Genetic and chemical characterization of ibuprofen degradation by Sphingomonas Ibu-2

Transformation of the drug ibuprofen by Priestia megaterium: reversible glycosylation and generation of hydroxylated metabolites

As one of the most-consumed drugs worldwide, ibuprofen (IBU) reaches the environment in considerable amounts as environmental pollutant, necessitating studies of its biotransformation as potential removal mechanism. Here, we screened bacteria with known capabilities to degrade aromatic environmental pollutants, belonging to the genera Bacillus, Priestia (formerly also Bacillus), Paenibacillus, Mycobacterium, and Cupriavidus, for their ability to transform ibuprofen. We identified seven transformation products, namely 2-hydroxyibuprofen, carboxyibuprofen, ibuprofen pyranoside, 2-hydroxyibuprofen pyranoside, 4-carboxy-α-methylbenzene-acetic acid, 1-[4-(2-hydroxy-2-methylpropyl)phenyl]ethanone, and 2-hydroxyibuprofenmethyl ester. Based on our screening results, we focused on ibuprofen biotransformation by Priestia megaterium SBUG 518, to identify structures of transformation products, and to shed light on the drug's impact on bacterial physiology. Biotransformation reactions by P. megaterium SBUG 518 involved (A) the hydroxylation of the isobutyl side chain at two positions, and (B) conjugate formation via esterification with a sugar molecule of the carboxylic group of ibuprofen and an ibuprofen hydroxylation product. Glycosylation seems to be a detoxification process, since the ibuprofen conjugate (ibuprofen pyranoside) was considerably less toxic than the parent compound to P. megaterium SBUG 518. Based on proteome profile changes and inhibition assays, cytochrome P450 systems appear to be central for ibuprofen transformation in P. megaterium SBUG 518. The toxic effect of ibuprofen appears to be caused by interference of the drug with different physiological pathways, especially sporulation.

Profiling trace organic chemical biotransformation genes, enzymes and associated bacteria in microbial model communities

Microbial biotransformation of trace organic chemicals (TOrCs) is an essential process in wastewater treatment to eliminate environmental pollution. Understanding TOrC biotransformation mechanisms, especially at their original concentrations, is important to optimize treatment performance, whereas our current knowledge is limited. Here, we investigated the biotransformation of seven TOrCs by 24 model communities. The genome-centric analyses unraveled potential biotransformation drivers concerning functional genes, enzymes, and responsible bacteria. We obtained efficient model communities for completely removing ibuprofen, caffeine, and atenolol, with transformation efficiencies between 0 % and 45 % for sulfamethoxazole, carbamazepine, trimethoprim, and gabapentin. Biotransformation performance was not fully reflected by the presence of known biotransformation genes and enzymes in the metagenomes of the communities. Functional similar homologs to existing biotransformation genes and enzymes (e.g., long-chain-fatty-acid-CoA ligase encoded by fadD and fadD13 gene) could play critical roles in TOrC metabolism. Finally, we identified previously undescribed degrading strains, e.g., Rhodococcus qingshengii for caffeine, carbamazepine, sulfamethoxazole, and ibuprofen biotransformation, and potential transformation enzymes, e.g., SDR family oxidoreductase targeting sulfamethoxazole and putative hypothetical proteins for caffeine, atenolol and gabapentin biotransformation. This study provides fundamental insights into naturally assembled low-complexity degrader communities that can help to identify and tackle the current research gaps on biotransformation.

Genetic and species rearrangements in microbial consortia impact biodegradation potential

Genomic reorganisation between species and horizontal gene transfer have been considered the most important mechanism of biological adaptation under selective pressure. Still, the impact of mobile genes in microbial ecology is far from being completely understood. Here we present the collection and characterisation of microbial consortia enriched from environments contaminated with emerging pollutants, such as non-steroidal anti-inflammatory drugs. We have obtained and further enriched two ibuprofen-degrading microbial consortia from two unrelated wastewater treatment plants. We have also studied their ability to degrade the drug and the dynamics of the re-organisations of the genetic information responsible for its biodegradation among the species within the consortium. Our results show that genomic reorganisation within microorganisms and species rearrangements occur rapidly and efficiently during the selection process, which may be facilitated by plasmids and/or transposable elements located within the sequences. We show the evolution of at least two different plasmid backbones on samples from different locations, showing rearrangements of genomic information, including genes encoding activities for IBU degradation. As a result, we found variations in the expression pattern of the consortia after evolution under selective pressure, as an adaptation process to the new conditions. This work provides evidence for changes in the metagenomes of microbial communities that allow adaptation under a selective constraint -ibuprofen as a sole carbon source- and represents a step forward in knowledge that can inspire future biotechnological developments for drug bioremediation.

Removal of Ibuprofen in Water by Bioaugmentation with Labrys neptuniae CSW11 Isolated from Sewage Sludge-Assessment of Biodegradation Pathway Based on Metabolite Formation and Genomic Analysis

Ibuprofen (IBP) is one of the most consumed drugs in the world. It is only partially removed in wastewater treatment plants (WWTPs), being present in effluent wastewater and sewage sludge, causing the widespread introduction of IBP as an emergent xenobiotic in different environmental compartments. This study describes the use of Labrys neptuniae CSW11, recently described as an IBP degrader, through bioaugmentation processes for the removal of IBP from water under different conditions (additional carbon sources, various concentrations of glucose and IBP). L. neptuniae CSW11 showed very good results in a wide range of IBP concentrations, with 100% removal in only 4 days for 1 and 5 mg L-1 IBP and 7 days for 10 mg L-1, and up to 48.4% removal in 28 days for IBP 100 mg L-1 when using glucose 3 g L-1 as an additional carbon source. Three IBP metabolites were identified during the biotransformation process: 1-hydroxyibuprofen (1-OH-IBP), 2-hydroxyibuprofen (2-OH-IBP), and carboxyibuprofen (CBX-IBP), whose concentrations declined drastically in the presence of glucose. IBP metabolites maintained a certain degree of toxicity in solution, even when IBP was completely removed. The results indicate that L. neptuniae CSW11 can be quite effective in degrading IBP in water, but the bioaugmentation method should be improved using CSW11 in consortia with other bacterial strains able to degrade the toxic metabolites produced. A genome-based analysis of L. neptuniae CSW11 revealed different enzymes that could be involved in IBP biodegradation, and a potential metabolic pathway was proposed based on the metabolites observed and genome analysis.

Identification of a Novel Ibuprofen Biotransformation Pathway in Streptomyces sp. D218 and Detoxification as Indicated by the Green Algae Scenedesmus obliquus

Ibuprofen, a widely used nonsteroidal anti-inflammatory drug, contaminates agricultural products and potentially threatens human health due to its frequent detection and poor biodegradability. Microbial metabolism dominates the elimination of residual ibuprofen in the environment. In mineral salt medium at pH 6 with 5 mM glucose, Streptomyces sp. D218 transformed ibuprofen concentrations ranging from 0.05 to 0.40 mM in 24 h. The optimal temperature, pH, and initial OD600 nm for ibuprofen transformation by strain D218 were 25-37 °C, 5.0-6.0, and 1.0-1.5, respectively. Strain D218 could simultaneously transform ibuprofen into the intermediates 2-hydroxyibuprofen and ibuprofen amide (IBUA). The two intermediates were further metabolized to 2-hydroxyibuprofen amide (2HIBUA), thus relieving the growth inhibition of ibuprofen in Scenedesmus obliquus. This is the first complete pathway reported for the detoxification of ibuprofen transformation by a Gram-positive strain. These findings further our understanding of the microbial catabolism of the IBU.

Microbial degradation of contaminants of emerging concern: metabolic, genetic and omics insights for enhanced bioremediation

The perpetual release of natural/synthetic pollutants into the environment poses major risks to ecological balance and human health. Amongst these, contaminants of emerging concern (CECs) are characterized by their recent introduction/detection in various niches, thereby causing significant hazards and necessitating their removal. Pharmaceuticals, plasticizers, cyanotoxins and emerging pesticides are major groups of CECs that are highly toxic and found to occur in various compartments of the biosphere. The sources of these compounds can be multipartite including industrial discharge, improper disposal, excretion of unmetabolized residues, eutrophication etc., while their fate and persistence are determined by factors such as physico-chemical properties, environmental conditions, biodegradability and hydrological factors. The resultant exposure of these compounds to microbiota has imposed a selection pressure and resulted in evolution of metabolic pathways for their biotransformation and/or utilization as sole source of carbon and energy. Such microbial degradation phenotype can be exploited to clean-up CECs from the environment, offering a cost-effective and eco-friendly alternative to abiotic methods of removal, thereby mitigating their toxicity. However, efficient bioprocess development for bioremediation strategies requires extensive understanding of individual components such as pathway gene clusters, proteins/enzymes, metabolites and associated regulatory mechanisms. "Omics" and "Meta-omics" techniques aid in providing crucial insights into the complex interactions and functions of these components as well as microbial community, enabling more effective and targeted bioremediation. Aside from natural isolates, metabolic engineering approaches employ the application of genetic engineering to enhance metabolic diversity and degradation rates. The integration of omics data will further aid in developing systemic-level bioremediation and metabolic engineering strategies, thereby optimising the clean-up process. This review describes bacterial catabolic pathways, genetics, and application of omics and metabolic engineering for bioremediation of four major groups of CECs: pharmaceuticals, plasticizers, cyanotoxins, and emerging pesticides.

Patulibacter defluvii sp. nov., Isolated from a Wastewater Treatment Plant in Guangzhou City, China

A novel Gram-stain-positive, aerobic, catalase-positive, oxidase-negative, non-motile, and rod-shaped bacterium with ibuprofen-degrading capacity, designated DM4T, was isolated from the sewage of a wastewater treatment plant (WWTP) in Guangzhou city, China. Strain DM4T grew optimally at 0% (w/v) NaCl, pH 5.0-7.0, and 30 °C, forming white colonies on trypticase soy agar. C18:1ω9c, C18:2ω9.12c and C15:1ω10c were the predominant fatty acids. Results of 16S rRNA gene alignment and phylogenetic analysis indicated that strain DM4T belonged to the genus Patulibacter, was closely related to Patulibacter medicamentivorans DSM 25692T (98.5%) and P. brassicae KCTC 39817T (98.1%). Strain DM4T had a genome size of 5.33Mbp, and the DNA G + C content was 75.0%. The average nucleotide identity (ANI), average amino acid identity (AAI), and digital DNA-DNA hybridisation (dDDH) values between strain DM4T and P. medicamentivorans were 85.2%, 83.9%, and 29.0% respectively, while those between strain DM4T and P. brassicae were 78.5%, 71.3%, and 22.2%, respectively. Strain DM4T could significantly degrade ibuprofen by almost 80% after 84 h of incubation, and the degradation kinetics was well fitted with the first-order kinetics. Evidence from phenotypic, phylogenetic and chemotaxonomic analyses support that strain DM4T (= GDMCC 1.4574T = KCTC 59145T) represents a new species of the genus Patulibacter, for which the name Patulibacter defluvii sp. nov. is proposed.

New bacterial strains for ibuprofen biodegradation: Drug removal, transformation, and potential catabolic genes

Ibuprofen (IBU) is a significant contaminant frequently found in wastewater treatment plants due to its widespread use and limited removal during treatment processes. This leads to its discharge into the environment, causing considerable environmental concerns. The use of microorganisms has recently been recognized as a sustainable method for mitigating IBU contamination in wastewater. In this study, new bacteria capable of growing in a solid medium with IBU as the only carbon source and removing IBU from a liquid medium were isolated from environmental samples, including soil, marine, mine, and olive mill wastewater. Four bacterial strains, namely Klebsiella pneumoniae TIBU2.1, Klebsiella variicola LOIBU1.1, Pseudomonas aeruginosa LOIBU1.2, and Mycolicibacterium aubagnense HPB1.1, were identified through 16S rRNA gene sequencing. These strains demonstrated significant IBU removal efficiencies, ranging from 60 to 100% within 14 days, starting from an initial IBU concentration of 5 mg per litre. These bacteria have not been previously reported in the literature as IBU degraders, making this work a valuable contribution to further studies in the field of bioremediation in environments contaminated by IBU. Based on the IBU removal results, the most promising bacteria, K. pneumoniae TIBU2.1 and M. aubagnense HPB1.1, were selected for an in silico analysis to identify genes potentially involved in IBU biodegradation. Interestingly, in the tests with TIBU2.1, a peak of IBU transformation product(s) was detected by high-performance liquid chromatography, while in the tests with HPB1.1, it was not detected. The emerging peak was analysed by liquid chromatography-mass spectrometry, indicating the presence of possible conjugates between intermediates of IBU biodegradation. The proteins encoded on their whole-genome sequences were aligned with proteins involved in an IBU-degrading pathway reported in bacteria with respective catabolic genes. The analysis indicated that strain HPB1.1 possesses genes encoding proteins similar to most enzymes reported associated with the IBU metabolic pathways used as reference bacteria, while strain TIBU2.1 has genes encoding proteins similar to enzymes involved in both the upper and the lower part of that pathway. Notably, in the tests with the strain having more candidate genes encoding IBU-catabolic enzymes, no IBU transformation products were detected, while in the tests with the strain having fewer of these genes, detection occurred.

Improving the production of 22-hydroxy-23,24-bisnorchol-4-ene-3-one in Mycolicibacterium smegmatis

The 22-hydroxy-23,24-bisnorchol-4-ene-3-one (4-HBC) is a C22 steroid synthon of pharmaceutical interest that can be produced as a lateral end-product of the catabolism of natural sterols (e.g., cholesterol or phytosterols). This work studies the role of an aldehyde dehydrogenase coded by the MSMEG_6563 gene of Mycolicibacterium smegmatis, named msRed, in 4-HBC production. This gene is located contiguously to the MSMEG_6561 encoding the aldolase msSal which catalyses the retroaldol elimination of acetyl-CoA of the metabolite intermediate 22-hydroxy-3-oxo-cholest-4-ene-24-carboxyl-CoA to deliver 3-oxo-4-pregnene-20-carboxyl aldehyde (3-OPA). We have demonstrated that msRed reduces 3-OPA to 4-HBC. Moreover, the role of msOpccR reductase encoded by MSMEG_1623 was also explored confirming that it also performs the reduction of 3-OPA into 4-HBC, but less efficiently than msRed. To obtain a M. smegmatis 4-HBC producer strain we deleted MSMEG_5903 (hsd4A) gene in strain MS6039-5941 (ΔkshB1, ΔkstD1) that produces 4-androstene-3,17-dione (AD) from natural sterols (cholesterol or phytosterols). The triple MS6039-5941-5903 mutant was able to produce 9 g/L of 4-HBC from 14 g/L of phytosterols in 2 L bioreactor, showing a productivity of 0.140 g/L h-1. To improve the metabolic flux of sterols towards the production of 4-HBC we have cloned and overexpressed the msSal and msRed enzymes in the MS6039-5941-5903 mutant rendering a production titter of 12.7 g/L with a productivity of 0.185 g/L h-1, and demonstrating that the new recombinant strain has a great potential for its industrial application.

Ibuprofen degradation by mixed bacterial consortia: Metabolic pathway and microbial community analysis

Degradation of ibuprofen, one of the most consumed drugs globally, by a mixed bacterial consortium was investigated. A contaminated hospital soil was used to enrich a bacterial consortium possessing the ability to degrade 4 mg/L ibuprofen in 6 days, fed on 6 mM acetate as a supplementary carbon source. Maximum ibuprofen degradation achieved was 99.51%, and for optimum ibuprofen degradation modelled statistically, the initial ibuprofen concentration, and temperature were determined to be 0.515 mg/L and 35 °C, respectively. The bacterial community analyses demonstrated an enrichment of Pseudomonas, Achromobacter, Bacillus, and Enterococcus in the presence of ibuprofen, suggesting their probable association with the biodegradation process. The biodegradation pathway developed using open-source metabolite predictors, GLORYx and BioTransformer suggested multiple degradation routes. Hydroxylation and oxidation were found to be the major mechanisms in ibuprofen degradation. Mono-hydroxylated metabolites were identified as well as predicted by the bioinformatics-based packages. Oxidation, dehydrogenation, super-hydroxylation, and hydrolysis were some other identified mechanisms.

Ibuprofen-enhanced biodegradation in solution and sewage sludge by a mineralizing microbial consortium. Shift in associated bacterial communities

Ibuprofen (IBP) is a widely used drug of environmental concern as emerging contaminant due to its low elimination rates by wastewater treatment plants (WWTPs), leading to the contamination of the environment, where IBP is introduced mainly from wastewater discharge and sewage sludge used as fertilizer. This study describes the application of a consortium from sewage sludge and acclimated with ibuprofen (consortium C7) to accelerate its biodegradation both in solution and sewage sludge. 500 mg L-1 IBP was degraded in solution in 28 h, and 66% mineralized in 3 days. IBP adsorbed in sewage sludge (10 mg kg-1) was removed after bioaugmentation with C7 up to 90% in 16 days, with a 5-fold increase in degradation rate. This is the first time that bioaugmentation with bacterial consortia or isolated bacterial strains have been used for IBP degradation in sewage sludge. The bacterial community of consortium C7 was significantly enriched in Sphingomonas wittichii, Bordetella petrii, Pseudomonas stutzeri and Bosea genosp. after IBP degradation, with a special increase in abundance of S. wittichii, probably the main potential bacterial specie responsible for IBP mineralization. Thirteen bacterial strains were isolated from C7 consortium. All of them degraded IBP in presence of glucose, especially Labrys neptuniae. Eight of these bacterial strains (B. tritici, L. neptuniae, S. zoogloeoides, B. petrii, A. denitrificans, S. acidaminiphila, P. nitroreducens, C. flaccumfaciens) had not been previously described as IBP-degraders. The bacterial community that makes up the indigenous consortium C7 appears to have a highly efficient biotic degradation potential to facilitate bioremediation of ibuprofen in contaminated effluents as well as in sewage sludge generated in WWTPs.

Diclofenac, ibuprofen, and paracetamol biodegradation: overconsumed non-steroidal anti-inflammatories drugs at COVID-19 pandemic

The consumption of non-steroidal anti-inflammatory drugs (NSAIDs) have increased significantly in the last years (2020-2022), especially for patients in COVID-19 treatment. NSAIDs such as diclofenac, ibuprofen, and paracetamol are often available without restrictions, being employed without medical supervision for basic symptoms of inflammatory processes. Furthermore, these compounds are increasingly present in nature constituting complex mixtures discarded at domestic and hospital sewage/wastewater. Therefore, this review emphasizes the biodegradation of diclofenac, ibuprofen, and paracetamol by pure cultures or consortia of fungi and bacteria at in vitro, in situ, and ex situ processes. Considering the influence of different factors (inoculum dose, pH, temperature, co-factors, reaction time, and microbial isolation medium) relevant for the identification of highly efficient alternatives for pharmaceuticals decontamination, since biologically active micropollutants became a worldwide issue that should be carefully addressed. In addition, we present a quantitative bibliometric survey, which reinforces that the consumption of these drugs and consequently their impact on the environment goes beyond the epidemiological control of COVID-19.

Analyzing microbial communities and their biodegradation of multiple pharmaceuticals in membrane bioreactors

Pharmaceuticals are of concern to our planet and health as they can accumulate in the environment. The impact of these biologically active compounds on ecosystems is hard to predict, and information on their biodegradation is necessary to establish sound risk assessment. Microbial communities are promising candidates for the biodegradation of pharmaceuticals such as ibuprofen, but little is known yet about their degradation capacity of multiple micropollutants at higher concentrations (100 mg/L). In this work, microbial communities were cultivated in lab-scale membrane bioreactors (MBRs) exposed to increasing concentrations of a mixture of six micropollutants (ibuprofen, diclofenac, enalapril, caffeine, atenolol, paracetamol). Key players of biodegradation were identified using a combinatorial approach of 16S rRNA sequencing and analytics. Microbial community structure changed with increasing pharmaceutical intake (from 1 to 100 mg/L) and reached a steady-state during incubation for 7 weeks on 100 mg/L. HPLC analysis revealed a fluctuating but significant degradation (30-100%) of five pollutants (caffeine, paracetamol, ibuprofen, atenolol, enalapril) by an established and stable microbial community mainly composed of Achromobacter, Cupriavidus, Pseudomonas and Leucobacter. By using the microbial community from MBR1 as inoculum for further batch culture experiments on single micropollutants (400 mg/L substrate, respectively), different active microbial consortia were obtained for each single micropollutant. Microbial genera potentially responsible for degradation of the respective micropollutant were identified, i.e. Pseudomonas sp. and Sphingobacterium sp. for ibuprofen, caffeine and paracetamol, Sphingomonas sp. for atenolol and Klebsiella sp. for enalapril. Our study demonstrates the feasibility of cultivating stable microbial communities capable of degrading simultaneously a mixture of highly concentrated pharmaceuticals in lab-scale MBRs and the identification of microbial genera potentially responsible for the degradation of specific pollutants. KEY POINTS: • Multiple pharmaceuticals were removed by stable microbial communities. • Microbial key players of five main pharmaceuticals were identified.

The Impact of Anti-Inflammatory Drugs on the Prokaryotic Community Composition and Selected Bacterial Strains Based on Microcosm Experiments

Non-steroidal anti-inflammatory drugs (NSAIDs) are increasingly recognized as potential environmental contaminants that may induce toxicity in aquatic ecosystems. This 3-week microcosm experiment explores the acute impacts of NSAIDs, including diclofenac (DCF), ibuprofen (IBU), and acetylsalicylic acid (ASA), on bacterial communities using a wide range of these substances (200-6000 ppm). The results showed that the NSAID-treated microcosms had higher cell count values than control samples, though the diversity of microbial communities decreased. The isolated heterotrophic bacteria mostly belonged to Proteobacteria, particularly Klebsiella. Next-generation sequencing (NGS) revealed that NSAIDs altered the structure of the bacterial community composition, with the proportion of Proteobacteria aligning with the selective cultivation results. Bacteria had higher resistance to IBU/ASA than to DCF. In DCF-treated microcosms, there has been a high reduction of the number of Bacteroidetes, whereas in the microcosms treated with IBU/ASA, they have remained abundant. The numbers of Patescibacteria and Actinobacteria have decreased across all NSAID-treated microcosms. Verrucomicrobia and Planctomycetes have tolerated all NSAIDs, even DCF. Cyanobacteria have also demonstrated tolerance to IBU/ASA treatment in the microcosms. The archaeal community structure was also impacted by the NSAID treatments, with Thaumarchaeota abundant in all microcosms, especially DCF-treated microcosms, while Nanoarchaeota is more typical of IBU/ASA-treated microcosms with lower NSAID concentrations. These results indicate that the presence of NSAIDs in aquatic environments could lead to changes in the composition of microbial communities.

Functional characterization of an efficient ibuprofen-mineralizing bacterial consortium

Ibuprofen (IBU) is a widely used non-steroidal anti-inflammatory drug (NSAID), which has attracted widespread attention due to its high frequency of environmental detection, non-degradability and potential ecological risks. However, little is known about the functional characterization of the highly efficient IBU-mineralizing consortium. In this study, an IBU-mineralizing consortium C6 was obtained by continuous enrichment of the original consortium C1 accumulated the metabolite of 2-Hydroxyibuprofen (2HIBU). Methylobacter, Pseudomonas, and Dokdonella spp. were significantly enriched in the consortium C6. Streptomyces sp. had a relative abundance of about 0.01 % in the consortium C1 but extremely low (< 0.001 %) in the consortium C6. Subsequently, two IBU degraders, Streptomyces sp. D218 and Pseudomonas sp. M20 with detection of 2HIBU or not, were isolated from the consortia C1 and C6, respectively. These results imply that the degradation of IBU in the consortia C1 and C6 may be mainly mediated by key players of Streptomyces and Pseudomonas, respectively. This study showed that the composition of the core functional strains of the bacterial community structure was changed by continuous enrichment, which affected the degradation process of IBU. These findings provide new insights into our understanding of the biotransformation process of NSAIDs and provide valuable strain resources for bioremediation.

Ibuprofen: Toxicology and Biodegradation of an Emerging Contaminant

The anti-inflammatory drug ibuprofen is considered to be an emerging contaminant because of its presence in different environments (from water bodies to soils) at concentrations with adverse effects on aquatic organisms due to cytotoxic and genotoxic damage, high oxidative cell stress, and detrimental effects on growth, reproduction, and behavior. Because of its high human consumption rate and low environmental degradation rate, ibuprofen represents an emerging environmental problem. Ibuprofen enters the environment from different sources and accumulates in natural environmental matrices. The problem of drugs, particularly ibuprofen, as contaminants is complicated because few strategies consider them or apply successful technologies to remove them in a controlled and efficient manner. In several countries, ibuprofen's entry into the environment is an unattended contamination problem. It is a concern for our environmental health system that requires more attention. Due to its physicochemical characteristics, ibuprofen degradation is difficult in the environment or by microorganisms. There are experimental studies that are currently focused on the problem of drugs as potential environmental contaminants. However, these studies are insufficient to address this ecological issue worldwide. This review focuses on deepening and updating the information concerning ibuprofen as a potential emerging environmental contaminant and the potential for using bacteria for its biodegradation as an alternative technology.

Biodegradation of Microtoxic Phenylpropanoids (Phenylpropanoic Acid and Ibuprofen) by Bacteria and the Relevance for Their Removal from Wastewater Treatment Plants

The NSAID ibuprofen (2-(4-isobutylphenyl)propanoic acid) and the structurally related 3-phenylpropanoic acid (3PPA), are widely used pharmaceutical and personal care products (PPCPs) which enter municipal waste streams but whose relatively low rates of elimination by wastewater treatment plants (WWTPs) are leading to the contamination of aquatic resources. Here, we report the isolation of three bacterial strains from a municipal WWTP, which as a consortium are capable of mineralizing ibuprofen. These were identified as the Pseudomonas citronellolis species, termed RW422, RW423 and RW424, in which the first two of these isolates were shown to contain the catabolic ipf operon responsible for the first steps of ibuprofen mineralization. These ipf genes which are associated with plasmids could, experimentally, only be transferred between other Sphingomonadaceae species, such as from the ibuprofen degrading Sphingopyxis granuli RW412 to the dioxins degrading Rhizorhabdus wittichii RW1, generating RW421, whilst a transfer from the P. citronellolis isolates to R. wittichii RW1 was not observed. RW412 and its derivative, RW421, as well as the two-species consortium RW422/RW424, can also mineralize 3PPA. We show that IpfF can convert 3PPA to 3PPA-CoA; however, the growth of RW412 with 3PPA produces a major intermediate that was identified by NMR to be cinnamic acid. This and the identification of other minor products from 3PPA allows us to propose the major pathway used by RW412 to mineralize 3PPA. Altogether, the findings in this study highlight the importance of ipf genes, horizontal gene transfer, and alternative catabolic pathways in the bacterial populations of WWTPs to eliminate ibuprofen and 3PPA.

Recombinant yeast for production of the pain receptor modulator nonivamide from vanillin

We report on the development of a method based on recombinant yeast Saccharomyces cerevisiae to produce nonivamide, a capsaicinoid and potent agonist of the pain receptor TRPV1. Nonivamide was produced in a two-step batch process where yeast was i) grown aerobically on glucose and ii) used to produce nonivamide from vanillin and non-anoic acid by bioconversion. The yeast was engineered to express multiple copies of an amine transaminase from Chromobacterium violaceum (CvTA), along with an NADH-dependent alanine dehydrogenase from Bacillus subtilis (BsAlaDH) to enable efficient reductive amination of vanillin. Oxygen-limited conditions and the use of ethanol as a co-substrate to regenerate NADH were identified to favour amination over the formation of the by-products vanillic alcohol and vanillic acid. The native alcohol dehydrogenase ADH6 was deleted to further reduce the formation of vanillic alcohol. A two-enzyme system consisting of an N-acyltransferase from Capsicum annuum (CaAT), and a CoA ligase from Sphingomonas sp. Ibu-2 (IpfF) was co-expressed to produce the amide. This study provides proof of concept for yeast-based production of non-ivamide by combined transamination and amidation of vanillin.

Weak electrostimulation enhanced the microbial transformation of ibuprofen and naproxen

Ibuprofen (IBU) and naproxen (NPX) are commonly used non-steroidal anti-inflammatory drugs (NSAIDs) with high-risk quotients and are frequently detected in various aquatic environments. A weak electrostimulated biofilm not only had improved removal efficiencies to IBU and NPX, but also transformed different enantiomers with comparable efficiency and without configuration inversion. IBU was transformed mainly by oxidation (hydroxyl-IBU, carboxy-IBU), while NPX was mainly detoxified. The microbial analysis of IBU and NPX biofilm showed that the shared core consortia (> 1%) contained typical electro-active bacteria (Geobacter, Desulfovibrio), fermenters (Petrimonas, Acetobacterium) and potential degraders (Pandoraea, Nocardiaceae), which exhibited synergistic interactions by exchanging the additional electrons, H⁺, coenzyme NAD(H) or NAD(P) (H) and energy. The fungal community has a significant correlation to those core bacteria and they may also play transformation roles with their diverse enzymes. Plenty of nonspecific oxidoreductase, decarboxylase, hydrolase, cytochrome P450, and other enzymes relating to xenobiotic degradation were high-abundance encoded by the core consortia and could potentially participate in IBU and NPX biotransformation. This study offers new insights into the functional microbes and enzymes working on complex NSAIDs biotransformation and provided a feasible strategy for the enhanced removal of NSAIDs (especially IBU and NPX).

Nocardioides carbamazepini sp. nov., an ibuprofen degrader isolated from a biofilm bacterial community enriched on carbamazepine

From the metagenome of a carbamazepine amended selective enrichment culture the genome of a new to science bacterial species affiliating with the genus Nocardioides was reconstructed. From the same enrichment an aerobic actinobacterium, strain CBZ_1^T, sharing 99.4% whole-genome sequence similarity with the reconstructed Nocardioides sp. bin genome was isolated. On the basis of 16S rRNA gene sequence similarity the novel isolate affiliated to the genus Nocardioides, with the closest relatives Nocardioides kongjuensis DSM19082^T (98.4%), Nocardioides daeguensis JCM17460^T (98.4%) and Nocardioides nitrophenolicus DSM15529^T (98.2%). Using a polyphasic approach it was confirmed that the isolate CBZ_1^T represents a new phyletic lineage within the genus Nocardioides. According to metagenomic, metatranscriptomic studies and metabolic analyses strain CZB_1^T was abundant in both carbamazepine and ibuprofen enrichments, and harbors biodegradative genes involved in the biodegradation of pharmaceutical compounds. Biodegradation studies supported that the new species was capable of ibuprofen biodegradation. After 7 weeks of incubation, in mineral salts solution supplemented with glucose (3 g l^-1) as co-substrate, 70% of ibuprofen was eliminated by strain CBZ_1^T at an initial conc. of 1.5 mg l^-1. The phylogenetic, phenotypic and chemotaxonomic data supported the classification of strain CBZ_1^T to the genus Nocardioides, for which the name Nocardioides carbamazepini sp. nov. (CBZ_1^T = NCAIM B.0.2663 = LMG 32395) is proposed. To the best of our knowledge, this is the first study that reports simultaneous genome reconstruction of a new to science bacterial species using metagenome binning and at the same time the isolation of the same novel bacterial species.

Genetic Characterization of the Ibuprofen-Degradative Pathway of Rhizorhabdus wittichii MPO218

Ibuprofen is one of the most common drugs found as a contaminant in soils, sediments, and waters. Although several microorganisms able to metabolize ibuprofen have been described, the metabolic pathways and factors limiting biodegradation in nature remain poorly characterized. Among the bacteria able to grow on ibuprofen, three different strains belonging to Sphingomonadaceae and isolated from different geographical locations carry the same set of genes required for the upper part of the ibuprofen metabolic pathway. Here, we have studied the metabolic pathway of Rhizorhabdus wittichii MPO218, identifying new genes required for the lower part of the ibuprofen metabolic pathway. We have identified two new DNA regions in MPO218 involved in the metabolism of ibuprofen. One is located on the MPO218 chromosome and appears to be required for the metabolism of propionyl-CoA through the methylmalonyl-CoA pathway. Although involved in ibuprofen metabolism, this region is not strictly necessary for growing using ibuprofen. The second region belongs to the pIBU218 plasmid and comprises two gene clusters containing aromatic compound biodegradation genes, part of which are necessary for ibuprofen degradation. We have identified two genes required for the first two steps of the lower part of the ibuprofen metabolic pathway (ipfL and ipfM), and, based on our results, we propose the putative complete pathway for ibuprofen metabolism in strain MPO218.

IMPORTANCE Ibuprofen, one of the most common pharmaceutical contaminants in natural environments, is toxic for some aquatic and terrestrial organisms. The main source of environmental ibuprofen is wastewater, so improving wastewater treatment is of relevant importance. Although several microorganisms capable of biodegrading ibuprofen have been described, the metabolic pathways and their genetic bases remain poorly understood. Three bacterial strains of the family Sphingomonadaceae capable of using ibuprofen as carbon and energy source have been described. Although the genes involved in the upper part of the degradation pathway (ipfABDEF cluster) have been identified, those required for the lower part of the pathway remained unknown. Here, we have confirmed the requirement of the ipf cluster for the generation of isobutyl catechol and have identified the genes involved in the subsequent transformation of the metabolic products. Identification of genes involved in ibuprofen degradation is essential to developing improved strains for the removal of this contaminant.

Characteristics and growth kinetics of biomass of Citrobacter freundii strains PYI-2 and Citrobacter portucalensis strain YPI-2 during the biodegradation of Ibuprofen

Ibuprofen (IBU) is the third most commonly used analgesic drug in the world. It enters the water system as a result of human excretion-based wastewater discharges. Hence, it attracts the attention of environmentalists for its ecological fate and degradation behavior. In this study, the two IBU degrading bacterial strains, Citrobacter freundii strain PYI-2 (MT039504) and Citrobacter portucalensis strain YPI-2 (MN744335), were isolated from industrial wastewater samples using an enrichment culture method, identified, and characterized. Physiological and batch culture degradation studies have indicated that these strains involved in IBU degradation and the intermediates produced during the process were analyzed. These strains degrade IBU in the batch culture. The optimum pH was reported for degradation of the PYI2 strain (6.9) and YPI2 strain (5.8), and the optimum temperatures were 42°C and 32°C, respectively. Biomass kinetic analysis of these strains was performed based on physical parameters (temperature, pH, and rpm) and confirmed by the experimental study. As indicated in the GC-MS chromatogram peaks, viz., hydroxyibuprofen, 2-(4-hydroxyphenylpropionic acid), 1,4-hydroquinone, and 2-hydroxy-1,4-quinol various intermediates compounds of degradation pathway were observed. Finally, through the GC-MS data, the metabolic pathway for degradation was predicted. In the study, it was confirmed that Citrobacter freundii strain PYI-2 and Citrobacter portucalensis strain YPI-2 exhibit metabolic potential for the biodegradation of IBU and can be further deployed in bioremediation.

Stable isotope probing reveals specific assimilating bacteria of refractory organic compounds in activated sludge

Activated sludge in wastewater treatment bioreactors contains diverse bacteria, while little is known about the community structure of bacteria responsible for degradation of refractory organic compounds (ROCs). In this study, 10 ROCs frequently detected in sewage were investigated, and the potential bacteria degrading these ROCs were analyzed by DNA stable isotope probing and high-throughput sequencing. The results showed that the bacterial communities responsible for degradation of different ROCs were largely different. A total of 84 bacterial genera were found to be involved in degrading at least one of the 10 ROCs, however, only six genera (Acinetobacter, Bacteroides, Bosea, Brevundimonas, Lactobacillus and Pseudomonas) were common to all 10 ROCs. This suggests that different ROCs may have specific assimilating bacteria in the activated sludge. Our results also showed that these ROC-degrading bacteria are difficult to isolate by conventional methods and that most of them have relatively low relative abundance in municipal wastewater treatment bioreactors. Development of new technologies to increase the abundance and activity of these bacteria may significantly improve the removal efficiency of ROCs from wastewater.

Metabolism of non-steroidal anti-inflammatory drugs by non-target wild-living organisms

The presence of the non-steroidal anti-inflammatory drugs (NSAIDs) in the environment is a fact, and aquatic and soil organisms are chronically exposed to trace levels of these emerging pollutants. This review presents the current state of knowledge on the metabolic pathways of NSAIDs in organisms at various levels of biological organisation. More than 150 publications dealing with target or non-target analysis of selected NSAIDs (mainly diclofenac, ibuprofen, and naproxen) were collected. The metabolites of phase I and phase II are presented. The similarity of NSAIDs metabolism to that in mammals was observed in bacteria, microalgae, fungi, higher plants, invertebrates, and vertebrates. The differences, such as newly detected metabolites, the extracellular metabolism observed in bacteria and fungi, or phase III metabolism in plants, are highlighted. Metabolites detected in plants (conjugates with sugars and amino acids) but not found in any other organisms are described. Selected, in-depth studies with isolated bacterial strains showed the possibility of transforming NSAIDs into assimilable carbon sources. It has been found that some of the metabolites show higher toxicity than their parent forms. The presence of metabolites of NSAIDs in the environment is the cumulative effect of their introduction with wastewaters, their formation in wastewater treatment plants, and their transformation by non-target wild-living organisms.

Clover Root Exudates Favor Novosphingobium sp. HR1a Establishment in the Rhizosphere and Promote Phenanthrene Rhizoremediation

Rhizoremediation is based on the ability of microorganisms to metabolize nutrients from plant root exudates and, thereby, to cometabolize or even mineralize toxic environmental contaminants. Novosphingobium sp. HR1a is a bacterial strain able to degrade a wide variety of polycyclic aromatic hydrocarbons (PAHs). Here, we have demonstrated that the number of CFU in microcosms vegetated with clover was almost 2 orders of magnitude higher than that in nonvegetated microcosms or microcosms vegetated with rye-grass or grass. Strain HR1a was able to eliminate 92% of the phenanthrene in the microcosms with clover after 9 days. We have studied the molecular basis of the interaction between strain HR1a and clover by phenomic, metabolomic, and transcriptomic analyses. By measuring the relative concentrations of several metabolites exudated by clover both in the presence and in the absence of the bacteria, we identified some compounds that were probably consumed in the rhizosphere; the transcriptomic analyses confirmed the expression of genes involved in the catabolism of these compounds. By using a transcriptional fusion of the green fluorescent protein (GFP) to the promoter of the gene encoding the dioxygenase involved in the degradation of PAHs, we have demonstrated that this gene is induced at higher levels in clover microcosms than in nonvegetated microcosms. Therefore, the positive interaction between clover and Novosphingobium sp. HR1a during rhizoremediation is a result of the bacterial utilization of different carbon and nitrogen sources released during seedling development and the capacity of clover exudates to induce the PAH degradation pathway. IMPORTANCE The success of an eco-friendly and cost-effective strategy for soil decontamination is conditioned by the understanding of the ecology of plant-microorganism interactions. Although many studies have been published about the bacterial metabolic capacities in the rhizosphere and about rhizoremediation of contaminants, there are fewer studies dealing with the integration of bacterial metabolic capacities in the rhizosphere during PAH bioremediation, and some aspects still remain controversial. Some authors have postulated that the presence of easily metabolizable carbon sources in root exudates might repress the expression of genes required for contaminant degradation, while others found that specific rhizosphere compounds can induce such genes. Novosphingobium sp. HR1a, which is our model organism, has two characteristics desirable in bacteria for use in remediation: its ubiquity and the capacity to degrade a wide variety of contaminants. We have demonstrated that this bacterium consumes several rhizospheric compounds without repression of the genes required for the mineralization of PAHs. In fact, some compounds even induced their expression.

Loading, transport, and treatment of emerging chemical and biological contaminants of concern in stormwater

Stormwater is a largely uncontrolled source of pollution in rural and urban environments across the United States. Concern regarding the growing diversity and abundance of pollutants in stormwater, as well as their impacts on water quality, has grown significantly over the past several decades. In addition to conventional contaminants like nutrients and heavy metals, stormwater is a well-documented source of many contaminants of emerging concern, which can be toxic to both aquatic and terrestrial organisms and remain a barrier to maintaining high quality water resources. Chemical pollutants like pharmaceuticals and personal care products, industrial pollutants such as per- and polyfluoroalkyl substances, and tire wear particles in stormwater are of great concern due to their toxic, genotoxic, mutagenic and carcinogenic properties. Emerging microbial contaminants such as pathogens and antibiotic resistance genes also represent significant threats to environmental water quality and human health. Knowledge regarding the transport, behavior, and the remediation capacity of these pollutants in runoff is key for addressing these pollutants in situ and minimizing ecosystem perturbations. To this end, this review paper will analyze current understanding of these contaminants in stormwater runoff in terms of their transport, behavior, and bioremediation potential.

Effluent decontamination by the ibuprofen-mineralizing strain, Sphingopyxis granuli RW412: Metabolic processes

The high global consumption of ibuprofen and its limited elimination by wastewater treatment plants (WWTPs), has led to the contamination of aquatic systems by this common analgesic and its metabolites. The potentially negative environmental and public health effects of this emerging contaminant have raised concerns, driving the demand for treatment technologies. The implementation of bacteria which mineralize organic contaminants in biopurification systems used to decontaminate water or directly in processes in WWTPs, is a cheap and sustainable means for complete elimination before release into the environment. In this work, an ibuprofen-mineralizing bacterial strain isolated from sediments of the River Elbe was characterized and assayed to remediate different ibuprofen-polluted media. Strain RW412, which was identified as Sphingopyxis granuli, has a 4.48 Mb genome which includes plasmid sequences which harbor the ipf genes that encode the first steps of ibuprofen mineralization. Here, we confirm that these genes encode enzymes which initiate CoA ligation to ibuprofen, followed by aromatic ring activation by a dioxygenase and retroaldol cleavage to unequivocally produce 4-isobutylcatechol and propionyl-CoA which then undergo further degradation. In liquid mineral salts medium, the strain eliminated more than 2 mM ibuprofen within 74 h with a generation time of 16 h. Upon inoculation into biopurification systems, it eliminated repeated doses of ibuprofen within a few days. Furthermore, in these systems the presence of RW412 avoided the accumulation of ibuprofen metabolites. In ibuprofen-spiked effluent from a municipal WWTP, ibuprofen removal by this strain was 7 times faster than by the indigenous microbiota. These results suggest that this strain can persist and remain active under environmentally relevant conditions, and may be a useful innovation to eliminate this emerging contaminant from urban wastewater treatment systems.

Fabrication of black TiO2-x /NiFe2O4 supported on diatomaceous earth with enhanced sonocatalytic activity for ibuprofen mitigation

This study reports a facile fabrication of black TiO_2-x /NiFe₂O₄ (Ti³⁺ self-doped titania coupled with nickel ferrite), an efficient sonocatalyst for ibuprofen (IBP) mitigation. Compared with TiO_2-x or NiFe₂O₄, TiO_2-x /NiFe₂O₄ heterojunction displayed higher sonocatalytic activity, and their immobilization onto diatomaceous earth further enhanced mitigation efficiency due to the synergy between adsorption and sonocatalysis. About 96.7% of 10 mg l^-1 IBP was removed in 100 min using 0.7 g l^-1 catalyst at pH = 6, with the ultrasonic power of 144 W and frequency of 60 KHz. Quenching experiment results demonstrated the roles of reactive species. The intermediates during IBP sono-oxidation were determined by HPLC-MS method, and the acute toxicity was evaluated. Furthermore, the reaction mechanism was proposed. The sonocatalyst revealed excellent reusability, suggesting itself promising for wastewater treatment.

Drug response in association with pharmacogenomics and pharmacomicrobiomics: towards a better personalized medicine

Researchers have long been presented with the challenge imposed by the role of genetic heterogeneity in drug response. For many years, Pharmacogenomics and pharmacomicrobiomics has been investigating the influence of an individual's genetic background to drug response and disposition. More recently, the human gut microbiome has proven to play a crucial role in the way patients respond to different therapeutic drugs and it has been shown that by understanding the composition of the human microbiome, we can improve the drug efficacy and effectively identify drug targets. However, our knowledge on the effect of host genetics on specific gut microbes related to variation in drug metabolizing enzymes, the drug remains limited and therefore limits the application of joint host-microbiome genome-wide association studies. In this paper, we provide a historical overview of the complex interactions between the host, human microbiome and drugs. While discussing applications, challenges and opportunities of these studies, we draw attention to the critical need for inclusion of diverse populations and the development of an innovative and combined pharmacogenomics and pharmacomicrobiomics approach, that may provide an important basis in personalized medicine.

Isolation and genomic characterization of the ibuprofen-degrading bacterium Sphingomonas strain MPO218

The presence of pharmaceutical compounds in waters and soils is of particular concern because these compounds can be biologically active, even at environmental concentrations. Most pharmaceutical contaminants result from inefficient removal of these compounds during wastewater treatment. Although microorganisms able to biodegrade pharmaceuticals compounds have been described, the isolation and characterization of new bacterial strains capable of degrading drugs remain important to improve the removal of this pollutant. In this work, we describe the Sphingomonas wittichii strain MPO218 as able to use ibuprofen as the sole carbon and energy source. The genome of MPO218 consists of a circular chromosome and two circular plasmids. Our analysis shows that the largest plasmid, named pIBU218, is conjugative and can horizontally transfer the capability of growing on ibuprofen after conjugation with another related bacterium, Sphingopyxis granuli TFA. This plasmid appears to be unstable since it undergoes different deletions in absence of selection when growth on ibuprofen is not selected. This is the first described example of a natural and conjugative plasmid that enables growth on ibuprofen and is another example of how horizontal gene transfer plays a crucial role in the evolution of bacteria.

Bacterial ecotoxicity and shifts in bacterial communities associated with the removal of ibuprofen, diclofenac and triclosan in biopurification systems

The proliferation and possible adverse effects of emerging contaminants such as pharmaceutical and personal care products (PPCPs) in waters and the environment is a cause for increasing concern. We investigated the dissipation of three PPCPs: ibuprofen (IBP), diclofenac (DCF) and triclosan (TCS), separately and in mixtures, in the ppm range in biopurification system (BPS) microcosms, paying special attention to their effect on bacterial ecotoxicity, as well as bacterial community structure and composition. The results reveal that BPS microcosms efficiently dissipate IBP and DCF with 90% removed after 45 and 84 days of incubation, respectively. However, removal of TCS required a longer incubation period of 127 days for 90% removal. Furthermore, dissipation of the PPCPs was slower when a mixture of all three was applied to BPS microcosms. TCS had an initial negative effect on bacterial viability by a decrease of 34-43% as measured by live bacterial cell counts using LIVE/DEAD® microscopy; however, this effect was mitigated when the three PPCPs were present simultaneously. The bacterial communities in BPS microcosms were more affected by incubation time than by the PPCPs used. Nonetheless, the PPCPs differentially affected the composition and relative abundance of bacterial taxa. IBP and DCF initially increased bacterial diversity and richness, while exposure to TCS generally provoked an opposite effect without full recovery at the end of the incubation period. TCS, which negatively affected the relative abundance of Acidobacteria, Methylophilales, and Legionellales, had the largest impact on bacterial groups. Biomarker OTUs were identified in the BPS microcosms which were constrained to higher concentrations of the PPCPs and thus are likely to harbour degradation and/or detoxification mechanisms. This study reveals for the first time the effect of PPCPs on bacterial ecotoxicity and diversity in biopurification system microcosms and also facilitates the design of further applications of biomixtures to eliminate PPCPs.

Ibuprofen Degradation and Associated Bacterial Communities in Hyporheic Zone Sediments

Ibuprofen, a non-steroidal anti-inflammatory pain reliever, is among pharmaceutical residues of environmental concern ubiquitously detected in wastewater effluents and receiving rivers. Thus, ibuprofen removal potentials and associated bacteria in the hyporheic zone sediments of an impacted river were investigated. Microbially mediated ibuprofen degradation was determined in oxic sediment microcosms amended with ibuprofen (5, 40, 200, and 400 µM), or ibuprofen and acetate, relative to an un-amended control. Ibuprofen was removed by the original sediment microbial community as well as in ibuprofen-enrichments obtained by re-feeding of ibuprofen. Here, 1-, 2-, 3-hydroxy- and carboxy-ibuprofen were the primary transformation products. Quantitative real-time PCR analysis revealed a significantly higher 16S rRNA abundance in ibuprofen-amended relative to un-amended incubations. Time-resolved microbial community dynamics evaluated by 16S rRNA gene and 16S rRNA analyses revealed many new ibuprofen responsive taxa of the Acidobacteria, Actinobacteria, Bacteroidetes, Gemmatimonadetes, Latescibacteria, and Proteobacteria. Two ibuprofen-degrading strains belonging to the genera Novosphingobium and Pseudomonas were isolated from the ibuprofen-enriched sediments, consuming 400 and 300 µM ibuprofen within three and eight days, respectively. The collective results indicated that the hyporheic zone sediments sustain an efficient biotic (micro-)pollutant degradation potential, and hitherto unknown microbial diversity associated with such (micro)pollutant removal.

Ibuprofen as an emerging organic contaminant in environment, distribution and remediation

Pharmaceutical and personal care products (PPCPs) are the one of sub-class under emerging organic contaminants (EOCs). Ibuprofen is the world's third most consumable drug. This drug enters into our water system through human pharmaceutical use. It attracts the attention of environmentalist on the basis of risk associated, presence and transformation in the environment. The detection and removal are the two key area where we need to focus. The concentration of such compounds in waterbodies detected through conventional and also by the advanced methods. This review we described the available technologies including chemical, physical and biological methods, etc used the for removal of Ibuprofen. The pure culture based method, mixed culture approach and activated sludge culture approach focused and pathway of degradation of ibuprofen was deciphered by using the various methods of structure determination. The various degradation methods used for Ibuprofen are discussed. The advanced methods coupled with physical, chemical, biological, chemical methods like ozonolysis, oxidation and adsorption, nanotechnology based methods, nanocatalysis and use of nonosensors to detect the presence of small amount in waterbodies can enhance the future degradation of this drug. It is necessary to develop the new detection methods to enhance the detection of such pollutants. With the developments in new detection methods based on GC-MS//MS, HPLC, LC/MS and nanotechnology based sensors makes easier detection of these compounds which can detect even very minute amount with great sensitivity and in less time. Also, the isolation and characterization of more potent microbial strains and nano-photocatalysis will significantly increase the future degradation of such harmful compounds from the environment.

From Laboratory Tests to the Ecoremedial System: The Importance of Microorganisms in the Recovery of PPCPs-Disturbed Ecosystems

The presence of a wide variety of emerging pollutants in natural water resources is an important global water quality challenge. Pharmaceuticals and personal care products (PPCPs) are known as emerging contaminants, widely used by modern society. This objective ensures availability and sustainable management of water and sanitation for all, according to the 2030 Agenda. Wastewater treatment plants (WWTP) do not always mitigate the presence of these emerging contaminants in effluents discharged into the environment, although the removal efficiency of WWTP varies based on the techniques used. This main subject is framed within a broader environmental paradigm, such as the transition to a circular economy. The research and innovation within the WWTP will play a key role in improving the water resource management and its surrounding industrial and natural ecosystems. Even though bioremediation is a green technology, its integration into the bio-economy strategy, which improves the quality of the environment, is surprisingly rare if we compare to other corrective techniques (physical and chemical). This work carries out a bibliographic review, since the beginning of the 21st century, on the biological remediation of some PPCPs, focusing on organisms (or their by-products) used at the scale of laboratory or scale-up. PPCPs have been selected on the basics of their occurrence in water resources. The data reveal that, despite the advantages that are associated with bioremediation, it is not the first option in the case of the recovery of systems contaminated with PPCPs. The results also show that fungi and bacteria are the most frequently studied microorganisms, with the latter being more easily implanted in complex biotechnological systems (78% of bacterial manuscripts vs. 40% fungi). A total of 52 works has been published while using microalgae and only in 7% of them, these organisms were used on a large scale. Special emphasis is made on the advantages that are provided by biotechnological systems in series, as well as on the need for eco-toxicological control that is associated with any process of recovery of contaminated systems.

Increasing ibuprofen degradation in constructed wetlands by bioaugmentation with gravel containing biofilms of an ibuprofen-degrading Sphingobium yanoikuyae

The aim of this study was to investigate the removal of ibuprofen in laboratory scale constructed wetlands. Four (planted and unplanted) laboratory-scale horizontal subsurface flow constructed wetlands were supplemented with ibuprofen in order to elucidate (i) the role of plants on ibuprofen removal and (ii) to evaluate the removal performance of a bioaugmented lab scale wetland. The planted systems showed higher ibuprofen removal efficiency than an unplanted one. The system planted with Juncus effusus was found to have a higher removal rate than the system planted with Phalaris arundinacea. The highest removal rate of ibuprofen was found after inoculation of gravel previously loaded with a newly isolated ibuprofen-degrading bacterium identified as Sphingobium yanoikuyae. This experiment showed that more than 80 days of CW community adaptation for ibuprofen treatment could be superseded by bioaugmentation with this bacterial isolate.

Metabolite identification of ibuprofen biodegradation by Patulibacter medicamentivorans under aerobic conditions

Ibuprofen (IBU) is a non-steroidal anti-inflammatory drug that is becoming increasingly recognized as an important micropollutant to be monitored in wastewater treatment plants (WWTP), since it has been detected in effluents at the µg L^-1 level. The IBU metabolites from biological degradation are not completely understood and can represent a threat to natural aquatic systems. P. medicamentivorans was previously isolated from WWTP sludge and found to be capable of IBU degradation. The aerobic biodegradation of ibuprofen by this organism was investigated in a batch lab-scale reactor for the identification of the metabolites formed. The metabolites were analysed and putatively identified by HPLC-DAD-MS/MS and GC-MS and biodegradation pathways were proposed. The toxicity and the biodegradability potential of the metabolites were also investigated. The results showed that IBU biotransformation was achieved by hydroxylation followed by the formation of a carboxylic acid in the IBU molecule and by the formation of a catechol, allowing the aromatic ring cleavage. Two biodegradation pathways were proposed: in one, the metabolites generated from the enzymatic action correspond to a less biodegradable chemical structure of the intermediate products (isobutylbenzene and 3-isobutylphenol), with comparatively higher toxicity; in the other mechanism, more oxidable chemical structures were formed with less toxicity and higher biodegradability. This suggests that the biodegradation of IBU by P. medicamentivorans can take place by more than one mechanism regarding the enzymes formed by this Gram-positive bacterium, with subsequent oxidation of the parent compound to overall more soluble and less toxic compounds to fish, daphnia and green algae.

Ibuprofen biodegradation by hospital, municipal, and distillery activated sludges

Ibuprofen (IBU) has been considered as one of emergent pharmaceutical contaminants in environments due to its occurrences in natural water bodies. Some reports suggested that the IBU was biodegradable but details about biodegradation pathways and functional microbial community were still not fully clear. This study was aimed to assess IBU biodegradation using three different activated sludges (i.e. H: hospital, M: municipal, and D: distillery) with foci on surmising degradation pathway based on UPLC/Q-ToF/MS (ultra-performance liquid chromatography quadrupole time of flight mass spectrometry) analyses and concluding microbial community according to high-throughput sequencing for partial 16S rRNA gene. Results showed that some IBU (∼5 mg/L) was able to be degraded only by sludges H and M during 2-5 days incubation under aerobic conditions. From LC/MS analysis of degradation byproducts, two major ring-opening precursors were identified in extracted ion chromatogram data. Ring-opening degradation pathways leading to the formation of low-molecular-weight carboxylic acids were elucidated. Additionally, the principal coordinate analyses using Fast UniFrac method for the partial 16S rRNA gene showed the microbial communities in the three sludges were significantly different but typically with high proportion of sequences matched gene fragments from Proteobacteria phylum. Some sequences with first matches with previously reported IBU degraders (i.e. Nocardia sp., Sphingomonas sp., and Variovorax sp.) were only found in the sludges H and M which showed capability for IBU biodegradation. These results demonstrated some functional microbes in activated sludges from hospital and municipal WWTPs had potential to break down IBU into smaller molecules.

The Future of Microbiome-Based Therapeutics in Clinical Applications

The microbiome, a collection of microorganisms, their genomes, and the surrounding environmental conditions, is akin to a human organ, and knowledge is emerging on its role in human health and diseases. The influence of the microbiome in drug response has only been investigated in detail for the last 10 years. The human microbiome is a complex and highly dynamic system, which varies dramatically between individuals, yet there exists a common core microbiome that is heritable and can be transmitted to progeny. Here, we review the role of the human microbiome, which is now widely accepted as a major factor that drives the interpersonal variation in therapeutic response. We describe examples in which the microbiome modifies drug action. Despite its complexity, the microbiome can be readily altered, with the potential to increase the benefits and reduce the toxicity and side effects associated with pharmaceutical drugs. The potential of new microbiome-based strategies, such as fecal microbiota transplant, probiotics, and phage therapy, as promising medical therapeutics are outlined. We also suggest a combination reductionist and system-level approaches that could be applied to further investigate the role of microbiota in drug metabolism modulation of drug response. Finally, we emphasize the importance of combining microbiome and pharmacology studies as a novel means to treat disease and reduce side effects.

Bioremoval of non-steroidal anti-inflammatory drugs by Pseudoxanthomonas sp. DIN-3 isolated from biological activated carbon process

The presence of non-steroidal anti-inflammatory drugs (NSAIDs) in the environment is an emerging concern owing to their potential threat on aquatic ecosystems and living organisms. To investigate the bioremoval potential of a biological activated carbon (BAC) filter for the removal of NSAIDs, removal of diclofenac (DCF), ibuprofen (IBU), and naproxen (NAP) by biofilms on a bench-scaled BAC column operated for 400 days was studied. The results showed that the BAC column effectively removed the three NSAIDs (>90%). One bacterial strain isolated from the BAC, Pseudoxanthomonas sp. DIN-3, was able to simultaneously remove DCF, IBU, and NAP, which were supplied as the sole carbon source. In 14 days, 23%, 41%, and 39% of DCF, IBU, and NAP (50 μg L^-1) were bioremoved, respectively, and strain DIN-3 eliminated IBU more rapidly than the other two NSAIDs. If only a single drug was added as the sole carbon source, ignoring the other drugs, the removal ability was overestimated by 5.0-27.0%. More efficient bioremoval was achieved, concomitantly with bacterial growth, via a co-metabolism with acetate, glucose, or methanol. Their intermediates were identified by UPLC-QQQ-MS, and their respective degradation pathways were also proposed. Moreover, based on the complete genome sequence of strain DIN-3, 49 related genes encoding the main enzymes involved in DCF, IBU, and NAP biodegradation were identified, including hemE, lpd, yihx, ligC, pobA, and ligA. These results suggested that Pseudoxanthomonas sp. DIN-3 is a potential degrader of DCF, IBU, and NAP, and to the best of our knowledge, this is the first report that demonstrates the bioremoval of DCF, IBU, and NAP simultaneously by an individual bacterial strain isolated from the environment. However, the bioremoval potential should be evaluated when assessing the applicability of the strain in the environment because of the combined effects of various pharmaceutical contaminants. The obtained results provide a foundation for the use of Pseudoxanthomonas sp. DIN-3 in the bioremoval of polycyclic NSAID-contaminated environments.

Removal of pharmaceuticals and personal care products using constructed wetlands: effective plant-bacteria synergism may enhance degradation efficiency

Post-industrial era has witnessed significant advancements at unprecedented rates in the field of medicine and cosmetics, which has led to affluent use of pharmaceuticals and personal care products (PPCPs). However, this has exacerbated the influx of various pollutants in the environment affecting living organisms through multiple routes. Thousands of PPCPs of various classes-prescription and non-prescription drugs-are discharged directly into the environment. In this review, we have surveyed literature investigating plant-based remediation practices to remove PPCPs from the environment. Our specific aim is to highlight the importance of plant-bacteria interplay for sustainable remediation of PPCPs. The green technologies not only are successfully curbing organic pollutants but also have displayed certain limitations. For example, the presence of biologically active compounds within plant rhizosphere may affect plant growth and hence compromise the phytoremediation potential of constructed wetlands. To overcome these hindrances, combined use of plants and beneficial bacteria has been employed. The microbes (both rhizo- and endophytes) in this type of system not only degrade PPCPs directly but also accelerate plant growth by producing growth-promoting enzymes and hence remediation potential of constructed wetlands.

Biotransformation of the Fluorinated Nonsteroidal Anti-Inflammatory Pharmaceutical Flurbiprofen in Activated Sludge Results in Accumulation of a Recalcitrant Fluorinated Aromatic Metabolite

Flurbiprofen is a fluorinated, nonsteroidal, anti-inflammatory pharmaceutical with potential application in a wide range of maladies. Currently, there is no information regarding its environmental fate. To address this, flurbiprofen is spiked at 500 and 50 ppm into activated sewage sludge taken from the municipal treatment plant of Ankara, Turkey. Flurbiprofen is partially degraded after 80 days, with removal proportion varying from 33% to 48%. Isolation of organisms able to use flurbiprofen as a sole carbon and energy source is unsuccessful. A transient, acid-labile yellow coloration appears in supernatants after addition of flurbiprofen. During disappearance, a novel potential metabolite is detected by high-performance liquid chromatography (HPLC) analyses, a chemical that does not appear in killed controls or in nonflurbiprofen-amended controls. Mass spectra of the novel chemical obtained at low and high collision energies are consistent with 4-(1-carboxyethyl)-2-fluorobenzoic acid, suggesting the application of a canonical metabolic paradigm for halogenated biphenyl metabolism by bacteria in which the nonhalogenated ring is metabolized by dioxygenation and metacleavage, leaving the halogenated aromatic ring behind. This metabolite shows no signs of disappearance after the 80-day monitoring period, implying that the environmental release of flurbiprofen might be of concern.

Pharmacomicrobiomics: The Holy Grail to Variability in Drug Response?

The human body, with 3.0 × 10¹³ cells and more than 3.8 × 10¹³ microorganisms, has nearly a one-to-one ratio of resident microbes to human cells. Initiatives like the Human Microbiome Project, American Gut, and Flemish Gut have identified associations between microbial taxa and human health. The study of interactions between microbiome and pharmaceutical agents, i.e., pharmacomicrobiomics, has revealed an instrumental role of the microbiome in modulating drug response that alters the therapeutic outcomes. In this review, we present our current comprehension of the relationship of the microbiome, host biology, and pharmaceutical agents such as cardiovascular drugs, analgesics, and chemotherapeutic agents to human disease and treatment outcomes. We also discuss the significance of studying diet-gene-drug interactions and further address the key challenges associated with pharmacomicrobiomics. Finally, we examine proposed models employing systems biology for the application of pharmacomicrobiomics and other -omics data, and provide approaches to elucidate microbiome-drug interactions to improve future translation to personalized medicine.

Sorption and Degradation Potential of Pharmaceuticals in Sediments from a Stormwater Retention Pond

Stormwater retention ponds commonly receive some wastewater through misconnections, sewer leaks, and sewer overloads, all of which leads to unintended loads of organic micropollutants, including pharmaceuticals. This study explores the role of pond sediment in removing pharmaceuticals (naproxen, carbamazepine, sulfamethoxazole, furosemide, and fenofibrate). It quantifies their sorption potential to the sediments and how it depends on pH. Then it addresses the degradability of the pharmaceuticals in microcosms holding sediment beds and pond water. The sediment-water partitioning coefficient of fenofibrate varied little with pH and was the highest (average log Kd: 4.42 L kg−1). Sulfamethoxazole had the lowest (average log Kd: 0.80 L kg−1), varying unsystematically with pH. The coefficients of naproxen, furosemide and carbamazepine were in between. The degradation by the sediments was most pronounced for sulfamethoxazole, followed by naproxen, fenofibrate, furosemide, and carbamazepine. The first three were all removed from the water phase with half-life of 2–8 days. Over the 38 days the experiment lasted, they were all degraded to near completion. The latter two were more resistant, with half-lives between 1 and 2 months. Overall, the study indicated that stormwater retention ponds have the potential to remove some but not all pharmaceuticals contained in wastewater contributions.

Photocatalytic degradation of ibuprofen over BiOCl nanosheets with identification of intermediates

Photocatalysis directed at the removal of persistent organic pollutants, including pharmaceuticals, has been the subject of intense recent research. Bismuth oxychloride (BiOCl) has emerged as a potential alternative to traditional photocatalysts and has shown competitive removal efficiencies. However, pathways responsible for BiOCl photodegradation have not been well characterized. The present work is the first to determine, using LC-MS/MS analysis, the pathways by which BiOCl removes ibuprofen (IBP) from water. HPLC-DAD and LC-MS/MS analyses show that BiOCl converts IBP to two primary photochemical products, 4-isobutylacetophenone (IBAP) and 1-(4-isobutylphenyl)ethanol (IBPE). The reactivity for BiOCl is attributed to interactions of the carboxylic acid group of IBP with holes in the valence band. Hydroxylated-IBP was not detected in BiOCl photocatalytic degradation experiments which would be expected in a process driven by the formation and reactivity of reactive oxygen species. These data were used to formulate a photocatalytic degradation pathway for IBP and highlight the importance of studying both primary and secondary degradation reactions for photocatalytic studies.

Organic micropollutants paracetamol and ibuprofen-toxicity, biodegradation, and genetic background of their utilization by bacteria

Currently, analgesics and nonsteroidal anti-inflammatory drugs (NSAIDs) are classified as one of the most emerging group of xenobiotics and have been detected in various natural matrices. Among them, monocyclic paracetamol and ibuprofen, widely used to treat mild and moderate pain are the most popular. Since long-term adverse effects of these xenobiotics and their biological and pharmacokinetic activity especially at environmentally relevant concentrations are better understood, degradation of such contaminants has become a major concern. Moreover, to date, conventional wastewater treatment plants (WWTPs) are not fully adapted to remove that kind of micropollutants. Bioremediation processes, which utilize bacterial strains with increased degradation abilities, seem to be a promising alternative to the chemical methods used so far. Nevertheless, despite the wide prevalence of paracetamol and ibuprofen in the environment, toxicity and mechanism of their microbial degradation as well as genetic background of these processes remain not fully characterized. In this review, we described the current state of knowledge about toxicity and biodegradation mechanisms of paracetamol and ibuprofen and provided bioinformatics analysis concerning the genetic bases of these xenobiotics decomposition.

Archaeal acetoacetyl-CoA thiolase/HMG-CoA synthase complex channels the intermediate via a fused CoA-binding site

Many reactions within a cell are thermodynamically unfavorable. To efficiently run some of those endergonic reactions, nature evolved intermediate-channeling enzyme complexes, in which the products of the first endergonic reactions are immediately consumed by the second exergonic reactions. Based on this concept, we studied how archaea overcome the unfavorable first reaction of isoprenoid biosynthesis-the condensation of two molecules of acetyl-CoA to acetoacetyl-CoA catalyzed by acetoacetyl-CoA thiolases (thiolases). We natively isolated an enzyme complex comprising the thiolase and 3-hydroxy-3-methylglutaryl (HMG)-CoA synthase (HMGCS) from a fast-growing methanogenic archaeon, Methanothermococcus thermolithotrophicus HMGCS catalyzes the second reaction in the mevalonate pathway-the exergonic condensation of acetoacetyl-CoA and acetyl-CoA to HMG-CoA. The 380-kDa crystal structure revealed that both enzymes are held together by a third protein (DUF35) with so-far-unknown function. The active-site clefts of thiolase and HMGCS form a fused CoA-binding site, which allows for efficient coupling of the endergonic thiolase reaction with the exergonic HMGCS reaction. The tripartite complex is found in almost all archaeal genomes and in some bacterial ones. In addition, the DUF35 proteins are also important for polyhydroxyalkanoate (PHA) biosynthesis, most probably by functioning as a scaffold protein that connects thiolase with 3-ketoacyl-CoA reductase. This natural and highly conserved enzyme complex offers great potential to improve isoprenoid and PHA biosynthesis in biotechnologically relevant organisms.

Exploring the Degradation of Ibuprofen by Bacillus thuringiensis B1(2015b): The New Pathway and Factors Affecting Degradation

Ibuprofen is one of the most often detected pollutants in the environment, particularly at landfill sites and in wastewaters. Contamination with pharmaceuticals is often accompanied by the presence of other compounds which may influence their degradation. This work describes the new degradation pathway of ibuprofen by Bacillus thuringiensis B1(2015b), focusing on enzymes engaged in this process. It is known that the key intermediate which transformation limits the velocity of the degradation process is hydroxyibuprofen. As the degradation rate also depends on various factors, the influence of selected heavy metals and aromatic compounds on ibuprofen degradation by the B1(2015b) strain was examined. Based on the values of non-observed effect concentration (NOEC) it was found that the toxicity of tested metals increases from Hg(II) < Cu(II) < Cd(II) < Co(II) < Cr(VI). Despite the toxic effect of metals, the biodegradation of ibuprofen was observed. The addition of Co²⁺ ions into the medium significantly extended the time necessary for the complete removal of ibuprofen. It was shown that Bacillus thuringiensis B1(2015b) was able to degrade ibuprofen in the presence of phenol, benzoate, and 2-chlorophenol. Moreover, along with the removal of ibuprofen, degradation of phenol and benzoate was observed. Introduction of 4-chlorophenol into the culture completely inhibits degradation of ibuprofen.