@article{Speth2024,

title = {GlobDB: a comprehensive species-dereplicated microbial genome resource},

author = {Daan R Speth and Nick Pullen and Samuel T N Aroney and Benjamin L Coltman and Jay Osvatic and Ben J Woodcroft and Thomas Rattei and Michael Wagner},

editor = {Nicola Mulder},

doi = {10.1093/bioadv/vbaf280},

issn = {2635-0041},

year  = {2025},

date = {2025-11-09},

urldate = {2025-11-09},

journal = {Bioinfo Adv},

volume = {5},

number = {1},

publisher = {Oxford University Press (OUP)},

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

                  <jats:sec>

                    <jats:title>Motivation</jats:title>

                    <jats:p>Over the past years, substantial numbers of microbial species’ genomes have been deposited outside of conventional INSDC databases.</jats:p>

                  </jats:sec>

                  <jats:sec>

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

                    <jats:p>The GlobDB aggregates 14 independent genomic catalogues to provide a comprehensive database of species-dereplicated microbial genomes, with consistent taxonomy, annotations, and additional analysis resources. The GlobDB more than doubles the number of microbial species represented by genomes relative to the field standard genome taxonomy database.</jats:p>

                  </jats:sec>

                  <jats:sec>

                    <jats:title>Availability and implementation</jats:title>

                    <jats:p>The GlobDB is available at https://globdb.org/.</jats:p>

                  </jats:sec>},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Holub2025,

title = {Not Just Better Resolution: A Detailed Study of the Signal Distribution in Mid-Infrared Optical Photothermal Imaging},

author = {Elisabeth Holub and Nikolaus Hondl and Sebastian Wöhrer and Bernhard Lendl and Georg Ramer},

doi = {10.1021/acs.analchem.5c03194},

issn = {1520-6882},

year  = {2025},

date = {2025-10-07},

urldate = {2025-10-07},

journal = {Anal. Chem.},

volume = {97},

number = {39},

pages = {21418--21427},

publisher = {American Chemical Society (ACS)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Bayer2025,

title = {Minor contribution of ammonia oxidizers to inorganic carbon fixation in the ocean},

author = {Barbara Bayer and Katharina Kitzinger and Nicola L. Paul and Justine B. Albers and Mak A. Saito and Michael Wagner and Craig A. Carlson and Alyson E. Santoro},

doi = {10.1038/s41561-025-01798-x},

issn = {1752-0908},

year  = {2025},

date = {2025-09-23},

journal = {Nat. Geosci.},

publisher = {Springer Science and Business Media LLC},

abstract = {Abstract

          Ammonia-oxidizing archaea are the most abundant chemolithoautotrophs in the ocean and are assumed to dominate carbon fixation below the sunlit surface layer. However, the supply of reduced nitrogen delivered from the surface in sinking particulate organic matter is insufficient to support the amount of nitrification required to sustain measured carbon fixation rates in the dark ocean. Here we attempt to reconcile this observed discrepancy by quantifying the contribution of ammonia oxidizers to dark carbon fixation in the eastern tropical and subtropical Pacific Ocean. We used phenylacetylene—a specific inhibitor of the ammonia monooxygenase enzyme—to selectively inhibit ammonia oxidizers in samples collected throughout the water column (60–600 m depth). We show that, despite their high abundances, ammonia oxidizers contribute only a small fraction to dark carbon fixation, accounting for 4–25% of the total depth-integrated rates in the eastern tropical Pacific. The highest contributions were observed within the upper mesopelagic zone (120–175 m depth), where ammonia oxidation could account for ~50% of dark carbon fixation at some stations. Our results challenge the current view that carbon fixation in the dark ocean is primarily sustained by nitrification and suggest that other microbial metabolisms, including heterotrophy, might play a larger role than previously assumed.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Kaiser2025,

title = {The role of ectomycorrhizal functional diversity in mediating soil carbon cycling under global change},

author = {Christina Kaiser and Mark A. Anthony},

doi = {10.1111/nph.70559},

issn = {1469-8137},

year  = {2025},

date = {2025-09-08},

journal = {New Phytologist},

publisher = {Wiley},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid40965358,

title = {Experimental and Theoretical Insights into Nanoscale AFM-IR Imaging of Complex Heterogeneous Structures},

author = {Yide Zhang and Ufuk Yilmaz and Artem S Vorobev and Simone Iadanza and Liam O'Faolain and Bernhard Lendl and Georg Ramer},

doi = {10.1021/acs.analchem.5c04707},

issn = {1520-6882},

year  = {2025},

date = {2025-09-01},

journal = {Anal Chem},

volume = {97},

number = {38},

pages = {21141--21149},

abstract = {Nanoscale chemical imaging enabled by atomic force microscopy-infrared spectroscopy (AFM-IR) provides valuable insights into the complex structures and chemical compositions of materials and biological samples. While AFM-IR has been applied to subsurface imaging, the underlying mechanisms, particularly in nonplanar geometries and complex heterogeneous structures, remain underexplored. This study presents a theoretical analysis and experimental validation of AFM-IR for imaging subsurface features within organic multilayer structures, uncovering how image broadening depends on whether the excitation occurs in the subsurface or the covering layer. An analytical model based on the sample geometry demonstrates that the lateral size of the absorber significantly impacts both the signal intensity and spatial resolution in AFM-IR chemical imaging. These findings are experimentally validated, and a more representative finite element method (FEM) model was subsequently created, resulting in strong agreement with the experimental data. The model reveals how irregular structures directly impact photothermal expansion, providing an explanation for the distinct image broadening observed with infrared excitation of different layers. Additionally, a linear relationship is observed between feature size, chemical images, and AFM-IR signal intensity. These findings contribute significantly to the understanding of the AFM-IR signal, providing insights into resolution and sensitivity, paving the way for more advanced nanoscale chemical imaging capabilities.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Sherman2025b,

title = {Uptake of tire-wear derived compounds by lettuce grown in three soils},

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

doi = {10.1016/j.envint.2025.109742},

issn = {0160-4120},

year  = {2025},

date = {2025-09-00},

journal = {Environment International},

volume = {203},

publisher = {Elsevier BV},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Chen2025,

title = {Microbial iron oxide respiration coupled to sulfide oxidation},

author = {Song-Can Chen and Xiao-Min Li and Nicola Battisti and Guoqing Guan and Maria A. Montoya and Jay Osvatic and Petra Pjevac and Shaul Pollak and Andreas Richter and Arno Schintlmeister and Wolfgang Wanek and Marc Mussmann and Alexander Loy},

doi = {10.1038/s41586-025-09467-0},

issn = {1476-4687},

year  = {2025},

date = {2025-08-27},

journal = {Nature},

publisher = {Springer Science and Business Media LLC},

abstract = {Abstract

          Microorganisms have driven Earth’s sulfur cycle since the emergence of life1–6, yet the sulfur-cycling capacities of microorganisms and their integration with other element cycles remain incompletely understood. One such uncharacterized metabolism is the coupling of sulfide oxidation with iron(iii) oxide reduction, a ubiquitous environmental process hitherto considered to be strictly abiotic7,8. Here we present a comprehensive genomic analysis of sulfur metabolism across prokaryotes, and reveal bacteria that are capable of oxidizing sulfide using extracellular solid phase iron(iii). Based on a phylogenetic framework of over hundred genes involved in dissimilatory transformation of sulfur compounds, we recorded sulfur-cycling capacity in most bacterial and archaeal phyla. Metabolic reconstructions predicted co-occurrence of sulfur compound oxidation and iron(iii) oxide respiration in diverse members of 37 prokaryotic phyla. Physiological and transcriptomic evidence demonstrated that a cultivated representative, Desulfurivibrio alkaliphilus, grows autotrophically by oxidizing dissolved sulfide or iron monosulfide (FeS) to sulfate with ferrihydrite as an extracellular iron(iii) electron acceptor. The biological process outpaced the abiotic process at environmentally relevant sulfide concentrations. These findings expand the known diversity of sulfur-cycling microorganisms and unveil a biological mechanism that links sulfur and iron cycling in anoxic environments, thus highlighting the fundamental role of microorganisms in global element cycles.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Rasoulimehrabani2025,

title = {Evaluating the prebiotic activity of arabinogalactan on the human gut microbiota using 16S rRNA gene sequencing and Raman-activated cell sorting},

author = {Hamid Rasoulimehrabani and Sanaz Khadem and Adnan Hodžić and Miriam Philipp and Rebecca Gallo and Georgi Nikolov and Joana Séneca and Julia Ramesmayer and Patrik Sivulič and David Berry},

doi = {10.20517/mrr.2025.29},

issn = {2771-5965},

year  = {2025},

date = {2025-08-14},

journal = {Microbiome Res Rep.},

volume = {4},

number = {3},

publisher = {OAE Publishing Inc.},

abstract = {

          Background: Arabinogalactan is a complex plant-derived polysaccharide proposed to function as a selective prebiotic, yet the microbial taxa directly involved in its metabolism and the cooperative dynamics within the gut microbiota remain incompletely defined.

          

          Methods: Here, we combined community-level sequencing with targeted single-cell activity profiling to investigate how arabinogalactan shapes gut microbial composition and function. Fecal samples from ten healthy individuals were incubated ex vivo with arabinogalactan, and microbial responses were assessed using 16S rRNA gene amplicon sequencing alongside Raman-activated cell sorting (RACS) and coculture experiments.

          

          Results: Arabinogalactan consistently enriched Bifidobacterium and Gemmiger across donors, with Bifidobacterium also responding to galactose and Gemmiger and Blautia stimulated by arabinose, the two monosaccharide components of arabinogalactan. RACS enabled the selective isolation of metabolically active arabinogalactan responders, including Bifidobacterium longum (B. longum) and Faecalibacterium prausnitzii, along with other strains from the phyla Actinomycetota, Bacteroidota, and Bacillota. Notably, coculture experiments revealed that B. longum not only degraded arabinogalactan efficiently but also supported the growth of non-degrading species via metabolic cross-feeding. These cooperative interactions highlight B. longum as a keystone species in arabinogalactan utilization and suggest broader community-level benefits from its activity.

          

          Conclusion: Together, our findings demonstrate arabinogalactan’s bifidogenic effect and its potential to promote functionally important microbes within the gut ecosystem. This study also highlights the utility of RACS for linking microbial identity to function, enabling the targeted recovery of active strains from complex communities.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Bale2025,

title = {Unusual Plastoquinones in Non‐Phototrophic Nitrifying Bacteria},

author = {Nicole J. Bale and Hayato Fujimura and Petra Pjevac and Michel Koenen and Hikaru Ikeda and Satohiro Itagaki and Yojiro Yamamoto and Johanna Palmetzhofer and Christopher J. Sedlacek and Hayk Palabikyan and Jaap S. Sinninghe Damsté and Michael Wagner and Hiroshi Shiigi and Holger Daims},

doi = {10.1111/1758-2229.70174},

issn = {1758-2229},

year  = {2025},

date = {2025-08-05},

urldate = {2025-08-00},

journal = {Environ Microbiol Rep},

volume = {17},

number = {4},

publisher = {Wiley},

abstract = {<jats:title>ABSTRACT</jats:title><jats:p>Isoprenoid quinones are important compounds in most organisms. They are essential in electron and proton transport in respiratory and photosynthetic electron transport chains, and additional functions include oxidative stress defence. The biologically most relevant quinones are naphthoquinones including menaquinone and benzoquinones including ubiquinone and plastoquinone. They differ in their polar headgroup structures, physicochemical properties, and distribution among organisms. Menaquinone is the most widespread quinone in prokaryotes, ubiquinone occurs only in bacteria of the phylum <jats:italic>Pseudomonadota</jats:italic> and eukaryotes, and plastoquinone exists in phototrophic <jats:italic>Cyanobacteria</jats:italic> and plants. We found that chemolithoautotrophic nitrifying bacteria of the genus <jats:italic>Nitrospira</jats:italic> (phylum <jats:italic>Nitrospirota</jats:italic>) exclusively possess unusual methyl‐plastoquinones with a standard redox potential below that of canonical plastoquinone and ubiquinone but above menaquinone, suggesting functional roles in reverse electron transport, ammonia oxidation, alternative energy metabolisms, and oxidative stress mitigation. This extends the known diversity of quinones and suggests that plastoquinone derivatives are essential in ecologically important, non‐phototrophic bacteria.</jats:p>},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Carr2025,

title = {Personalized Clostridioides difficile colonization risk prediction and probiotic therapy assessment in the human gut},

author = {Alex V. Carr and Nitin S. Baliga and Christian Diener and Sean M. Gibbons},

doi = {10.1016/j.cels.2025.101367},

issn = {2405-4712},

year  = {2025},

date = {2025-08-04},

urldate = {2025-08-00},

journal = {Cell Systems},

volume = {16},

number = {8},

publisher = {Elsevier BV},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{FMKop2025,

title = {Comparative genome analysis reveals broad phylogenetic and functional diversity within the order Nitrospirales},

author = {Linnea F M Kop and Hanna Koch and Daan Speth and Claudia Lüke and Eva Spieck and Mike S M Jetten and Holger Daims and Sebastian Lücker},

doi = {10.1093/ismejo/wraf151},

issn = {1751-7370},

year  = {2025},

date = {2025-07-24},

urldate = {2025-07-22},

journal = {The ISME Journal},

volume = {19},

issue = {1},

pages = {wraf151},

publisher = {Oxford University Press (OUP)},

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

 <jats:p>Nitrification, a key process in the nitrogen cycle, involves the oxidation of ammonia to nitrite and nitrate by a diverse group of chemolithoautotrophic microorganisms. The order Nitrospirales (referred to in literature as the genus Nitrospira), which includes both nitrite-oxidizing and complete ammonia-oxidizing bacteria, plays a central role in this process. We sequenced the genomes of nine Nitrospirales members, incorporating genomes from previously unsequenced taxonomic Nitrospirales lineages. A comprehensive genomic analysis of these new Nitrospirales was conducted, which included an examination of their habitat distribution, phylogenetic diversity, and functional capabilities. This was complemented by the construction of and comparison to a database of 446 non-redundant, high-quality Nitrospirales genomes. Our phylogenomic analysis uncovered the presence of additional unclassified lineages and provided a comparison between genome-based and 16S rRNA gene-based taxonomies. Whereas some Nitrospirales lineages seem to exhibit habitat preferences, others are found across a wide variety of ecosystems, suggesting a broad niche spectrum. This capacity to adapt to different environmental conditions is also reflected in the high variability and modularity of the respiratory chain and nitrogen assimilation mechanisms. Additionally, we found evidence of quorum sensing systems in species beyond lineage II, implying a broader ecological role for this communication mechanism within the Nitrospirales. Finally, we identified a set of conserved genes unique to nitrite oxidoreductase-containing Nitrospirales, providing insights into the emergence of this functional group. In conclusion, our study emphasizes the adaptability of the various nitrifying classes of the order Nitrospirales to diverse environments and reveals the presence of new taxonomic lineages.</jats:p>},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid40296371b,

title = {The Fecal Microbiome of IBD Patients Is Less Divertible by Bowel Preparation Compared to Healthy Controls: Results From a Prospective Study},

author = {Andreas Blesl and Lukas Binder and Bettina Halwachs and Franziska Baumann-Durchschein and Stefan Fürst and Patrizia Constantini-Kump and Heimo Wenzl and Gregor Gorkiewicz and Christoph Högenauer},

doi = {10.1093/ibd/izaf053},

issn = {1536-4844},

year  = {2025},

date = {2025-07-01},

journal = {Inflamm Bowel Dis},

volume = {31},

number = {7},

pages = {2007--2018},

abstract = {BACKGROUND: The fecal microbiome of patients with inflammatory bowel diseases (IBD) is characterized by longitudinal variability. It remains unknown if this is caused by decreased resilience of the microbiome to external factors. We investigated the influence of osmotic diarrhea induced by bowel preparation as a disruptive factor on the fecal microbiome in IBD patients and healthy comparators.nnMETHODS: We conducted a prospective, single-center study including IBD patients and healthy controls scheduled for colonoscopy with uniform bowel preparation. Fecal samples were collected at 7 time points prior, during, and until 3 months after the intervention. 16S rRNA was isolated from stool and sequenced using the Illumina technique.nnRESULTS: Twenty-two IBD patients and 17 healthy controls were included in the study. Baseline diversity was higher in healthy controls. Bowel preparation longitudinally decreased alpha diversity and altered beta diversity and taxonomic composition in both groups. Alterations were more pronounced in healthy controls, and the microbial composition converged between the 2 groups. Bowel preparation resulted in an increased relative abundance of Anaerostipes and Coprococcus in both groups and in decreased relative abundance of Bifidobacterium and Clostridium sensu stricto in IBD patients and of Eubacterium hallii group and Ruminococcus in healthy controls. Changes largely restored to baseline composition within 1 week in both groups and remained stable thereafter.nnCONCLUSIONS: Bowel preparation induced reversible short-term microbial perturbations which were less pronounced in IBD patients than in healthy comparators suggesting that a single external disruptive factor may have less impact on an already altered fecal microbiome.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid40511921,

title = {Mimivirus transcription and translation occur at well-defined locations within amoeba host cells},

author = {Lotte Mayer and Georgi Nikolov and Martin Kunert and Matthias Horn and Anouk Willemsen},

doi = {10.1128/jvi.00554-25},

issn = {1098-5514},

year  = {2025},

date = {2025-07-01},

journal = {J Virol},

volume = {99},

number = {7},

pages = {e0055425},

abstract = {Many giant viruses replicate in the cytoplasm in viral factories. How exactly these viral factories are established and where the different steps of the replication cycle occur remain largely obscure. We have developed a single-molecule messenger RNA fluorescence  hybridization (smFISH) protocol for giant viruses in an  host. Combined with other labeling techniques (FUNCAT, DiD, rRNA FISH, and DAPI), we show the Mimivirus transcription and translation sites during an infection cycle in the amoeba host cell. Although viral mRNA localization changes depend on the infection stage, transcription occurs at well-defined spots within the viral factory. The original viral cores released within the cytoplasm most likely define these spots. When transported outside of the viral factory, the translation of viral mRNA takes place in a well-defined ring surrounding it. With this study, we obtained novel insights into giant virus replication, of which the methods are widely applicable to other viruses for the visualization and quantification of RNA molecules.IMPORTANCEGiant viruses have massive particle and genome sizes, which are known to infect unicellular eukaryotes. Although most viruses replicate in the host cell's nucleus, the giant Mimivirus replicates in viral factories established in the host cell's cytoplasm. Before this study, the location of the various steps in the Mimivirus replication cycle was largely unknown. By developing new protocols to label giant virus mRNA, protein synthesis, host cell membranes and rRNA, we demonstrate that Mimivirus transcription occurs at well-defined sites within the viral factory. In contrast, translation takes place directly outside of it. This is different from other viruses known to have a cytoplasmic life cycle. These results bring us a step closer to understanding how the genome complexity of viruses influences the virus-host interactions and viral replication strategies.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid40296371,

title = {The Fecal Microbiome of IBD Patients Is Less Divertible by Bowel Preparation Compared to Healthy Controls: Results From a Prospective Study},

author = {Andreas Blesl and Lukas Binder and Bettina Halwachs and Franziska Baumann-Durchschein and Stefan Fürst and Patrizia Constantini-Kump and Heimo Wenzl and Gregor Gorkiewicz and Christoph Högenauer},

doi = {10.1093/ibd/izaf053},

issn = {1536-4844},

year  = {2025},

date = {2025-07-01},

journal = {Inflamm Bowel Dis},

volume = {31},

number = {7},

pages = {2007--2018},

abstract = {BACKGROUND: The fecal microbiome of patients with inflammatory bowel diseases (IBD) is characterized by longitudinal variability. It remains unknown if this is caused by decreased resilience of the microbiome to external factors. We investigated the influence of osmotic diarrhea induced by bowel preparation as a disruptive factor on the fecal microbiome in IBD patients and healthy comparators.nnMETHODS: We conducted a prospective, single-center study including IBD patients and healthy controls scheduled for colonoscopy with uniform bowel preparation. Fecal samples were collected at 7 time points prior, during, and until 3 months after the intervention. 16S rRNA was isolated from stool and sequenced using the Illumina technique.nnRESULTS: Twenty-two IBD patients and 17 healthy controls were included in the study. Baseline diversity was higher in healthy controls. Bowel preparation longitudinally decreased alpha diversity and altered beta diversity and taxonomic composition in both groups. Alterations were more pronounced in healthy controls, and the microbial composition converged between the 2 groups. Bowel preparation resulted in an increased relative abundance of Anaerostipes and Coprococcus in both groups and in decreased relative abundance of Bifidobacterium and Clostridium sensu stricto in IBD patients and of Eubacterium hallii group and Ruminococcus in healthy controls. Changes largely restored to baseline composition within 1 week in both groups and remained stable thereafter.nnCONCLUSIONS: Bowel preparation induced reversible short-term microbial perturbations which were less pronounced in IBD patients than in healthy comparators suggesting that a single external disruptive factor may have less impact on an already altered fecal microbiome.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Becher2025,

title = {A cost-effective vessel-on-a-chip for high shear stress applications in vascular biology},

author = {Clarissa Becher and Martin Frauenlob and Florian Selinger and Peter Ertl and Marie-José Goumans and Gonzalo Sanchez-Duffhues},

doi = {10.1016/j.mvr.2025.104814},

issn = {0026-2862},

year  = {2025},

date = {2025-07-01},

urldate = {2025-05-00},

journal = {Microvascular Research},

volume = {160},

pages = {104814},

publisher = {Elsevier BV},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Breyer2025,

title = {The contribution of pelagic fungi to ocean biomass},

author = {Eva Breyer and Constanze Stix and Sophie Kilker and Benjamin R. K. Roller and Fragkiski Panagou and Charlotte Doebke and Chie Amano and Daniel E. M. Saavedra and Guillem Coll-García and Barbara Steger-Mähnert and Jordi Dachs and Naiara Berrojalbiz and Maria Vila-Costa and Cristina Sobrino and Antonio Fuentes-Lema and Franz Berthiller and Martin F. Polz and Federico Baltar},

doi = {10.1016/j.cell.2025.05.004},

issn = {0092-8674},

year  = {2025},

date = {2025-07-00},

journal = {Cell},

volume = {188},

number = {15},

pages = {3992–4002.e13},

publisher = {Elsevier BV},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Xu2025,

title = {Eco-Corona Formation Enhances Cotransport of Nanoplastics and Organic Contaminants in Porous Media},

author = {Shengkai Xu and Meiling Zhu and Lihua Fan and Yao Yao and Tianchi Cao and Rong Ji and Thilo Hofmann and Tong Zhang and Wei Chen},

doi = {10.1021/acs.est.5c02378},

issn = {1520-5851},

year  = {2025},

date = {2025-06-15},

urldate = {2025-07-01},

journal = {Environ. Sci. Technol.},

volume = {59},

number = {25},

pages = {12978--12989},

publisher = {American Chemical Society (ACS)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Tomin2025,

title = {Increased antioxidative defense and reduced advanced glycation end-product formation by metabolic adaptation in non-small-cell-lung-cancer patients},

author = {Tamara Tomin and Sophie Elisabeth Honeder and Laura Liesinger and Daniela Gremel and Bernhard Retzl and Joerg Lindenmann and Luka Brcic and Matthias Schittmayer and Ruth Birner-Gruenberger},

doi = {10.1038/s41467-025-60326-y},

issn = {2041-1723},

year  = {2025},

date = {2025-06-03},

urldate = {2025-12-00},

journal = {Nat Commun},

volume = {16},

number = {1},

publisher = {Springer Science and Business Media LLC},

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

 <jats:p>Reactive oxygen species can oxidatively modify enzymes to reroute metabolism according to tumor needs, rendering identification of oxidized proteins important for understanding neoplastic survival mechanisms. Thiol groups are most susceptible to oxidative modifications but challenging to analyze in clinical settings. We here describe the protein and small-molecular thiol oxidation landscape of 70 human lung tumors (and their paired healthy counter parts) and demonstrate that cancer adapts metabolism to increase glutathione synthesis to counteract oxidative stress. Glyoxalases, the key enzymes in the detoxification of methylglyoxal, a byproduct of glycolysis and precursor of advanced glycation end-products, are compromised by oxidation and downregulation. Despite decreased methylglyoxal detoxification capacity, cancers do not accumulate advanced glycation end-products. Since in vitro downregulation or inhibition of GAPDH upregulates glyoxalases, we propose that tumors reduce methylglyoxal by activating GAPDH.</jats:p>},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Gruseck2025,

title = {Flavonoid Stability and Biotransformation in Agricultural Soils: Effects of Hydroxylation, Methoxylation, and Glycosylation},

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

doi = {10.1021/acs.jafc.5c02814},

issn = {1520-5118},

year  = {2025},

date = {2025-06-02},

urldate = {2025-06-11},

journal = {J. Agric. Food Chem.},

volume = {73},

number = {23},

pages = {14245–14252},

publisher = {American Chemical Society (ACS)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Ódor2025,

title = {Epidemic-induced local awareness behavior inferred from surveys and genetic sequence data},

author = {Gergely Ódor and Márton Karsai},

doi = {10.1038/s41467-025-59508-5},

issn = {2041-1723},

year  = {2025},

date = {2025-05-22},

urldate = {2025-12-00},

journal = {Nat Commun},

volume = {16},

number = {1},

publisher = {Springer Science and Business Media LLC},

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

 <jats:p>Behavior-disease models suggest that pandemics can be contained cost-effectively if individuals take preventive actions when disease prevalence rises among their close contacts. However, assessing local awareness behavior in real-world datasets remains a challenge. Through the analysis of mutation patterns in clinical genetic sequence data, we propose an efficient approach to quantify the impact of local awareness by identifying superspreading events and assigning containment scores to them. We validate the proposed containment score as a proxy for local awareness in simulation experiments, and find that it was correlated positively with policy stringency during the COVID-19 pandemic. Finally, we observe a temporary drop in the containment score during the Omicron wave in the United Kingdom, matching a survey experiment we carried out in Hungary during the corresponding period of the pandemic. Our findings bring important insight into the field of awareness modeling through the analysis of large-scale genetic sequence data, one of the most promising data sources in epidemics research.</jats:p>},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid40305857,

title = { Daphnia magna as an Alternative Model for (Simultaneous) Bioaccumulation and Chronic Toxicity Assessment─Controlled Exposure Study Indicates High Hazard of Heterocyclic PAHs},

author = {Göksu Çelik and Schylar Alexandra Healy and Stefan Stolte and Philipp Mayer and Marta Markiewicz},

doi = {10.1021/acs.est.5c00384},

issn = {1520-5851},

year  = {2025},

date = {2025-05-01},

urldate = {2025-05-01},

journal = {Environ Sci Technol},

volume = {59},

number = {18},

pages = {8984--8996},

abstract = {Testing the bioaccumulation and chronic toxicity of (highly) hydrophobic compounds is extremely challenging, but crucial for hazard assessment. Fish are used as a model organism in these tests, but have many limitations, including a long time to reach steady-state, difficulty in maintaining constant exposure, and ethical concerns. We developed a method for the (simultaneous) assessment of chronic reproductive toxicity and bioaccumulation using  as a model organism. As test chemicals, we selected heterocyclic polyaromatic hydrocarbons (heterocyclic PAHs), which are often persistent and show high acute aquatic toxicity, raising concerns about their long-term effects. In this study, we developed a robust passive dosing method to maintain constant exposure in chronic toxicity and bioaccumulation tests of four heterocyclic PAHs in . Passive dosing maintained stable exposure concentrations in the ng to μg L range, even after reusing disks up to three times. All chemicals were toxic to  with EC values between 0.1 and 15 μg L. Bioaccumulation tests showed that steady-state was not reached, and the uptake rate constant () could not be reliably determined due to complex exposure routes (both via water and diet). However, depuration rates in  were about 2 orders of magnitude higher than in fish, which is advantageous in the assessment of highly hydrophobic compounds. We propose to use the depuration rate constant (), which is independent of the uptake route, as an indicator of bioaccumulation potential. The  thresholds for  were estimated to identify (very) bioaccumulative compounds by correlating  values with bioconcentration factors (BCFs) for  and applying fish BCF thresholds. We suggest that a  bioaccumulation test can be used as a screening tool to trigger further bioaccumulation testing in fish, as it offers higher throughput, is more ethical, and reaches steady-state faster. However, further validation with reference test protocols and substances is essential.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Sherman2025,

title = {The Invisible Footprint of Climbing Shoes: High Exposure to Rubber Additives in Indoor Facilities},

author = {Anya Sherman and Thibault Masset and Lukas Wimmer and Leah K. Maruschka and Lea Ann Dailey and Thorsten Hüffer and Florian Breider and Thilo Hofmann},

doi = {10.1021/acsestair.5c00017},

issn = {2837-1402},

year  = {2025},

date = {2025-04-24},

journal = {ACS EST Air},

publisher = {American Chemical Society (ACS)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Krammer2025,

title = {A general approach for activity-based protein profiling of oxidoreductases with redox-differentiated diarylhalonium warheads},

author = {Leo Krammer and Barbara Darnhofer and Marko Kljajic and Laura Liesinger and Matthias Schittmayer and Dmytro Neshchadin and Georg Gescheidt and Alexander Kollau and Bernd Mayer and Roland C. Fischer and Silvia Wallner and Peter Macheroux and Ruth Birner-Gruenberger and Rolf Breinbauer},

doi = {10.1039/d4sc08454c},

issn = {2041-6539},

year  = {2025},

date = {2025-04-21},

urldate = {2025-04-09},

journal = {Chem. Sci.},

volume = {16},

number = {15},

pages = {6240–6256},

publisher = {Royal Society of Chemistry (RSC)},

abstract = {<jats:p>A general chemoproteomic profiling approach for oxidoreductases with conceptually novel probes based on diarylhalonium salts is reported.</jats:p>},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Weinberger2025,

title = {Expanding the cultivable human archaeome: Methanobrevibacter intestini sp. nov. and strain Methanobrevibacter smithii ‘GRAZ-2’ from human faeces},

author = {Viktoria Weinberger and Rokhsareh Mohammadzadeh and Marcus Blohs and Kerstin Kalt and Alexander Mahnert and Sarah Moser and Marina Cecovini and Polona Mertelj and Tamara Zurabishvili and Bhawna Arora and Jacqueline Wolf and Tejus Shinde and Tobias Madl and Hansjörg Habisch and Dagmar Kolb and Dominique Pernitsch and Kerstin Hingerl and William Metcalf and Christine Moissl-Eichinger},

doi = {10.1099/ijsem.0.006751},

issn = {1466-5034},

year  = {2025},

date = {2025-04-16},

urldate = {2025-04-16},

journal = {International Journal of Systematic and Evolutionary Microbiology},

volume = {75},

number = {4},

publisher = {Microbiology Society},

abstract = {<jats:p>Two mesophilic, hydrogenotrophic methanogens, WWM1085 and <jats:italic>M. smithii</jats:italic> GRAZ-2, were isolated from human faecal samples. WWM1085 was isolated from an individual in the United States and represents a novel species within the genus <jats:italic>Methanobrevibacter. M. smithii</jats:italic> GRAZ-2 (=DSM 116045) was retrieved from a faecal sample of a European, healthy woman and represents a novel strain within this species. Both <jats:italic>Methanobrevibacter</jats:italic> representatives form non-flagellated, short rods with variable morphologies and the capacity to form filaments. Both isolates showed the typical fluorescence of F<jats:sub>420</jats:sub> and methane production. Compared to <jats:italic>M. smithii</jats:italic> GRAZ-2, WWM1085 did not accumulate formate when grown with H<jats:sub>2</jats:sub> and CO<jats:sub>2</jats:sub>. The optimal growth conditions were at 35–39 °C and pH 6.5–7.5. Full genome sequencing revealed a genomic difference of WWM1085 to the type strain of <jats:italic>M. smithii</jats:italic> DSM 861 (=PS<jats:sup>T</jats:sup>), with 93.55% average nucleotide identity (ANI) and major differences in the sequence of its <jats:italic>mcrA</jats:italic> gene (3.3% difference in nucleotide sequence). Differences in the 16S rRNA gene sequence were very minor, and thus distinction based on this gene marker might not be possible. <jats:italic>M. smithii</jats:italic> GRAZ-2 was identified as a novel strain within the species <jats:italic>Methanobrevibacter smithii</jats:italic> (ANI 99.04% to <jats:italic>M. smithii</jats:italic> DSM 861 [=PS<jats:sup>T</jats:sup>]). Due to the major differences between WWM1085 and <jats:italic>M. smithii</jats:italic> type strain <jats:italic>M. smithii</jats:italic> DSM 861 (=PS<jats:sup>T</jats:sup>) in phenotypic, genomic and metabolic features, we propose <jats:italic>Methanobrevibacter intestini</jats:italic> sp. nov. as a novel species with WWM1085 as the type strain (DSM 116060<jats:sup>T</jats:sup> = CECT 30992<jats:sup>T</jats:sup>).</jats:p>},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@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 = {2025-04-15},

urldate = {2025-04-00},

journal = {Water Research},

volume = {274},

publisher = {Elsevier BV},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Wichmann2025,

title = {Conserved specificity of extracellular wastewater peptidases revealed by multiplex substrate profiling by mass spectrometry},

author = {Natalie Wichmann and Josephine Meibom and Tamar Kohn and Michael Zumstein},

doi = {10.1007/s10311-025-01834-7},

issn = {1610-3661},

year  = {2025},

date = {2025-04-12},

journal = {Environ Chem Lett},

publisher = {Springer Science and Business Media LLC},

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

 <jats:p> Peptide-based chemicals are promising for numerous applications including home and personal care and medical treatments. To better understand and control the environmental fate of peptide-based chemicals, in-depth knowledge on the specificity of wastewater peptidases is needed. Here, we employed multiplex substrate profiling by mass spectrometry to obtain specificity profiles of extracellular peptidases derived from influent and aeration tanks of three full-scale wastewater treatment plants. Specificities were confirmed by fluorogenic peptidase substrates. Our results revealed highly similar specificity profiles across wastewater treatment plants. We found that hydrolysis by extracellular wastewater peptidases is favored when positively charged amino acid residues surround the cleavage site and disfavored when negatively charged amino acid residues surround the cleavage site.</jats:p>},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Quinn-Bohmann2025,

title = {Moving from genome-scale to community-scale metabolic models for the human gut microbiome},

author = {Nick Quinn-Bohmann and Alex V. Carr and Christian Diener and Sean M. Gibbons},

doi = {10.1038/s41564-025-01972-2},

issn = {2058-5276},

year  = {2025},

date = {2025-04-11},

urldate = {2025-05-00},

journal = {Nat Microbiol},

volume = {10},

number = {5},

pages = {1055–1066},

publisher = {Springer Science and Business Media LLC},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Kwon2025,

title = {Vertical DNA Nanostructure Arrays: Facilitating Functionalization on Macro-Scale Surfaces},

author = {Hyeonjun Kwon and Jihoon Shin and Siqi Sun and Rong Zhu and Sarah Stainer and Peter Hinterdorfer and Sang-Joon Cho and Dong-Hwan Kim and Yoo Jin Oh},

doi = {10.1021/acsnano.5c03100},

issn = {1936-086X},

year  = {2025},

date = {2025-04-09},

journal = {ACS Nano},

publisher = {American Chemical Society (ACS)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Mohammadzadeh2025,

title = {Age-related dynamics of predominant methanogenic archaea in the human gut microbiome},

author = {Rokhsareh Mohammadzadeh and Alexander Mahnert and Tejus Shinde and Christina Kumpitsch and Viktoria Weinberger and Helena Schmidt and Christine Moissl-Eichinger},

doi = {10.1186/s12866-025-03921-9},

issn = {1471-2180},

year  = {2025},

date = {2025-04-04},

urldate = {2025-12-00},

journal = {BMC Microbiol},

volume = {25},

number = {1},

publisher = {Springer Science and Business Media LLC},

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

 <jats:sec> 

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

 <jats:p>The reciprocal relationship between aging and alterations in the gut microbiota is a subject of ongoing research. While the role of bacteria in the gut microbiome is well-documented, specific changes in the composition of methanogens during extreme aging and the impact of high methane production in general on health remain unclear. This study was designed to explore the association of predominant methanogenic archaea within the human gut and aging.</jats:p> 

 </jats:sec> 

 <jats:sec> 

 <jats:title>Methods</jats:title> <jats:p>Shotgun metagenomic data from the stool samples of young adults (<jats:italic>n</jats:italic> = 127, Age: 19–59 y), older adults (<jats:italic>n</jats:italic> = 86, Age: 60–99 y), and centenarians (<jats:italic>n</jats:italic> = 34, age: 100–109 years) were analyzed.</jats:p> 

 </jats:sec> 

 <jats:sec> 

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

 <jats:p>Our findings reveal a compelling link between age and the prevalence of high methanogen phenotype, while overall archaeal diversity diminishes. Surprisingly, the archaeal composition of methanogens in the microbiome of centenarians appears more akin to that of younger adults, showing an increase in <jats:italic>Methanobrevibacter smithii</jats:italic>, rather than <jats:italic>Candidatus</jats:italic> Methanobrevibacter intestini. Remarkably, <jats:italic>Ca.</jats:italic> M. intestini emerged as a central player in the stability of the archaea-bacteria network in adults, paving the way for <jats:italic>M. smithii</jats:italic> in older adults and centenarians. Notably, centenarians exhibit a highly complex and stable network of these two methanogens with other bacteria. The mutual exclusion between <jats:italic>Lachnospiraceae</jats:italic> and these methanogens throughout all age groups suggests that these archaeal communities may compensate for the age-related drop in <jats:italic>Lachnospiraceae</jats:italic> by co-occurring with <jats:italic>Oscillospiraceae</jats:italic>.</jats:p> 

 </jats:sec> 

 <jats:sec> 

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

 <jats:p>This study underscores the dynamics of archaeal microbiome in human physiology and aging. It highlights age-related shifts in methanogen composition, emphasizing the significance of both <jats:italic>M. smithii</jats:italic> and <jats:italic>Ca.</jats:italic> M. intestini and their partnership with butyrate-producing bacteria for potential enhanced health.</jats:p> 

 </jats:sec>},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Savchenko2025,

title = {Chitinivorax: The New Kid on the Block of Bacterial 2-Alkyl-4(1textitH)-quinolone Producers},

author = {Viktoriia Savchenko and Xiaoqian Annie Yu and Martin F. Polz and Thomas Böttcher},

doi = {10.1021/acschembio.5c00046},

issn = {1554-8937},

year  = {2025},

date = {2025-03-27},

journal = {ACS Chem. Biol.},

publisher = {American Chemical Society (ACS)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Burger2025,

title = {Discovery of the antifungal compound ilicicolin K through genetic activation of the ilicicolin biosynthetic pathway in Trichoderma reesei},

author = {Isabella Burger and Matthias Schmal and Kathrin Peikert and Lukas Fourtis and Christoph Suster and Christian Stanetty and Dominik Schnalzer and Barbara Hufnagel and Thomas Böttcher and Ruth Birner-Gruenberger and Robert L. Mach and Astrid R. Mach-Aigner and Matthias Schittmayer and Christian Zimmermann},

doi = {10.1186/s13068-025-02628-3},

issn = {2731-3654},

year  = {2025},

date = {2025-03-11},

urldate = {2025-12-00},

journal = {Biotechnol. Biofuels Bioprod.},

volume = {18},

number = {1},

publisher = {Springer Science and Business Media LLC},

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

 <jats:sec> 

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

 <jats:p>Given the global rise in antimicrobial resistance, the discovery of novel antimicrobial agents and production processes thereof are of utmost importance. To this end we have activated the gene cluster encoding for the biosynthesis of the potent antifungal compound ilicicolin H in the fungus <jats:italic>Trichoderma reesei</jats:italic>. While the biosynthetic gene cluster (BGC) is silent under standard cultivation conditions, we achieved BGC activation by genetically overexpressing the transcription factor TriliR.</jats:p> 

 </jats:sec> 

 <jats:sec> 

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

 <jats:p>Successful activation was confirmed by RT-qPCR, proteomic and metabolomic analyses. Metabolomic profiling upon BGC expression revealed high-yield production of ilicicolin H. To elucidate the enzymatically highly diverse functionality of this BGC, we employed a combination of overexpression and deletions of individual genes in the BGC. While we hardly observed any of the previously reported side- or shunt products associated with heterologous ilicicolin H expression, we discovered that <jats:italic>Trichoderma reesei</jats:italic> produces a novel member of the ilicicolin family using a metabolomic molecular networking approach. This new compound, ilicicolin K, is expressed in substantial amounts in the genetically engineered <jats:italic>Trichoderma reesei</jats:italic>. Ilicicolin K differs from ilicicolin H in its structure by a second hydroxylation of the tyrosine derived phenol and an additional ring formed by an intramolecular ether bridge of the hydroxyl group at the pyridone towards the tyrosine moiety of the molecule. Bioactivity tests of ilicicolin K revealed a strong antifungal activity against <jats:italic>Saccharomyces cerevisiae</jats:italic> and a moderate activity against the human pathogen <jats:italic>Candida auris</jats:italic>, an emerging multi-drug resistant fungus.</jats:p> 

 </jats:sec> 

 <jats:sec> 

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

 <jats:p>By activating a silent BGC in <jats:italic>T. reesei</jats:italic>, we obtained a high-yielding strain for the production of the antifungal compounds ilicicolin H and the novel ilicicolin K. These two compounds share some structural properties and are thus highly likely to act on the fungal cytochrome bc1 complex, a component of the mitochondrial repository chain. However, they possess different bioactive properties, which might suggest that ilicicolin K may overcome certain limitations of ilicicolin H.</jats:p> 

 </jats:sec> 

 <jats:sec> 

 <jats:title>Graphical Abstract</jats:title> 

 </jats:sec>},

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{Woh2025,

title = {Reevaluation of the gastrointestinal methanogenic archaeome in multiple sclerosis and its association with treatment},

author = {Pei Yee Woh and Yehao Chen and Christina Kumpitsch and Rokhsareh Mohammadzadeh and Laura Schmidt and Christine Moissl-Eichinger},

editor = {Henning Seedorf},

doi = {10.1128/spectrum.02183-24},

issn = {2165-0497},

year  = {2025},

date = {2025-02-25},

journal = {Microbiol Spectr},

publisher = {American Society for Microbiology},

abstract = {<jats:title>ABSTRACT</jats:title> 

 <jats:sec> 

 <jats:title/> 

 <jats:p> 

 The role of the gut archaeal microbiome (archaeome) in health and disease remains poorly understood. Methanogenic archaea have been linked to multiple sclerosis (MS), but prior studies were limited by small cohorts and inconsistent methodologies. To address this, we re-evaluated the association between methanogenic archaea and MS using metagenomic data from the International Multiple Sclerosis Microbiome Study. We analyzed gut microbiome profiles from 115 MS patients and 115 healthy household controls across Buenos Aires (27.8%), Edinburgh (33.9%), New York (10.4%), and San Francisco (27.8%). Metagenomic sequences were taxonomically classified using kraken2/bracken and a curated profiling database to detect archaea, specifically 

 <jats:italic>Methanobrevibacter</jats:italic> 

 species. Most MS patients were female (80/115), aged 25–72 years (median: 44.5), and 70% were undergoing treatment, including dimethyl fumarate ( 

 <jats:italic>n</jats:italic> = 21), fingolimod ( 

 <jats:italic>n</jats:italic> = 20), glatiramer acetate ( 

 <jats:italic>n</jats:italic> = 14), interferon ( 

 <jats:italic>n</jats:italic> = 18), natalizumab ( 

 <jats:italic>n</jats:italic> = 6), or ocrelizumab/rituximab ( 

 <jats:italic>n</jats:italic> = 1). We found no significant differences in overall archaeome profiles between MS patients and controls. However, treated MS patients exhibited higher abundances of 

 <jats:italic>Methanobrevibacter smithii</jats:italic> 

 and 

 <jats:italic>M.</jats:italic> 

 sp900766745 compared to untreated patients. Notably, 

 <jats:italic>M.</jats:italic> 

 sp900766745 abundance correlated with lower disease severity scores in treated patients. Our results suggest that gut methanogens are not directly associated with MS onset or progression but may reflect microbiome health during treatment. These findings highlight potential roles for 

 <jats:italic>M. smithii</jats:italic> 

 and 

 <jats:italic>M.</jats:italic> 

 sp900766745 in modulating treatment outcomes, warranting further investigation into their relevance to gut microbiome function and MS management. 

 </jats:p> 

 <jats:sec> 

 <jats:title>IMPORTANCE</jats:title> 

 <jats:p>Multiple sclerosis (MS) is a chronic neuroinflammatory disease affecting the central nervous system, with approximately 2.8 million people diagnosed worldwide, mainly young adults aged 20–30 years. While recent studies have focused on bacterial changes in the MS microbiome, the role of gut archaea has been less explored. Previous research suggested a potential link between methanogenic archaea and MS disease status, but these findings remained inconclusive. Our study addresses this gap by investigating the gut archaeal composition in MS patients and examining how it changes in response to treatment. By focusing on methanogens, we aim to uncover novel insights into their role in MS, potentially revealing new biomarkers or therapeutic targets. This research is crucial for enhancing our understanding of the gut microbiome’s impact on MS and improving patient management.</jats:p> 

 </jats:sec> 

 </jats:sec>},

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 = {2025-02-18},

urldate = {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}

}