@article{Zhou2026,

title = {Zinc accumulation as a primary contributor to co-exposure toxicity with 6PPD-quinone in earthworms: Multi-level evidence},

author = {Hanghai Zhou and Zhendong Li and Zhou Wu and Lihua Zou and Hong Sun and Hua Li and Xin Wang and Yuan Wang and Junwei Jin and Thilo Hofmann and Jiangwu Tang},

doi = {10.1016/j.jhazmat.2026.142749},

issn = {0304-3894},

year  = {2026},

date = {2026-08-00},

urldate = {2026-08-00},

journal = {Journal of Hazardous Materials},

volume = {514},

publisher = {Elsevier BV},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Koch2026,

title = {From “synthetic” to defined microbial communities for clearer terminology},

author = {Hanna Koch and Thomas Clavel and Cintia Mayr and Benjamin L. Coltman and Michael Schloter and Julia A. Vorholt and Yolanda Sanz and Tomislav Cernava and Gwyn A. Beattie and Lene Lange and Stéphane Chaillou and Ákos T. Kovács and Hauke Smidt and Corné M. J. Pieterse and Tanja Kostic and Omri M. Finkel and Christopher E. Lawson and Luca Cocolin and Jesús Mercado-Blanco and Robert D. Finn and Kalliope K. Papadopoulou and Matthew Ryan and Marco Candela and Paul D. Cotter and Gabriele Berg and Orla O’Sullivan and Manuel Delgado-Baquerizo and Pankaj Trivedi and Trevor C. Charles and Brajesh K. Singh and Günter Brader and Malek Marian and Angela Sessitsch},

doi = {10.1038/s41467-026-74251-1},

issn = {2041-1723},

year  = {2026},

date = {2026-06-08},

urldate = {2026-12-00},

journal = {Nat Commun},

volume = {17},

number = {1},

publisher = {Springer Science and Business Media LLC},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Chen2026,

title = {From Particles to Chemicals: Redefining the Impact of Agricultural Plastics on Water Quality},

author = {Wei Chen and Thilo Hofmann},

doi = {10.1021/acs.est.6c05931},

issn = {1520-5851},

year  = {2026},

date = {2026-06-08},

journal = {Environ. Sci. Technol.},

publisher = {American Chemical Society (ACS)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Karner2026,

title = {Gut microbial diversity and inferred capacity to produce short-chain fatty acids are associated with acute stress reactivity in healthy adults},

author = {Thomas Karner and Paul A.G. Forbes and David Berry and Isabella C. Wagner},

doi = {10.1016/j.ynstr.2026.100807},

issn = {2352-2895},

year  = {2026},

date = {2026-06-01},

urldate = {2026-06-00},

journal = {Neurobiology of Stress},

volume = {42},

publisher = {Elsevier BV},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Kralova2026b,

title = {Kineochelins—A New Group of Siderophores From an Antarctic Bacterium},

author = {Stanislava Kralova and Peter Spacek and Johannes Gafriller and Matej Bezdicek and Viktoria Medvedcova and Joana Séneca and Jay Osvatic and Ulrike Grienke and Thomas Rattei and Olga N. Sekurova and Sergey B. Zotchev and Martin Zehl and Alexander Loy},

doi = {10.1111/1751-7915.70386},

issn = {1751-7915},

year  = {2026},

date = {2026-05-28},

urldate = {2026-06-00},

journal = {Microbial Biotechnology},

volume = {19},

number = {6},

publisher = {Wiley},

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

                  <jats:p>

                    The global rise of antimicrobial resistance has intensified the search for new microbial metabolites from underexplored environments and taxonomic groups. Extreme and geographically isolated habitats such as Antarctic terrestrial ecosystems represent promising reservoirs of biosynthetic diversity, particularly among rare and difficult‐to‐cultivate actinomycetes that may produce chemically diverse metabolites with potential biotechnological applications. Here, we report the characterization of kineochelins, a previously undescribed group of siderophores produced by the Antarctic isolate

                    <jats:italic>Actinokineospora</jats:italic>

                    sp. UV203, representing a difficult‐to‐cultivate actinomycete lineage. Structural elucidation revealed a set of closely related congeners with a mixed‐ligand architecture consistent with metal‐chelating activity. Genome mining combined with transcriptomic analysis identified a dedicated nonribosomal peptide synthetase‐encoding biosynthetic gene cluster responsible for kineochelin production. Comparative genomic analyses indicated that, although kineochelin biosynthetic genes share limited similarity with known mixed‐ligand siderophores, their gene content and organization differ substantially, suggesting a distinct biosynthetic lineage. Functional characterization of the culture supernatant and an enriched pre‐purified kineochelin fraction demonstrated strong and selective iron chelation, with high affinity for ferric and ferrous iron. Crude culture extracts inhibited the growth of bacterial strains isolated from the same Antarctic environment, indicating that kineochelins may contribute to iron‐mediated microbial competition. In addition, kineochelin‐enriched pre‐purified fractions showed moderate selective inhibitory activity against the opportunistic yeast pathogen

                    <jats:italic>Nakaseomyces glabratus</jats:italic>

                    and a clinical isolate of

                    <jats:styled-content style="fixed-case">

                      <jats:italic>Saccharomyces cerevisiae</jats:italic>

                    </jats:styled-content>

                    associated with invasive infection. These findings expand the chemical and biosynthetic diversity known within the genus

                    <jats:italic>Actinokineospora</jats:italic>

                    and demonstrate that Antarctic rare actinomycetes represent valuable sources of previously unexplored natural products. The discovery of kineochelins highlights the potential of genome‐guided exploration of polar microorganisms for identifying bioactive metabolites with relevance for antimicrobial discovery and biotechnology.

                  </jats:p>},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Plum-Jensen2026,

title = {Distribution of a novel DsrEFH sulfur transferase suggests widespread sulfur oxidation capacity in sulfate reducers},

author = {Lea Emilie Plum-Jensen and Marc Gregor Mohr and Tomohisa Sebastian Tanabe and Bo Wang and Simon Gregersen Echers and Nikoline Sanggård Madsen and Casper Thorup and Markéta Linhartova and Lars Peter Nielsen and Morten Kam Dahl Dueholm and Thomas Boesen and Ian Philip George Marshall and Christiane Dahl and Andreas Schramm},

doi = {10.1093/ismejo/wrag130},

issn = {1751-7370},

year  = {2026},

date = {2026-05-23},

urldate = {2026-05-23},

journal = {The ISME Journal},

publisher = {Oxford University Press (OUP)},

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

                  <jats:p>Microbial sulfur cycling is typically divided into an oxidative and a reductive branch, with microbes driving either sulfide oxidation or sulfate reduction distinguished by their genomic setup. Paradoxically, filamentous cable bacteria perform electrogenic sulfide oxidation but contain genes indicative of sulfate reduction, including the reductive type of dissimilatory sulfite reductase (DsrAB), whereas they apparently lack the canonical sulfur transferase DsrEFH essential for sulfur oxidation. AlphaFold2 structure prediction of conserved cable bacteria proteins with unknown functions identified a protein complex resembling canonical DsrEFH (hereafter termed DsrEFH type II). In vitro characterization of heterologously expressed DsrEFH type II confirmed its sulfur transferase function and, together with site-directed mutagenesis, verified that the conserved cysteine, Cys67, is the active sulfur transfer residue. Genes encoding the novel DsrEFH type II were found in 985 prokaryotic genomes. They typically co-occurred with genes for reductive DsrAB in microbes characterized as sulfate reducers or sulfur disproportionators. This study not only fills an important gap in the sulfide oxidation pathway of cable bacteria, but also suggests that a wide range of sulfate reducing bacteria may be more metabolically versatile than currently understood, representing a major shift in the perception of this globally significant physiological group of microorganisms.</jats:p>},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Hu2026,

title = {Revised 16S rRNA V4 hypervariable region targeting primers enhance detection of Patescibacteria and other lineages across diverse environments},

author = {Huifeng Hu and Clemens Karwautz and Kalina Duszka and Thomas Karner and Isabella C Wagner and Christoph Grander and Wilhelm Grander and Laura Steinwidder and Lucilla Boito and Viktor Van de Velde and Marijn Bauters and Pascal Boeckx and David Seki and Bettina Glasl and Stefan Thiele and Hannes Schmidt and Joana Séneca and Michael Wagner and Petra Pjevac},

doi = {10.1093/ismeco/ycag141},

issn = {2730-6151},

year  = {2026},

date = {2026-05-21},

urldate = {2026-05-21},

journal = {The ISME Journal},

volume = {6},

number = {1},

publisher = {Oxford University Press (OUP)},

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

                  <jats:p>Primer bias in 16S rRNA gene amplicon sequencing can distort microbial diversity estimates by underrepresenting key taxa. We introduce a modified primer pair (V4-EXT) targeting the hypervariable V4 region of bacterial and archaeal 16S rRNA genes, with improved in silico taxonomic inclusivity. To benchmark performance, we analyzed 938 samples from terrestrial, aquatic, and host-associated habitats, comparing microbial community profiles derived with V4-EXT and the currently most widely used V4-targeted primers. V4-EXT substantially improved the detection of Patescibacteria and other underrepresented lineages, such as Chloroflexi and Iainarchaeota, while enhancing recovery of novel amplicon sequence variants across sample types. Overall, V4-EXT provides broader taxonomic coverage and more inclusive microbial community profiles, particularly in high-diversity ecosystems such as groundwater and soils. We propose V4-EXT as a robust successor for comprehensive microbial community analysis across diverse habitats.</jats:p>},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Cao2026,

title = {Defining the “Point of No Return”: Thickness-Dependent Fragmentation Controls Nonlinear Microplastics Emissions from Agricultural Mulch Films},

author = {Tianchi Cao and Xiaoxia Zhang and Yan Lin and Thilo Hofmann and Wei Chen},

doi = {10.1021/acs.est.6c00814},

issn = {1520-5851},

year  = {2026},

date = {2026-05-12},

journal = {Environ. Sci. Technol.},

volume = {60},

number = {18},

pages = {13645--13655},

publisher = {American Chemical Society (ACS)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Yu2026,

title = {Genome-wide sweeps create ecological units in the human gut microbiome},

author = {Xiaoqian Annie Yu and Cameron R. Strachan and Craig W. Herbold and Michaela Lang and Christoph Gasche and Athanasios Makristathis and Nicola Segata and Shaul Pollak and Adrian Tett and Martin F. Polz},

doi = {10.1038/s41586-026-10476-w},

issn = {1476-4687},

year  = {2026},

date = {2026-05-06},

journal = {Nature},

publisher = {Springer Science and Business Media LLC},

abstract = {Abstract

                  

                    The human gut microbiome is shaped by diverse selective forces that originate from host and environmental factors and it substantially influences health and disease. Whereas the association of microbial lineages with various health conditions has been shown at different taxonomic levels

                    1–5

                    , the extent to which unifying adaptive mechanisms sort microbial lineages into ecologically differentiated populations remains poorly understood. Here we show that genome-wide selective sweeps are a pervasive mechanism that differentiates bacteria in the microbiome. This mechanism leads to population structures akin to global epidemics across geographically and ethnically diverse human populations. Such sweeps arise when an adaptation allows a clone to outcompete others in its niche followed by rediversification, and they manifest as clusters of closely related genomes on long branches in phylogenetic trees. This structure is revealed by excluding recombination events that mask the clonal descent of the genomes. Indeed, we show that genome-wide sweeps originate under a wide range of recombination rates in at least 66 taxa from 25 bacterial families. Estimated ages of divergence suggest that sweep clusters can spread globally within decades and that this process has occurred throughout human history. Sweep clusters are associated with different host conditions—such as age, colorectal cancer, inflammatory bowel diseases and type 2 diabetes—as an indication of their ecological differentiation. Our results reveal an evolutionary mechanism for the observation of stably inherited strains with differential associations and provide a theoretical foundation for analysing adaptation among microbial populations.

                  },

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Liu2026b,

title = {Retreaded tires are an overlooked source of microplastics with distinct additive leaching and ecotoxicity},

author = {Hao Liu and Tianchi Cao and Yan Lin and Guoliang Shi and Kaiwei Huang and Zhi Cao and Tong Zhang and Thilo Hofmann and Wei Chen},

doi = {10.1038/s43247-026-03566-0},

issn = {2662-4435},

year  = {2026},

date = {2026-04-28},

urldate = {2026-04-28},

journal = {Commun Earth Environ},

publisher = {Springer Science and Business Media LLC},

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

                  <jats:p>

                    Retreaded tires constitute a substantial segment of the commercial tire market and are an important source of tire wear particles (TWPs), yet the environmental risks of this major microplastic category remain uninvestigated. Here, we show that although the total additive mass is generally lower in TWPs from retreaded tires, these particles exhibit a markedly greater additive leaching potential, particularly for

                    <jats:italic>p</jats:italic>

                    -phenylenediamines (PPDs). Notably, the highly water-soluble additive

                    <jats:italic>N</jats:italic>

                    -isopropyl-

                    <jats:italic>N’</jats:italic>

                    -phenyl-p-phenylenediamine (IPPD), present at high concentrations in some retreaded-tire TWPs, is especially leachable. Correspondingly, leachates from retreaded-tire TWPs cause greater growth inhibition in

                    <jats:italic>Vibrio fischeri</jats:italic>

                    and

                    <jats:italic>Chlorella vulgaris</jats:italic>

                    than those from new or used tires. Furthermore, our numerical model projections under the Shared Socioeconomic Pathway 2 (SSP2) scenario show that global emissions of retreaded-tire TWPs could increase several hundred-fold by 2060. The substantial and growing risks identified in our study underscore the urgent need for broader investigations into the environmental impacts of these particles.

                  </jats:p>},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Seki2026,

title = {Human milk oligosaccharide mediates mutualism between Escherichia coli and Bifidobacterium bifidum},

author = {David Seki and Shaul Pollak and Magdalena Kujawska and Raymond Kiu and Antia Acuna-Gonzalez and Lucy I. Crouch and Cassie R. Bakshani and Peter T. Chivers and Monique Mommers and Nils van Best and John Penders and Lindsay J. Hall},

doi = {10.1038/s41467-026-71764-7},

issn = {2041-1723},

year  = {2026},

date = {2026-04-22},

urldate = {2026-12-00},

journal = {Nat Commun},

volume = {17},

number = {1},

publisher = {Springer Science and Business Media LLC},

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

                  <jats:p>

                    Infant gut microbiota development involves frequent colonization by

                    <jats:italic>Enterobacteriaceae</jats:italic>

                    , particularly

                    <jats:italic>Escherichia coli</jats:italic>

                    , yet their ecological role in healthy infants is unclear. Here, we analyse longitudinal stool samples from healthy, term-born, breastfed infants (n = 41) and related mothers (n = 30) using shotgun metagenomics and novel computational approaches. Strain-resolved profiling indicates that

                    <jats:italic>Bifidobacterium</jats:italic>

                    species are frequently shared within families, whereas

                    <jats:italic>E. coli</jats:italic>

                    derive from external sources, but often persist within individuals. Despite differing ecological strategies, these genera co-exist and share evolutionary adaptations related to lactose acquisition in the infant gut. In vitro, we demonstrate that interactions between

                    <jats:italic>E. coli</jats:italic>

                    and

                    <jats:italic>Bifidobacterium bifidum</jats:italic>

                    are mutualistic in co-culture, where

                    <jats:italic>E. coli</jats:italic>

                    supplies cysteine to its auxotrophic partner, facilitating cooperative degradation of 2′-fucosyllactose, the predominant human milk oligosaccharide. In turn, the liberated monosaccharides sustain

                    <jats:italic>E. coli</jats:italic>

                    growth, highlighting a cooperative cross-feeding interaction that may contribute to regulating

                    <jats:italic>E. coli</jats:italic>

                    abundance within the infant host.

                  </jats:p>},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Treichel2026,

title = {Benchmarking of shotgun sequencing depth reveals the potential and limitations of shallow metagenomics and strain-level analysis},

author = {Nicole S. Treichel and Charlie Pauvert and Joana Séneca and Petra Pjevac and David Berry and John Penders and Thomas C. A. Hitch and Thomas Clavel},

doi = {10.1038/s41564-026-02334-2},

issn = {2058-5276},

year  = {2026},

date = {2026-04-21},

urldate = {2026-04-21},

journal = {Nat Microbiol},

publisher = {Springer Science and Business Media LLC},

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

                  <jats:p>Shotgun metagenomics can provide both taxonomic and functional insights, but benchmarking is necessary to determine the sequencing depth appropriate for specific analyses. Here we used complex mixtures of DNA from cultured bacteria and analysed taxonomic composition, strain-level resolution and functional profiles at up to 11 sequencing depths (0.1–50.0 Gb). Reference-based analysis provided accurate strain-level taxonomy at 0.5–1.0 Gb. By contrast, de novo metagenome-assembled genome (MAG) reconstruction required deep sequencing (>10 Gb), and even MAGs deemed high quality by standard metrics were chimeric, with 54.5–81.8% accurately representing original strains, depending on the bioinformatic approach. Functionally, 2 Gb provided reliable insights at the pathway level for each of the mock communities tested, but sufficient proteome coverage was achieved only at or above 10 Gb. Library preparation and host DNA contamination were identified as confounders in shallow metagenomic analysis. This analysis highlights the potential and limitations of shallow metagenomics and provides guidance to accurately capture strain-level diversity using MAGs.</jats:p>},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Vogel2026,

title = {Symbiont diversity within Loripes orbiculatus and the case for multiple hosts},

author = {Margaret A Vogel and Fragkiskos Machairas and Sophia Ferchiou and Jay Osvatic and Hanin Alzubaidy and Joana Séneca and Bela Hausmann and Katja Klun and Jillian M Petersen},

doi = {10.1093/ismejo/wrag094},

issn = {1751-7370},

year  = {2026},

date = {2026-04-15},

urldate = {2026-04-15},

journal = {The ISME Journal},

publisher = {Oxford University Press (OUP)},

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

                  <jats:p>Seagrasses support immense biodiversity and are critical for maintaining coastal ecosystem health. These foundation species benefit from a ‘three-way’ facultative relationship with one of the common inhabitants of seagrass meadows, lucinid bivalves, which host specific bacterial Ca. Thiodiazotropha symbionts. Relatives of the bivalve symbionts have been detected on seagrass roots raising the possibility that these symbionts may colonize both animals and plants; however, no study has yet compared bivalve- and seagrass-associated symbionts at the same site and time. Our combination of 16S rRNA gene amplicon and metagenome sequencing revealed a greater diversity than was previously observed within both lucinid bivalves and on seagrass roots from the Adriatic Sea and resulted in the closed genome of one prominent symbiont species. We show that two of the Ca. Thiodiazotropha ASVs found on seagrass roots are identical to those found in bivalve hosts at the same site. This suggests that symbiont sharing may occur in the seagrass habitat between these two host species, which has important evolutionary and ecological implications for both hosts and symbionts.</jats:p>},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Mahnert2026,

title = {Cultivation and molecular profiling reveal ammonia-oxidizing archaea as skin commensals},

author = {Alexander Mahnert and Maximilian Dreer and Ülkü Perier and Michael Melcher and Stefanie Duller and Adina Lehnen and Theodora Goessler and Daniela Brunner and Thomas Graier and Peter Wolf and Rafael I Ponce-Toledo and Logan H Hodgskiss and Melina Kerou and Christine Moissl-Eichinger and Christa Schleper},

doi = {10.1093/ismejo/wrag078},

issn = {1751-7370},

year  = {2026},

date = {2026-04-11},

urldate = {2026-01-14},

journal = {The ISME Journal},

volume = {20},

number = {1},

publisher = {Oxford University Press (OUP)},

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

                  <jats:p>Ammonia-oxidizing archaea (AOA) have repeatedly been detected with molecular methods on human skin, yet their persistence, physiological traits, and adaptations remain poorly understood. This is mostly owed to a lack of cultured representatives of AOA taxa from healthy human skin. Using a customized enrichment scheme, we cultivated two autotrophic strains, Candidatus Nitrosocosmicus epidermidis and Ca. Nitrosocosmicus unguis, from human skin samples. Genomic analyses revealed specific adaptations for skin colonization, including genomic islands, and expanded gene families linked to interactions with host proteins, and signaling pathways, distinguishing these AOA from their soil-dwelling relatives. Profiling of >700 samples from 8 body sites in cross-sectional and longitudinal cohorts consistently validated the detection of Ca. Nitrosocosmicus species with up to 100% prevalence in a longitudinal cohort, particularly in sebaceous areas. Co-occurrence patterns with specific bacterial taxa reinforce their role as stable components of the skin microbiome. Our results establish Ca. Nitrosocosmicus species as common skin commensals that are evolutionarily capable of transitioning from soil to human skin. They likely play a critical role in the skin ecosystem by recovering nitrogen from the sebum through utilization of urea and ammonia. This sheds new light on the role of archaeal species in maintaining the nitrogen balance in the human skin microbiome, which might be of importance in maintaining healthy skin.</jats:p>},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Spieck2026,

title = {Cultivation‐Based Detection of a Novel High‐GC Nitrospira Derived From the Argentinian Copahue Volcano Area},

author = {Eva Spieck and Hanna Koch and Linnea F. M. Kop and Sabine Keuter and Marcel Malinowski and Katharina Sass and Wolfgang Sand and Edgardo Donati and Pablo Perez Garcia and Sebastian Lücker and Alejandra Giaveno},

doi = {10.1111/1462-2920.70290},

issn = {1462-2920},

year  = {2026},

date = {2026-04-03},

urldate = {2026-04-03},

journal = {Environmental Microbiology},

volume = {28},

number = {4},

publisher = {Wiley},

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

                  <jats:p>

                    Nitrification is an essential process within the global nitrogen cycle and also occurs under extreme conditions, such as in geothermal environments. The nitrite‐oxidizing group

                    <jats:italic>Nitrospira</jats:italic>

                    represents key nitrifiers in these systems, as several species inhabit hot springs worldwide. Using different initial incubation temperatures, two novel moderately thermophilic

                    <jats:italic>Nitrospira</jats:italic>

                    enrichments,

                    <jats:italic>Nitrospira</jats:italic>

                    sp. Vd2 and

                    <jats:italic>Ca</jats:italic>

                    .

                    <jats:styled-content style="fixed-case">

                      N.

                      <jats:italic>neuquenensis</jats:italic>

                    </jats:styled-content>

                    E2OT, were obtained from sulfur‐rich mud pools in the geothermal field Las Máquinas (Neuquén Province, Argentina).

                    <jats:italic>Nitrospira</jats:italic>

                    sp. Vd2 belongs to the N.

                    <jats:italic>bockiana</jats:italic>

                    lineage V, whereas the second enrichment (E2OT) represents the novel taxonomic lineage VIII, together with cultures from Kamchatka (Kam‐Ns4a) and Garga hot springs (Ga3a). The vibrioid morphology of

                    <jats:italic>Ca</jats:italic>

                    .

                    <jats:styled-content style="fixed-case">

                      N.

                      <jats:italic>neuquenensis</jats:italic>

                    </jats:styled-content>

                    E2OT is strikingly different from all described, twisted rod‐shaped

                    <jats:italic>Nitrospira</jats:italic>

                    . Our study expands the knowledge of the taxonomic and genomic diversity of moderately thermophilic

                    <jats:italic>Nitrospira</jats:italic>

                    , by comparing the high‐quality draft genomes with those of previously described species. The recent discovery of quorum‐sensing genes outside the

                    <jats:italic>Nitrospira</jats:italic>

                    lineage II was confirmed for both Argentinian cultures. Notably, the genome GC contents of the enrichments Vd2 and E2OT are 60.6% and 69.4%, respectively. The latter is the highest observed for

                    <jats:italic>Nitrospira</jats:italic>

                    to date and might support thermotolerance up to 50°C.

                  </jats:p>},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Schmelz2026,

title = {Host depletion kits improve microbiome analyses in environmental samples: Seagrass as a test case},

author = {Philipp Schmelz and Stefan Eckensperger and Jay Osvatic and Joana Séneca and Hanin Alzubaidy and Jillian Petersen},

doi = {10.1093/ismeco/ycag082},

issn = {2730-6151},

year  = {2026},

date = {2026-03-28},

urldate = {2026-03-28},

journal = {ISME Communications},

publisher = {Oxford University Press (OUP)},

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

                  <jats:p>All plants and animals associate with specific communities of symbiotic microorganisms. Characterizing the diversity and functions of these communities is essential for understanding their roles in host health, however such efforts are often hindered by the dominance of host-derived material in e.g., DNA extractions. Although various commercial host DNA depletion kits have been developed to overcome these challenges, they have not yet been systematically tested on environmental samples. We used Zostera marina, globally the most widespread seagrass species, as a test case to assess the effectiveness of three different commercially available host DNA depletion kits: QIAamp DNA Microbiome Kit, HostZero Microbial Enrichment Kit, and NEBNext Microbiome Enrichment Kit, when compared to the widely used DNeasy PowerSoil Pro Kit. All three host depletion kits substantially reduced the relative proportion of host DNA, as assessed by 16S rRNA gene amplicon sequencing, and enriched previously identified seagrass-associated bacteria. Furthermore, in metagenomes, only samples processed with host depletion methods allowed for the assembly of metagenome-assembled genomes (MAGs) with high completeness and low contamination. Metagenomic analysis further enabled the recovery of seagrass root core microbiome members, including previously undetected members of the family Sedimenticolaceae, highlighting the value of these techniques for uncovering novel host-associated microbial diversity in environmental samples such as marine plants.</jats:p>},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Krasenbrink2026,

title = {Sulfoquinovose degradation by cow rumen microbiota},

author = {Julia Krasenbrink and Song-Can Chen and Tomohisa Sebastian Tanabe and Hüseyin Sarikeçe and Pleun Meurs and Sabrina Borusak and Rahul Samrat and Guoqing Guan and Clara Priemer and Jay Osvatic and Joana Séneca and Bela Hausmann and Daan R Speth and Evelyne Selberherr and Wolfgang Wanek and David Schleheck and Marc Mussmann and Alexander Loy},

doi = {10.1093/ismejo/wrag069},

issn = {1751-7370},

year  = {2026},

date = {2026-03-27},

urldate = {2026-03-27},

journal = {ISME J},

publisher = {Oxford University Press (OUP)},

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

                  <jats:p>Sulfoquinovose, a sulfonated sugar derived from the thylakoid membrane lipid sulfoquinovosyl diacylglycerol, is abundant in photosynthetic organisms and plays a key role in global sulfur cycling. Its degradation in nature is mediated by specialized bacteria, many of which rely on the enzyme sulfoquinovosidase (YihQ) to release sulfoquinovose from sulfoquinovosyl (diacyl)glycerol. Despite its ecological importance, the diversity and functional roles of sulfoquinovose-degrading microorganisms remain poorly characterized in natural environments. Here, we developed a yihQ-targeted amplicon sequencing approach to investigate the richness and distribution of SQ-degrading bacteria across selected environments. We revealed high richness of yihQ-containing microorganisms in the analyzed cow rumen samples, far exceeding that observed in human and mouse gut microbiomes, suggesting an important role of sulfoquinovose metabolism in ruminant digestion. Anoxic microcosm experiments with sulfoquinovose-amended rumen fluid revealed cooperative microbial degradation of sulfoquinovose to sulfide via isethionate cross-feeding. Amplicon sequencing and genome-resolved metagenomics and metatranscriptomics identified yet undescribed and uncultured sulfoquinovose-degrading taxa. Members of Caproiciproducens (Acutalibacteraceae), Candidatus Limivicinus (Oscillospiraceae), and Sphaerochaetaceae transcribed the isethionate-producing sulfo-transketolase pathway, whereas isethionate was likely respired by a Candidatus Mailhella bacterium (Desulfovibrionaceae). This study presents a functional gene-based assay for tracking environmental yihQ richness, highlights sulfoquinovose degradation as a central metabolic process in the cow rumen, describes previously unknown sulfoquinovose-metabolizing bacteria, and advances understanding of sulfur physiology in complex microbial communities.</jats:p>},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Kück2026,

title = {Host species-specific gene expression by a widespread and flexible chemosynthetic symbiont},

author = {A Carlotta Kück and Lukas Leibrecht and Isidora Morel-Letelier and Olivier Gros and Laetitia G E Wilkins and Benedict Yuen-Simović and Jillian M Petersen},

doi = {10.1093/ismejo/wrag065},

issn = {1751-7370},

year  = {2026},

date = {2026-03-24},

urldate = {2026-03-24},

journal = {The ISME Journal},

publisher = {Oxford University Press (OUP)},

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

                  <jats:p>Associations with microbial symbionts shape the ecology and evolution of almost all eukaryotes. One of their defining features is their specificity, but despite this, many symbioses show a degree of flexibility, with some symbiont species capable of colonizing multiple (often closely related) host species. Although widespread, the functional and evolutionary consequences of flexibility in host-symbiont pairings is poorly understood. Bivalves from the diverse, globally distributed, and ecologically important family Lucinidae are ideal for investigating this, as multiple host species can associate with the same symbiont species, often at the same location. We used metatranscriptomics to investigate the molecular responses of one symbiont species, Candidatus Thiodiazotropha endolucinida, in association with three different host species that co-occur in seagrass meadows in the Caribbean Sea. In replicated experiments, we identified host species-specific patterns of symbiont gene expression including those for key functions such as carbon fixation, cell division, and sulfide oxidation. Our work shows that the symbiont consistently responds in different ways to association with different host species. Because all samples were collected at the same site on the same day, and were thus exposed to the same environmental conditions, these differences are likely driven by host rather than environmental factors. In addition, host species had significantly different carbon isotope signatures, which were consistent with distinct modes of host-microbe interaction indicated by transcriptomics. Our results show that not only symbiont genotype, but also symbiont phenotype may enable coexistence of closely related host species, demonstrating the power of symbiosis in promoting and maintaining biodiversity.</jats:p>},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Liu2026,

title = {Per- and polyfluoroalkyl substances-driven enhancement of colloid-facilitated contaminant transport in groundwater},

author = {Jiameng Liu and Tianchi Cao and Tong Zhang and Thilo Hofmann and Wei Chen},

doi = {10.1016/j.watres.2026.125335},

issn = {0043-1354},

year  = {2026},

date = {2026-03-15},

urldate = {2026-03-00},

journal = {Water Research},

volume = {292},

publisher = {Elsevier BV},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid41766386,

title = {Arbuscular mycorrhizal fungal families and exploration-based guilds exhibit distinct responses to long-term N, P and K deficiencies and imbalances},

author = {Kian Jenab and Lauren Alteio and Ksenia Guseva and Stefan Gorka and Sean Darcy and Lucia Fuchslueger and Alberto Canarini and Victoria Martin and Julia Wiesenbauer and Felix Spiegel and Bruna Imai and Hannes Schmidt and Karin Hage-Ahmed and Erich M Pötsch and Andreas Richter and Jan Jansa and Christina Kaiser},

doi = {10.1111/nph.70969},

issn = {1469-8137},

year  = {2026},

date = {2026-03-02},

urldate = {2026-03-01},

journal = {New Phytol},

abstract = {Many agroecosystems face nitrogen (N), phosphorus (P) or potassium (K) deficiencies due to imbalanced or insufficient nutrient replenishment after biomass harvest. How this affects the symbiosis between plants and arbuscular mycorrhizal fungi (AMF) and the abundance of exploration-based AMF guilds (rhizophilic, edaphophilic and ancestral) remains largely unknown. We studied a 70-yr nutrient deficiency experiment in a managed grassland in central Austria, where aboveground biomass was harvested three times annually. N, P and K were fully, partially or not replenished, causing long-term nutrient deficiencies and imbalances. We analysed AMF communities in soil and roots by DNA/RNA amplicon sequencing and fatty acid biomarkers, alongside soil and plant community properties. Soil AMF communities were affected by N and P deficiencies, while root AMF communities were most susceptible to K deficiency, showing up to 50% biomass reduction, particularly when N was abundant. We observed a shift from rhizophilic to ancestral guilds under P deficiency in soil, and under K deficiency in roots. Families within each guild, particularly ancestral, showed differential responses, indicating complementary nutrient specializations at the family level. Our findings underscore the previously unrecognized role of K deficiency in AMF symbiosis and suggest the existence of nutrient-related functional subgroups within exploration-based AMF guilds.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Lee2026,

title = {Kinetic Plasticity of Nitrite-Oxidizing Bacteria Containing Cytoplasmic Nitrite Oxidoreductase},

author = {Ui-Ju Lee and Joo-Han Gwak and Christiana Abiola and Seongjun Lee and Jin-Sun Yoo and Ok-Ja Si and Hyo Je Cho and Zhe-Xue Quan and Katharina Kitzinger and Holger Daims and Michael Wagner and Man-Young Jung and Sung-Keun Rhee},

doi = {10.1093/ismejo/wrag040},

issn = {1751-7370},

year  = {2026},

date = {2026-02-27},

urldate = {2026-02-27},

journal = {ISME J},

publisher = {Oxford University Press (OUP)},

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

                  <jats:p>Nitrite-oxidizing bacteria (NOB) use either periplasmic (pNXR) or cytoplasmic (cNXR) nitrite oxidoreductase to oxidize nitrite, and this distinction influences nitrite affinity and energy yield. cNXR-containing NOB have historically been considered low-affinity, copiotrophic nitrifiers adapted to high nitrite and neutral pH. Here, we report a previously uncharacterized pH- and substrate-dependent modulation of nitrite affinity in cNXR NOB that is not observed in pNXR NOB and is not a universal microbial trait. Nitrobacter winogradskyi Nb-255, grown at low nitrite (1 mM), had a high apparent affinity (Km(app) = 25.9 μM; specific affinity ao = 440.5 l g cells−1 h−1) comparable to oligotrophic pNXR NOB. However, when grown at high nitrite (10 mM), these cells showed a low affinity at pH 7.5 (Km(app) = 388.0 μM) but exhibited a rapid increase in affinity upon immediate exposure to pH 5.5 (Km(app) = 19.2 μM) without prior acid adaptation. In contrast, pNXR NOB exhibited consistent kinetic behavior across different pH conditions, underscoring that this kinetic plasticity is unique to cNXR NOB. Kinetic inhibition assays revealed that this plasticity is mechanistically underpinned by a shift from a low-affinity nitrite/nitrate antiporter (NarK) to a high-affinity nitrite channel (NirC), coupled with enhanced HNO2 diffusion at low pH, together increasing intracellular nitrite availability. These findings establish that cNXR NOB can dynamically tune nitrite affinity via transporter-level regulation in response to nitrite concentration and pH. This novel mechanism provides a mechanistic explanation for the unexpected prevalence of Nitrobacter in acidic, low-nitrite environments, highlighting its ecological relevance.</jats:p>},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Wang2026,

title = {Elevated Temperature Simulating Heatwaves Restructures Active Nitrifying Communities and Associated Viruses in Tidal Flats and Agricultural Soils},

author = {Baozhan Wang and Ping Gao and Ping Zhang and Yue Zheng and Xu Liu and Ning Ling and Jun Shan and Rongjiang Yao and Shuai Zhao and Zhiguo Zhang and Guibing Zhu and Man-Young Jung and Jianwen Zou and Xiaoyuan Yan and Sungeun Lee and Christina Hazard and Graeme W Nicol and Jizhong Zhou and Yunfeng Yang and Yongguan Zhu and David A Stahl and Michael Wagner and Yanzheng Gao and Jiandong Jiang and Wei Qin},

doi = {10.1093/ismejo/wrag037},

issn = {1751-7370},

year  = {2026},

date = {2026-02-20},

urldate = {2026-02-20},

journal = {ISME J},

publisher = {Oxford University Press (OUP)},

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

                  <jats:p>Global heatwave intensification under climate change will impact the nitrogen cycle, yet its effect on active nitrifier groups or their interactions with viruses remains unclear. Using 13CO2-DNA-based stable-isotope probing coupled with metagenomics, we show that elevated temperatures under heatwave conditions fundamentally restructure active nitrifying communities and their associated viruses in Yangtze River estuary upper tidal flats and adjacent agricultural soils. In tidal flats, sustained high temperature constrained nitrification by reducing the abundance of active ammonia-oxidizing archaea and bacteria (AOA, AOB) and canonical nitrite-oxidizing bacteria (NOB). This was accompanied by a shift in the active community from marine to more thermotolerant but less salt-tolerant terrestrial ecotypes. Conversely, heatwave conditions in agricultural soils suppressed AOB but enhanced nitrification activity in thermotolerant terrestrial AOA ecotypes. Across both ecosystems, inferred virus-nitrifier interactions were temperature dependent. 13C-labeled nitrifier-infecting viruses exhibited coordinated shifts in virus-to-host abundance ratios and predicted lifestyles with their hosts, with sustained high temperatures reducing virus-to-host abundance ratios and favoring temperate infections, relative to higher abundance ratios and a greater proportion of predicted lytic cycles at lower temperatures. We identified AOA-infecting viruses that carry plastocyanin (pcy), encoding a key copper-dependent electron carrier in the AOA respiratory chain, with conserved active sites and a predicted protein fold that supports its capacity for electron transfer, potentially augmenting host energy metabolism. Together, our findings demonstrate that prolonged heatwaves drive coupled shifts in nitrifier community composition and virus–host interaction strategies in a land-use–dependent manner, with implications for nitrogen transformations and ecosystem feedbacks under climate extremes.</jats:p>},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Mohammadzadeh2026,

title = {Cross-domain metabolic interactions link Methanobrevibacter smithii to colorectal cancer microbial ecosystems},

author = {Rokhsareh Mohammadzadeh and Alexander Mahnert and Tamara Zurabishvili and Lisa Wink and Christina Kumpitsch and Hansjoerg Habisch and Jannik Sprengel and Klara Filek and Polona Mertelj and Dominique Pernitsch and Kerstin Hingerl and Marija Durdevic and Gregor Gorkiewicz and Christian Diener and Alexander Loy and Dagmar Kolb and Christoph Trautwein and Tobias Madl and Christine Moissl-Eichinger},

doi = {10.1038/s41467-026-69711-7},

issn = {2041-1723},

year  = {2026},

date = {2026-02-20},

urldate = {2026-02-20},

journal = {Nat Commun},

publisher = {Springer Science and Business Media LLC},

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

                  <jats:p>

                    The human gut is colonized by trillions of microbes that influence the health of their human host. Whereas many bacterial species have now been linked to a variety of different diseases, the involvement of Archaea, an evolutionarily distinct group of microbes, in human disease remains elusive. By analyzing 19 independent clinical studies, we demonstrate that associations between Archaea and human diseases are widespread yet highly heterogeneous, with a pronounced and consistent enrichment of

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

                    in colorectal cancer (CRC) patients. Metabolic modelling and in vitro co-culture identified distinct mutualistic interactions of

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

                    with CRC-causing bacteria such as

                    <jats:italic>Fusobacterium nucleatum</jats:italic>

                    , including metabolic enhancement. Metabolomics further reveal archaeal-derived compounds with tumor-modulating properties. Together, our results provide mechanistic insights into how the human gut archaeome may participate in CRC-associated microbial networks through metabolic cooperation with bacteria.

                  </jats:p>},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid40897862,

title = {Cell membrane cholesterol affects serotonin transporter efflux due to altered transporter oligomerization},

author = {Deborah Rudin and Dino Luethi and Marco Niello and Jae-Won Yang and Isabella Burger and Walter Sandtner and Ruth Birner-Gruenberger and Gerhard J Schütz and Harald H Sitte},

doi = {10.1038/s41380-025-03201-y},

issn = {1476-5578},

year  = {2026},

date = {2026-02-01},

journal = {Mol Psychiatry},

volume = {31},

number = {2},

pages = {963--975},

abstract = {The human monoamine transporters (MATs) for serotonin (SERT), dopamine (DAT), and norepinephrine (NET) play a key role in neurotransmission by transporting neurotransmitters from the synaptic cleft back into the neuron. MATs are embedded in the cell membrane's lipid bilayer, encompassing cholesterol, phospholipids, and sphingolipids as main components. Membrane cholesterol association has been shown for all MATs impacting transporter conformation, substrate affinity, transport velocity, and turnover rates. In the present study, we compared the regulatory impact of cholesterol on the uptake and efflux function, binding affinity, and transporter oligomerization across all three MATs. We observed that cholesterol depletion impairs transporter-mediated uptake in human transporter-transfected HEK293 cells and reduces the binding affinity of all MATs. Electrophysiological investigations in SERT-expressing cells revealed that cholesterol alterations affect the transition of the transporter from the outward to the inward-facing conformation in the presence of substrate. Upon cholesterol depletion, FRET imaging and single molecule microscopy studies indicated altered oligomerization behavior exclusively for SERT. Interestingly, reduction of membrane cholesterol selectively increased amphetamine-induced efflux via SERT, while efflux via DAT and NET was reduced. This effect was diminished in a mutant with reduced PIP binding capacity. Hence, the increased efflux at SERT due to cholesterol depletion appears to depend on the ability of PIP to bind to SERT. Thus, we hypothesize that the interaction profile between cholesterol and MATs may fine-tune the transporter functionality and influence MAT-dependent disorders.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Cuparencu2026,

title = {Integration of modern technologies to advance dietary assessment},

author = {Catalina Cuparencu and Christian Diener and Thomas Wilson and Sean M. Gibbons and Desiree A. Lucassen},

doi = {10.1038/s43016-025-01290-0},

issn = {2662-1355},

year  = {2026},

date = {2026-01-26},

urldate = {2026-01-00},

journal = {Nat Food},

volume = {7},

number = {1},

pages = {17--26},

publisher = {Springer Science and Business Media LLC},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Holub2026,

title = {Investigating Spectral Biomarker Candidates for Migratory Potential in Cancer Cells Using Micro-FTIR and O-PTIR Spectroscopy},

author = {Elisabeth Holub and Nikolaus Hondl and Kai-Lan Lin and Marjaana Parikainen and Cecilia Sahlgren and Bernhard Lendl and Georg Ramer},

doi = {10.1021/acsmeasuresciau.5c00132},

issn = {2694-250X},

year  = {2026},

date = {2026-01-21},

journal = {ACS Meas. Sci. Au},

publisher = {American Chemical Society (ACS)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Ye2026,

title = {Associations between gut microbiota and personality traits: insights from a captive common marmoset (                    \textit{Callithrix jacchus}                    ) colony},

author = {Huimin Ye and Vedrana Šlipogor and Buck T. Hanson and Joana Séneca and Bela Hausmann and Craig W. Herbold and Petra Pjevac and Thomas Bugnyar and Alexander Loy},

editor = {Qi Su},

doi = {10.1128/spectrum.00443-25},

issn = {2165-0497},

year  = {2026},

date = {2026-01-06},

urldate = {2026-01-06},

journal = {Microbiol Spectr},

volume = {14},

number = {1},

publisher = {American Society for Microbiology},

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

                  <jats:sec>

                    <jats:title/>

                    <jats:p>

                      Recent studies have suggested associations between consistent inter-individual behavioral variation (i.e., animal personality) and gut microbiota. Non-human primates living under controlled conditions are valuable models to investigate diet-independent microbiome-host interactions. In this study, we investigated associations between specific gut microbiota members and personality traits, as well as group membership, sex, age class, breeding status, and relatedness of 26 captive common marmosets (

                      <jats:italic toggle="yes">Callithrix jacchus</jats:italic>

                      ), maintained under the same diet and housing conditions. Personality was assessed using an established testing battery in repeated tests. Then, we collected a total of 225 fecal samples during the summers of 2017 and 2019 from five marmoset social groups for 16S rRNA gene amplicon sequencing. Within-individual microbiota variance was smaller than that between group members. Group members also exhibited more similar gut microbiota than individuals from different groups in each sampling year. Beta diversity of the gut microbiota was linked with personality traits, age class, sex, and breeding status, but not with genetic relatedness. We identified specific bacterial taxa associated with personality traits. In particular, members of the sulfite-reducing genus

                      <jats:italic toggle="yes">Desulfovibrio</jats:italic>

                      were enriched in more avoidant marmosets. Amplicon sequencing of the dissimilatory sulfite reductase gene

                      <jats:italic toggle="yes">dsrB</jats:italic>

                      confirmed this pattern, yet additionally revealed an unknown uncultured bacterium that was the predominant sulfite-reducing bacterium in the fecal samples and was linked to more explorative individuals. These findings highlight specific association patterns between identified microbial taxa and personality traits in captive common marmosets.

                    </jats:p>

                    <jats:sec>

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

                      <jats:p>This study provides valuable insights into the intricate relationship between gut microbiota and host personality traits, using captive common marmosets as a model. By controlling for diet and housing conditions, it probes key host factors such as personality, age, sex, and social group membership, offering a robust framework for understanding microbiome-host interactions. The discovery of specific microbial taxa associated with personality traits, particularly the enrichment of sulfite-reducing genera in more avoidant individuals, underscores the potential of the gut microbiome to reflect or be associated with personality differences. These findings advance our understanding of microbiome-host dynamics and pave the way for future research on the mechanistic links between behavior and gut microbiota in other animal models and across broader ecological contexts.</jats:p>

                    </jats:sec>

                  </jats:sec>},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Sherman2026,

title = {Minor influence of climbing hall characteristics on rubber-derived compound contamination highlights a need for material-level solutions},

author = {Anya Sherman and Laura Lotteraner and Leah K. Maruschka and Thilo Hofmann},

doi = {10.1039/d5em00812c},

issn = {2050-7895},

year  = {2026},

date = {2026-01-06},

urldate = {2026-00-00},

journal = {Environ. Sci.: Processes Impacts},

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

abstract = {<jats:p>Climbing shoe abrasion generates fine rubber particles, leading to elevated concentrations of rubber-derived compounds (RDCs) in airborne particulate matter and settled dust of indoor climbing halls, in some cases comparable...</jats:p>},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Lotteraner2026,

title = {The Importance of Being Thorough: How Data Analysis Choices Impact the Perceived Relationship between Pollutants and Predictors},

author = {Laura Lotteraner and Torsten Möller and Thilo Hofmann},

doi = {10.1016/j.watres.2025.124639},

issn = {0043-1354},

year  = {2026},

date = {2026-01-01},

urldate = {2026-01-00},

journal = {Water Research},

volume = {288},

publisher = {Elsevier BV},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Bauchinger2025,

title = {Metatranscriptomic-driven insights into mucosal glycan degradation by the human gut microbiota},

author = {Franziska Bauchinger and David Berry},

editor = {Leluo Guan},

doi = {10.1093/femsec/fiaf118},

issn = {1574-6941},

year  = {2025},

date = {2025-12-22},

volume = {102},

number = {1},

publisher = {Oxford University Press (OUP)},

abstract = {Abstract

                  The secreted mucus layer in the human gastrointestinal tract constitutes both a protective boundary between gut lumen and epithelium as well as an important nutrient source for members of the gut microbiota. While many gut microbes possess the genetic potential to degrade mucin, it is still unclear which species transcribe the respective genes. Here, we systematically analysed publicly available metagenome and metatranscriptome datasets to characterize the gut microbial community involved in mucosal glycan degradation. We utilized cooccurrence network analysis and linear regression to elucidate the ecological strategies of, and relationship between, mucus degraders. We found that although ~60% of species carrying genes encoding for mucosal-glycan-degrading enzymes have detectable transcription of these genes, only 21 species prevalently transcribe more than 1 gene. Furthermore, the transcription of individual genes was frequently dominated by single species in individual samples. Transcription patterns suggested the presence of competitive mucosal glycan degraders characterized by abundance-driven transcription that were negative predictors for the transcription of other degraders as well as opportunistic species with decoupled abundance and transcription profiles. These findings provide insights into the ecology of the mucosal glycan degradation niche in the human gut microbiota.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Singleton2025,

title = {The Microflora Danica atlas of Danish environmental microbiomes},

author = {C. M. Singleton and T. B. N. Jensen and F. Delogu and K. S. Knudsen and E. A. Sørensen and V. R. Jørgensen and S. M. Karst and Y. Yang and M. Sereika and F. Petriglieri and S. Knutsson and S. M. Dall and R. H. Kirkegaard and J. M. Kristensen and C. K. Overgaard and B. J. Woodcroft and D. R. Speth and S. T. N. Aroney and and Henning C. Thomsen and Bent T. Christensen and Lis W. de Jonge and Anne-Cathrine S. Danielsen and Cecilie Hermansen and Mogens H. Greve and Rasmus Ejrnæs and Thomas A. Davidson and Signe Normand and Urs A. Treier and Bjarke Madsen and Andreas Schramm and Ian P. G. Marshall and Ann-Sofie Dam and Kasper U. Kjeldsen and Kai Finster and Philip F. Thomsen and Eva E. Sigsgaard and Martin J. Klepke and Marie Vestergård and Erik Aude and Lene Thomsen and Camilla Lemming and Rita Hørfarter and Marlene M. Jensen and Tobias G. Frøslev and Lone Gram and Peter B. Svendsen and Morten Dencker Schostag and Sanne Kjellerup and Torben L. Skovhus and Ditte A. Søborg and Kasper Reitzel and Jørgen F. Pedersen and Andrew Giguere and Inge S. Pedersen and Mads Sønderkær and Jes Vollertsen and Fan Liu and Peter Roslev and Niels Iversen and Kåre L. Nielsen and Nadieh de Jonge and Dan Bruhn and Jeppe L. Nielsen and Torsten N. Kristensen and Chenjing Jiang and Marta A. Nierychlo and Giulia Dottorini and M. Wagner and M. K. D. Dueholm and P. H. Nielsen and M. Albertsen},

doi = {10.1038/s41586-025-09794-2},

issn = {1476-4687},

year  = {2025},

date = {2025-12-03},

urldate = {2025-12-03},

journal = {Nature},

publisher = {Springer Science and Business Media LLC},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid41425875,

title = {Single-Mode Ring Resonator-Based Optomechanical Transducers for Advanced Atomic Force Sensing},

author = {Yide Zhang and Artem S Vorobev and Savda Sam and S Hadi Badri and Mauro David and Bernhard Lendl and Georg Ramer and Liam O'Faolain},

doi = {10.1021/acsphotonics.5c01914},

issn = {2330-4022},

year  = {2025},

date = {2025-12-01},

journal = {ACS Photonics},

volume = {12},

number = {12},

pages = {6778--6787},

abstract = {Atomic force microscopy (AFM) is a widely used technique for high-resolution imaging and force sensing, yet its performance is fundamentally constrained by the cantilever size, spring constants, and mechanical frequencies. To overcome these limitations, we present a compact and highly efficient single-mode ring resonator-based optomechanical transducer on an silicon-on-insulator (SOI) platform. Unlike conventional designs that rely on whispering gallery modes (WGMs) resonators, our approach ensures mode stability, facilitates straightforward signal interpretation, and enhances measurement reliability by eliminating mode-splitting effects and complex optical responses. Coupled with a picogram-scale cantilever, our system achieves exceptional displacement resolution of 6.7 × 10 m/Hz and force detection down to 5.0 × 10 N, providing a high-performance alternative to existing optomechanical AFM transducers. The tunable mechanical resonance frequency (1.3 to 22.5 MHz) and adjustable stiffness (0.46 to 3.54 N/m) enable precise force sensing across a broad range of applications, from soft matter characterization to high-speed imaging. Importantly, our results exhibit strong agreement with theoretical predictions, ensuring accurate and direct displacement measurements. Our results establish this single-mode optomechanical transducer as a robust, high-sensitivity platform for next-generation AFM and nanoscale sensing applications, offering a compact, scalable, and highly precise alternative to traditional free-space optical detection methods. The combination of high displacement resolution, mode stability, and tunable performance establishes this optomechanical transducer as a promising advancement in integrated nanoscale sensing and AFM applications.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Plöchl2025,

title = {A novel class of small-molecule inhibitors targeting bacteriophage infection},

author = {Konstantin Plöchl and Thomas Böttcher},

doi = {10.1039/d5cb00120j},

issn = {2633-0679},

year  = {2025},

date = {2025-12-01},

urldate = {2025-00-00},

journal = {RSC Chem. Biol.},

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

abstract = {<jats:p>Discovery of benzimidazylpyrazoles as a new class of synthetic bacteriophage antivirals provides a chemical tool enabling the study of disease-related phage–host interactions.</jats:p>},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Wang2025,

title = {Methane-cycling microbiomes in soils of the pan-Arctic and their response to permafrost degradation},

author = {Haitao Wang and Erik Lindemann and Patrick Liebmann and Milan Varsadiya and Mette Marianne Svenning and Muhammad Waqas and Sebastian Petters and Andreas Richter and Georg Guggenberger and Jiri Barta and Tim Urich},

doi = {10.1038/s43247-025-02765-5},

issn = {2662-4435},

year  = {2025},

date = {2025-12-00},

journal = {Commun Earth Environ},

volume = {6},

number = {1},

publisher = {Springer Science and Business Media LLC},

abstract = {Abstract

          The methane-cycling microbiomes play crucial roles in methane dynamics. However, little is known about their distributions on a pan-Arctic scale as well as their responses to the widespread permafrost degradation. Based on 621 datasets of 16S rRNA gene amplicons from intact permafrost soils across the pan-Arctic, we identified only 22 methanogen and 26 methanotroph phylotypes. Their relative abundances varied significantly between sites and soil horizons. Only four methanogen phylotypes were detected at all locations. Remarkably, the permafrost soil methane filter was almost exclusively dominated by some obligate methanotroph (Methylobacter-like) phylotypes. However, a case study in Alaska suggests that atmospheric methane oxidizing bacteria (Methylocapsa-like phylotypes) dominated methanotrophs in a drier condition after permafrost degradation. These findings point towards a few key microbes particularly relevant for future studies on Arctic methane dynamics in a warming climate and that under future dry conditions, increased atmospheric methane uptake in Arctic upland soils may occur.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Krasenbrink2025,

title = {Sulfoquinovose is exclusively metabolized by the gut microbiota and degraded differently in mice and humans},

author = {Julia Krasenbrink and Buck T. Hanson and Anna S. Weiss and Sabrina Borusak and Tomohisa Sebastian Tanabe and Michaela Lang and Georg Aichinger and Bela Hausmann and David Berry and Andreas Richter and Doris Marko and Marc Mussmann and David Schleheck and Bärbel Stecher and Alexander Loy},

doi = {10.1186/s40168-025-02175-x},

issn = {2049-2618},

year  = {2025},

date = {2025-12-00},

journal = {Microbiome},

volume = {13},

number = {1},

publisher = {Springer Science and Business Media LLC},

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

 <jats:sec> 

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

 <jats:p>Sulfoquinovose (SQ) is a green-diet-derived sulfonated glucose and a selective substrate for a limited number of human gut bacteria. Complete anaerobic SQ degradation via interspecies metabolite transfer to sulfonate-respiring bacteria produces hydrogen sulfide, which has dose- and context-dependent health effects. Here, we studied potential SQ degradation by the mammalian host and the impact of SQ supplementation on human and murine gut microbiota diversity and metabolism.</jats:p> 

 </jats:sec> 

 <jats:sec> 

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

 <jats:p> 

 <jats:sup>13</jats:sup>CO<jats:sub>2</jats:sub> breath tests with germ-free C57BL/6 mice gavaged with <jats:sup>13</jats:sup>C-SQ were negative. Also, SQ was not degraded by human intestinal cells in vitro, indicating that SQ is not directly metabolized by mice and humans. Addition of increasing SQ concentrations to human fecal microcosms revealed dose-dependent responses of the microbiota and corroborated the relevance of <jats:italic>Agathobacter rectalis</jats:italic> and <jats:italic>Bilophila wadsworthia</jats:italic> in cooperative degradation of SQ to hydrogen sulfide via interspecies transfer of 2,3-dihydroxy-1-propanesulfonate (DHPS). Similar to the human gut microbiome, the genetic capacity for SQ or DHPS degradation is sparsely distributed among bacterial species in the gut of conventional laboratory mice. <jats:italic>Escherichia coli</jats:italic> and <jats:italic>Enterocloster clostridioformis</jats:italic> were identified as primary SQ degraders in the mouse gut. SQ and DHPS supplementation experiments with conventional laboratory mice and their intestinal contents showed that SQ was incompletely catabolized to DHPS. Although some <jats:italic>E. clostridioformis</jats:italic> genomes encode an extended sulfoglycolytic pathway for both SQ and DHPS fermentation, SQ was only degraded to DHPS by a mouse-derived <jats:italic>E. clostridioformis</jats:italic> strain.</jats:p> 

 </jats:sec> 

 <jats:sec> 

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

 <jats:p>Our findings suggest that SQ is solely a nutrient for the gut microbiota and not for mice and humans, emphasizing its potential as a prebiotic. SQ degradation by the microbiota of conventional laboratory mice differs from the human gut microbiota by absence of DHPS degradation activity. Hence, the microbiota of conventional laboratory mice does not fully represent the SQ metabolism in humans, indicating the need for alternative model systems to assess the impact of SQ on human health. This study advances our understanding of how individual dietary compounds shape the microbial community structure and metabolism in the gut and thereby potentially influence host health.</jats:p> 

 </jats:sec>},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Weinberger2025b,

title = {Proteomic and metabolomic profiling of extracellular vesicles produced by human gut archaea},

author = {Viktoria Weinberger and Barbara Darnhofer and Himadri B. Thapa and Polona Mertelj and Régis Stentz and Emily Jones and Gerlinde Grabmann and Rokhsareh Mohammadzadeh and Tejus Shinde and Christina Karner and Jennifer Ober and Rokas Juodeikis and Dominique Pernitsch and Kerstin Hingerl and Tamara Zurabishvili and Christina Kumpitsch and Torben Kuehnast and Beate Rinner and Heimo Strohmaier and Dagmar Kolb and Kathryn Gotts and Thomas Weichhart and Thomas Köcher and Harald Köfeler and Simon R. Carding and Stefan Schild and Christine Moissl-Eichinger},

doi = {10.1038/s41467-025-60271-w},

issn = {2041-1723},

year  = {2025},

date = {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>Gastrointestinal bacteria interact with the host and each other through various mechanisms, including the production of extracellular vesicles (EVs). However, the composition and potential roles of EVs released by gut archaea are poorly understood. Here, we study EVs produced by four strains of human gut-derived methanogenic archaea: <jats:italic>Methanobrevibacter smithii</jats:italic> ALI, <jats:italic>M. smithii</jats:italic> GRAZ-2, <jats:italic>M. intestini</jats:italic>, and <jats:italic>Methanosphaera stadtmanae</jats:italic>. The size (~130 nm) and morphology of these EVs are comparable to those of bacterial EVs. Proteomic and metabolomic analyses reveal that the archaeal EVs are enriched in putative adhesins or adhesin-like proteins, free glutamic and aspartic acid, and choline glycerophosphate. The archaeal EVs are taken up by macrophages in vitro and elicit species-specific responses in immune and epithelial cell lines, including production of chemokines such as CXCL9, CXCL11, and CX3CL1. The EVs produced by <jats:italic>M. intestini</jats:italic> strongly induce pro-inflammatory cytokine IL-8 in epithelial cells. Future work should examine whether archaeal EVs play roles in the interactions of archaea with other gut microbes and with the host.</jats:p>},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Jancheva2025,

title = {A phage-selective trigger hints at an SOS-independent mechanism of prophage induction by oxidative stress},

author = {Magdalena Jancheva and Thi-Hong Nhung Nguyen and Felix Anderl and Shubham Joge and Jessica Neubauer and Clarissa Rominger-Baumann and Alexandra Walter and Golo Storch and Thomas Böttcher},

doi = {10.1039/d5sc04923g},

issn = {2041-6539},

year  = {2025},

date = {2025-11-29},

urldate = {2025-00-00},

journal = {Chem. Sci.},

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

abstract = {<jats:p>

                    We report an SOS-independent mechanism of selective prophage induction in a poly-lysogenic

                    <jats:italic>Staphylococcus aureus</jats:italic>

                    host triggered by redox cycling of phenazine compounds.

                  </jats:p>},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@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}

}