A Gated TIMS FTICR MS Instrument to Decipher Isomeric Content of Complex Organic Mixtures.

Modern research faces increasingly complex materials with a constant need for new analytical strategies that can provide deeper levels of chemical insight. Ultrahigh resolution mass spectrometry (MS), particularly Fourier transform ion cyclotron resonance (FTICR) MS, has provided a robust analytical foundation. However, MS alone offers limited structural information. Here, we present the first implementation and results from an FTICR MS with fully integrated dual accumulation analysis with gated trapped ion mobility spectrometry (gTIMS) capability. The drastically extended charge capacity and parallel accumulation facilitate the analysis of complex mixtures. We achieved a high dynamic range of 4 orders of magnitude within a single FTICR acquisition event. Simultaneously, the valuable linear relationship between the TIMS elution voltage and reduced mobility was retained over a wide mobility range. Benchmarking the instrument performance with Suwannee River fulvic acid (SRFA) by variable ramp gTIMS analysis allowed separation and unambiguous assignment of different charge state distributions. Application to bio-oils has proven the capability to distinguish the isomeric diversity in these ultracomplex samples, while maintaining the expected FTICR MS resolving power and mass accuracy. Valuable information about the molecular distribution, isomeric diversity, and main molecular differences could directly be extracted within the analysis time of a classical "dilute and shoot" direct infusion experiment. The development of this fully integrated and flexible gTIMS with FTICR MS analysis possesses the potential to significantly change the current landscape of high-resolution mass spectrometric analysis of complex mixtures through the added insight of isomeric complexity afforded by TIMS. The exploration of the added IMS dimension promises transformative effects across diverse fields including energy transition, environmental studies, and biological research.

Utility of combining OLIG2 and SOX10 IHC expression in CNS tumours: promising biomarkers for subtyping paediatric- and adult-type gliomas.

AIMS: The SOX10 transcription factor is important for the maturation of oligodendrocytes involved in central nervous system (CNS) myelination. Currently, very little information exists about its expression and potential use in CNS tumour diagnoses. The aim of our study was to characterize the expression of SOX10 in a large cohort of CNS tumours and to evaluate its potential use as a biomarker. METHODS: We performed immunohistochemistry (IHC) for SOX10 and OLIG2 in a series of 683 cases of adult- and paediatric-type CNS tumours from different subtypes. The nuclear immunostaining results for SOX10 and OLIG2 were scored as positive (≥10% positive tumour cells) or negative. RESULTS: OLIG2 and SOX10 were positive in diffuse midline gliomas (DMG), H3-mutant, and EZHIP-overexpressed. However, in all DMG, EGFR-mutant, SOX10 was constantly negative. In diffuse paediatric-type high-grade gliomas (HGG), all RTK1 cases were positive for both OLIG2 and SOX10. RTK2 cases were all negative for both OLIG2 and SOX10. MYCN cases variably expressed OLIG2 and were all immunonegative for SOX10. In glioblastoma, IDH-wildtype, OLIG2 was mostly positive, but SOX10 was variably expressed, depending on the epigenetic subtype. All circumscribed astrocytic gliomas were positive for both OLIG2 and SOX10 except pleomorphic xanthoastrocytomas, astroblastomas, MN1-altered, and subependymal giant cell astrocytomas. SOX10 was negative in ependymomas, meningiomas, pinealoblastomas, choroid plexus tumours, intracranial Ewing sarcomas, and embryonal tumours except neuroblastoma, FOXR2-activated. CONCLUSION: To conclude, SOX10 can be incorporated into the IHC panel routinely used by neuropathologists in the diagnostic algorithm of embryonal tumours and for the subtyping of paediatric and adult-type HGG.

Structure of a membrane-bound menaquinol:organohalide oxidoreductase.

Organohalide-respiring bacteria are key organisms for the bioremediation of soils and aquifers contaminated with halogenated organic compounds. The major players in this process are respiratory reductive dehalogenases, corrinoid enzymes that use organohalides as substrates and contribute to energy conservation. Here, we present the structure of a menaquinol:organohalide oxidoreductase obtained by cryo-EM. The membrane-bound protein was isolated from Desulfitobacterium hafniense strain TCE1 as a PceA2B2 complex catalysing the dechlorination of tetrachloroethene. Two catalytic PceA subunits are anchored to the membrane by two small integral membrane PceB subunits. The structure reveals two menaquinone molecules bound at the interface of the two different subunits, which are the starting point of a chain of redox cofactors for electron transfer to the active site. In this work, the structure elucidates how energy is conserved during organohalide respiration in menaquinone-dependent organohalide-respiring bacteria.

GC-FTICR mass spectrometry with dopant assisted atmospheric pressure photoionization: application to the characterization of plastic pyrolysis oil.

Pyrolysis is a promising way to convert plastic waste into valuable resources. However, for downstream upgrading processes, many undesirable species, such as conjugated diolefins or heteroatom-containing compounds, can be generated during this pyrolysis. In-depth chemical characterization is therefore required to improve conversion and valorization. Because of the high molecular diversity found in these samples, advanced analytical instrumentation is needed to provide accurate and complete characterization. Generally, direct infusion Fourier transform mass spectrometry is used to gather information at the molecular level, but it has the disadvantage of limited structural insights. To overcome this drawback, gas chromatography has been coupled to Fourier transform ion cyclotron resonance mass spectrometry. By taking advantage of soft atmospheric pressure photoionization, which preserves molecular information, and the use of different dopants (pyrrole, toluene, and benzene), selective ionization of different chemical families was achieved. Differences in the ionization energy of the dopants will only allow the ionization of the molecules of the pyrolysis oil which have lower ionization energy, or which are accessible via specific chemical ionization pathways. With a selective focus on hydrocarbon species and especially hydrocarbon species having a double bond equivalent (DBE) value of 2, pyrrole is prone to better ionize low-mass molecules with lower retention times compared to the dopant benzene, which allowed better ionization of high-mass molecules with higher retention times. The toluene dopant presented the advantage of ionizing both low and high mass molecules.

Physics-based scintillations for outdoor sound auralization.

The sound propagating in a turbulent atmosphere fluctuates in amplitude and phase. This phenomenon, known as acoustic scintillation, is caused by random fluctuations in the acoustic refractive index of the air induced by atmospheric turbulence. Auralization techniques should consider this phenomenon to increase the realism of the synthetic sound. This paper proposes a physics-based formulation to model sequences of log-amplitude and phase fluctuations of a sound propagating in a turbulent atmosphere. This method applies to slanted and vertical propagation of the sound, which is useful for simulating elevated noise sources such as aircraft, drones, and wind turbines. The theoretical framework is based on the spatial correlation functions for the log-amplitude and phase fluctuations for spherical waves, the von Kármán spectrum, and similarity theories to model atmospheric turbulence. Two applications with audio files are presented to demonstrate the applicability of this method to tonal and broadband noise.

Contribution of LDI and MALDI for the Characterization of a Lignocellulosic-Based Pyrolysis Bio-Oil.

In recent years, various alternatives to fossil fuels have been developed. One of them involves the production of bio-oils from lignocellulosic-based biomass through pyrolysis. However, bio-oils present numerous heteroatoms and, in particular, oxygen atoms that need to be removed by an upgrading process. To optimize these processes, it is necessary to have good knowledge of the composition of the bio-oils at the molecular level. This work aims to establish the usefulness of laser desorption ionization (LDI) and matrix-assisted laser desorption/ionization (MALDI) techniques on lignocellulosic biomass-based bio-oils. Using a Fourier transform ion cyclotron mass spectrometer (FTICR MS), we showed that MALDI gives more information than LDI. The selectivity of a series of MALDI matrices was investigated, showing that some matrices are selective toward compound families and others ionize a wider range of compounds. In this study, nine proton-transfer matrices and three electron-transfer matrices were used and compared to results obtained in LDI. Dithranol, acetosyringone, and graphene oxide were the three promising matrices selected from all matrices, giving an overall characterization of oxygenated classes in a bio-oil. They allowed the ionization of many more species covering a wide range of polarity, aromaticity, and mass with a homogeneous relative intensity for all molecular classes such as lignin-derivative species, sugars, and lipid-derivative species.

Microsynt: Exploring the syntax of EEG microstates.

Microstates represent electroencephalographic (EEG) activity as a sequence of switching, transient, metastable states. Growing evidence suggests the useful information on brain states is to be found in the higher-order temporal structure of these sequences. Instead of focusing on transition probabilities, here we propose "Microsynt", a method designed to highlight higher-order interactions that form a preliminary step towards understanding the syntax of microstate sequences of any length and complexity. Microsynt extracts an optimal vocabulary of "words" based on the length and complexity of the full sequence of microstates. Words are then sorted into classes of entropy and their representativeness within each class is statistically compared with surrogate and theoretical vocabularies. We applied the method on EEG data previously collected from healthy subjects undergoing propofol anesthesia, and compared their "fully awake" (BASE) and "fully unconscious" (DEEP) conditions. Results show that microstate sequences, even at rest, are not random but tend to behave in a more predictable way, favoring simpler sub-sequences, or "words". Contrary to high-entropy words, lowest-entropy binary microstate loops are prominent and favored on average 10 times more than what is theoretically expected. Progressing from BASE to DEEP, the representation of low-entropy words increases while that of high-entropy words decreases. During the awake state, sequences of microstates tend to be attracted towards "A - B - C" microstate hubs, and most prominently A - B binary loops. Conversely, with full unconsciousness, sequences of microstates are attracted towards "C - D - E" hubs, and most prominently C - E binary loops, confirming the putative relation of microstates A and B to externally-oriented cognitive processes and microstate C and E to internally-generated mental activity. Microsynt can form a syntactic signature of microstate sequences that can be used to reliably differentiate two or more conditions.

Humid Evolution of Haze in the Atmosphere of Super-Earths in the Habitable Zone.

Abstract Photochemical hazes are expected to form and significantly contribute to the chemical and radiative balance of exoplanets with relatively moderate temperatures, possibly in the habitable zone of their host star. In the presence of humidity, haze particles might thus serve as cloud condensation nuclei and trigger the formation of water droplets. In the present work, we are interested in the chemical impact of such a close interaction between photochemical hazes and humidity on the organic content composing the hazes and on the capacity to generate organic molecules with high prebiotic potential. For this purpose, we explore experimentally the sweet spot by combining N-dominated super-Earth exoplanets in agreement with Titan's rich organic photochemistry and humid conditions expected for exoplanets in habitable zones. A logarithmic increase with time is observed for the relative abundance of oxygenated species, with O-containing molecules dominating after 1 month only. The rapidity of the process suggests that the humid evolution of N-rich organic haze provides an efficient source of molecules with high prebiotic potential.

PyC2MC: An Open-Source Software Solution for Visualization and Treatment of High-Resolution Mass Spectrometry Data.

Complex molecular mixtures are encountered in almost all research disciplines, such as biomedical 'omics, petroleomics, and environmental sciences. State-of-the-art characterization of sample materials related to these fields, deploying high-end instrumentation, allows for gathering large quantities of molecular composition data. One established technological platform is ultrahigh-resolution mass spectrometry, e.g., Fourier-transform mass spectrometry (FT-MS). However, the huge amounts of data acquired in FT-MS often result in tedious data treatment and visualization. FT-MS analysis of complex matrices can easily lead to single mass spectra with more than 10,000 attributed unique molecular formulas. Sophisticated software solutions to conduct these treatment and visualization attempts from commercial and noncommercial origins exist. However, existing applications have distinct drawbacks, such as focusing on only one type of graphic representation, being unable to handle large data sets, or not being publicly available. In this respect, we developed a software, within the international complex matrices molecular characterization joint lab (IC2MC), named "python tools for complex matrices molecular characterization" (PyC2MC). This piece of software will be open-source and free to use. PyC2MC is written under python 3.9.7 and relies on well-known libraries such as pandas, NumPy, or SciPy. It is provided with a graphical user interface developed under PyQt5. The two options for execution, (1) a user-friendly route with a prepacked executable file or (2) running the main python script through a Python interpreter, ensure a high applicability but also an open characteristic for further development by the community. Both are available on the GitHub platform (https://github.com/iC2MC/PyC2MC_viewer).

Proteome adaptations of the organohalide-respiring Desulfitobacterium hafniense strain DCB-2 to various energy metabolisms.

Introduction: Desulfitobacterium hafniense was isolated for its ability to use organohalogens as terminal electron acceptors via organohalide respiration (OHR). In contrast to obligate OHR bacteria, Desulfitobacterium spp. show a highly versatile energy metabolism with the capacity to use different electron donors and acceptors and to grow fermentatively. Desulfitobacterium genomes display numerous and apparently redundant members of redox enzyme families which confirm their metabolic potential. Nonetheless, the enzymes responsible for many metabolic traits are not yet identified. Methods: In the present work, we conducted an extended proteomic study by comparing the proteomes of Desulfitobacterium hafniense strain DCB-2 cultivated in combinations of electron donors and acceptors, triggering five alternative respiratory metabolisms that include OHR, as well as fermentation. Tandem Mass Tag labelling proteomics allowed us to identify and quantify almost 60% of the predicted proteome of strain DCB-2 (2,796 proteins) in all six growth conditions. Raw data are available via ProteomeXchange with identifier PXD030393. Results and discussion: This dataset was analyzed in order to highlight the proteins that were significantly up-regulated in one or a subset of growth conditions and to identify possible key players in the different energy metabolisms. The addition of sodium sulfide as reducing agent in the medium - a very widespread practice in the cultivation of strictly anaerobic bacteria - triggered the expression of the dissimilatory sulfite reduction pathway in relatively less favorable conditions such as fermentative growth on pyruvate, respiration with H2 as electron donor and OHR conditions. The presence of H2, CO2 and acetate in the medium induced several metabolic pathways involved in carbon metabolism including the Wood-Ljungdahl pathway and two pathways related to the fermentation of butyrate that rely on electron-bifurcating enzymes. While the predicted fumarate reductase appears to be constitutively expressed, a new lactate dehydrogenase and lactate transporters were identified. Finally, the OHR metabolism with 3-chloro-4-hydroxyphenylacetate as electron acceptor strongly induced proteins encoded in several reductive dehalogenase gene clusters, as well as four new proteins related to corrinoid metabolism. We believe that this extended proteomic database represents a new landmark in understanding the metabolic versatility of Desulfitobacterium spp. and provides a solid basis for addressing future research questions.

Changes of health-related quality of life 6 months after high-risk oncological upper gastrointestinal and hepatobiliary surgery: a single-centre prospective observational study (ChangeQol Study).

INTRODUCTION: Postoperative health-related quality of life (HRQoL) is an essential outcome in oncological surgery, particularly for elderly patients undergoing high-risk surgery. Previous studies have suggested that, on average, HRQoL returns to premorbid normal levels in the months following major surgery. However, the averaging of effect over a studied cohort may hide the variation of individual HRQoL changes. The proportions of patients who have a varied HRQoL response (stable, improvement, or a deterioration) after major oncological surgery is poorly understood. The study aims to describe the patterns of these HRQoL changes at 6 months after surgery, and to assess the patients and next-of-kin regret regarding the decision to undergo surgery. METHODS AND ANALYSIS: This prospective observational cohort study is carried out at the University Hospitals of Geneva, Switzerland. We include patients over 18 years old undergoing gastrectomy, esophagectomy, pancreas resection or hepatectomy. The primary outcome is the proportion of patients in each group with changes in HRQoL (improvement, stability or deterioration) 6 months after surgery, using a validated minimal clinically important difference of 10 points in HRQoL. The secondary outcome is to assess whether patients and their next-of-kin may regret their decision to undergo surgery at 6 months. We measure the HRQoL using the EORTC QLQ-C30 questionnaire before and 6 months after surgery. We assess regret with the Decision Regret Scale (DRS) at 6 months after surgery. Key other perioperative data include preoperative and postoperative place of residence, preoperative anxiety and depression (HADS scale), preoperative disability (WHODAS V.2.0), preoperative frailty (Clinical Frailty Scale), preoperative cognitive function (Mini-Mental State Examination) and preoperative comorbidities. A follow-up at 12 months is planned. ETHICS AND DISSEMINATION: The study was first approved by the Geneva Ethical Committee for Research (ID 2020-00536) on 28 April 2020. The results of this study will be presented at national and international scientific meetings, and publications will be submitted to an open-access peer-reviewed journal. TRIAL REGISTRATION NUMBER: NCT04444544.

Reviewing next of kin regrets in surgical decision-making: cross-sectional analysis of systematically searched literature.

BACKGROUND: Decision-making concerning relatives undergoing surgery is challenging. It remains unclear to what extent implicated next of kin eventually regret their decisions and how this regret is assessed. Our aim was to systematically review the literature on decisional regret of next of kin and to describe the assessment tools used and the surgical populations studied. METHODS: We included interventional or observational, quantitative or qualitative studies reporting the measurement of decisional regret of next of kin concerning relatives undergoing surgery. We searched a variety of databases without restriction on publication year. We assessed the quality of reporting of quantitative studies using the NIH Quality Assessment Tool for Observational Cohort and Cross-Sectional Studies and of qualitative studies using the Critical Appraisal Skills Program Checklist. RESULTS: Thirteen cross-sectional, five prospective cohorts and five qualitative studies matched our inclusion criteria. In 18 studies (78%), patients were children, in five (22%), young or middle-aged adults. No study included elderly or frail patients. Thirteen studies (57%) used the original Decision Regret Scale which was validated for patients, but not for next of kin. Only 3 of the 18 (17%) quantitative studies and only one of the 4 (25%) qualitative studies were rated as "good" in the quality assessment. CONCLUSION: None of the retrieved studies used validated tools to assess the decisional regret of next of kin and none of them examined this issue in elderly or frail surgical patients.

Prediction of Structures of Compounds Encountered in Complex Organic Matter with Highly Flexible Alkyl Chains Using Ion Mobility-Mass Spectrometry.

The chemical structure of an organic molecule has a direct influence on its three-dimensional conformation. One way to obtain information on this conformation is to use ion mobility spectrometry. This technique allows the separation of different isomers according to their collision cross section (CCS) with an inert gas. Smaller or more compact molecules will have lower collision cross section values than larger molecules. The CCS is an intrinsic ion parameter for a specific gas and is thus predictable. Today, calculations of rigid molecules are commonly performed to obtain additional structural information on an ion. However, calculations are more complex with very flexible molecules. In particular, molecules presenting long alkyl chains can yield a high number of conformers. Each conformer is then associated with a CCS value that is specific to it. We report, here, a methodology to predict CCS of flexible molecules. The used approach is based on automatic conformers research followed by geometry optimization and CCS calculations. Determination of theoretical and experimental CCS values for a rigid polycyclic aromatic hydrocarbons (PAHs) standard was used to calibrate the Mobcal software. Then, 13 standard molecules ranging from 4 to 19 carbon alkyl chains, including three long alkyl chain isomers of C22H38, were analyzed on a TWIMS-ToF and calculated using our methodology. CCS deviations between experimental and theoretical values were found to be less than 1.5% over the whole studied CCS range. This method was finally applied for structural analysis of petroleum compounds refractory to the hydro-denitrogenation process.

Visualization and identification of single meteoritic organic molecules by atomic force microscopy.

Using high-resolution atomic force microscopy (AFM) with CO-functionalized tips, we atomically resolved individual molecules from Murchison meteorite samples. We analyzed powdered Murchison meteorite material directly, as well as processed extracts that we prepared to facilitate characterization by AFM. From the untreated Murchison sample, we resolved very few molecules, as the sample contained mostly small molecules that could not be identified by AFM. By contrast, using a procedure based on several trituration and extraction steps with organic solvents, we isolated a fraction enriched in larger organic compounds. The treatment increased the fraction of molecules that could be resolved by AFM, allowing us to identify organic constituents and molecular moieties, such as polycyclic aromatic hydrocarbons and aliphatic chains. The AFM measurements are complemented by high-resolution mass spectrometry analysis of Murchison fractions. We provide a proof of principle that AFM can be used to image and identify individual organic molecules from meteorites and propose a method for extracting and preparing meteorite samples for their investigation by AFM. We discuss the challenges and prospects of this approach to study extraterrestrial samples based on single-molecule identification.

Comparing propofol anaesthesia guided by Bispectral Index monitoring and frontal EEG wave analysis with standard monitoring in laparoscopic surgery: protocol for the 'EEG in General Anaesthesia - More Than Only a Bispectral Index' Trial, a multicentre, double-blind, randomised controlled trial.

INTRODUCTION: The use of Bispectral Index (BIS) monitors for assessing depth of sedation has led to a reduction in both the incidence of awareness and anaesthetic consumption in total intravenous anaesthesia. However, these monitors are vulnerable to artefacts. In addition to the processed number, the raw frontal electroencephalogram (EEG) can be displayed as a curve on the same monitor. Anaesthesia practitioners can learn to interpret the EEG in a short tutorial and may be quicker and more accurate thanBIS in assessing anaesthesia depth by recognising EEG patterns. We hypothesise that quality of recovery (QoR) in patients undergoing laparoscopic surgery is better, if propofol is titrated by anaesthesia practitioners able to interpret the EEG. METHODS AND ANALYSIS: This is a multicentre, double-blind (patients and outcome assessors) randomised controlled trial taking place in four Swiss hospitals. Patients aged 18 years or older undergoing laparoscopic procedures with general anaesthesia using propofol and anaesthesia practitioners with more than 2 years experience will be eligible. The primary study outcome is the difference in QoR 24 hours after surgery. Secondary outcomes are propofol consumption, incidence of postoperative nausea and vomiting (PONV) and postoperative delirium.QoR and propofol consumption are compared between both groups using a two-sample t-test. Fisher's exact test is used to compare the incidences of PONV and delirium. A total of 200 anaesthesia practitioners (and 200 patients) are required to have an 80% chance of detecting the minimum relevant difference for the QoR-15 as significant at the 5% level assuming a SD of 20. ETHICS AND DISSEMINATION: Ethical approval has been obtained from all responsible ethics committees (lead committee: Ethikkommission Nordwest- und Zentralschweiz, 16 January 2021). The findings of the trial will be published in a peer-reviewed journal, presented at international conferences, and may lead to a change in titrating propofol in clinical practice. TRIAL REGISTRATION NUMBER: www. CLINICALTRIALS: gov:NCT04105660.

Speciation and Semiquantification of Nitrogen-Containing Species in Complex Mixtures: Application to Plastic Pyrolysis Oil.

Plastic pyrolysis oil is of particular interest for waste management in the current context of a circular economy. Due to their uncontrolled origin, these oils may contain significant amount of unwanted compounds such as nitrogen-containing species. These compounds are known to be catalyst poisons during refining processes. Therefore, the removal of these species is crucial, and their characterization from structural and quantification points of view is essential for this purpose. This study presents a method to specify and quantify nitrogen-containing classes in a plastic pyrolysis oil by direct infusion mass spectrometry. Two steps were used, namely structural characterization to select suitable standards and semiquantification. The structural speciation of nitrogen-containing compounds was first performed by electrospray ionization Fourier transform mass spectrometry, followed by tandem mass spectrometry using high-resolution mass isolation and infrared multiphoton dissociation fragmentation. A semiquantification is then performed by the standard addition method, which is very appropriate for such complex matrices. Aromatic cores such as quinoline and quinoxaline were evidenced for both N1 and N2 classes, allowing 2-methylquinoxaline and 2-butylquinoline to be proposed as standards for the semiquantification of N2- and N1-containing compounds, respectively. The amount of nitrogen detected from the sum of the individual species was consistent with the bulk analysis. The reported methodology can be applied to numerous other families of compounds in various other complex matrices.

EEG microstate dynamics indicate a U-shaped path to propofol-induced loss of consciousness.

Evidence suggests that the stream of consciousness is parsed into transient brain states manifesting themselves as discrete spatiotemporal patterns of global neuronal activity. Electroencephalographical (EEG) microstates are proposed as the neurophysiological correlates of these transiently stable brain states that last for fractions of seconds. To further understand the link between EEG microstate dynamics and consciousness, we continuously recorded high-density EEG in 23 surgical patients from their awake state to unconsciousness, induced by step-wise increasing concentrations of the intravenous anesthetic propofol. Besides the conventional parameters of microstate dynamics, we introduce a new implementation of a method to estimate the complexity of microstate sequences. The brain activity under the surgical anesthesia showed a decreased sequence complexity of the stereotypical microstates, which became sparser and longer-lasting. However, we observed an initial increase in microstates' temporal dynamics and complexity with increasing depth of sedation leading to a distinctive "U-shape" that may be linked to the paradoxical excitation induced by moderate levels of propofol. Our results support the idea that the brain is in a metastable state under normal conditions, balancing between order and chaos in order to flexibly switch from one state to another. The temporal dynamics of EEG microstates indicate changes of this critical balance between stability and transition that lead to altered states of consciousness.

Disentangle genus microdiversity within a complex microbial community by using a multi-distance long-read binning method: example of Candidatus Accumulibacter.

Complete genomes can be recovered from metagenomes by assembling and binning DNA sequences into metagenome assembled genomes (MAGs). Yet, the presence of microdiversity can hamper the assembly and binning processes, possibly yielding chimeric, highly fragmented and incomplete genomes. Here, the metagenomes of four samples of aerobic granular sludge bioreactors containing Candidatus (Ca.) Accumulibacter, a phosphate-accumulating organism of interest for wastewater treatment, were sequenced with both PacBio and Illumina. Different strategies of genome assembly and binning were investigated, including published protocols and a binning procedure adapted to the binning of long contigs (MuLoBiSC). Multiple criteria were considered to select the best strategy for Ca. Accumulibacter, whose multiple strains in every sample represent a challenging microdiversity. In this case, the best strategy relies on long-read only assembly and a custom binning procedure including MuLoBiSC in metaWRAP. Several high-quality Ca. Accumulibacter MAGs, including a novel species, were obtained independently from different samples. Comparative genomic analysis showed that MAGs retrieved in different samples harbour genomic rearrangements in addition to accumulation of point mutations. The microdiversity of Ca. Accumulibacter, likely driven by mobile genetic elements, causes major difficulties in recovering MAGs, but it is also a hallmark of the panmictic lifestyle of these bacteria.