize undigested gluten fragments that have escaped digestion by human enzymatic activities. The aim of this work was obtaining and culturing complex human gut microbial communities derived from gluten metabolism to model the dynamics of healthy human large intestine microbiota associated with different gluten forms. For this purpose, stool samples from six healthy volunteers were inoculated in media containing predigested gluten or predigested gluten plus non-digested gluten. Passages were carried out every 24 h for 15 days in the same medium and community composition along time was studied via V3-V4 16S rDNA sequencing. Diverse microbial communities were successfully obtained. Moreover, communities were shown to be maintained in culture with stable composition for 14 days. Under non-digested gluten presence, communities were enriched in members of Bacillota, such as Lachnospiraceae, Clostridiaceae, Streptococcaceae, Peptoniphilaceae, Selenomonadaceae or Erysipelotrichaceae, and members of Actinomycetota, such as Bifidobacteriaceae and Eggerthellaceae. Contrarily, communities exposed to digested gluten were enriched in Pseudomonadota. Hence, this study shows a method for culture and stable maintenance of gut communities derived from gluten metabolism. This method enables the analysis of microbial metabolism of gluten in the gut from a community perspective.

Development of a flow-cell bioreactor for immobilized sulfidogenic sludge characterization using electrochemical H2S microsensors

The sulfate-reduction process plays a crucial role in the biological valorization of SOx gases. However, a complete understanding of the sulfidogenic process in bioreactors is limited by the lack of technologies for characterizing the sulfate-reducing activity of immobilized biomass. In this work, we propose a flow-cell bioreactor (FCB) for characterizing sulfate-reducing biomass using H2S microsensors to monitor H2S production in real-time within a biofilm. To replace natural immobilization through extracellular polymeric substance production, sulfidogenic sludge was artificially immobilized using polymers. Physical and sulfate-reducing activity studies were performed to select a polymer-biomass matrix that maintained sulfate-reducing activity of biomass while providing strong microbial retention and mechanical strength. Several operational conditions of the sulfidogenic reactor allowed to obtain a H2S profiles under different inlet sulfate loads and, additionally, 3D mapping was assessed in order to perform a hydraulic characterization. Besides, the effects of artificial immobilization on biodiversity were investigated through the characterization of microbial communities. This study demonstrated the appropriateness of immobilized-biomass for characterization of sulfidogenic biomass in FCB using H2S electrochemical microsensors, and beneficial microbiological communities shifts as well as enrichment of sulfate-reducing bacteria have been confirmed.

Microbial interactions facilitating efficient methane driven denitrification via in-situ utilization of short chain fatty acids

High nitrate pollution in agriculture and industry poses a challenge to emerging methane oxidation coupled denitrification. In this study, an efficient nitrate removal efficiency of 100 % was achieved at an influent loading rate of 400 mg-N/L·d, accompanied by the production of short chain fatty acids (SCFAs) with a maximum value of 80.9 mg/L. Batch tests confirmed that methane was initially converted to acetate, which then served as a carbon source for denitrification. Microbial community characterization revealed the dominance of heterotrophic denitrifiers, including Simplicispira (22.8 %), Stappia (4.9 %), and the high‑nitrogen-tolerant heterotrophic denitrifier Diaphorobacter (19.0 %), at the nitrate removal rate of 400 mg-N/L·d. Notably, the low abundance of methanotrophs ranging from 0.24 % to 3.75 % across all operational stages does not fully align with the abundance of pmoA genes, suggesting the presence of other functional microorganisms capable of methane oxidation and SCFAs production. These findings could facilitate highly efficient denitrification driven by methane and contributed to the development of denitrification using methane as an electron donor.

Metagenomic sequencing sheds light on microbes putatively associated with pneumonia-related fatalities of white-tailed deer (Odocoileus virginianus).

With emerging infectious disease outbreaks in human, domestic and wild animal populations on the rise, improvements in pathogen characterization and surveillance are paramount for the protection of human and animal health, as well as the conservation of ecologically and economically important wildlife. Genomics offers a range of suitable tools to meet these goals, with metagenomic sequencing facilitating the characterization of whole microbial communities associated with emerging and endemic disease outbreaks. Here, we use metagenomic sequencing in a case-control study to identify microbes in lung tissue associated with newly observed pneumonia-related fatalities in 34 white-tailed deer (Odocoileus virginianus) in Wisconsin, USA. We identified 20 bacterial species that occurred in more than a single individual. Of these, only Clostridium novyi was found to substantially differ (in number of detections) between case and control sample groups; however, this difference was not statistically significant. We also detected several bacterial species associated with pneumonia and/or other diseases in ruminants (Mycoplasma ovipneumoniae, Trueperella pyogenes, Pasteurella multocida, Anaplasma phagocytophilum, Fusobacterium necrophorum); however, these species did not substantially differ between case and control sample groups. On average, we detected a larger number of bacterial species in case samples than controls, supporting the potential role of polymicrobial infections in this system. Importantly, we did not detect DNA of viruses or fungi, suggesting that they are not significantly associated with pneumonia in this system. Together, these results highlight the utility of metagenomic sequencing for identifying disease-associated microbes. This preliminary list of microbes will help inform future research on pneumonia-associated fatalities of white-tailed deer.

Coupling Partial Nitritation, Anammox and n-DAMO in a membrane aerated biofilm reactor for simultaneous dissolved methane and nitrogen removal

Anaerobic technologies with downstream autotrophic nitrogen removal have been proposed to enhance bioenergy recovery and transform a wastewater treatment plant from an energy consumer to an energy exporter. However, approximately 20–50 % of the produced methane is dissolved in the anaerobically treated effluent and is easily stripped into the atmosphere in the downstream aerobic process, contributing to the release of greenhouse gas emissions. This study aims to develop a solution to beneficially utilize dissolved methane to support high-level nitrogen removal from anaerobically treated mainstream wastewater. A novel technology, integrating Partial Nitritation, Anammox and Methane-dependent nitrite/nitrate reduction (i.e. PNAM) was demonstrated in a membrane-aerated biofilm reactor (MABR). With the feeding of ∼50 mg NH4+-N/L and ∼20 mg/L dissolved methane at a hydraulic retention time of 15 h, around 90 % of nitrogen and ∼100 % of dissolved methane can be removed together in the MABR. Microbial community characterization revealed that ammonia-oxidizing bacteria (AOB), nitrite-oxidizing bacteria (NOB), anammox bacteria, nitrite/nitrate-dependent anaerobic methane oxidation microorganisms (n-DAMO bacteria and archaea) and aerobic methanotrophs co-existed in the established biofilm. Batch tests confirmed the active microbial pathways and showed that AOB, anammox bacteria and n-DAMO microbes were jointly responsible for the nitrogen removal, and dissolved methane was mainly removed by the n-DAMO process, with aerobic methane oxidation making a minor contribution. In addition, the established system was robust against dynamic changes in influent composition. The study provides a promising technology for the simultaneous removal of dissolved methane and nitrogen from domestic wastewater, which can support the transformation of wastewater treatment from an energy- and carbon-intensive process, to one that is energy- and carbon-neutral.

Integrated annotation prioritizes metabolites with bioactivity in inflammatory bowel disease.

Microbial biochemistry is central to the pathophysiology of inflammatory bowel diseases (IBD). Improved knowledge of microbial metabolites and their immunomodulatory roles is thus necessary for diagnosis and management. Here, we systematically analyzed the chemical, ecological, and epidemiological properties of ~82k metabolic features in 546 Integrative Human Microbiome Project (iHMP/HMP2) metabolomes, using a newly developed methodology for bioactive compound prioritization from microbial communities. This suggested >1000 metabolic features as potentially bioactive in IBD and associated ~43% of prevalent, unannotated features with at least one well-characterized metabolite, thereby providing initial information for further characterization of a significant portion of the fecal metabolome. Prioritized features included known IBD-linked chemical families such as bile acids and short-chain fatty acids, and less-explored bilirubin, polyamine, and vitamin derivatives, and other microbial products. One of these, nicotinamide riboside, reduced colitis scores in DSS-treated mice. The method, MACARRoN, is generalizable with the potential to improve microbial community characterization and provide therapeutic candidates.

Recent molecular techniques to strengthen ecological studies in echinoderms

Introduction: Echinoderms, an integral component of marine ecosystems worldwide, have captivated scientific interest for centuries. Despite this longstanding attention, comprehending key facets such as trophic relationships, diet composition, and host-microbiota relationships still represents a challenge using traditional techniques. Recent years, however, have witnessed a transformative shift, thanks to the emergence of advanced molecular techniques, offering new approaches to strengthen ecological studies in echinoderms.
 Objective: Explore how recent advancements in molecular tools have impacted ecological research on echinoderms. Specifically, we aim to investigate the potential of these tools to shed light on trophic interactions, diet composition, and the characterization of gut microbial communities in these organisms.
 Methods: Available literature was used to clarify how novel molecular techniques can improve ecological studies. The focus is diet, trophic relationships, and gut microbiota.
 Results: Traditionally, studies of stomach contents using compound microscopy have provided an idea of ingested material; nevertheless, sometimes a simple magnified visualization of dietary content does not allow exhaustive identification of the entire food spectrum, as it is limited due to the rapid digestion and maceration of food items within the echinoderm’s digestive tract. The use of DNA-metabarcoding, targeting specific DNA regions, such as the mitochondrial COI gene, has allowed us to enhance the accuracy and precision of diet characterization by enabling the identification of prey items down to the species or even genetic variant level, providing valuable insights into specific dietary preferences. Another approach is the use of stable isotopes, particularly carbon and nitrogen, which provide a powerful tool to trace the origin and flow of nutrients through food webs. By analyzing the isotopic signatures in muscular tissues and food items, we can discern the sources of their primary food items and gain insights into their trophic position within the ecosystem. Lastly, a third new technique used to elucidate the characterization of the prokaryotic community is 16S rRNA sequencing. This method allows us to explore the composition and dynamics of the digestive tract microbial communities.
 Conclusions: This is a promising era for ecological research on echinoderms, where advances of molecular tools have enabled an unprecedented level of detail, resolving longstanding challenges in comprehending their trophic interactions, diet composition, and host-microbiota relationships, and opening new avenues of investigation in ecological studies.

Benchmarking a targeted 16S ribosomal RNA gene enrichment approach to reconstruct ancient microbial communities.

The taxonomic characterization of ancient microbiomes is a key step in the rapidly growing field of paleomicrobiology. While PCR amplification of the 16S ribosomal RNA (rRNA) gene is a widely used technique in modern microbiota studies, this method has systematic biases when applied to ancient microbial DNA. Shotgun metagenomic sequencing has proven to be the most effective method in reconstructing taxonomic profiles of ancient dental calculus samples. Nevertheless, shotgun sequencing approaches come with inherent limitations that could be addressed through hybridization enrichment capture. When employed together, shotgun sequencing and hybridization capture have the potential to enhance the characterization of ancient microbial communities. Here, we develop, test, and apply a hybridization enrichment capture technique to selectively target 16S rRNA gene fragments from the libraries of ancient dental calculus samples generated with shotgun techniques. We simulated data sets generated from hybridization enrichment capture, indicating that taxonomic identification of fragmented and damaged 16S rRNA gene sequences was feasible. Applying this enrichment approach to 15 previously published ancient calculus samples, we observed a 334-fold increase of ancient 16S rRNA gene fragments in the enriched samples when compared to unenriched libraries. Our results suggest that 16S hybridization capture is less prone to the effects of background contamination than 16S rRNA amplification, yielding a higher percentage of on-target recovery. While our enrichment technique detected low abundant and rare taxa within a given sample, these assignments may not achieve the same level of specificity as those achieved by unenriched methods.

Microbial Community Profiling Protocol with Full-length 16S rRNA Sequences and Emu.

16S rRNA targeted amplicon sequencing is an established standard for elucidating microbial community composition. While high-throughput short-read sequencing can elicit only a portion of the 16S rRNA gene due to their limited read length, third generation sequencing can read the 16S rRNA gene in its entirety and thus provide more precise taxonomic classification. Here, we present a protocol for generating full-length 16S rRNA sequences with Oxford Nanopore Technologies (ONT) and a microbial community profile with Emu. We select Emu for analyzing ONT sequences as it leverages information from the entire community to overcome errors due to incomplete reference databases and hardware limitations to ultimately obtain species-level resolution. This pipeline provides a low-cost solution for characterizing microbiome composition by exploiting real-time, long-read ONT sequencing and tailored software for accurate characterization of microbial communities. © 2024 Wiley Periodicals LLC. Basic Protocol: Microbial community profiling with Emu Support Protocol 1: Full-length 16S rRNA microbial sequences with Oxford Nanopore Technologies sequencing platform Support Protocol 2: Building a custom reference database for Emu.

The Decorated Garden Grotto of Condes de Basto Palace in Évora, Portugal: Microbial Community Characterization and Biocide Tests for Conservation

The Eugénio de Almeida Foundation’s Casa de Fresco is a historical monument of valuable historic–artistic significance, which currently reveals an assortment of biofilms due to the proliferation of microorganisms in the stone and rocaille elements. The biodeterioration in this area was studied as part of the Conservation and Restoration Project. We effectively characterized the local microbial community using modern high-throughput DNA analysis. Our results suggested the existence of a variety of lichens or lichenized fungi, including genera such as Variospora, Verrucaria, Circinaria, and Caloplaca. Furthermore, we detected several prokaryote microorganisms related to the identification of these lichens. To properly deal with this microbiological issue and avoid fungal recolonization, we evaluated available commercial antimicrobial treatments.

Characterization of microbial communities in urban subway: connotation for indoor environment quality and public health

Characterization of microbial communities in urban subway: connotation for indoor environment quality and public health

Characterisation of flavour profiles and microbial communities of fermented peppers with different fermentation years by combining flavouromics and metagenomics

The changes in flavours, volatile aromas and microbial communities of fermented peppers with different fermentation years and their relationships were investigated in this study. Results indicated a gradual increase in organic acids during fermentation, whereas free amino acids and capsaicinoids reached stability after 1 year of fermentation. Overall, the analysis detected 340 volatile compounds in fermented peppers and regarded 69 of them as differential compounds. Peppers fermented for 2 (FY2) and 4 years (FY4) possessed a greater number of differential volatiles with large odour activity values, thus endowing them with more favourable flavours. Hence, metagenomic analysis compared their microbial communities and functional annotations. Results revealed that Lactiplantibacillus plantarum and Zygosaccharomyces rouxii were the dominant bacterium and fungus, and metabolism was the main Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway in FY2. Correlation analysis demonstrated that Hyphopichia, Kazachstania and Clavispora were highly positively correlated with 12 key aroma flavours.

Inflammatory Bowel Disease and Gut Microbiota Dysbiosis: Current understanding and Future Direction

Inflammatory Bowel Disease (IBD) represents a group of chronic, relapsing inflammatory disorders primarily affecting the gastrointestinal tract. The pathogenesis of IBD is multifaceted, involving genetic predisposition, environmental triggers, and dysregulation of the immune response. Recent research has illuminated the pivotal role of gut microbiota dysbiosis in the development and perpetuation of IBD. The human gut harbors a complex and dynamic ecosystem of microorganisms that profoundly influences host health and disease. Alterations in the composition, diversity, and function of the gut microbiota, termed dysbiosis, have been consistently linked to IBD. Shifts in microbial composition, reduction in microbial diversity, and imbalances in beneficial versus pathogenic microorganisms characterize the dysbiotic state associated with IBD.The intricate interplay between the host immune system and the gut microbiota is a key determinant in IBD pathogenesis. Dysbiosis triggers aberrant immune responses, leading to chronic mucosal inflammation and tissue damage. Furthermore, dysbiotic alterations disrupt essential microbial-derived metabolites and signaling molecules crucial for gut homeostasis, further exacerbating the disease. Advancements in high-throughput sequencing technologies and metagenomic analysis have enabled comprehensive characterization of microbial communities in IBD, uncovering microbial signatures and functional pathways associated with disease phenotypes and treatment responses. Therapeutic interventions targeting the gut microbiota, such as probiotics, prebiotics, fecal microbiota transplantation, and microbial-based therapies, have shown promise in preclinical and clinical studies for modulating dysbiosis and ameliorating IBD symptoms.
 Keywords: Inflammatory Bowel Disease, Dysbiosis, Fecal microbiota, Probiotics

Contaminants of emerging concern reduction and microbial community characterization across a three-barrier advanced water treatment system

This research investigated the removal of contaminants of emerging concern (CECs) and characterized the microbial community across an advanced water treatment (AWT) train consisting of Coagulation/Flocculation/Clarification/Granular Media Filtration (CFCGMF), Ozone-Biological Activated Carbon Filtration (O3/BAC), Granular Activated Carbon filtration, Ultraviolet Disinfection, and Cartridge Filtration (GAC/UV/CF). The AWT train successfully met the goals of CECs and bulk organics removal. The microbial community at each treatment step of the AWT train was characterized using 16S rRNA sequencing on the Illumina MiSeq platform generated from DNA extracted from liquid and solid (treatment media) samples taken along the treatment train. Differences in the microbial community structure were observed. The dominant operational taxonomic units (OTU) decreased along the treatment train, but the treatment steps did impact the microbial community composition downstream of each unit process. These results provide insights into microbial ecology in advanced water treatment systems, which are influenced and shaped by each treatment step, the microbial community interactions, and their potential metabolic contribution to CECs degradation.

Characterization of Microbial Decay and Microbial Communities in Waterlogged Archaeological Wood Excavated from the Wetland

Anatomical and chemical changes due to microbial decay and microbial communities in three waterlogged archaeological woods, namely Dongnim 1, Dongnim 2, and Dongnim 3, excavated from the wetland of the Dongnim-dong archaeological site in Gwangju, were investigated. Dongnim 1−3 exhibited a maximum moisture content approximately 6 to 8 times higher than that of undecayed recent wood, and there was no correlation with the burial period. Chemical analysis revealed an increase in ash and hot water extractive content in Dongnim 1−3 compared to undecayed recent wood, while the solvent extractive content tended to decrease. Additionally, there was a significant decrease in holocellulose content with a relative increase in lignin concentration in Dongnim 1−3. Microscopic observations showed erosion bacteria decay and soft rot decay in Dongnim 1−3. The microbial community analysis of Dongnim 2 and 3 revealed the dominance of Ascomycota (98% to 99%) in the fungal community and Proteobacteria (34% to 55%) as the predominant bacterial phylum. Nonetheless, significant differences in microbial community structure and diversity were observed between Dongnim 2 and Dongnim 3.

Characterization of microbial communities during Grifola frondosa (maitake) wood log cultivation

The method used to cultivate the popular Japanese mushroom Grifola frondosa (maitake), called 'wood log cultivation', comprised two steps: (1) the mycelium is grown around a wood log in a plastic bag, and (2) the mycelium that has spread on the wood log is transferred into casing substrates in a forest. This method is still popular in Japan due to its low cost and high-quality crop production. The importance of the microbiome that inhabits mushroom-cultivation surroundings has recently attracted attention, but no study of the microbial communities in maitake cultivation has been published. We investigated how the bacterial communities changed in wood logs in comparison with a control group (without inoculation) and their interaction with maitake during the first to fourth years of maitake wood log cultivation. A maitake biomass was detected by quantitative PCR in wood logs but not in the casings, and we thus decided to investigate the bacterial communities in wood log samples for control and first- to fourth-year cultivation. The results indicate that the phyla Proteobacteria, Firmicutes, and Gemmatimonadota play key roles in changes of the microbiome composition for maitake wood log cultivation. In a functional profile, bacteria communities in the wood logs during maitake cultivation showed higher relative abundance in cellulolysis, glycolysis, TCA cycle, and many biosynthesis pathways, whereas the control group showed higher relative abundance in fermentation. These results suggested that (i) the bacterial communities which inhabited maitake cultivated wood logs may help the maitake degrade wood cellulose, and (ii) part of the glucose from the cellulose degraded by both maitake and bacteria was used for the bacterial TCA cycle instead of fermentation. Bacteria also produce some chemicals that maitake mycelium may need. It is also likely that some potential intracellular parasites dwell with maitake. The different cultivation stages showed different network structures. A network analysis indicated that Class Gammaproteobacteria is a potential keystone taxon for the microbiome network stability of maitake cultivated wood logs. These results contribute to the understanding of the microbiome in maitake-cultivation surroundings and will improve maitake wood log cultivation.

Compositional shifts in fresh-cut apples microbiome in response to application of Lactiplantibacillus plantarum assessed by next-generation sequencing

Spoilage caused by microorganisms is the main problem of fresh-cut fruits during storage, leading to quality deterioration and short shelf life. Lactic acid bacteria (LAB) contribute to fruit preservation by producing secondary metabolites with antibacterial activity, like bactericins, organic acids, and extracellular polysaccharides, etc. In the study, the effects of Lactiplantibacillus plantarum BX62 and LP1-4 on the composition and dynamics of the microbiome on the surface of fresh-cut apples were investigated. L. plantarum survived and remained stable (>7 log CFU/mL). The cell suspensions (9 log cells/mL) of BX62, LP1-4, and BX62+LP1-4 showed varying degrees of antagonistic activity against microorganisms on the surface of fresh-cut apples during cold storage. Moreover, L. plantarum treatment inhibited the increase of bacterial diversity, and their cell suspensions also reduced the relative abundance of Actinobacteria, Acidobacteria, Basidiomycota, Rhodococcus, Pantoea, Ralstonia, Vishniacozyma, and Cystofilobasidium on the surface of fresh-cut apples. The results provide new insight into the characterization of microbial communities on the surface of fresh-cut apples after LAB treatment, which might assist in developing new biocontrol agents to control the microbial contamination of fruits.

Assessing the Ecotoxicity of Eight Widely Used Antibiotics on River Microbial Communities

Global prevalence of antibiotic residues (ABX) in rivers requires ecotoxicological impact assessment. River microbial communities serve as effective bioindicators for this purpose. We quantified the effects of eight commonly used ABXs on a freshwater river microbial community using Biolog EcoPlates™, enabling the assessment of growth and physiological profile changes. Microbial community characterization involved 16S rRNA gene sequencing. The river community structure was representative of aquatic ecosystems, with the prevalence of Cyanobacteria, Proteobacteria, Actinobacteria, and Bacteroidetes. Our findings reveal that all ABXs at 100 µg/mL reduced microbial community growth and metabolic capacity, particularly for polymers, carbohydrates, carboxylic, and ketonic acids. Chloramphenicol, erythromycin, and gentamicin exhibited the highest toxicity, with chloramphenicol notably impairing the metabolism of all studied metabolite groups. At lower concentrations (1 µg/mL), some ABXs slightly enhanced growth and the capacity to metabolize substrates, such as carbohydrates, carboxylic, and ketonic acids, and amines, except for amoxicillin, which decreased the metabolic capacity across all metabolites. We explored potential correlations between physicochemical parameters and drug mechanisms to understand drug bioavailability. Acute toxicity effects at the river-detected low concentrations (ng/L) are unlikely. However, they may disrupt microbial communities in aquatic ecosystems. The utilization of a wide array of genetically characterized microbial communities, as opposed to a single species, enables a better understanding of the impact of ABXs on complex river ecosystems.