@article{Saeidi2025,

title = {Towards a better understanding of sorption of persistent and mobile contaminants to activated carbon: Applying data analysis techniques with experimental datasets of limited size},

author = {Navid Saeidi and Laura Lotteraner and Gabriel Sigmund and Thilo Hofmann and Martin Krauss and Katrin Mackenzie and Anett Georgi},

url = {https://doi.org/10.1016/j.watres.2024.123032},

doi = {10.1016/j.watres.2024.123032},

issn = {0043-1354},

year  = {2025},

date = {2025-04-00},

urldate = {2025-04-00},

journal = {Water Research},

volume = {274},

publisher = {Elsevier BV},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Lintner2025,

title = {Tire-derived compounds, phthalates, and trace metals in the Kiel Fjord (Germany)},

author = {Michael Lintner and Charlotte Henkel and Ruoting Peng and Petra Heinz and Martin Stockhausen and Thilo Hofmann and Thorsten Hüffer and Nina Keul},

url = {https://www.sciencedirect.com/science/article/pii/S0025326X25000566#ab0015},

doi = {10.1016/j.marpolbul.2025.117581},

issn = {0025-326X},

year  = {2025},

date = {2025-03-00},

urldate = {2025-03-00},

journal = {Marine Pollution Bulletin},

volume = {212},

publisher = {Elsevier BV},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid39966520,

title = {Metagenomic estimation of dietary intake from human stool},

author = {Christian Diener and Hannah D Holscher and Klara Filek and Karen D Corbin and Christine Moissl-Eichinger and Sean M Gibbons},

doi = {10.1038/s42255-025-01220-1},

issn = {2522-5812},

year  = {2025},

date = {2025-02-01},

journal = {Nat Metab},

abstract = {Dietary intake is tightly coupled to gut microbiota composition, human metabolism and the incidence of virtually all major chronic diseases. Dietary and nutrient intake are usually assessed using self-reporting methods, including dietary questionnaires and food records, which suffer from reporting biases and require strong compliance from study participants. Here, we present Metagenomic Estimation of Dietary Intake (MEDI): a method for quantifying food-derived DNA in human faecal metagenomes. We show that DNA-containing food components can be reliably detected in stool-derived metagenomic data, even when present at low abundances (more than ten reads). We show how MEDI dietary intake profiles can be converted into detailed metabolic representations of nutrient intake. MEDI identifies the onset of solid food consumption in infants, shows significant agreement with food frequency questionnaire responses in an adult population and shows agreement with food and nutrient intake in two controlled-feeding studies. Finally, we identify specific dietary features associated with metabolic syndrome in a large clinical cohort without dietary records, providing a proof-of-concept for detailed tracking of individual-specific, health-relevant dietary patterns without the need for questionnaires.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid39707459,

title = {pH-FISH: coupled microscale analysis of microbial identity and acid-base metabolism in complex biofilm samples},

author = {Yumi Chokyu Del Rey and Katharina Kitzinger and Marie Braad Lund and Andreas Schramm and Rikke Louise Meyer and Michael Wagner and Sebastian Schlafer},

doi = {10.1186/s40168-024-01977-9},

issn = {2049-2618},

year  = {2024},

date = {2024-12-01},

journal = {Microbiome},

volume = {12},

number = {1},

pages = {266},

abstract = {BACKGROUND: Correlative structural and chemical imaging of biofilms allows for the combined analysis of microbial identity and metabolism at the microscale. Here, we developed pH-FISH, a method that combines pH ratiometry with fluorescence in situ hybridization (FISH) in structurally intact biofilms for the coupled investigation of microbial acid metabolism and biofilm composition. Careful biofilm handling and modified sample preparation procedures for FISH allowed preservation of the three-dimensional biofilm structure throughout all processing and imaging steps. We then employed pH-FISH to investigate the relationship between local biofilm pH and the distribution of acid-producing (streptococci) and acid-consuming (Veillonella spp.) bacteria in dental biofilms from healthy subjects and caries-active patients.nnRESULTS: The relative abundance of streptococci correlated with low biofilm pH at the field-of-view level, while the opposite trend was observed for Veillonella spp. These results suggest that clusters of streptococci contribute to the formation of acidic pockets inside dental biofilms, whereas Veillonella spp. may have a protective role against biofilm acidification.nnCONCLUSIONS: pH-FISH combines microscale mapping of biofilm pH in real time with structural imaging of the local microbial architecture, and is a powerful method to explore the interplay between biofilm composition and metabolism in complex biological systems. Video Abstract.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid39435044,

title = {Quantification of guanidine in environmental samples using benzoin derivatization and LC-MS analysis},

author = {Richard Gruseck and Marton Palatinszky and Michael Wagner and Thilo Hofmann and Michael Zumstein},

doi = {10.1016/j.mex.2024.102972},

issn = {2215-0161},

year  = {2024},

date = {2024-12-01},

journal = {MethodsX},

volume = {13},

pages = {102972},

abstract = {The recent discovery of guanidine-dependent riboswitches in many microbes raised interest in the biological function and metabolism of this nitrogen-rich compound. However, very little is known about the concentrations of guanidine in the environment. Several methods have been published for quantifying guanidine and guanidino compounds in human urine and blood, often relying on derivatization followed by fluorescence detection. We adapted this analytical approach using benzoin as the derivatization agent to sensitively and selectively quantify guanidine in environmental samples, thereby facilitating future research on the biological and environmental roles of guanidine. This adapted method was applied to human urine, raw wastewater, and biological growth media as relevant matrices. Our liquid chromatography-tandem mass spectrometry analyses of the derivatized solutions identified a different major derivatization product than previously reported. This product was consistently observed across various substrates (guanidine, methylguanidine, and arginine) and derivatization agents (benzoin and anisoin). We observed a constant background signal, restricting our analyses to a lower limit of quantification of 50 nM. Despite this limitation, our method allowed for the quantification of guanidine concentrations significantly lower than those reported in previous derivatization-based studies.•Selective and sensitive detection of guanidine by LC-MS.•Method development and validation for robust detection of guanidine in environmental samples.•Reduction of sample preparation steps and reduced usage of toxic chemicals compared to previous methods.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Canarini2024,

title = {Soil fungi remain active and invest in storage compounds during drought independent of future climate conditions},

author = {Alberto Canarini and Lucia Fuchslueger and Jörg Schnecker and Dennis Metze and Daniel B. Nelson and Ansgar Kahmen and Margarete Watzka and Erich M. Pötsch and Andreas Schaumberger and Michael Bahn and Andreas Richter},

url = {https://pubmed.ncbi.nlm.nih.gov/39613745/},

doi = {10.1038/s41467-024-54537-y},

issn = {2041-1723},

year  = {2024},

date = {2024-12-00},

urldate = {2024-12-00},

journal = {Nat Commun},

volume = {15},

number = {1},

publisher = {Springer Science and Business Media LLC},

abstract = {<jats:title>Abstract</jats:title><jats:p>Microbial growth is central to soil carbon cycling. However, how microbial communities grow under climate change is still largely unexplored. Here we use a unique field experiment simulating future climate conditions (increased atmospheric CO<jats:sub>2</jats:sub> and temperature) and drought concomitantly and investigate impacts on soil microbial activity. We trace <jats:sup>2</jats:sup>H or <jats:sup>18</jats:sup>O applied via water-vapor exchange into membrane (and storage) fatty acids or DNA, respectively, to assess community- and group-level adjustments in soil microbial physiology (replication, storage product synthesis, and carbon use efficiency). We show that, while bacterial growth decreases by half during drought, fungal growth remains stable, demonstrating a remarkable resistance against soil moisture changes. In addition, fungal investment into storage triglycerides increases more than five-fold under drought. Community-level carbon use efficiency (the balance between anabolism and catabolism) is unaffected by drought but decreases in future climate conditions, favoring catabolism. Our results highlight that accounting for different microbial growth strategies can foster our understanding of soil microbial contributions to carbon cycling and feedback on the climate system.</jats:p>},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Fian2024,

title = {Microplastics in food and drink: perceptions of the risks, challenges, and solutions among individuals in the ‘farm-to-fork’ food chain},

author = {Leonie Fian and Lena M. Schmidlechner and Ulrike Felt and Thilo Hofmann and Mathew P. White and Sabine Pahl},

url = {https://www.tandfonline.com/doi/full/10.1080/13669877.2024.2431900},

doi = {10.1080/13669877.2024.2431900},

issn = {1466-4461},

year  = {2024},

date = {2024-11-26},

urldate = {2024-11-26},

journal = {Journal of Risk Research},

pages = {1--24},

publisher = {Informa UK Limited},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Bauchinger2024,

title = {Characteristics of putative keystones in the healthy adult human gut microbiota as determined by correlation network analysis},

author = {Franziska Bauchinger and David Seki and David Berry},

url = {https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2024.1454634/full},

doi = {10.3389/fmicb.2024.1454634},

issn = {1664-302X},

year  = {2024},

date = {2024-11-20},

urldate = {2024-11-20},

journal = {Front. Microbiol.},

volume = {15},

publisher = {Frontiers Media SA},

abstract = {<jats:p>Keystone species are thought to play a critical role in determining the structure and function of microbial communities. As they are important candidates for microbiome-targeted interventions, the identification and characterization of keystones is a pressing research goal. Both empirical as well as computational approaches to identify keystones have been proposed, and in particular correlation network analysis is frequently utilized to interrogate sequencing-based microbiome data. Here, we apply an established method for identifying putative keystone taxa in correlation networks. We develop a robust workflow for network construction and systematically evaluate the effects of taxonomic resolution on network properties and the identification of keystone taxa. We are able to identify correlation network keystone species and genera, but could not detect taxa with high keystone potential at lower taxonomic resolution. Based on the correlation patterns observed, we hypothesize that the identified putative keystone taxa have a stabilizing effect that is exerted on correlated taxa. Correlation network analysis further revealed subcommunities present in the dataset that are remarkably similar to previously described patterns. The interrogation of available metatranscriptomes also revealed distinct transcriptional states present in all putative keystone taxa. These results suggest that keystone taxa may have stabilizing properties in a subset of community members rather than global effects. The work presented here contributes to the understanding of correlation network keystone taxa and sheds light on their potential ecological significance.</jats:p>},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid39352455,

title = {What determines transfer of carbon from plants to mycorrhizal fungi?},

author = {Rebecca A Bunn and Ana Corrêa and Jaya Joshi and Christina Kaiser and Ylva Lekberg and Cindy E Prescott and Anna Sala and Justine Karst},

doi = {10.1111/nph.20145},

issn = {1469-8137},

year  = {2024},

date = {2024-11-01},

journal = {New Phytol},

volume = {244},

number = {4},

pages = {1199--1215},

abstract = {Biological Market Models are common evolutionary frameworks to understand the maintenance of mutualism in mycorrhizas. 'Surplus C' hypotheses provide an alternative framework where stoichiometry and source-sink dynamics govern mycorrhizal function. A critical difference between these frameworks is whether carbon transfer from plants is regulated by nutrient transfer from fungi or through source-sink dynamics. In this review, we: provide a historical perspective; summarize studies that asked whether plants transfer more carbon to fungi that transfer more nutrients; conduct a meta-analysis to assess whether mycorrhizal plant growth suppressions are related to carbon transfer; and review literature on cellular mechanisms for carbon transfer. In sum, current knowledge does not indicate that carbon transfer from plants is directly regulated by nutrient delivery from fungi. Further, mycorrhizal plant growth responses were linked to nutrient uptake rather than carbon transfer. These findings are more consistent with 'Surplus C' hypotheses than Biological Market Models. However, we also identify research gaps, and future research may uncover a mechanism directly linking carbon and nutrient transfer. Until then, we urge caution when applying economic terminology to describe mycorrhizas. We present a synthesis of ideas, consider knowledge gaps, and suggest experiments to advance the field.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid39572788,

title = {The Parkinson's disease drug entacapone disrupts gut microbiome homoeostasis via iron sequestration},

author = {Fátima C Pereira and Xiaowei Ge and Jannie M Kristensen and Rasmus H Kirkegaard and Klara Maritsch and Dávid Szamosvári and Stefanie Imminger and David Seki and Juwairiyah B Shazzad and Yifan Zhu and Marie Decorte and Bela Hausmann and David Berry and Kenneth Wasmund and Arno Schintlmeister and Thomas Böttcher and Ji-Xin Cheng and Michael Wagner},

doi = {10.1038/s41564-024-01853-0},

issn = {2058-5276},

year  = {2024},

date = {2024-11-01},

journal = {Nat Microbiol},

abstract = {Many human-targeted drugs alter the gut microbiome, leading to implications for host health. However, the mechanisms underlying these effects are not well known. Here we combined quantitative microbiome profiling, long-read metagenomics, stable isotope probing and single-cell chemical imaging to investigate the impact of two widely prescribed drugs on the gut microbiome. Physiologically relevant concentrations of entacapone, a treatment for Parkinson's disease, or loxapine succinate, used to treat schizophrenia, were incubated ex vivo with human faecal samples. Both drugs significantly impact microbial activity, more so than microbial abundance. Mechanistically, entacapone can complex and deplete available iron resulting in gut microbiome composition and function changes. Microbial growth can be rescued by replenishing levels of microbiota-accessible iron. Further, entacapone-induced iron starvation selected for iron-scavenging gut microbiome members encoding antimicrobial resistance and virulence genes. These findings reveal the impact of two under-investigated drugs on whole microbiomes and identify metal sequestration as a mechanism of drug-induced microbiome disturbance.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid39423289,

title = {Tailless and filamentous prophages are predominant in marine Vibrio},

author = {Kerrin Steensen and Joana Séneca and Nina Bartlau and Xiaoqian A Yu and Fatima A Hussain and Martin F Polz},

doi = {10.1093/ismejo/wrae202},

issn = {1751-7370},

year  = {2024},

date = {2024-10-01},

urldate = {2024-10-01},

journal = {ISME J},

abstract = {Although tailed bacteriophages (phages) of the class Caudoviricetes are thought to constitute the most abundant and ecologically relevant group of phages that can integrate their genome into the host chromosome, it is becoming increasingly clear that other prophages are widespread. Here, we show that prophages derived from filamentous and tailless phages with genome sizes below 16 kb make up the majority of prophages in marine bacteria of the genus Vibrio. To estimate prophage prevalence unaffected by database biases, we combined comparative genomics and chemical induction of 58 diverse Vibrio cyclitrophicus isolates, resulting in 107 well-curated prophages. Complemented with computationally predicted prophages, we obtained 1,158 prophages from 931 naturally co-existing strains of the family Vibrionaceae. Prophages resembling tailless and filamentous phages predominated, accounting for 80% of all prophages in V. cyclitrophicus and 60% across the Vibrionaceae. In our experimental model, prophages of all three viral realms actively replicated upon induction indicating their ability to transfer to new hosts. Indeed, prophages were rapidly gained and lost, as suggested by variable prophage content between closely related V. cyclitrophicus. Prophages related to filamentous and tailless phages were integrated into only three genomic locations and restored the function of their integration site. Despite their small size, they contained highly diverse accessory genes that may contribute to host fitness, such as phage defense systems. We propose that, like their well-studied tailed equivalent, tailless and filamentous temperate phages are active and highly abundant drivers of host ecology and evolution in marine Vibrio, which have been largely overlooked.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Protsak2024b,

title = {Enhanced selective extraction of indium and gallium using mesoporous sorbents},

author = {Iryna Protsak and Martin Stockhausen and Aaron Brewer and Martin Owton and Thilo Hofmann and Freddy Kleitz},

url = {https://www.sciencedirect.com/science/article/pii/S138589472405959X?via%3Dihub},

doi = {10.1016/j.cej.2024.154468},

issn = {1385-8947},

year  = {2024},

date = {2024-10-00},

urldate = {2024-10-00},

journal = {Chemical Engineering Journal},

volume = {498},

publisher = {Elsevier BV},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid39333700,

title = {Photoaging enhances the leaching of di(2-ethylhexyl) phthalate and transformation products from polyvinyl chloride microplastics into aquatic environments},

author = {Charlotte Henkel and Thorsten Hüffer and Ruoting Peng and Xiaoyu Gao and Subhasis Ghoshal and Thilo Hofmann},

doi = {10.1038/s42004-024-01310-3},

issn = {2399-3669},

year  = {2024},

date = {2024-09-01},

journal = {Commun Chem},

volume = {7},

number = {1},

pages = {218},

abstract = {Increasing chemical pollution is a threat to sustainable water resources worldwide. Plastics and harmful additives released from plastics add to this burden and might pose a risk to aquatic organisms, and human health. Phthalates, which are common plasticizers and endocrine-disrupting chemicals, are released from polyvinyl chloride (PVC) microplastics and are a cause of concern. Therefore, the leaching kinetics of additives, including the influence of environmental weathering, are key to assessing exposure concentrations but remain largely unknown. We show that photoaging strongly enhances the leaching rates of di(2-ethylhexyl) phthalate (DEHP) by a factor of 1.5, and newly-formed harmful transformation products, such as mono(2-ethylhexyl) phthalate (MEHP), phthalic acid, and phthalic anhydride from PVC microplastics into the aquatic environment. Leaching half-lives of DEHP reduced from 449 years for pristine PVC to 121 years for photoaged PVC. Aqueous boundary layer diffusion (ABLD) is the limiting mass transfer process for the release of DEHP from pristine and photoaged PVC microplastics. The leaching of transformation products is limited by intraparticle diffusion (IPD). The calculated mass transfer rates can be used to predict exposure concentrations of harmful additives in the aquatic environment.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Protsak2024,

title = {Advancing Selective Extraction: A Novel Approach for Scandium, Thorium, and Uranium Ion Capture},

author = {Iryna Protsak and Martin Stockhausen and Aaron Brewer and Martin Owton and Thilo Hofmann and Freddy Kleitz},

url = {https://onlinelibrary.wiley.com/doi/10.1002/smsc.202400171},

doi = {10.1002/smsc.202400171},

issn = {2688-4046},

year  = {2024},

date = {2024-08-28},

urldate = {2024-08-28},

journal = {Small Science},

publisher = {Wiley},

abstract = {<jats:p>The potential use of thorium (Th) and uranium (U) as nuclear fuels underscores the importance of developing materials for their sustainable recovery. The production of Th and U requires the separation of these elements from rare‐earth elements (REEs) as they often coexist in various feedstocks. Equally crucial is efficiently isolating scandium (Sc) from REEs, considering its high‐value status and pivotal role in advanced alloy technologies. This study introduces a new selective ligand‐functionalized silica sorbent for extracting Sc, other REEs, Th, and U from solutions with varying pH and elemental compositions. The functionalized sorbent exhibits exceptional selectivity for Sc ions at pH 4 across solutions containing 3–20 elements. It also shows excellent selectivity for Th at pH 2 in 18‐ and 20‐element solutions and substantial selectivity for U in 18‐ and 20‐element solutions at pH 4. Additionally, it efficiently adsorbs neodymium (Nd), dysprosium (Dy), and lanthanum (La) in Sc‐free solutions with a given preference for Nd. The ligand‐functionalized sorbent successfully undergoes ten cycles of reuse which along with its enhanced recovery performance toward targeted elements highlights its industrial application potential.</jats:p>},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid39217206,

title = {Targeted isolation of Methanobrevibacter strains from fecal samples expands the cultivated human archaeome},

author = {Stefanie Duller and Simone Vrbancic and Lukasz Szydlowski and Alexander Mahnert and Marcus Blohs and Michael Predl and Christina Kumpitsch and Verena Zrim and Christoph Högenauer and Tomasz Kosciolek and Ruth A Schmitz and Anna Eberhard and Melanie Dragovan and Laura Schmidberger and Tamara Zurabischvili and Viktoria Weinberger and Adrian Mathias Moser and Dagmar Kolb and Dominique Pernitsch and Rokhsareh Mohammadzadeh and Torben Kühnast and Thomas Rattei and Christine Moissl-Eichinger},

doi = {10.1038/s41467-024-52037-7},

issn = {2041-1723},

year  = {2024},

date = {2024-08-01},

urldate = {2024-08-01},

journal = {Nat Commun},

volume = {15},

number = {1},

pages = {7593},

abstract = {Archaea are vital components of the human microbiome, yet their study within the gastrointestinal tract (GIT) is limited by the scarcity of cultured representatives. Our study presents a method for the targeted enrichment and isolation of methanogenic archaea from human fecal samples. The procedure combines methane breath testing, in silico metabolic modeling, media optimization, FACS, dilution series, and genomic sequencing through Nanopore technology. Additional analyzes include the co-cultured bacteriome, comparative genomics of archaeal genomes, functional comparisons, and structure-based protein function prediction of unknown differential traits. Successful establishment of stable archaeal cultures from 14 out of 16 fecal samples yielded nine previously uncultivated strains, eight of which are absent from a recent archaeome genome catalog. Comparative genomic and functional assessments of Methanobrevibacter smithii and Candidatus Methanobrevibacter intestini strains from individual donors revealed features potentially associated with gastrointestinal diseases. Our work broadens available archaeal representatives for GIT studies, and offers insights into Candidatus Methanobrevibacter intestini genomes' adaptability in critical microbiome contexts.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid39143220,

title = {Growth of complete ammonia oxidizers on guanidine},

author = {Marton Palatinszky and Craig W Herbold and Christopher J Sedlacek and Dominic Pühringer and Katharina Kitzinger and Andrew T Giguere and Kenneth Wasmund and Per H Nielsen and Morten K D Dueholm and Nico Jehmlich and Richard Gruseck and Anton Legin and Julius Kostan and Nesrete Krasnici and Claudia Schreiner and Johanna Palmetzhofer and Thilo Hofmann and Michael Zumstein and Kristina Djinović-Carugo and Holger Daims and Michael Wagner},

doi = {10.1038/s41586-024-07832-z},

issn = {1476-4687},

year  = {2024},

date = {2024-08-01},

urldate = {2024-08-01},

journal = {Nature},

volume = {633},

issue = {8030},

pages = {646-653},

abstract = {Guanidine is a chemically stable nitrogen compound that is excreted in human urine and is widely used in manufacturing of plastics, as a flame retardant and as a component of propellants, and is well known as a protein denaturant in biochemistry. Guanidine occurs widely in nature and is used by several microorganisms as a nitrogen source, but microorganisms growing on guanidine as the only substrate have not yet been identified. Here we show that the complete ammonia oxidizer (comammox) Nitrospira inopinata and probably most other comammox microorganisms can grow on guanidine as the sole source of energy, reductant and nitrogen. Proteomics, enzyme kinetics and the crystal structure of a N. inopinata guanidinase homologue demonstrated that it is a bona fide guanidinase. Incubation experiments with comammox-containing agricultural soil and wastewater treatment plant microbiomes suggested that guanidine serves as substrate for nitrification in the environment. The identification of guanidine as a growth substrate for comammox shows an unexpected niche of these globally important nitrifiers and offers opportunities for their isolation.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid38747602,

title = {SoxY gene family expansion underpins adaptation to diverse hosts and environments in symbiotic sulfide oxidizers},

author = {Marta Sudo and Jay Osvatic and John D Taylor and Suzanne C Dufour and Anchana Prathep and Laetitia G E Wilkins and Thomas Rattei and Benedict Yuen and Jillian M Petersen},

doi = {10.1128/msystems.01135-23},

issn = {2379-5077},

year  = {2024},

date = {2024-06-01},

urldate = {2024-06-01},

journal = {mSystems},

volume = {9},

number = {6},

pages = {e0113523},

abstract = {Sulfur-oxidizing bacteria (SOB) have developed distinct ecological strategies to obtain reduced sulfur compounds for growth. These range from specialists that can only use a limited range of reduced sulfur compounds to generalists that can use many different forms as electron donors. Forming intimate symbioses with animal hosts is another highly successful ecological strategy for SOB, as animals, through their behavior and physiology, can enable access to sulfur compounds. Symbioses have evolved multiple times in a range of animal hosts and from several lineages of SOB. They have successfully colonized a wide range of habitats, from seagrass beds to hydrothermal vents, with varying availability of symbiont energy sources. Our extensive analyses of sulfur transformation pathways in 234 genomes of symbiotic and free-living SOB revealed widespread conservation in metabolic pathways for sulfur oxidation in symbionts from different host species and environments, raising the question of how they have adapted to such a wide range of distinct habitats. We discovered a gene family expansion of  in these genomes, with up to five distinct copies per genome. Symbionts harboring only the "canonical"  were typically ecological "specialists" that are associated with specific host subfamilies or environments (e.g., hydrothermal vents, mangroves). Conversely, symbionts with multiple divergent  genes formed versatile associations across diverse hosts in various marine environments. We hypothesize that expansion and diversification of the  gene family could be one genomic mechanism supporting the metabolic flexibility of symbiotic SOB enabling them and their hosts to thrive in a range of different and dynamic environments.IMPORTANCESulfur metabolism is thought to be one of the most ancient mechanisms for energy generation in microorganisms. A diverse range of microorganisms today rely on sulfur oxidation for their metabolism. They can be free-living, or they can live in symbiosis with animal hosts, where they power entire ecosystems in the absence of light, such as in the deep sea. In the millions of years since they evolved, sulfur-oxidizing bacteria have adopted several highly successful strategies; some are ecological "specialists," and some are "generalists," but which genetic features underpin these ecological strategies are not well understood. We discovered a gene family that has become expanded in those species that also seem to be "generalists," revealing that duplication, repurposing, and reshuffling existing genes can be a powerful mechanism driving ecological lifestyle shifts.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Sherman2024b,

title = {Uptake of tire-derived compounds in leafy vegetables and implications for human dietary exposure},

author = {Anya Sherman and Luzian Elijah Hämmerle and Evyatar Ben Mordechay and Benny Chefetz and Thorsten Hüffer and Thilo Hofmann},

url = {https://www.frontiersin.org/journals/environmental-science/articles/10.3389/fenvs.2024.1384506/full},

doi = {10.3389/fenvs.2024.1384506},

issn = {2296-665X},

year  = {2024},

date = {2024-05-28},

urldate = {2024-05-28},

journal = {Front. Environ. Sci.},

volume = {12},

publisher = {Frontiers Media SA},

abstract = {<jats:sec><jats:title>Introduction</jats:title><jats:p>Tire and road wear particles are one of the most abundant types of microplastic entering the environment. The toxicity of tire and road wear particles has been linked to their organic additives and associated transformation products. Tire and road wear particles, and associated tire-derived compounds are introduced to the agricultural environment via atmospheric deposition, irrigation with reclaimed wastewater, and the use of biosolids (treated sewage sludge) as fertilizer. In the agricultural environment, these tire-derived compounds could be taken up by edible plants, leading to human exposure.</jats:p></jats:sec><jats:sec><jats:title>Methods</jats:title><jats:p>Sixteen tire-derived compounds were measured in twenty-eight commercial leafy vegetable samples from four countries. Based on the results, the estimated daily intake of these tire-derived compounds was calculated due to leafy vegetable consumption based on local diets under a mean and maximum concentration scenario.</jats:p></jats:sec><jats:sec><jats:title>Results</jats:title><jats:p>In commercial leafy vegetables, six tire-derived compounds were detected: benzothiazole (maximum concentration—238 ng/g dry weight), 2-hydroxybenzothiazole (maximum concentration—665 ng/g dry weight), 1,3-diphenylguanidine (maximum concentration—2.1 ng/g dry weight), N-(1,3-dimethylbutyl)-N′-phenyl-p-phenylenediamine (6PPD, maximum concentration—0.4 ng/g dry weight), N-Isopropyl-N-phenyl-4-phenylenediamine (IPPD, maximum concentration—0.1 ng/g dry weight), and N-phenyl-N-cyclohexyl-p-phenylenediamine (CPPD, maximum concentration—0.3 ng/g dry weight). At least one compound was present in 71% of samples analyzed. The estimated daily intake for 1,3-diphenylguanidine ranged from 0.05 ng/person/day in the mean scenario to 4.0 ng/person/day in the maximum scenario; benzothiazole ranged from 12 to 1,296 ng/person/day; 6PPD ranged from 0.06 to 2.6 ng/person/day; IPPD ranged from 0.04 to 1.1 ng/person/day; CPPD ranged from 0.05 to 2.6 ng/person/day.</jats:p></jats:sec><jats:sec><jats:title>Discussion</jats:title><jats:p>Statistical analyses did not reveal correlation between known growth conditions and tire-derived compound concentrations in the leafy vegetable samples. The estimated daily intake via leafy vegetable consumption was generally lower than or comparable to the estimated daily intake via other known sources. However, we show that tire-derived compounds are taken up by foodstuff, and exposure might be higher for other produce. Future studies are needed to uncover pathways of tire-derived compounds from road to food, assess the exposure to transformation products, and investigate the biological effects associated with this exposure.</jats:p></jats:sec>},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid38762502,

title = {Nitrous oxide respiration in acidophilic methanotrophs},

author = {Samuel Imisi Awala and Joo-Han Gwak and Yongman Kim and Man-Young Jung and Peter F Dunfield and Michael Wagner and Sung-Keun Rhee},

doi = {10.1038/s41467-024-48161-z},

issn = {2041-1723},

year  = {2024},

date = {2024-05-01},

journal = {Nat Commun},

volume = {15},

number = {1},

pages = {4226},

abstract = {Aerobic methanotrophic bacteria are considered strict aerobes but are often highly abundant in hypoxic and even anoxic environments. Despite possessing denitrification genes, it remains to be verified whether denitrification contributes to their growth. Here, we show that acidophilic methanotrophs can respire nitrous oxide (NO) and grow anaerobically on diverse non-methane substrates, including methanol, C-C substrates, and hydrogen. We study two strains that possess NO reductase genes: Methylocella tundrae T4 and Methylacidiphilum caldifontis IT6. We show that NO respiration supports growth of Methylacidiphilum caldifontis at an extremely acidic pH of 2.0, exceeding the known physiological pH limits for microbial NO consumption. Methylocella tundrae simultaneously consumes NO and CH in suboxic conditions, indicating robustness of its NO reductase activity in the presence of O. Furthermore, in O-limiting conditions, the amount of CH oxidized per O reduced increases when NO is added, indicating that Methylocella tundrae can direct more O towards methane monooxygenase. Thus, our results demonstrate that some methanotrophs can respire NO independently or simultaneously with O, which may facilitate their growth and survival in dynamic environments. Such metabolic capability enables these bacteria to simultaneously reduce the release of the key greenhouse gases CO, CH and NO.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid38113742,

title = {Tire materials disturb transformations of nitrogen compounds and affect the structure of biomass in aerobic granular sludge reactors},

author = {Piotr Jachimowicz and Ruoting Peng and Thorsten Hüffer and Thilo Hofmann and Agnieszka Cydzik-Kwiatkowska},

doi = {10.1016/j.jhazmat.2023.133223},

issn = {1873-3336},

year  = {2024},

date = {2024-03-01},

journal = {J Hazard Mater},

volume = {465},

pages = {133223},

abstract = {Tire materials (TMs) present a notable hazard due to their potential to release harmful chemicals and microplastics into the environment. They can infiltrate wastewater treatment plants, where their effects remain inadequately understood, raising concerns regarding their influence on treatment procedures. Thus, this study investigated the impact of TMs in wastewater (10, 25, 50 mg/L) on wastewater treatment efficiency, biomass morphology, and microbial composition in aerobic granular sludge (AGS) reactors. TM dosage negatively correlated with nitrification and denitrification efficiencies, reducing overall nitrogen removal, but did not affect the efficiency of chemical-oxygen-demand removal. The presence of TMs increased the diameter of the granules due to TM incorporation into the biomass. The most frequently leached additives from TMs were N-(1,3-dimethylbutyl)-N'-phenyl-1,4-phenylenediamine, benzothiazole (BTH), and 2-hydroxybenzothiazole. In the treated wastewater, only BTH and aniline were detected in higher concentrations, which indicates that tire additives were biodegraded by AGS. The microbial community within the AGS adapted to TMs and their chemicals, highlighting the potential for efficient degradation of tire additives by bacteria belonging to the genera Rubrivivax, Ferruginibacter, and Xanthomonas. Additionally, our research underscores AGS's ability to incorporate TMs into biomass and effectively biodegrade tire additives, offering a promising solution for addressing environmental concerns related to TMs.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid38555566,

title = {Exploring the human archaeome: its relevance for health and disease, and its complex interplay with the human immune system},

author = {Torben Kuehnast and Christina Kumpitsch and Rokhsareh Mohammadzadeh and Thomas Weichhart and Christine Moissl-Eichinger and Holger Heine},

doi = {10.1111/febs.17123},

issn = {1742-4658},

year  = {2024},

date = {2024-03-01},

journal = {FEBS J},

abstract = {This Review aims to coalesce existing knowledge on the human archaeome, a less-studied yet critical non-bacterial component of the human microbiome, with a focus on its interaction with the immune system. Despite a largely bacteria-centric focus in microbiome research, archaea present unique challenges and opportunities for understanding human health. We examine the archaeal distribution across different human body sites, such as the lower gastrointestinal tract (LGT), upper aerodigestive tract (UAT), urogenital tract (UGT), and skin. Variability in archaeal composition exists between sites; methanogens dominate the LGT, while Nitrososphaeria are prevalent on the skin and UAT. Archaea have yet to be classified as pathogens but show associations with conditions such as refractory sinusitis and vaginosis. In the LGT, methanogenic archaea play critical metabolic roles by converting bacterial end-products into methane, correlating with various health conditions, including obesity and certain cancers. Finally, this work looks at the complex interactions between archaea and the human immune system at the molecular level. Recent research has illuminated the roles of specific archaeal molecules, such as RNA and glycerolipids, in stimulating immune responses via innate immune receptors like Toll-like receptor 8 (TLR8) and 'C-type lectin domain family 4 member E' (CLEC4E; also known as MINCLE). Additionally, metabolic by-products of archaea, specifically methane, have demonstrated immunomodulatory effects through anti-inflammatory and anti-oxidative pathways. Despite these advancements, the mechanistic underpinnings of how archaea influence immune activity remain a fertile area for further investigation.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid38493180,

title = {Global abundance patterns, diversity, and ecology of Patescibacteria in wastewater treatment plants},

author = {Huifeng Hu and Jannie Munk Kristensen and Craig William Herbold and Petra Pjevac and Katharina Kitzinger and Bela Hausmann and Morten Kam Dahl Dueholm and Per Halkjaer Nielsen and Michael Wagner},

doi = {10.1186/s40168-024-01769-1},

issn = {2049-2618},

year  = {2024},

date = {2024-03-01},

journal = {Microbiome},

volume = {12},

number = {1},

pages = {55},

abstract = {BACKGROUND: Microorganisms are responsible for nutrient removal and resource recovery in wastewater treatment plants (WWTPs), and their diversity is often studied by 16S rRNA gene amplicon sequencing. However, this approach underestimates the abundance and diversity of Patescibacteria due to the low coverage of commonly used PCR primers for this highly divergent bacterial phylum. Therefore, our current understanding of the global diversity, distribution, and ecological role of Patescibacteria in WWTPs is very incomplete. This is particularly relevant as Patescibacteria are considered to be associated with microbial host cells and can therefore influence the abundance and temporal variability of other microbial groups that are important for WWTP functioning.nnRESULTS: Here, we evaluated the in silico coverage of widely used 16S rRNA gene-targeted primer pairs and redesigned a primer pair targeting the V4 region of bacterial and archaeal 16S rRNA genes to expand its coverage for Patescibacteria. We then experimentally evaluated and compared the performance of the original and modified V4-targeted primers on 565 WWTP samples from the MiDAS global sample collection. Using the modified primer pair, the percentage of ASVs classified as Patescibacteria increased from 5.9 to 23.8%, and the number of detected patescibacterial genera increased from 560 to 1576, while the detected diversity of the remaining microbial community remained similar. Due to this significantly improved coverage of Patescibacteria, we identified 23 core genera of Patescibacteria in WWTPs and described the global distribution pattern of these unusual microbes in these systems. Finally, correlation network analysis revealed potential host organisms that might be associated with Patescibacteria in WWTPs. Interestingly, strong indications were found for an association between Patescibacteria of the Saccharimonadia and globally abundant polyphosphate-accumulating organisms of the genus Ca. Phosphoribacter.nnCONCLUSIONS: Our study (i) provides an improved 16S rRNA gene V4 region-targeted amplicon primer pair inclusive of Patescibacteria with little impact on the detection of other taxa, (ii) reveals the diversity and distribution patterns of Patescibacteria in WWTPs on a global scale, and (iii) provides new insights into the ecological role and potential hosts of Patescibacteria in WWTPs. Video Abstract.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid38461313,

title = {Interindividual differences in aronia juice tolerability linked to gut microbiome and metabolome changes-secondary analysis of a randomized placebo-controlled parallel intervention trial},

author = {Sonja Lackner and Alexander Mahnert and Christine Moissl-Eichinger and Tobias Madl and Hansjörg Habisch and Nathalie Meier-Allard and Christina Kumpitsch and Theresa Lahousen and Alexandra Kohlhammer-Dohr and Sabrina Mörkl and Herbert Strobl and Sandra Holasek},

doi = {10.1186/s40168-024-01774-4},

issn = {2049-2618},

year  = {2024},

date = {2024-03-01},

journal = {Microbiome},

volume = {12},

number = {1},

pages = {49},

abstract = {BACKGROUND: Aronia melanocarpa is a berry rich in polyphenols known for health benefits. However, the bioavailability of polyphenols has been questioned, and the individual taste acceptance of the fruit with its specific flavor varies. We recently observed substantial differences in the tolerability of aronia juice among healthy females, with half of the individuals tolerating aronia juice without complaints. Given the importance of the gut microbiome in food digestion, we investigated in this secondary analysis of the randomized placebo-controlled parallel intervention study (ClinicalTrials.gov registration: NCT05432362) if aronia juice tolerability was associated with changes in intestinal microbiota and bacterial metabolites, seeking for potential mechanistic insights into the impact on aronia polyphenol tolerance and metabolic outcomes.nnRESULTS: Forty females were enrolled for this 6-week trial, receiving either 100 ml natural aronia juice (verum, V) twice daily or a polyphenol-free placebo (P) with a similar nutritional profile, followed by a 6-week washout. Within V, individuals were categorized into those who tolerated the juice well (Vt) or reported complaints (Vc). The gut microbiome diversity, as analyzed by 16S rRNA gene-based next-generation sequencing, remained unaltered in Vc but changed significantly in Vt. A MICOM-based flux balance analysis revealed pronounced differences in the 40 most predictive metabolites post-intervention. In Vc carbon-dioxide, ammonium and nine O-glycans were predicted due to a shift in microbial composition, while in Vt six bile acids were the most likely microbiota-derived metabolites. NMR metabolomics of plasma confirmed increased lipoprotein subclasses (LDL, VLDL) post-intervention, reverting after wash out. Stool samples maintained a stable metabolic profile.nnCONCLUSION: In linking aronia polyphenol tolerance to gut microbiota-derived metabolites, our study explores adaptive processes affecting lipoprotein profiles during high polyphenol ingestion in Vt and examines effects on mucosal gut health in response to intolerance to high polyphenol intake in Vc. Our results underpin the importance of individualized hormetic dosing for beneficial polyphenol effects, demonstrate dynamic gut microbiome responses to aronia juice, and emphasize personalized responses in polyphenol interventions.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid39679616,

title = {Gut microbiota genome features associated with brain injury in extremely premature infants},

author = {David Seki and Rasmus Kirkegaard and Jay Osvatic and Bela Hausmann and Joana Séneca and Petra Pjevac and Angelika Berger and Lindsay J Hall and Lukas Wisgrill and David Berry},

doi = {10.1080/19490976.2024.2410479},

issn = {1949-0984},

year  = {2024},

date = {2024-01-01},

journal = {Gut Microbes},

volume = {16},

number = {1},

pages = {2410479},

abstract = {Severe brain damage is common among premature infants, and the gut microbiota has been implicated in its pathology. Although the order of colonizing bacteria is well described, the mechanisms underlying aberrant assembly of the gut microbiota remain elusive. Here, we employed long-read nanopore sequencing to assess abundances of microbial species and their functional genomic potential in stool samples from a cohort of 30 extremely premature infants. We identify several key microbial traits significantly associated with severe brain damage, such as the genomic potential for nitrate respiration and iron scavenging. Members of the  were prevalent across the cohort and displayed a versatile metabolic potential, including pathogenic and nonpathogenic traits. Predominance of  and  were associated with an overall loss of genomic functional redundancy as well as poor neurophysiological outcome. These findings reveal microbial traits that may be involved in exacerbating brain injury in extremely premature infants and provide suitable targets for therapeutic interventions.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid39244747,

title = {Metabolite release by nitrifiers facilitates metabolic interactions in the ocean},

author = {Barbara Bayer and Shuting Liu and Katherine Louie and Trent R Northen and Michael Wagner and Holger Daims and Craig A Carlson and Alyson E Santoro},

doi = {10.1093/ismejo/wrae172},

issn = {1751-7370},

year  = {2024},

date = {2024-01-01},

journal = {ISME J},

volume = {18},

number = {1},

abstract = {Microbial chemoautotroph-heterotroph interactions may play a pivotal role in the cycling of carbon in the deep ocean, reminiscent of phytoplankton-heterotroph associations in surface waters. Nitrifiers are the most abundant chemoautotrophs in the global ocean, yet very little is known about nitrifier metabolite production, release, and transfer to heterotrophic microbial communities. To elucidate which organic compounds are released by nitrifiers and potentially available to heterotrophs, we characterized the exo- and endometabolomes of the ammonia-oxidizing archaeon Nitrosopumilus adriaticus CCS1 and the nitrite-oxidizing bacterium Nitrospina gracilis Nb-211. Nitrifier endometabolome composition was not a good predictor of exometabolite availability, indicating that metabolites were predominately released by mechanisms other than cell death/lysis. Although both nitrifiers released labile organic compounds, N. adriaticus preferentially released amino acids, particularly glycine, suggesting that its cell membranes might be more permeable to small, hydrophobic amino acids. We further initiated co-culture systems between each nitrifier and a heterotrophic alphaproteobacterium, and compared exometabolite and transcript patterns of nitrifiers grown axenically to those in co-culture. In particular, B vitamins exhibited dynamic production and consumption patterns in nitrifier-heterotroph co-cultures. We observed an increased production of vitamin B2 and the vitamin B12 lower ligand dimethylbenzimidazole by N. adriaticus and N. gracilis, respectively. In contrast, the heterotroph likely produced vitamin B5 in co-culture with both nitrifiers and consumed the vitamin B7 precursor dethiobiotin when grown with N. gracilis. Our results indicate that B vitamins and their precursors could play a particularly important role in governing specific metabolic interactions between nitrifiers and heterotrophic microbes in the ocean.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid39469462,

title = {Burkholderia pseudomallei produces 2-alkylquinolone derivatives important for host virulence and competition with bacteria that employ naphthoquinones for aerobic respiration},

author = {Sherry Mou and Viktoriia Savchenko and Verena Filz and Thomas Böttcher and David DeShazer},

doi = {10.3389/fmicb.2024.1474033},

issn = {1664-302X},

year  = {2024},

date = {2024-01-01},

urldate = {2024-01-01},

journal = {Front Microbiol},

volume = {15},

pages = {1474033},

abstract = {Melioidosis is caused by , an opportunistic Gram-negative pathogen that inhabits soil and water in tropical and subtropical regions.  infections often occur following contact with contaminated water or soil or by inhalation of contaminated dust and water droplets. There is limited knowledge about how  is able to survive in harsh environmental conditions and compete with the microbes that inhabit these niches. Previous research demonstrated that 3-methyl-2-alkylquinolones (MAQs), and their corresponding -oxides (MAQNOs), are produced by  and provide a competitive advantage when grown in the presence of Gram-positive bacteria. In this study, 39 Gram-negative environmental bacteria in the  and  phyla were isolated and characterized. Intriguingly,  inhibited 71% of bacteria in the phylum  in zone of inhibition and coculture competition assays, but no  isolates were similarly inhibited. Transposon mutagenesis was utilized to identify  genes required for the inhibition of  sp. ST4, a representative member of the . Three mutations mapped to , the locus encoding 2-alkylquinolone derivatives, and two mutations were identified in , a gene encoding a quorum-sensing controlled LysR-type transcriptional regulator.  strains with deletion mutations in  and  were unable to produce 2-alkylquinolone derivatives or inhibit  isolates in competition assays. RAW264.7 murine macrophage cells were infected with  1026b and 1026b  and there was a 94-fold reduction in the number of intracellular 1026b  bacteria relative to 1026b. The 50% lethal dose (LD) of 1026b and 1026b  in BALB/c mice was determined to be 3 x 10 colony forming units (CFU) and > 1 x 10 CFU, respectively. Taken together, the results indicate that the products of the  locus are important for intracellular replication in murine macrophages, virulence in a mouse model of melioidosis, and competition with bacteria that utilize naphthoquinones for aerobic respiration.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid38318189,

title = {Immune evasion by proteolytic shedding of natural killer group 2, member D ligands in  infection},

author = {Margit Anthofer and Markus Windisch and Rosa Haller and Sandra Ehmann and Sebastian Wrighton and Michael Miller and Lorenz Schernthanner and Iris Kufferath and Silvia Schauer and Barbara Jelušić and Sabine Kienesberger and Ellen L Zechner and Gernot Posselt and Mar Vales-Gomez and Hugh T Reyburn and Gregor Gorkiewicz},

doi = {10.3389/fimmu.2024.1282680},

issn = {1664-3224},

year  = {2024},

date = {2024-01-01},

journal = {Front Immunol},

volume = {15},

pages = {1282680},

abstract = {BACKGROUND:  () uses various strategies that attenuate mucosal immunity to ensure its persistence in the stomach. We recently found evidence that  might modulate the natural killer group 2, member 2 (NKG2D) system. The NKG2D receptor and its ligands are a major activation system of natural killer and cytotoxic T cells, which are important for mucosal immunity and tumor immunosurveillance. The NKG2D system allows recognition and elimination of infected and transformed cells, however viruses and cancers often subvert its activation. Here we aimed to identify a potential evasion of the NKG2D system in  infection.nnMETHODS: We analyzed expression of NKG2D system genes in gastric tissues of  gastritis and gastric cancer patients, and performed cell-culture based infection experiments using  isogenic mutants and epithelial and NK cell lines.nnRESULTS: In biopsies of  gastritis patients, NKG2D receptor expression was reduced while NKG2D ligands accumulated in the lamina propria, suggesting NKG2D evasion. ,  induced the transcription and proteolytic shedding of NKG2D ligands in stomach epithelial cells, and these effects were associated with specific  virulence factors. The -driven release of soluble NKG2D ligands reduced the immunogenic visibility of infected cells and attenuated the cytotoxic activity of effector immune cells, specifically the anti-tumor activity of NK cells.nnCONCLUSION:  manipulates the NKG2D system. This so far unrecognized strategy of immune evasion by  could potentially facilitate chronic bacterial persistence and might also promote stomach cancer development by allowing transformed cells to escape immune recognition and grow unimpeded to overt malignancy.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid38255855,

title = {Human Sterols Are Overproduced, Stored and Excreted in Yeasts},

author = {Astrid Radkohl and Veronika Schusterbauer and Lukas Bernauer and Gerald N Rechberger and Heimo Wolinski and Matthias Schittmayer and Ruth Birner-Gruenberger and Gerhard G Thallinger and Erich Leitner and Melanie Baeck and Harald Pichler and Anita Emmerstorfer-Augustin},

doi = {10.3390/ijms25020781},

issn = {1422-0067},

year  = {2024},

date = {2024-01-01},

journal = {Int J Mol Sci},

volume = {25},

number = {2},

abstract = {Sterols exert a profound influence on numerous cellular processes, playing a crucial role in both health and disease. However, comprehending the effects of sterol dysfunction on cellular physiology is challenging. Consequently, numerous processes affected by impaired sterol biosynthesis still elude our complete understanding. In this study, we made use of yeast strains that produce cholesterol instead of ergosterol and investigated the cellular response mechanisms on the transcriptome as well as the lipid level. The exchange of ergosterol for cholesterol caused the downregulation of phosphatidylethanolamine and phosphatidylserine and upregulation of phosphatidylinositol and phosphatidylcholine biosynthesis. Additionally, a shift towards polyunsaturated fatty acids was observed. While the sphingolipid levels dropped, the total amounts of sterols and triacylglycerol increased, which resulted in 1.7-fold enlarged lipid droplets in cholesterol-producing yeast cells. In addition to internal storage, cholesterol and its precursors were excreted into the culture supernatant, most likely by the action of ABC transporters Snq2, Pdr12 and Pdr15. Overall, our results demonstrate that, similarly to mammalian cells, the production of non-native sterols and sterol precursors causes lipotoxicity in , mainly due to upregulated sterol biosynthesis, and they highlight the different survival and stress response mechanisms on multiple, integrative levels.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Kang2023,

title = {Stability of Coumarins and Determination of the Net Iron Oxidation State of Iron–Coumarin Complexes: Implications for Examining Plant Iron Acquisition Mechanisms},

author = {Kyounglim Kang and Walter D. C. Schenkeveld and Guenther Weber and Stephan M. Kraemer},

doi = {10.1021/acsearthspacechem.3c00199},

issn = {2472-3452},

year  = {2023},

date = {2023-12-21},

journal = {ACS Earth Space Chem.},

volume = {7},

number = {12},

pages = {2339--2352},

publisher = {American Chemical Society (ACS)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid37850721,

title = {Engineered yeasts and lignocellulosic biomaterials: shaping a new dimension for biorefinery and global bioeconomy},

author = {Michael Dare Asemoloye and Tunde Sheriffdeen Bello and Peter Olusakin Oladoye and Muideen Remilekun Gbadamosi and Segun Oladiran Babarinde and Gboyega Ebenezer Adebami and Olumayowa Mary Olowe and Marta Elisabetta Eleonora Temporiti and Wolfgang Wanek and Mario Andrea Marchisio},

doi = {10.1080/21655979.2023.2269328},

issn = {2165-5987},

year  = {2023},

date = {2023-12-01},

journal = {Bioengineered},

volume = {14},

number = {1},

pages = {2269328},

abstract = {The next milestone of synthetic biology research relies on the development of customized microbes for specific industrial purposes. Metabolic pathways of an organism, for example, depict its chemical repertoire and its genetic makeup. If genes controlling such pathways can be identified, scientists can decide to enhance or rewrite them for different purposes depending on the organism and the desired metabolites. The lignocellulosic biorefinery has achieved good progress over the past few years with potential impact on global bioeconomy. This principle aims to produce different bio-based products like biochemical(s) or biofuel(s) from plant biomass under microbial actions. Meanwhile, yeasts have proven very useful for different biotechnological applications. Hence, their potentials in genetic/metabolic engineering can be fully explored for lignocellulosic biorefineries. For instance, the secretion of enzymes above the natural limit (aided by genetic engineering) would speed-up the down-line processes in lignocellulosic biorefineries and the cost. Thus, the next milestone would greatly require the development of synthetic yeasts with much more efficient metabolic capacities to achieve basic requirements for particular biorefinery. This review gave comprehensive overview of lignocellulosic biomaterials and their importance in bioeconomy. Many researchers have demonstrated the engineering of several ligninolytic enzymes in heterologous yeast hosts. However, there are still many factors needing to be well understood like the secretion time, titter value, thermal stability, pH tolerance, and reactivity of the recombinant enzymes. Here, we give a detailed account of the potentials of engineered yeasts being discussed, as well as the constraints associated with their development and applications.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid37847076,

title = {Chiral Monitoring Across Both Enantiomeric Excess and Concentration Space: Leveraging Quantum Cascade Lasers for Sensitive Vibrational Circular Dichroism Spectroscopy},

author = {Daniel-Ralph Hermann and Georg Ramer and Lisa Riedlsperger and Bernhard Lendl},

doi = {10.1177/00037028231206186},

issn = {1943-3530},

year  = {2023},

date = {2023-12-01},

journal = {Appl Spectrosc},

volume = {77},

number = {12},

pages = {1362--1370},

abstract = {Recently, high-throughput quantum cascade laser-based vibrational circular dichroism (QCL-VCD) technology has reduced the measurement time for high-quality vibrational circular dichroism spectra from hours to a few minutes. This study evaluates QCL-VCD for chiral monitoring using flow-through measurement of a changing sample in a circulating loop. A balanced detection QCL-VCD system was applied to the enantiomeric pair R/S-1,1'-bi-2-naphthol in solution. Different mixtures of the two components were used to simulate a racemization process, collecting spectral data at a time resolution of 6 min, and over three concentration levels. The goal of this experimental setup was to evaluate QCL-VCD in terms of both molar and enantiomeric excess (EE) sensitivity at a time resolution relevant to chiral monitoring in chemical processes. Subsequent chemometric evaluation by partial least squares regression revealed a cross-validated prediction accuracy of 2.8% EE with a robust prediction also for the test data set (error = 3.5% EE). In addition, the data set was also treated with the least absolute shrinkage and selection operator (LASSO), which also achieved a robust prediction. Due to the operating principle of LASSO, the obtained coefficients constituted a few discrete spectral frequencies, which represent the most variance. This information can be used in the future for dedicated QCL-based instrument design, gaining a higher time resolution without sacrificing predictive capabilities.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid37427803,

title = {Hydrolyzable tannins are incorporated into the endocarp during sclerification of the water caltrop Trapa natans},

author = {Jessica C Huss and Sebastian J Antreich and Martin Felhofer and Konrad Mayer and Michaela Eder and Ana Catarina Vieira Dias Dos Santos and Georg Ramer and Bernhard Lendl and Notburga Gierlinger},

doi = {10.1093/plphys/kiad408},

issn = {1532-2548},

year  = {2023},

date = {2023-12-01},

journal = {Plant Physiol},

volume = {194},

number = {1},

pages = {94--105},

abstract = {The water caltrop (Trapa natans) develops unique woody fruits with unusually large seeds among aquatic plants. During fruit development, the inner fruit wall (endocarp) sclerifies and forms a protective layer for the seed. Endocarp sclerification also occurs in many land plants with large seeds; however, in T. natans, the processes of fruit formation, endocarp hardening, and seed storage take place entirely underwater. To identify potential chemical and structural adaptations for the aquatic environment, we investigated the cell-wall composition in the endocarp at a young developmental stage, as well as at fruit maturity. Our work shows that hydrolyzable tannins-specifically gallotannins-flood the endocarp tissue during secondary wall formation and are integrated into cell walls along with lignin during maturation. Within the secondary walls of mature tissue, we identified unusually strong spectroscopic features of ester linkages, suggesting that the gallotannins and their derivatives are cross-linked to other wall components via ester bonds, leading to unique cell-wall properties. The synthesis of large amounts of water-soluble, defensive aromatic metabolites during secondary wall formation might be a fast way to defend seeds within the insufficiently lignified endocarp of T. natans.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid38097563b,

title = {Identification of inulin-responsive bacteria in the gut microbiota via multi-modal activity-based sorting},

author = {Alessandra Riva and Hamid Rasoulimehrabani and José Manuel Cruz-Rubio and Stephanie L Schnorr and Cornelia von Baeckmann and Deniz Inan and Georgi Nikolov and Craig W Herbold and Bela Hausmann and Petra Pjevac and Arno Schintlmeister and Andreas Spittler and Márton Palatinszky and Aida Kadunic and Norbert Hieger and Giorgia Del Favero and Martin von Bergen and Nico Jehmlich and Margarete Watzka and Kang Soo Lee and Julia Wiesenbauer and Sanaz Khadem and Helmut Viernstein and Roman Stocker and Michael Wagner and Christina Kaiser and Andreas Richter and Freddy Kleitz and David Berry},

doi = {10.1038/s41467-023-43448-z},

issn = {2041-1723},

year  = {2023},

date = {2023-12-01},

journal = {Nat Commun},

volume = {14},

number = {1},

pages = {8210},

abstract = {Prebiotics are defined as non-digestible dietary components that promote the growth of beneficial gut microorganisms. In many cases, however, this capability is not systematically evaluated. Here, we develop a methodology for determining prebiotic-responsive bacteria using the popular dietary supplement inulin. We first identify microbes with a capacity to bind inulin using mesoporous silica nanoparticles functionalized with inulin. 16S rRNA gene amplicon sequencing of sorted cells revealed that the ability to bind inulin was widespread in the microbiota. We further evaluate which taxa are metabolically stimulated by inulin and find that diverse taxa from the phyla Firmicutes and Actinobacteria respond to inulin, and several isolates of these taxa can degrade inulin. Incubation with another prebiotic, xylooligosaccharides (XOS), in contrast, shows a more robust bifidogenic effect. Interestingly, the Coriobacteriia Eggerthella lenta and Gordonibacter urolithinfaciens are indirectly stimulated by the inulin degradation process, expanding our knowledge of inulin-responsive bacteria.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid37619685,

title = {Targeting structural flexibility in low density lipoprotein by integrating cryo-electron microscopy and high-speed atomic force microscopy},

author = {Aline Cisse and Ambroise Desfosses and Sarah Stainer and Eaazhisai Kandiah and Daouda A K Traore and Armel Bezault and Anna-Laurence Schachner-Nedherer and Gerd Leitinger and Gerd Hoerl and Peter Hinterdorfer and Irina Gutsche and Ruth Prassl and Judith Peters and Karin Kornmueller},

doi = {10.1016/j.ijbiomac.2023.126345},

issn = {1879-0003},

year  = {2023},

date = {2023-12-01},

journal = {Int J Biol Macromol},

volume = {252},

pages = {126345},

abstract = {Low-density lipoprotein (LDL) plays a crucial role in cholesterol metabolism. Responsible for cholesterol transport from the liver to the organs, LDL accumulation in the arteries is a primary cause of cardiovascular diseases, such as atherosclerosis. This work focuses on the fundamental question of the LDL molecular structure, as well as the topology and molecular motions of apolipoprotein B-100 (apo B-100), which is addressed by single-particle cryo-electron microscopy (cryo-EM) and high-speed atomic force microscopy (HS-AFM). Our results suggest a revised model of the LDL core organization with respect to the cholesterol ester (CE) arrangement. In addition, a high-density region close to the flattened poles could be identified, likely enriched in free cholesterol. The most remarkable new details are two protrusions on the LDL surface, attributed to the protein apo B-100. HS-AFM adds the dimension of time and reveals for the first time a highly dynamic direct description of LDL, where we could follow large domain fluctuations of the protrusions in real time. To tackle the inherent flexibility and heterogeneity of LDL, the cryo-EM maps are further assessed by 3D variability analysis. Our study gives a detailed explanation how to approach the intrinsic flexibility of a complex system comprising lipids and protein.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid38114492,

title = {Single-cell transcriptome sequencing of plant leaf expressing anti-HER2 VHH-FcK cancer therapeutic protein},

author = {Myung-Shin Kim and Seung-Won Lee and Kibum Kim and Yerin Kim and Hyunjoo Hwang and Peter Hinterdorfer and Doil Choi and Kisung Ko},

doi = {10.1038/s41597-023-02833-5},

issn = {2052-4463},

year  = {2023},

date = {2023-12-01},

journal = {Sci Data},

volume = {10},

number = {1},

pages = {911},

abstract = {The transgenic plant is a promising strategy for the production of highly valuable biotherapeutic proteins such as recombinant vaccines and antibodies. To achieve an efficient level of protein production, codon sequences and expression cassette elements need to be optimized. However, the systematical expression of recombinant proteins in plant biomass can generally be controlled for the production of therapeutic proteins after the generation of transgenic plants. Without understanding the transgene expression patterns in plant tissue, it is difficult to enhance further production levels. In this study, single-cell RNA-sequencing (scRNA-seq) analysis of transgenic tobacco (Nicotiana tabacum) leaf, expressing an immunotherapeutic llama antibody against breast cancer, anti-HER2 VHH-Fc, was conducted to obtain data on the expression pattern of tissue-specific cells. These high-quality scRNA-seq data enabled the identification of gene expression patterns by cell types, which can be applied to select the best cell types or tissues for the high production of these recombinant antibodies. These data provide a foundation to elucidate the mechanisms that regulate the biosynthesis of recombinant proteins in N. tabacum.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid38205347,

title = {Extracellular Matrix Protein-1 as a Mediator of Inflammation-Induced Fibrosis After Myocardial Infarction},

author = {Sean A Hardy and Laura Liesinger and Ralph Patrick and Maria Poettler and Lavinia Rech and Juergen Gindlhuber and Nishani S Mabotuwana and DiyaaEldin Ashour and Verena Stangl and Mark Bigland and Lucy A Murtha and Malcolm R Starkey and Daniel Scherr and Philip M Hansbro and Gerald Hoefler and Gustavo Campos Ramos and Clement Cochain and Richard P Harvey and Ruth Birner-Gruenberger and Andrew J Boyle and Peter P Rainer},

doi = {10.1016/j.jacbts.2023.05.010},

issn = {2452-302X},

year  = {2023},

date = {2023-12-01},

journal = {JACC Basic Transl Sci},

volume = {8},

number = {12},

pages = {1539--1554},

abstract = {Irreversible fibrosis is a hallmark of myocardial infarction (MI) and heart failure. Extracellular matrix protein-1 (ECM-1) is up-regulated in these hearts, localized to fibrotic, inflammatory, and perivascular areas. ECM-1 originates predominantly from fibroblasts, macrophages, and pericytes/vascular cells in uninjured human and mouse hearts, and from M1 and M2 macrophages and myofibroblasts after MI. ECM-1 stimulates fibroblast-to-myofibroblast transition, up-regulates key fibrotic and inflammatory pathways, and inhibits cardiac fibroblast migration. ECM-1 binds HuCFb cell surface receptor LRP1, and LRP1 inhibition blocks ECM-1 from stimulating fibroblast-to-myofibroblast transition, confirming a novel ECM-1-LRP1 fibrotic signaling axis. ECM-1 may represent a novel mechanism facilitating inflammation-fibrosis crosstalk.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Sun2023b,

title = {Exogenous nitrogen input skews estimates of microbial nitrogen use efficiency by ecoenzymatic stoichiometry},

author = {Lifei Sun and Daryl L. Moorhead and Yongxing Cui and Wolfgang Wanek and Shuailin Li and Chao Wang},

url = {https://www.microplanet.at/},

doi = {10.1186/s13717-023-00457-6},

issn = {2192-1709},

year  = {2023},

date = {2023-12-00},

urldate = {2023-12-00},

journal = {Ecol Process},

volume = {12},

number = {1},

publisher = {Springer Science and Business Media LLC},

abstract = {<jats:title>Abstract</jats:title><jats:sec>

                <jats:title>Background</jats:title>

                <jats:p>Ecoenzymatic stoichiometry models (EEST) are often used to evaluate microbial nutrient use efficiency, but the validity of these models under exogenous nitrogen (N) input has never been clarified. Here, we investigated the effects of long-term N addition (as urea) on microbial N use efficiency (NUE), compared EEST and <jats:sup>18</jats:sup>O-labeling methods for determining NUE, and evaluated EEST’s theoretical assumption that the ratios of standard ecoenzymatic activities balance resource availability with microbial demand.</jats:p>

              </jats:sec><jats:sec>

                <jats:title>Results</jats:title>

                <jats:p>We found that NUE estimated by EEST ranged from 0.94 to 0.98. In contrast, estimates of NUE by the <jats:sup>18</jats:sup>O-labeling method ranged from 0.07 to 0.30. The large differences in NUE values estimated by the two methods may be because the sum of β-N-acetylglucosaminidase and leucine aminopeptidase activities in the EEST model was not limited to microbial N acquisition under exogenous N inputs, resulting in an overestimation of microbial NUE by EEST. In addition, the acquisition of carbon by N-acquiring enzymes also likely interferes with the evaluation of NUE by EEST.</jats:p>

              </jats:sec><jats:sec>

                <jats:title>Conclusions</jats:title>

                <jats:p>Our results demonstrate that caution must be exercised when using EEST to evaluate NUE under exogenous N inputs that may skew standard enzyme assays.</jats:p>

              </jats:sec>},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Gorka2023b,

title = {Beyond PLFA: Concurrent extraction of neutral and glycolipid fatty acids provides new insights into soil microbial communities},

author = {Stefan Gorka and Sean Darcy and Julia Horak and Bruna Imai and Moritz Mohrlok and Erika Salas and Andreas Richter and Hannes Schmidt and Wolfgang Wanek and Christina Kaiser and Alberto Canarini},

doi = {10.1016/j.soilbio.2023.109205},

issn = {0038-0717},

year  = {2023},

date = {2023-12-00},

journal = {Soil Biology and Biochemistry},

volume = {187},

publisher = {Elsevier BV},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Savchenko2023,

title = {Biosynthetic flexibility of Pseudomonas aeruginosa leads to hydroxylated 2-alkylquinolones with proinflammatory host response},

author = {Viktoriia Savchenko and Dávid Szamosvári and Yifan Bao and Marc Pignitter and Thomas Böttcher},

doi = {10.1038/s42004-023-00937-y},

issn = {2399-3669},

year  = {2023},

date = {2023-12-00},

journal = {Commun Chem},

volume = {6},

number = {1},

publisher = {Springer Science and Business Media LLC},

abstract = {AbstractThe human pathogen Pseudomonas aeruginosa produces various 4(1H)-quinolones with diverse functions. Among these, 2-nonyl-4(1H)-quinolone (NQ) and its N-oxide (NQNO) belong to the main metabolites. Their biosynthesis involves substrates from the fatty acid metabolism and we hypothesized that oxidized fatty acids could be responsible for a so far undetected class of metabolites. We developed a divergent synthesis strategy for 2′-hydroxy (2′-OH) and 2′-oxo- substituted quinolones and N-oxides and demonstrated for the first time that 2′-OH-NQ and 2′-OH-NQNO but not the corresponding 2′-oxo compounds are naturally produced by PAO1 and PA14 strains of P. aeruginosa. The main metabolite 2′-OH-NQ is produced even in concentrations comparable to NQ. Exogenous availability of β-hydroxydecanoic acid can further increase the production of 2′-OH-NQ. In contrast to NQ, 2′-OH-NQ potently induced the cytokine IL-8 in a human cell line at 100 nм, suggesting a potential role in host immune modulation.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Metz2023,

title = {Rates and Mechanism of Vivianite Dissolution under Anoxic Conditions},

author = {Rouven Metz and Naresh Kumar and Walter D. C. Schenkeveld and Stephan M. Kraemer},

doi = {10.1021/acs.est.3c04474},

issn = {1520-5851},

year  = {2023},

date = {2023-11-14},

journal = {Environ. Sci. Technol.},

volume = {57},

number = {45},

pages = {17266--17277},

publisher = {American Chemical Society (ACS)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}