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Motivation: Metagenomics characterizes microbial communities by random shotgun sequencing of DNA isolated directly from an environment of interest. An essential step in computational metagenome analysis is taxonomic sequence assignment, which allows identifying the sequenced community members and reconstructing taxonomic bins with sequence data for the individual taxa. For the massive datasets generated by next-generation sequencing technologies, this cannot be performed with de-novo phylogenetic inference methods. We describe an algorithm and the accompanying software, taxator-tk, which performs taxonomic sequence assignment by fast approximate determination of evolutionary neighbors from sequence similarities. Results: Taxator-tk was precise in its taxonomic assignment across all ranks and taxa for a range of evolutionary distances and for short as well as for long sequences. In addition to the taxonomic binning of metagenomes, it is well suited for profiling microbial communities from metagenome samples because it identifies bacterial, archaeal and eukaryotic community members without being affected by varying primer binding strengths, as in marker gene amplification, or copy number variations of marker genes across different taxa. Taxator-tk has an efficient, parallelized implementation that allows the assignment of 6Gb of sequence data per day on a standard multiprocessor system with 10 CPU cores and microbial RefSeq as the genomic reference data. [ABSTRACT FROM AUTHOR]

Due to their metabolic versatility in substrate utilization, acetogenic bacteria represent industrially significant production platforms for biotechnological applications such as syngas fermentation, microbial electrosynthesis or transformation of one-carbon substrates. However, acetogenic strains from the genera Terrisporobacter and Acetoanaerobium remained poorly investigated for biotechnological applications. We report the isolation and characterization of four acetogenic Terrisporobacter strains and one Acetoanaerobium strain. All Terrisporobacter isolates showed a characteristic growth pattern under a H 2  + CO 2 atmosphere. An initial heterotrophic growth phase was followed by a stationary growth phase, where continuous acetate production was indicative of H 2 -dependent acetogenesis. One of the novel Terrisporobacter isolates obtained from compost (strain COM T ) additionally produced ethanol besides acetate in the stationary growth phase in H 2 -supplemented cultures. Genomic and physiological characterizations showed that strain COM T represented a novel Terrisporobacter species and the name Terrisporobacter vanillatitrophus is proposed (=DSM 116160 T  = CCOS 2104 T ). Phylogenomic analysis of the novel isolates and reference strains implied the reclassification of the T. petrolearius / T. hibernicus phylogenomic cluster to the species T. petrolearius and of the A. noterae/A. sticklandii phylogenomic cluster to the species A. sticklandii . Furthermore, we provide first insights into active prophages of acetogens from the genera Terrisporobacter and Acetoanaerobium ., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2024 Böer, Schüler, Lüschen, Eysell, Dröge, Heinemann, Engelhardt, Basen, Daniel and Poehlein.)

Exposure to ultrafine particles has a significant influence on human health. In regions with large commercial airports, air traffic and ground operations can represent a potential particle source. The particle number concentration was measured in a low-traffic residential area about 7 km from Frankfurt Airport with a Condensation Particle Counter in a long-term study. In addition, the particle number size distribution was determined using a Fast Mobility Particle Sizer. The particle number concentrations showed high variations over the entire measuring period and even within a single day. A maximum 24 h-mean of 24,120 cm -3 was detected. Very high particle number concentrations were in particular measured when the wind came from the direction of the airport. In this case, the particle number size distribution showed a maximum in the particle size range between 5 and 15 nm. Particles produced by combustion in jet engines typically have this size range and a high potential to be deposited in the alveoli. During a period with high air traffic volume, significantly higher particle number concentrations could be measured than during a period with low air traffic volume, as in the COVID-19 pandemic. A large commercial airport thus has the potential to lead to a high particle number concentration even in a distant residential area. Due to the high particle number concentrations, the critical particle size, and strong concentration fluctuations, long-term measurements are essential for a realistic exposure analysis., Competing Interests: Declaration of competing interest The authors declare the following financial interests/personal relationships which may be considered as potential competing interests: Janis Dröge reports financial support was provided by Dr. Senckenbergische Stiftung. Janis Dröge reports financial support was provided by Alfons und Gertrund Kassel-Stiftung., (Copyright © 2024 The Authors. Published by Elsevier Ltd.. All rights reserved.)

Introduction: Cannabis is a widely used drug like tobacco and alcohol. In the meantime, it is also prescribed for medical treatment in some countries. Tobacco smoke contains chemical carcinogens and particulate matter (PM) that are both harmful to health. Method: In this study, we investigated PM levels in second-hand smoke (SHS) of hand-tamped cannabis cigarettes compared to cigarettes with tubing tobacco and the 3R4F reference cigarette. Results: It could be demonstrated that the largest proportion of the particle mass is attributable to particles with a diameter of less than 1μm and that every tested cigarette emitted more PM than the 3R4F reference cigarette. In addition, our data clearly revealed that cannabis smoke contains higher PM levels in SHS than tobacco cigarettes. Compared to the reference cigarette, the PM 1 emissions of cannabis were 105% higher. Also, the cannabis mixed cigarettes had higher PM levels than the 3R4F cigarettes. For instance, the PM 10 emissions were 93% higher. Also, the Gauloises Mélange tubing tobacco also reached higher PM concentrations than the 3R4F cigarette. Discussion: Regardless of negative health effects, cannabis is seen as a harmless drug in the public eye. We found strong indications for potential health risks by PM from cannabis products and, therefore, the public should be educated about a potential harm.

Single amino acid changes in the parasite protein Kelch13 (K13) result in reduced susceptibility of P. falciparum parasites to artemisinin and its derivatives (ART). Recent work indicated that K13 and other proteins co-localising with K13 (K13 compartment proteins) are involved in the endocytic uptake of host cell cytosol (HCCU) and that a reduction in HCCU results in reduced susceptibility to ART. HCCU is critical for parasite survival but is poorly understood, with the K13 compartment proteins among the few proteins so far functionally linked to this process. Here we further defined the composition of the K13 compartment by analysing more hits from a previous BioID, showing that MyoF and MCA2 as well as Kelch13 interaction candidate (KIC) 11 and 12 are found at this site. Functional analyses, tests for ART susceptibility as well as comparisons of structural similarities using AlphaFold2 predictions of these and previously identified proteins showed that vesicle trafficking and endocytosis domains were frequent in proteins involved in resistance or endocytosis (or both), comprising one group of K13 compartment proteins. While this strengthened the link of the K13 compartment to endocytosis, many proteins of this group showed unusual domain combinations and large parasite-specific regions, indicating a high level of taxon-specific adaptation of this process. Another group of K13 compartment proteins did not influence endocytosis or ART susceptibility and lacked detectable vesicle trafficking domains. We here identified the first protein of this group that is important for asexual blood stage development and showed that it likely is involved in invasion. Overall, this work identified novel proteins functioning in endocytosis and at the K13 compartment. Together with comparisons of structural predictions it provides a repertoire of functional domains at the K13 compartment that indicate a high level of adaption of endocytosis in malaria parasites., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2023 Schmidt et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Despite antagonizing attempts from the tobacco industry, passive inhalation of tobacco smoke is known to be cancerogenic and toxic to human health for decades. Nonetheless, millions of non-smoking adults and children are still victims of second-hand smoke. Accumulation of particulate matter (PM) in confined spaces such as the car are particularly harmful due to high concentrations. We here aimed to analyze the specific effects of ventilation conditions in the setting of a car. By the use of the measuring platform TAPaC (tobacco-associated particulate matter emissions inside a car cabin), 3R4F reference cigarettes, Marlboro red, and Marlboro gold were smoked in a car interior with a volume of 3.709 m 3 . Seven different ventilation conditions (C1-C7) were analyzed. Under C1, all windows were closed. Under C2-C7, the car ventilation was turned on power level 2/4 with the air directed towards the windshield. Only the passenger side window was opened, where an outer placed fan could create an airstream speed of 15.9-17.4 km/h at one meter distance to simulate a driving car. C2: Window 10 cm opened. C3: Window 10 cm opened with the fan turned on. C4: Window half-opened. C5: Window half-opened with the fan turned on. C6: Window fully opened. C7: Window fully opened with the fan turned on. Cigarettes were remotely smoked by an automatic environmental tobacco smoke emitter and a cigarette smoking device. Depending on the ventilation condition the cigarettes emitted different mean PM concentrations after 10 min under condition C1 (PM 10 : 1272-1697 µg/m 3 , PM 2.5 : 1253-1659 µg/m 3 , PM 1 : 964-1263 µg/m 3 ) under C2, C4, and C6 (PM 10 : 68.7-196.2 µg/m 3 , PM 2.5 : 68.2-194.7 µg/m 3 , PM 1 : 66.1-183.8 µg/m 3 ) C3, C5, and C7 (PM 10 : 73.7-139 µg/m 3 , PM 2.5 : 72-137.9 µg/m 3 , PM 1 :68.9-131.9 µg/m 3 ). Vehicle ventilation is insufficient to protect passengers from toxic second-hand smoke completely. Brand-specific variations of tobacco ingredients and mixtures markedly influence PM emissions under ventilation conditions. The most efficient ventilation mode to reduce PM exposure was achieved by opening the passenger´s window 10 cm and turning the onboard ventilation on power level 2/4. In-vehicle smoking should be banned to preserve innocent risk groups (e.g., children) from harm., (© 2023. The Author(s).)

The present review of the biomarkers BNP and NT-pro-BNP is published in the series "biomarkers" of the Zentralblatt für Arbeitsmedizin, Arbeitsschutz und Ergonomie , which deals with the increasing use of the determination of specific markers in so-called manager preventive and check-up examinations. In principle, BNP and NT-pro-BNP are fundamentally suitable as markers for diagnosing acute and chronic heart failure and for assessing the course. In this context these show a high sensitivity and specificity., (© The Author(s) 2023.)

Background: Unlike most other commodities, rare earth elements (REEs) are part of a wide range of applications needed for daily life all over the world. These applications range from cell phones to electric vehicles to wind turbines. They are often declared as part of "green technology" and, therefore, often called "green elements". However, their production and use are not only useful but also risky to the environment and human health, as many studies have shown. Consequently, the range of global research efforts is broad and highly variable, and therefore difficult to capture and assess. Hence, this study aims to assess the global parameters of global research on REE in the context of environment and health (REE eh ). In addition to established bibliometric parameters, advanced analyses using market driver and scientific infrastructure values were carried out to provide deep insight into incentives, necessities, and barriers to international research., Results: The focus of REE research is in line with national aspirations, especially from the major global players, China and the USA. Whereas globally, regional research interests are related to market interests, as evidenced by the inclusion of drivers such as electric vehicles, wind turbines, and permanent magnets. The topics receiving the most attention are related to gadolinium used for magnetic resonance imaging and the use of ceria nanoparticles. Since both are used for medical purposes, the medical research areas are equally profiled and mainly addressed in high-income countries. Nevertheless, environmental issues are increasingly in focus., Conclusions: There is still a need for research that is independent and open-ended. For this, market-independent technologies, substitutes and recycling of REEs need to be addressed scientifically. The results of this study are relevant for all stakeholders, from individual scientists to planners to funders, to improve future research strategies in line with these research mandates., (© 2022. The Author(s).)

Background: Particulate matter (PM) emission caused by tobacco combustion leads to severe health burdens worldwide. Second-hand smoke exposure is extraordinarily high in enclosed spaces (e.g., indoor rooms, car cabins) and poses a particular threat to the health of vulnerable individuals (e.g., children, elderly, etc.). This study aimed to establish a new measuring platform and investigate PM emissions under four different ventilation conditions inside a car cabin without exposing any person to harmful tobacco smoke., Methods: PM concentrations were measured during the smoking of 3R4F reference cigarettes in a Mitsubishi Space Runner (interior volume 3.709 m 3 ). The cigarettes were smoked with a machine, eliminating exposure of the researchers. Cigarettes were extinguished 4.5 min after ignition, and PM measurements continued until 10 min after ignition., Results: High mean PM concentrations were measured for cigarettes without ventilation after 4.5 min (PM 10 : 1150 µg/m 3 , PM 2.5 : 1132 µg/m 3 , PM 1 : 861.6 µg/m 3 ) and after 10 min (PM 10 : 1608 µg/m 3 , PM 2.5 : 1583 µg/m 3 , PM 1 : 1133 µg/m 3 ). 3R4F smoked under conditions with turned on ventilation resulted in reduction of PM compared to those smoked without ventilation after 4.5 min (PM 10 :-47.5 to -58.4%, PM 2.5 :-47.2 to -58%, PM 1 :-39.6 to -50.2%) and after 10 min (PM 10 :-70.8 to -74.4%, PM 2.5 :-70.6 to -74.3%, PM 1 :-64.0 to -68.0%). Cigarettes smoked without ventilation generated high PM peaks at 4.5 min (PM 10 : 2207 µg/m 3 , PM 2.5 : 2166 µg/m 3 , PM 1 : 1421 µg/m 3 ) and at 10 min (PM 10 : 1989 µg/m 3 , PM 2.5 : 1959 µg/m 3 , PM 1 : 1375 µg/m 3 ). PM peaks of cigarettes smoked under different ventilation modes varied at 4.5 min (PM 10 : 630-845 µg/m 3 , PM 2.5 : 625-836 µg/m 3 , PM 1 : 543 - 693 µg/m 3 ) and 10 min (PM 10 : 124 - 130 µg/m 3 , PM 2.5 : 124 - 129 µg/m 3 , PM 1 : 118 - 124 µg/m 3 )., Conclusion: The new measuring platform provides a safer way for researchers to investigate PM emissions of cigarettes. These data are comparable to published research and show that smoking in a parked vehicle with the windows closed generates harmful PM emissions even when the vehicle ventilation is in operation. Future studies should be carried out using the new measuring platform investigating PM exposure and PM distribution of in-vehicle smoking under a wide range of conditions., (© 2022. The Author(s).)

Particulate matter emitted during autopsies can serve as a vector for numerous viruses or bacteria and can lead to infections. Reducing the exposure of those particles in indoor working environments is, therefore, an important issue. To assess the health risk for employees in forensic medicine, we measure particulate matter in the ambient air during autopsies by using an aerosol spectrometer. The autopsies were performed with either an ordinary oscillating saw or an adapted saw with a suction unit. The particle emissions from both saws were compared to each other in order to evaluate whether a technical adaption leads to a particle reduction. Furthermore, the particle exposure reduction by wearing a face mask and variations in the background concentration in the room were analyzed. High particle concentrations were measured while using the ordinary saw. By using the adapted saw or wearing a face mask, the particle exposure could mostly be avoided. On the majority of the working days, an increase in the background concentration could be observed. Based on this knowledge, the use of a proper suction unit and wearing a face mask during autopsies is necessary. Besides, it is important to have sufficient ventilation in the room so that long-lasting high background concentrations can be prevented., (© 2022. The Author(s).)

Private-label cigarettes are cigarettes that belong to the retailer itself. Private-label cigarettes from discounters or supermarkets are cheaper than brand-name cigarettes, and their lower price has allowed them to garner an ever-increasing share of the tobacco product market, especially among lower socioeconomic groups. Particulate matter (PM), a considerable component of air pollution, is a substantial health-damaging factor. Smoking is the primary source of PM in smokers’ homes. In a 2.88 m3 measuring chamber, the PM emission fractions PM10, PM2.5, and PM1 from three private-label cigarette brands and three brand-name cigarette brands with identical nicotine, tar, and carbon monoxide content were measured and compared to those of a reference cigarette by laser aerosol spectroscopy. All cigarette brands emitted PM in health-threatening quantities. The measurement results ranged from 1394 µg/m3 to 1686 µg/m3 PM10, 1392 µg/m3 to 1682 µg/m3 PM2.5, and 1355 µg/m3 to 1634 µg/m3 PM1, respectively. Only one private-label brand differed significantly (p < 0.001) from the other cigarette brands, which were tested with slightly lower PM levels. All other brands differed only marginally (not significant, p > 0.05) from one another. Significant (p < 0.05) negative correlations between private-label and brand-name cigarettes were found for PM10, PM2.5, and PM1 when accounting for tobacco filling densities, and for PM1 when accounting for filter lengths. The especially health-hazardous fraction PM1 accounted for the largest proportion of PM emissions from the cigarettes tested. The results of this study suggest that- cheaper tobacco products are as harmful as more expensive ones, at least regarding PM emissions. This highlights the importance of anti-smoking campaigns, especially for lower socioeconomic groups, where smoking is more widespread. Governments should reduce the price gap between cheap and more expensive tobacco products by implementing specific tobacco taxes. In such a case, at increasing prices of tobacco products, a downward shift to private-label cigarettes would probably decrease.

Beneficial modulation of the gut microbiome has high-impact implications not only in humans, but also in livestock that sustain our current societal needs. In this context, we have tailored an acetylated galactoglucomannan (AcGGM) fibre to match unique enzymatic capabilities of Roseburia and Faecalibacterium species, both renowned butyrate-producing gut commensals. Here, we test the accuracy of AcGGM within the complex endogenous gut microbiome of pigs, wherein we resolve 355 metagenome-assembled genomes together with quantitative metaproteomes. In AcGGM-fed pigs, both target populations differentially express AcGGM-specific polysaccharide utilization loci, including novel, mannan-specific esterases that are critical to its deconstruction. However, AcGGM-inclusion also manifests a "butterfly effect", whereby numerous metabolic changes and interdependent cross-feeding pathways occur in neighboring non-mannanolytic populations that produce short-chain fatty acids. Our findings show how intricate structural features and acetylation patterns of dietary fibre can be customized to specific bacterial populations, with potential to create greater modulatory effects at large.

Shiga toxin-producing Escherichia coli (STEC) and Shigella spp./enteroinvasive E. coli (EIEC) are common diarrheagenic bacteria that cause sporadic diseases and outbreaks. Clinical manifestations vary from mild symptoms to severe complications. For microbiological diagnosis, culture confirmation of a positive stool screening PCR test is challenging because of time-consuming methods for isolation of strains, wide variety of STEC pathotypes, and increased emergence of non-classical strains with unusual serotypes. Therefore, molecular assays for the rapid identification of suspect colonies growing on selective media are very useful. In this study, the performance of the newly introduced eazyplex® EHEC assay based on loop-mediated isothermal amplification (LAMP) was evaluated using 18 representative STEC and Shigella strains and 31 isolates or positive-enrichment broths that were collected from clinical stool samples following screening by BD MAX™ EBP PCR. Results were compared to real-time PCR as a reference standard. Overall, sensitivities and specificities of the eazyplex® EHEC were as follows: 94.7% and 100% for Shiga toxin 1 (stx1), 100% and 100% for stx2, 93.3% and 97.1% for intimin (eae), 100% and 100% for enterohemolysin A (ehlyA), and 100% and 100% for invasion-associated plasmid antigen H (ipaH) as Shigella spp./EIEC target, respectively. Sample preparation for LAMP took only some minutes, and the time to result of the assay ranged from 8.5 to 13 min. This study shows that eazyplex® EHEC is a very fast and easy to perform molecular assay that provides reliable results as a culture confirmation assay for the diagnosis of STEC and Shigella spp./EIEC infections.

From a global viewpoint, a lot of time is spent within the indoor air compartment of vehicles. A German study on mobility has revealed that, on average, people spend 45 minutes per day inside vehicles. In recent years the number of cars has increased to around 43 million vehicles in private households. This means that more than one car can be used in every household. The ratio has been growing, especially in eastern Germany and rural areas. "Overall and especially outside the cities, the car remains by far number one mode of transport, especially in terms of mileage". Therefore, numerous international studies have addressed different aspects of indoor air hygiene, in the past years. In this paper, meaningful original studies on car indoor air pollution, related to VOCs, COx, PMs, microbials, BFRs, OPFRs, cigarettes, electronic smoking devices, high molecular weight plasticizer, and NOx are summarized in the form of a review. This present review aimed to summarize recently published studies in this important field of environmental medicine and points to the need for further studies with special recommendations for optimizing the interior air hygiene.

Background: Hospital wastewaters contain fecal material from a large number of individuals, of which many are undergoing antibiotic therapy. It is, thus, plausible that hospital wastewaters could provide opportunities to find novel carbapenemases and other resistance genes not yet described in clinical strains. Our aim was therefore to investigate the microbiota and antibiotic resistome of hospital effluent collected from the city of Mumbai, India, with a special focus on identifying novel carbapenemases., Results: Shotgun metagenomics revealed a total of 112 different mobile antibiotic resistance gene types, conferring resistance against almost all classes of antibiotics. Beta-lactamase genes, including encoding clinically important carbapenemases, such as NDM, VIM, IMP, KPC, and OXA-48, were abundant. NDM (0.9% relative abundance to 16S rRNA genes) was the most common carbapenemase gene, followed by OXA-58 (0.84% relative abundance to 16S rRNA genes). Among the investigated mobile genetic elements, class 1 integrons (11% relative abundance to 16S rRNA genes) were the most abundant. The genus Acinetobacter accounted for as many as 30% of the total 16S rRNA reads, with A. baumannii accounting for an estimated 2.5%. High throughput sequencing of amplified integron gene cassettes identified a novel functional variant of an IMP-type (proposed IMP-81) carbapenemase gene (eight aa substitutions) along with recently described novel resistance genes like sul4 and bla RSA1 . Using a computational hidden Markov model, we detected 27 unique metallo-beta-lactamase (MBL) genes in the shotgun data, of which nine were novel subclass B1 genes, one novel subclass B2, and 10 novel subclass B3 genes. Six of the seven novel MBL genes were functional when expressed in Escherichia coli., Conclusion: By exploring hospital wastewater from India, our understanding of the diversity of carbapenemases has been extended. The study also demonstrates that the microbiota of hospital wastewater can serve as a reservoir of novel resistance genes, including previously uncharacterized carbapenemases with the potential to spread further.

Background: Shotgun metagenome data sets of microbial communities are highly diverse, not only due to the natural variation of the underlying biological systems, but also due to differences in laboratory protocols, replicate numbers, and sequencing technologies. Accordingly, to effectively assess the performance of metagenomic analysis software, a wide range of benchmark data sets are required., Results: We describe the CAMISIM microbial community and metagenome simulator. The software can model different microbial abundance profiles, multi-sample time series, and differential abundance studies, includes real and simulated strain-level diversity, and generates second- and third-generation sequencing data from taxonomic profiles or de novo. Gold standards are created for sequence assembly, genome binning, taxonomic binning, and taxonomic profiling. CAMSIM generated the benchmark data sets of the first CAMI challenge. For two simulated multi-sample data sets of the human and mouse gut microbiomes, we observed high functional congruence to the real data. As further applications, we investigated the effect of varying evolutionary genome divergence, sequencing depth, and read error profiles on two popular metagenome assemblers, MEGAHIT, and metaSPAdes, on several thousand small data sets generated with CAMISIM., Conclusions: CAMISIM can simulate a wide variety of microbial communities and metagenome data sets together with standards of truth for method evaluation. All data sets and the software are freely available at https://github.com/CAMI-challenge/CAMISIM.

Air pollution of particulate matter (PM) from traffic emissions has a significant impact on human health. Risk assessments for different traffic participants are often performed on the basis of data from local air quality monitoring stations. Numerous studies demonstrated the limitation of this approach. To assess the risk of PM exposure to a car driver more realistically, we measure the exposure to PM in a car cabin with a mobile aerosol spectrometer in Frankfurt am Main under different settings (local variations, opened versus a closed window) and compare it with data from stationary measurement. A video camera monitored the surroundings for potential PM source detection. In-cabin concentrations peaked at 508 µg m -3 for PM 10 , 133.9 µg m -3 for PM 2.5 , and 401.3 µg m -3 for coarse particles, and strongly depended on PM size and PM concentration in ambient air. The concentration of smaller particles showed low fluctuations, but the concentration of coarse particles showed high fluctuations with maximum values on busy roads. Several of these concentration peaks were assigned to the corresponding sources with characteristic particle size distribution profiles. The closure of the car window reduced the exposure to PM, and in particular to coarse particles. The mobile measured PM values differed significantly from stationary PM measures, although good correlations were computed for finer particles. Mobile rather than stationary measurements are essential to assess the risk of PM exposure for car passengers.

Methods for assembly, taxonomic profiling and binning are key to interpreting metagenome data, but a lack of consensus about benchmarking complicates performance assessment. The Critical Assessment of Metagenome Interpretation (CAMI) challenge has engaged the global developer community to benchmark their programs on highly complex and realistic data sets, generated from ∼700 newly sequenced microorganisms and ∼600 novel viruses and plasmids and representing common experimental setups. Assembly and genome binning programs performed well for species represented by individual genomes but were substantially affected by the presence of related strains. Taxonomic profiling and binning programs were proficient at high taxonomic ranks, with a notable performance decrease below family level. Parameter settings markedly affected performance, underscoring their importance for program reproducibility. The CAMI results highlight current challenges but also provide a roadmap for software selection to answer specific research questions.

The enrichment culture BPL is able to degrade benzene with sulfate as electron acceptor and is dominated by an organism of the genus Pelotomaculum. Members of Pelotomaculum are usually known to be fermenters, undergoing syntrophy with anaerobic respiring microorganisms or methanogens. By using a metagenomic approach, we reconstructed a high-quality genome (∼2.97 Mbp, 99% completeness) for Pelotomaculum candidate BPL. The proteogenomic data suggested that (1) anaerobic benzene degradation was activated by a yet unknown mechanism for conversion of benzene to benzoyl-CoA; (2) the central benzoyl-CoA degradation pathway involved reductive dearomatization by a class II benzoyl-CoA reductase followed by hydrolytic ring cleavage and modified β-oxidation; (3) the oxidative acetyl-CoA pathway was utilized for complete oxidation to CO2. Interestingly, the genome of Pelotomaculum candidate BPL has all the genes for a complete sulfate reduction pathway including a similar electron transfer mechanism for dissimilatory sulfate reduction as in other Gram-positive sulfate-reducing bacteria. The proteome analysis revealed that the essential enzymes for sulfate reduction were all formed during growth with benzene. Thus, our data indicated that, besides its potential to anaerobically degrade benzene, Pelotomaculum candidate BPL is the first member of the genus that can perform sulfate reduction., (© FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)