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Publications in peer reviewed journals

8 Publications found
  • The maternal microbiome in pregnancy, delivery, and early-stage development of neonatal microbiome after cesarean section: A prospective longitudinal study

    Foessleitner P, Pjevac P, Granser S, Wisgrill L, Pummer L, Eckel F, Seki D, Berry D, Hausmann B, Farr A
    2024 - AOGS, in press



    Changes within the maternal microbiome during the last trimester of pregnancy and the determinants of the subsequent neonatal microbiome establishment after delivery by elective cesarean section are described.

    Material and methods

    Maternal vaginal and rectal microbiome samples were collected in the last trimester and before cesarean section; intrauterine cavity, placenta, neonatal buccal mucosa, skin, and meconium samples were obtained at birth; neonatal sample collection was repeated 2–3 days postnatally. Microbial community composition was analyzed by 16S rRNA gene amplicon sequencing. Relative abundance measurements of amplicon sequencing variants and sum counts at higher taxonomic levels were compared to test for significant overlap or differences in microbial community compositions. ID: NCT04489056.


    A total of 30 mothers and their neonates were included with available microbiome samples for all maternal, intrauterine cavity and placenta samples, as well as for 18 of 30 neonates. The composition of maternal vaginal and rectal microbiomes during the last trimester of healthy pregnancies did not significantly change (permutational multivariate analysis of variance [PERMANOVA], p > 0.05). No robust microbial signature was detected in the intrauterine cavity, placenta, neonatal buccal mucosa, skin swabs, or meconium samples collected at birth. After birth, the neonatal microbiome was rapidly established, and significantly different microbial communities were detectable 2–3 days postnatally in neonate buccal mucosa and stool samples (PERMANOVA, p < 0.01).


    Maternal vaginal and rectal microbiomes in healthy pregnancies remain stable during the third trimester. No microbial colonization of the neonate was observed before birth in healthy pregnancies. Neonatal microbiomes in infants delivered by cesarean section displayed a taxonomic composition distinct from maternal vaginal and rectal microbiomes at birth, indicating that postnatal exposure to the extrauterine environment is the driving source of initial neonatal microbiome development in this cohort.

  • Reevaluation and novel insights into amino sugar and neutral sugar necromass biomarkers in archaea, bacteria, fungi, and plants

    Salas E, Gorfer M, Bandian D, Eichorst SA, Schmidt H, Horak J, Rittmann SKMR, Schleper C, Reischl B, Pribasnig T, Jansa J, Kaiser C, Wanek W
    2024 - Sci. Total Environ, 906: 167463


    Soil microbial necromass is an important contributor to soil organic matter (>50%) and it is largely composed of microbial residues. In soils, fragmented cell wall residues are mostly found in their polysaccharide forms of fungal chitin and bacterial peptidoglycan. Microbial necromass biomarkers, particularly amino sugars (AS) such as glucosamine (GlcN) and muramic acid (MurA) have been used to trace fungal and bacterial residues in soils, and to distinguish carbon (C) found in microbial residues from non-microbial organic C. Neutral sugars (NS), particularly the hexose/pentose ratio, have also been proposed as tracers of plant polysaccharides in soils. In our study, we extended the range of biomarkers to include AS and NS compounds in the biomass of 120 species belonging to archaea, bacteria, fungi, or plants. GlcN was the most common AS found in all taxa, contributing 42–91% to total AS content, while glucose was the most common NS found, contributing 56–79% to total NS. We identified talosaminuronic acid, found in archaeal pseudopeptidoglycan, as a new potential biomarker specific for Euryarchaeota. We compared the variability of these compounds between the different taxonomic groups using multivariate approaches, such as non-metric multidimensional scaling (NMDS) and partial least squares discriminant analysis (PLS-DA) and statistically evaluated their biomarker potential via indicator species analysis. Both NMDS and PLS-DA showcased the variability in the AS and NS contents between the different taxonomic groups, highlighting their potential as necromass residue biomarkers and allowing their extension from separating bacterial and fungal necromass to separating microbes from plants. Finally, we estimated new conversion factors where fungal GlcN is converted to fungal C by multiplying by 10 and MurA is converted to bacterial C by multiplying by 54. Conversion factors for talosaminuronic acid and galactosamine are also proposed to allow estimation of archaeal or all-microbial necromass residue C, respectively.

  • The efficacy of Pb, As(V) and Sb(III ) removal by biochar is determined by solution chemistry

    Sampriti Chaudhuri, Gabriel Sigmund, Naresh Kumar, Thorsten Hüffer, Andreas Mautner, Thilo Hofmann
    2024 - Environmental Science: Water Research & Technology, in press


    Biochars (BC) are cost-effective and sustainable sorbents to clean up waters polluted with metal(loid)s. Understanding the influence of water chemistry is critical in identifying processes that limit metal(loid) removal. To address this, we investigated the removal of lead [Pb], arsenate [As(V)], and antimonite [Sb(III)] using BC in the presence of various solution constituents. A design of experiments approach was used to investigate sorption for each metal(loid)-BC setup (Pb with a straw BC, As(V) with charred wood-dolomite and Sb(III) with a steam-activated wood BC) with twenty-five different background solutions varying in calcium (Ca), natural organic matter (NOM), phosphorus (P), and iron [Fe(III)] content. Background solution composition affected removal of Pb (29 to 100%) more strongly than that of As(V) (37 to 92%) and Sb(III) (20 to 70%), with the selected BC at the metal(loid) concentrations studied. Pb removal was associated with Fe(III)–NOM–Ca organo-mineral phases for solutions containing Fe(III), NOM and Ca. As(V) sorption was enhanced by Ca due to cation-bridging and reducing the competition for sorption sites by NOM and P in high NOM and/or P containing solutions. Sb(III) sorption was hindered by oxidation to Sb(V) through redox active moieties in the BC in all solutions. Sb(III) removal decreased in the presence of high Fe(III), because Fe(III)/Fe(III)–NOM phases blocked accessibility to sorption sites in the highly porous BC, and/or due to enhanced oxidation of Sb(III) to the more mobile (but less toxic) Sb(V). Ideally, the design of BC sorbents for the removal of metal(loid)s from contaminated waters should a priori consider complex solution compositions.

  • Biomonitoring of Dietary Mycotoxin Exposure and Associated Impact on the Gut Microbiome in Nigerian Infants

    Ayeni KI, Seki D, Pjevac P, Hausmann B, Krausová M, Braun D, Wisgrill L, Berry D, Warth B, Ezekiel CN
    2024 - Environmental Science & Technology, in press


    Mycotoxins are toxic chemicals that adversely affect human health. Here, we assessed the influence of mycotoxin exposure on the longitudinal development of early life intestinal microbiota of Nigerian neonates and infants (NIs). Human biomonitoring assays based on liquid chromatography tandem mass spectrometry were applied to quantify mycotoxins in breast milk (n = 68) consumed by the NIs, their stool (n = 82), and urine samples (n = 15), which were collected longitudinally from month 1–18 postdelivery. Microbial community composition was characterized by 16S rRNA gene amplicon sequencing of stool samples and was correlated to mycotoxin exposure patterns. Fumonisin B1 (FB1), FB2, and alternariol monomethyl ether (AME) were frequently quantified in stool samples between months 6 and 18. Aflatoxin M1 (AFM1), AME, and citrinin were quantified in breast milk samples at low concentrations. AFM1, FB1, and ochratoxin A were quantified in urine samples at relatively high concentrations. Klebsiella and Escherichia/Shigella were dominant in very early life stool samples (month 1), whereas Bifidobacterium was dominant between months 3 and 6. The total mycotoxin levels in stool were significantly associated with NIs’ gut microbiome composition (PERMANOVA, p < 0.05). However, no significant correlation was observed between specific microbiota and the detection of certain mycotoxins. Albeit a small cohort, this study demonstrates that mycotoxins may influence early life gut microbiome composition.

  • Tire Materials Disturb Transformations of Nitrogen Compounds and Affect the Structure of Biomass in Aerobic Granular Sludge Reactors

    Piotr Jachimowicz, Ruoting Peng, Thorsten Hüffer, Thilo Hofmann, Agnieszka Cydzik-Kwiatkowska
    2024 - Journal of Hazardous Materials, 465: 133223


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

  • An integrated approach to testing and assessment (IATA) to support grouping and read-across of nanomaterials in aquatic systems

    Richard K. Cross, Dave Spurgeon, Claus Svendsen, Elma Lahive, Simon Little, Frank von der Kammer, Frédéric Loosli, Marianne Matzke, Teresa F. Fernandes, Vicki Stone, Willie J.G.M. Peijnenburg, Eric A.J. Bleeker
    2024 - Nano Today, 54: 102065


    Even small changes in physicochemical properties of nanoforms (NFs), can drive differences in their environmental fate and hazard. The large number of new materials being developed means it will not be feasible to test and characterise the fate, behaviour and (eco)toxicity of each individual NF. This is further amplified by transformations of NFs over their lifecycle, changing the processes governing their risk. A common complexity arises from dissolution, where the combined toxicity of the exposure arises from both the solutes and any remaining particles contribution to the overall toxicity of the exposure. For efficient and effective risk assessment, it is the most relevant form of the NF for a given exposure that should be targeted for testing and assessment. In aquatic systems, functional fate processes (including dissolution, dispersion stability and chemical and biological transformations) determine the NF’s exposure relevant form. Whilst transformations in the environment alter the initial properties of an NF, different NFs may follow a shared functional fate pathway and ultimately present a similar fate and hazard profile in the environment. Therefore, these processes may be used to scientifically justify grouping NFs and read-across for specific endpoints from data rich NF(s) to verified members of the group that have not been tested yet. Integrated Approaches to Testing and Assessment (IATA) have been used in other regulatory contexts to support the collection and integration of relevant existing information as well as the targeted generation of new data to support grouping and read-across. Here, a new IATA is presented consisting of decision nodes focused on dissolution, dispersion stability, chemical transformations and the relative contribution to toxicity of the particle and dissolved component of the overall exposure. The IATA focuses on the fate of NFs in aquatic systems outside of the body, but it can be considered a template for future assessment of in vivo kinetics, which will require further development. Guidance on tiered testing approaches and thresholds for grouping within each decision node are critically discussed. Worked examples for ecotoxicity of metal oxide NFs in aqueous systems (in microbial communities isolated from soils and for lettuce plants in hydroponic systems) demonstrate successful identification of the exposure relevant form of the NF in these case studies and allows for different grouping of NFs through application of the IATA.

  • Global abundance patterns, diversity, and ecology of Patescibacteria in wastewater treatment plants

    Hu H, Kristensen JM, Herbold CW, Pjevac P, Kitzinger K, Hausmann B, Dueholm MKD, Nielsen PH, Wagner M
    2024 - Microbiome, in press
    Patescibacteria co-occurrence network



    Microorganisms are responsible for nutrient removal and resource recovery in wastewater treatment plants (WWTPs), and their diversity is often studied by 16S rRNA gene amplicon sequencing. However, this approach underestimates the abundance and diversity of Patescibacteria due to the low coverage of commonly used PCR primers for this highly divergent bacterial phylum. Therefore, our current understanding of the global diversity, distribution, and ecological role of Patescibacteria in WWTPs is very incomplete. This is particularly relevant as Patescibacteria are considered to be associated with microbial host cells and can therefore influence the abundance and temporal variability of other microbial groups that are important for WWTP functioning.


    Here, we evaluated the in silico coverage of widely used 16S rRNA gene-targeted primer pairs and redesigned a primer pair targeting the V4 region of bacterial and archaeal 16S rRNA genes to expand its coverage for Patescibacteria. We then experimentally evaluated and compared the performance of the original and modified V4-targeted primers on 565 WWTP samples from the MiDAS global sample collection. Using the modified primer pair, the percentage of ASVs classified as Patescibacteria increased from 5.9% to 23.8%, and the number of detected patescibacterial genera increased from 560 to 1,576, while the detected diversity of the remaining microbial community remained similar. Due to this significantly improved coverage of Patescibacteria, we identified 23 core genera of Patescibacteria in WWTPs and described the global distribution pattern of these unusual microbes in these systems. Finally, correlation network analysis revealed potential host organisms that might be associated with Patescibacteria in WWTPs. Interestingly, strong indications were found for an association between Patescibacteria of the Saccharimonadia and globally abundant polyphosphate-accumulating organisms of the genus Ca. Phosporibacter.


    Our study (i) provides an improved 16S rRNA gene V4 region-targeted amplicon primer pair inclusive of Patescibacteria with little impact on the detection of other taxa, (ii) reveals the diversity and distribution patterns of Patescibacteria in WWTPs on a global scale, and (iii) provides new insights into the ecological role and potential hosts of Patescibacteria in WWTPs.


  • Hydrolysis of Antimicrobial Peptides by Extracellular Peptidases in Wastewater

    Natalie Wichmann, Richard Gruseck, Michael Zumstein
    2024 - Environ. Sci. Technol., 1: 717–726


    Several antimicrobial peptides (AMPs) are emerging as promising novel antibiotics. When released into wastewater streams after use, AMPs might be hydrolyzed and inactivated by wastewater peptidases─resulting in a reduced release of active antimicrobials into wastewater-receiving environments. A key step towards a better understanding of the fate of AMPs in wastewater systems is to investigate the activity and specificity of wastewater peptidases. Here, we quantified peptidase activity in extracellular extracts from different stages throughout the wastewater treatment process. For all four tested municipal wastewater treatment plants, we detected highest activity in raw wastewater. Complementarily, we assessed the potential of enzymes in raw wastewater extracts to biotransform 10 selected AMPs. We found large variations in the susceptibility of AMPs to enzymatic transformation, indicating substantial substrate specificity of extracted enzymes. To obtain insights into peptidase specificities, we searched for hydrolysis products of rapidly biotransformed AMPs and quantified selected products using synthetic standards. We found that hydrolysis occurred at specific sites and that these sites were remarkably conserved across the four tested wastewaters. Together, these findings provide insights into the fate of AMPs in wastewater systems and can inform the selection and design of peptide-based antibiotics that are hydrolyzable by wastewater peptidases.

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