Publications by authors named "Nico Jehmlich"

140 Publications

Insights into Autotrophic Activities and Carbon Flow in Iron-Rich Pelagic Aggregates (Iron Snow).

Microorganisms 2021 Jun 23;9(7). Epub 2021 Jun 23.

Institute of Biodiversity, Friedrich Schiller University Jena, Dornburger Strasse 159, 07743 Jena, Germany.

Pelagic aggregates function as biological carbon pumps for transporting fixed organic carbon to sediments. In iron-rich (ferruginous) lakes, photoferrotrophic and chemolithoautotrophic bacteria contribute to CO fixation by oxidizing reduced iron, leading to the formation of iron-rich pelagic aggregates (iron snow). The significance of iron oxidizers in carbon fixation, their general role in iron snow functioning and the flow of carbon within iron snow is still unclear. Here, we combined a two-year metatranscriptome analysis of iron snow collected from an acidic lake with protein-based stable isotope probing to determine general metabolic activities and to trace CO incorporation in iron snow over time under oxic and anoxic conditions. mRNA-derived metatranscriptome of iron snow identified four key players (, , , ) with relative abundances (59.6-85.7%) encoding ecologically relevant pathways, including carbon fixation and polysaccharide biosynthesis. No transcriptional activity for carbon fixation from archaea or eukaryotes was detected. CO incorporation studies identified active chemolithoautotroph under both conditions. Only 1.0-5.3% relative C abundances were found in heterotrophic and under oxic conditions. These data show that iron oxidizers play an important role in CO fixation, but the majority of fixed C will be directly transported to the sediment without feeding heterotrophs in the water column in acidic ferruginous lakes.
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http://dx.doi.org/10.3390/microorganisms9071368DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8305228PMC
June 2021

A workflow to identify novel proteins based on the direct mapping of peptide-spectrum-matches to genomic locations.

BMC Bioinformatics 2021 May 26;22(1):277. Epub 2021 May 26.

German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig and Competence Center for Scalable Data Services and Solutions Dresden-Leipzig and Leipzig Research Center for Civilization Diseases, University Leipzig, 04107, Leipzig, Germany.

Background: Small Proteins have received increasing attention in recent years. They have in particular been implicated as signals contributing to the coordination of bacterial communities. In genome annotations they are often missing or hidden among large numbers of hypothetical proteins because genome annotation pipelines often exclude short open reading frames or over-predict hypothetical proteins based on simple models. The validation of novel proteins, and in particular of small proteins (sProteins), therefore requires additional evidence. Proteogenomics is considered the gold standard for this purpose. It extends beyond established annotations and includes all possible open reading frames (ORFs) as potential sources of peptides, thus allowing the discovery of novel, unannotated proteins. Typically this results in large numbers of putative novel small proteins fraught with large fractions of false-positive predictions.

Results: We observe that number and quality of the peptide-spectrum matches (PSMs) that map to a candidate ORF can be highly informative for the purpose of distinguishing proteins from spurious ORF annotations. We report here on a workflow that aggregates PSM quality information and local context into simple descriptors and reliably separates likely proteins from the large pool of false-positive, i.e., most likely untranslated ORFs. We investigated the artificial gut microbiome model SIHUMIx, comprising eight different species, for which we validate 5114 proteins that have previously been annotated only as hypothetical ORFs. In addition, we identified 37 non-annotated protein candidates for which we found evidence at the proteomic and transcriptomic level. Half (19) of these candidates have close functional homologs in other species. Another 12 candidates have homologs designated as hypothetical proteins in other species. The remaining six candidates are short (< 100 AA) and are most likely bona fide novel proteins.

Conclusions: The aggregation of PSM quality information for predicted ORFs provides a robust and efficient method to identify novel proteins in proteomics data. The workflow is in particular capable of identifying small proteins and frameshift variants. Since PSMs are explicitly mapped to genomic locations, it furthermore facilitates the integration of transcriptomics data and other sources of genome-level information.
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http://dx.doi.org/10.1186/s12859-021-04159-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8157683PMC
May 2021

Explorative Meta-Analysis of 417 Extant Archaeal Genomes to Predict Their Contribution to the Total Microbiome Functionality.

Microorganisms 2021 Feb 13;9(2). Epub 2021 Feb 13.

Molecular Systems Biology, Helmholtz-Center for Environmental Research, UFZ, 04318 Leipzig, Germany.

Revealing the relationship between taxonomy and function in microbiomes is critical to discover their contribution to ecosystem functioning. However, while the relationship between taxonomic and functional diversity in bacteria and fungi is known, this is not the case for archaea. Here, we used a meta-analysis of 417 completely annotated extant and taxonomically unique archaeal genomes to predict the extent of microbiome functionality on Earth contained within archaeal genomes using accumulation curves of all known level 3 functions of KEGG Orthology. We found that intergenome redundancy as functions present in multiple genomes was inversely related to intragenome redundancy as multiple copies of a gene in one genome, implying the tradeoff between additional copies of functionally important genes or a higher number of different genes. A logarithmic model described the relationship between functional diversity and species richness better than both the unsaturated and the saturated model, which suggests a limited total number of archaeal functions in contrast to the sheer unlimited potential of bacteria and fungi. Using the global archaeal species richness estimate of 13,159, the logarithmic model predicted 4164.1 ± 2.9 KEGG level 3 functions. The non-parametric bootstrap estimate yielded a lower bound of 2994 ± 57 KEGG level 3 functions. Our approach not only highlighted similarities in functional redundancy but also the difference in functional potential of archaea compared to other domains of life.
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http://dx.doi.org/10.3390/microorganisms9020381DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7918521PMC
February 2021

Discovery of novel community-relevant small proteins in a simplified human intestinal microbiome.

Microbiome 2021 02 23;9(1):55. Epub 2021 Feb 23.

Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research - UFZ GmbH, Leipzig, Germany.

Background: The intestinal microbiota plays a crucial role in protecting the host from pathogenic microbes, modulating immunity and regulating metabolic processes. We studied the simplified human intestinal microbiota (SIHUMIx) consisting of eight bacterial species with a particular focus on the discovery of novel small proteins with less than 100 amino acids (= sProteins), some of which may contribute to shape the simplified human intestinal microbiota. Although sProteins carry out a wide range of important functions, they are still often missed in genome annotations, and little is known about their structure and function in individual microbes and especially in microbial communities.

Results: We created a multi-species integrated proteogenomics search database (iPtgxDB) to enable a comprehensive identification of novel sProteins. Six of the eight SIHUMIx species, for which no complete genomes were available, were sequenced and de novo assembled. Several proteomics approaches including two earlier optimized sProtein enrichment strategies were applied to specifically increase the chances for novel sProtein discovery. The search of tandem mass spectrometry (MS/MS) data against the multi-species iPtgxDB enabled the identification of 31 novel sProteins, of which the expression of 30 was supported by metatranscriptomics data. Using synthetic peptides, we were able to validate the expression of 25 novel sProteins. The comparison of sProtein expression in each single strain versus a multi-species community cultivation showed that six of these sProteins were only identified in the SIHUMIx community indicating a potentially important role of sProteins in the organization of microbial communities. Two of these novel sProteins have a potential antimicrobial function. Metabolic modelling revealed that a third sProtein is located in a genomic region encoding several enzymes relevant for the community metabolism within SIHUMIx.

Conclusions: We outline an integrated experimental and bioinformatics workflow for the discovery of novel sProteins in a simplified intestinal model system that can be generically applied to other microbial communities. The further analysis of novel sProteins uniquely expressed in the SIHUMIx multi-species community is expected to enable new insights into the role of sProteins on the functionality of bacterial communities such as those of the human intestinal tract. Video abstract.
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http://dx.doi.org/10.1186/s40168-020-00981-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7903761PMC
February 2021

The structure and function of soil archaea across biomes.

J Proteomics 2021 04 11;237:104147. Epub 2021 Feb 11.

CEBAS-CSIC, Campus Universitario de Espinardo, Murcia E-30100, Spain.

We lack a predictive understanding of the environmental drivers determining the structure and function of archaeal communities as well as the proteome associated with these important soil organisms. Here, we characterized the structure (by 16S rRNA gene sequencing) and function (by metaproteomics) of archaea from 32 soil samples across terrestrial ecosystems with contrasting climate and vegetation types. Our multi-"omics" approach unveiled that genes from Nitrosophaerales and Thermoplasmata dominated soils collected from four continents, and that archaea comprise 2.3 ± 0.3% of microbial proteins in these soils. Aridity positively correlated with the proportion of Nitrosophaerales genes and the number of archaeal proteins. The interaction of climate x vegetation shaped the functional profile of the archaeal community. Our study provides novel insights into the structure and function of soil archaea across climates, and highlights that these communities may be influenced by increasing global aridity.
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http://dx.doi.org/10.1016/j.jprot.2021.104147DOI Listing
April 2021

Interspecies metabolite transfer and aggregate formation in a co-culture of Dehalococcoides and Sulfurospirillum dehalogenating tetrachloroethene to ethene.

ISME J 2021 06 21;15(6):1794-1809. Epub 2021 Jan 21.

Department of Applied and Ecological Microbiology, Institute of Microbiology, Friedrich Schiller University, Jena, Germany.

Microbial communities involving dehalogenating bacteria assist in bioremediation of areas contaminated with halocarbons. To understand molecular interactions between dehalogenating bacteria, we co-cultured Sulfurospirillum multivorans, dechlorinating tetrachloroethene (PCE) to cis-1,2-dichloroethene (cDCE), and Dehalococcoides mccartyi strains BTF08 or 195, dehalogenating PCE to ethene. The co-cultures were cultivated with lactate as electron donor. In co-cultures, the bacterial cells formed aggregates and D. mccartyi established an unusual, barrel-like morphology. An extracellular matrix surrounding bacterial cells in the aggregates enhanced cell-to-cell contact. PCE was dehalogenated to ethene at least three times faster in the co-culture. The dehalogenation was carried out via PceA of S. multivorans, and PteA (a recently described PCE dehalogenase) and VcrA of D. mccartyi BTF08, as supported by protein abundance. The co-culture was not dependent on exogenous hydrogen and acetate, suggesting a syntrophic relationship in which the obligate hydrogen consumer D. mccartyi consumes hydrogen and acetate produced by S. multivorans. The cobamide cofactor of the reductive dehalogenase-mandatory for D. mccartyi-was also produced by S. multivorans. D. mccartyi strain 195 dechlorinated cDCE in the presence of norpseudo-B produced by S. multivorans, but D. mccartyi strain BTF08 depended on an exogenous lower cobamide ligand. This observation is important for bioremediation, since cofactor supply in the environment might be a limiting factor for PCE dehalogenation to ethene, described for D. mccartyi exclusively. The findings from this co-culture give new insights into aggregate formation and the physiology of D. mccartyi within a bacterial community.
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http://dx.doi.org/10.1038/s41396-020-00887-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8163811PMC
June 2021

Comparative Proteomics of sp. TT1 Reveals Corexit Impacts on Hydrocarbon Metabolism, Chemotactic Motility, and Biofilm Formation.

Microorganisms 2020 Dec 22;9(1). Epub 2020 Dec 22.

Microbial Ecology, Center for Applied Geosciences, University of Tübingen, 72076 Tübingen, Germany.

The application of chemical dispersants during marine oil spills can affect the community composition and activity of marine microorganisms. Several studies have indicated that certain marine hydrocarbon-degrading bacteria, such as spp., can be inhibited by chemical dispersants, resulting in lower abundances and/or reduced biodegradation rates. However, a major knowledge gap exists regarding the mechanisms underlying these physiological effects. Here, we performed comparative proteomics of the Deepwater Horizon isolate sp. TT1 grown under different conditions. Strain TT1 received different carbon sources (pyruvate vs. -hexadecane) with and without added dispersant (Corexit EC9500A). Additional treatments contained crude oil in the form of a water-accommodated fraction (WAF) or chemically-enhanced WAF (CEWAF; with Corexit). For the first time, we identified the proteins associated with alkane metabolism and alginate biosynthesis in strain TT1, report on its potential for aromatic hydrocarbon biodegradation and present a protein-based proposed metabolism of Corexit components as carbon substrates. Our findings revealed that Corexit exposure affects hydrocarbon metabolism, chemotactic motility, biofilm formation, and induces solvent tolerance mechanisms, like efflux pumps, in strain TT1. This study provides novel insights into dispersant impacts on microbial hydrocarbon degraders that should be taken into consideration for future oil spill response actions.
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http://dx.doi.org/10.3390/microorganisms9010003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7822026PMC
December 2020

HumanMetagenomeDB: a public repository of curated and standardized metadata for human metagenomes.

Nucleic Acids Res 2021 01;49(D1):D743-D750

Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ GmbH, Leipzig, Saxony 04318, Germany.

Metagenomics became a standard strategy to comprehend the functional potential of microbial communities, including the human microbiome. Currently, the number of metagenomes in public repositories is increasing exponentially. The Sequence Read Archive (SRA) and the MG-RAST are the two main repositories for metagenomic data. These databases allow scientists to reanalyze samples and explore new hypotheses. However, mining samples from them can be a limiting factor, since the metadata available in these repositories is often misannotated, misleading, and decentralized, creating an overly complex environment for sample reanalysis. The main goal of the HumanMetagenomeDB is to simplify the identification and use of public human metagenomes of interest. HumanMetagenomeDB version 1.0 contains metadata of 69 822 metagenomes. We standardized 203 attributes, based on standardized ontologies, describing host characteristics (e.g. sex, age and body mass index), diagnosis information (e.g. cancer, Crohn's disease and Parkinson), location (e.g. country, longitude and latitude), sampling site (e.g. gut, lung and skin) and sequencing attributes (e.g. sequencing platform, average length and sequence quality). Further, HumanMetagenomeDB version 1.0 metagenomes encompass 58 countries, 9 main sample sites (i.e. body parts), 58 diagnoses and multiple ages, ranging from just born to 91 years old. The HumanMetagenomeDB is publicly available at https://webapp.ufz.de/hmgdb/.
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http://dx.doi.org/10.1093/nar/gkaa1031DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7778935PMC
January 2021

Synergistic biodegradation of aromatic-aliphatic copolyester plastic by a marine microbial consortium.

Nat Commun 2020 11 13;11(1):5790. Epub 2020 Nov 13.

Junior Research Group Microbial Biotechnology, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124, Braunschweig, Germany.

The degradation of synthetic polymers by marine microorganisms is not as well understood as the degradation of plastics in soil and compost. Here, we use metagenomics, metatranscriptomics and metaproteomics to study the biodegradation of an aromatic-aliphatic copolyester blend by a marine microbial enrichment culture. The culture can use the plastic film as the sole carbon source, reaching maximum conversion to CO and biomass in around 15 days. The consortium degrades the polymer synergistically, with different degradation steps being performed by different community members. We identify six putative PETase-like enzymes and four putative MHETase-like enzymes, with the potential to degrade aliphatic-aromatic polymers and their degradation products, respectively. Our results show that, although there are multiple genes and organisms with the potential to perform each degradation step, only a few are active during biodegradation.
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http://dx.doi.org/10.1038/s41467-020-19583-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7666164PMC
November 2020

Seasonal Patterns of Dominant Microbes Involved in Central Nutrient Cycles in the Subsurface.

Microorganisms 2020 Oct 30;8(11). Epub 2020 Oct 30.

Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research GmbH-UFZ, 04318 Leipzig, Germany.

Microbial communities play a key role for central biogeochemical cycles in the subsurface. Little is known about whether short-term seasonal drought and rewetting events influence the dominant microbes involved in C- and N-cycles. Here, we applied metaproteomics at different subsurface sites in winter, summer and autumn from surface litter layer, seepage water at increasing subsoil depths and remote located groundwater from two wells within the Hainich Critical Zone Exploratory, Germany. We observed changes in the dominance of microbial families at subsurface sampling sites with increasing distances, i.e., dominated in topsoil seepage, while dominated at deeper and more distant groundwater wells. Nitrifying bacteria showed a shift in dominance from drought to rewetting events from summer by to autumn by . We further observed that the reductive pentose phosphate pathway was a prominent CO-fixation strategy, dominated by in wet early winter, which decreased under drought conditions and changed to a dominance of under rewetting conditions. This study shows that increasing subsurface sites and rewetting event after drought alter the dominances of key subsurface microbes. This helps to predict the consequences of annual seasonal dynamics on the nutrient cycling microbes that contribute to ecosystem functioning.
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http://dx.doi.org/10.3390/microorganisms8111694DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7716230PMC
October 2020

Rational design of a microbial consortium of mucosal sugar utilizers reduces Clostridiodes difficile colonization.

Nat Commun 2020 10 9;11(1):5104. Epub 2020 Oct 9.

University of Vienna, Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, Althanstrasse 14, 1090, Vienna, Austria.

Many intestinal pathogens, including Clostridioides difficile, use mucus-derived sugars as crucial nutrients in the gut. Commensals that compete with pathogens for such nutrients are therefore ecological gatekeepers in healthy guts, and are attractive candidates for therapeutic interventions. Nevertheless, there is a poor understanding of which commensals use mucin-derived sugars in situ as well as their potential to impede pathogen colonization. Here, we identify mouse gut commensals that utilize mucus-derived monosaccharides within complex communities using single-cell stable isotope probing, Raman-activated cell sorting and mini-metagenomics. Sequencing of cell-sorted fractions reveals members of the underexplored family Muribaculaceae as major mucin monosaccharide foragers, followed by members of Lachnospiraceae, Rikenellaceae, and Bacteroidaceae families. Using this information, we assembled a five-member consortium of sialic acid and N-acetylglucosamine utilizers that impedes C. difficile's access to these mucosal sugars and impairs pathogen colonization in antibiotic-treated mice. Our findings underscore the value of targeted approaches to identify organisms utilizing key nutrients and to rationally design effective probiotic mixtures.
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http://dx.doi.org/10.1038/s41467-020-18928-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7547075PMC
October 2020

Environmentally Relevant Concentration of Bisphenol S Shows Slight Effects on SIHUMIx.

Microorganisms 2020 Sep 19;8(9). Epub 2020 Sep 19.

Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research GmbH - UFZ, 04318 Leipzig, Germany.

Bisphenol S (BPS) is an industrial chemical used in the process of polymerization of polycarbonate plastics and epoxy resins and thus can be found in various plastic products and thermal papers. The microbiota disrupting effect of BPS on the community structure of the microbiome has already been reported, but little is known on how BPS affects bacterial activity and function. To analyze these effects, we cultivated the simplified human intestinal microbiota (SIHUMIx) in bioreactors at a concentration of 45 µM BPS. By determining biomass, growth of SIHUMIx was followed but no differences during BPS exposure were observed. To validate if the membrane composition was affected, fatty acid methyl esters (FAMEs) profiles were compared. Changes in the individual membrane fatty acid composition could not been described; however, the saturation level of the membranes slightly increased during BPS exposure. By applying targeted metabolomics to quantify short-chain fatty acids (SCFA), it was shown that the activity of SIHUMIx was unaffected. Metaproteomics revealed temporal effect on the community structure and function, showing that BPS has minor effects on the structure or functionality of SIHUMIx.
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http://dx.doi.org/10.3390/microorganisms8091436DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7564734PMC
September 2020

Protein stable isotope probing with H O differentiated cold stress response at permissive temperatures from general growth at optimal conditions in Escherichia coli K12.

Rapid Commun Mass Spectrom 2021 Jan;35(1):e8941

Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research - UFZ, Leipzig, Germany.

Rationale: Tracing isotopically labeled water into proteins allows for the detection of species-specific metabolic activity in complex communities. However, a stress response may alter the newly synthesized proteins.

Methods: We traced 18-oxygen from heavy water into proteins of Escherichia coli K12 grown from permissive to retardant temperatures. All samples were analyzed using UPLC/Orbitrap Q-Exactive-MS/MS operating in positive electrospray ionization mode.

Results: We found that warmer temperatures resulted in significantly (P-value < 0.05) higher incorporation of 18-oxygen as seen by both substrate utilization as relative isotope abundance (RIA) and growth as labeling ratio (LR). However, the absolute number of peptides with incorporation of 18-oxygen showed no significant correlation to temperature, potentially caused by the synthesis of different proteins at low temperatures, namely, proteins related to cold stress response.

Conclusions: Our results unveil the species-specific cold stress response of E. coli K12 that could be misinterpreted as general growth; this is why the quantity as RIA and LR but also the quality as absolute number of peptides with incorporation (relative abundance, RA) and their function must be considered to fully understand the activity of microbial communities.
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http://dx.doi.org/10.1002/rcm.8941DOI Listing
January 2021

Channeling C1 Metabolism toward -Adenosylmethionine-Dependent Conversion of Estrogens to Androgens in Estrogen-Degrading Bacteria.

mBio 2020 08 25;11(4). Epub 2020 Aug 25.

Faculty of Biology-Microbiology, Albert-Ludwigs-Universität Freiburg, Freiburg im Breisgau, Germany

Bacterial degradation of endocrine disrupting and carcinogenic estrogens is essential for their elimination from the environment. Recent studies of the denitrifying, estrogen-degrading strain DHT3 revealed the conversion of estrogens to androgens by a putative cobalamin-dependent methyltransferase encoded by the genes. The methyl donor and its continuous regeneration to initiate estradiol catabolism have remained unknown. Here, large-scale cultivation of the denitrifying bacterium with estrogen provided the biomass required for quantitative biochemical analyses. Soluble fractions of extracts from estradiol-grown cells catalyzed the -adenosyl-l-methionine (SAM)- and Ti(III)-citrate-dependent conversion of 17β-estradiol/estrone to the respective androgens at 0.15 nmol minmg Kinetic studies of 17β-estradiol methylation and reverse 1-dehydrotestosterone demethylation reactions indicated that the exergonic methyl transfer from SAM to the putative cobalamin drives the endergonic methyl transfer from the methylcobalamin intermediate to the phenolic ring A. Based on a high-quality circular genome from , proteogenomic analyses identified a 17β-estradiol-induced gene cluster comprising genes together with genes involved in SAM regeneration via l-serine and l-methionine. Consistent with this finding, l-methionine/ATP or l-serine/ATP/tetrahydrofolate/l-homocysteine substituted for SAM as methyl donors, further confirmed by the incorporation of the C-methyl-group from C-l-methonine into methyl(III)cobalamine and the estrone methylation product androsta-1,4-diene-3-one. This work demonstrates that during bacterial estrogen catabolism, the C1 pool is channeled toward the initiating methyl transfer to ring A. The effective cellular SAM regeneration system may serve as a model for whole-cell SAM-dependent methylation reactions of biotechnological interest. Estrogens comprise a group of related hormones occurring in predominantly female vertebrates, with endocrine disrupting and carcinogenic potential. Microbial biodegradation of estrogens is essential for their elimination from surface waters and wastewater. Aerobic bacteria employ oxygenases for the initial cleavage of the aromatic ring A. In contrast, anaerobic degradation of estrogens is initiated by methyl transfer-dependent conversion into androgens involving a putative cobalamin-dependent methyltransferase system. The methyl donor for this unprecedented reaction and its stoichiometric regeneration have remained unknown. With the biomass obtained from large-scale fermentation of an estrogen-degrading denitrifying bacterium, we identified -adenosyl-methionine (SAM) as the methyl donor for the cobalamin-mediated methyl transfer to estrogens. To continuously supply C1 units to initiate estrogen degradation, genes for SAM regeneration from estradiol-derived catabolites are highly upregulated. Data presented here shed light into biochemical processes involved in the globally important microbial degradation of estrogens.
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http://dx.doi.org/10.1128/mBio.01259-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7448270PMC
August 2020

The glyphosate formulation Roundup® LB plus influences the global metabolome of pig gut microbiota in vitro.

Sci Total Environ 2020 Nov 17;745:140932. Epub 2020 Jul 17.

Helmholtz-Centre for Environmental Research - UFZ, Department of Molecular Systems Biology, Leipzig, Germany; Institute of Biochemistry, Faculty of Biosciences, Pharmacy and Psychology, University of Leipzig, Germany. Electronic address:

Glyphosate is the world's most widely used herbicide, and its potential side effects on the intestinal microbiota of various animals, from honeybees to livestock and humans, are currently under discussion. Pigs are among the most abundant livestock animals worldwide and an impact of glyphosate on their intestinal microbiota function can have serious consequences on their health, not to mention the economic effects. Recent studies that addressed microbiota-disrupting effects focused on microbial taxonomy but lacked functional information. Therefore, we chose an experimental design with a short incubation time in which effects on the community structure are not expected, but functional effects can be detected. We cultivated intestinal microbiota derived from pig colon in chemostats and investigated the acute effect of 228 mg/d glyphosate acid equivalents from Roundup® LB plus, a frequently applied glyphosate formulation. The applied glyphosate concentration resembles a worst-case scenario for an 8-9 week-old pig and relates to the maximum residue levels of glyphosate on animal fodder. The effects were determined on the functional level by metaproteomics, targeted and untargeted meta-metabolomics, while variations in community structure were analyzed by 16S rRNA gene profiling and on the single cell level by microbiota flow cytometry. Roundup® LB plus did not affect the community taxonomy or the enzymatic repertoire of the cultivated microbiota in general or on the expression of the glyphosate target enzyme 5-enolpyruvylshikimate-3-phosphate synthase in detail. On the functional level, targeted metabolite analysis of short chain fatty acids (SCFAs), free amino acids and bile acids did not reveal significant changes, whereas untargeted meta-metabolomics did identify some effects on the functional level. This multi-omics approach provides evidence for subtle metabolic effects of Roundup® LB plus under the conditions applied.
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http://dx.doi.org/10.1016/j.scitotenv.2020.140932DOI Listing
November 2020

Soil protein as a potential antimicrobial agent against methicillin -resistant Staphylococcus aureus.

Environ Res 2020 09 28;188:109320. Epub 2020 Feb 28.

Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, CZ-613 00, Brno, Czech Republic; Central European Institute of Technology, Brno University of Technology, Purkynova 123, CZ-612 00, Brno, Czech Republic. Electronic address:

Recently, the interest is increasing to find alternatives to replace the usage of antibiotics since their massive and improper usage enhance the antibiotic resistance in human pathogens. In this study, for the first time we showed that the soil proteins have very high antibacterial activity (98% of growth inhibition) against methicillin resistant Staphylococcus aureus (MRSA), one of the most threatening human pathogens. We found that the protein extract (C3) from the forest with past intensive management showed higher antibacterial activity than that of unmanaged forest. The MIC and IC were found to be 30 and 15.0 μg protein g dry soil respectively. C3 was found to kill the bacteria by cell wall disruption and genotoxicity which was confirmed by optical and fluorescent microscopy and comet assay. According to qPCR study, the mecA (the antibiotic resistant gene) expression in MRSA was found to be down-regulated after C3 treatment. In contrast, C3 showed no hemolytic toxicity on human red blood cells which was confirmed by hemolytic assay. According to ultra-high performance liquid chromatography-mass spectrometry (UHPLC-MS), 144 proteins were identified in C3 among which the majority belonged to Gram negative bacteria (45.8%). Altogether, our results will help to develop novel, cost-effective, non-toxic and highly efficient antibacterial medicines from natural sources against antibiotic resistant infections.
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http://dx.doi.org/10.1016/j.envres.2020.109320DOI Listing
September 2020

Corrigendum to Tracing incorporation of heavy water into proteins for species-specific metabolic activity in complex communities.

J Proteomics 2020 Jul 25;224:103829. Epub 2020 May 25.

Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research - UFZ, Leipzig, Germany; Institute of Biochemistry, Faculty of Biosciences, Pharmacy and Psychology, University of Leipzig, Leipzig, Germany. Electronic address:

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http://dx.doi.org/10.1016/j.jprot.2020.103829DOI Listing
July 2020

Mechanistic insight to mycoremediation potential of a metal resistant fungal strain for removal of hazardous metals from multimetal pesticide matrix.

Environ Pollut 2020 Jul 6;262:114255. Epub 2020 Mar 6.

Helmholtz-Centre for Environmental Research-UFZ, Department of Molecular Systems Biology, 04318, Permoserstr. 15, Leipzig, Germany.

Fungi have an exceptional capability to flourish in presence of heavy metals and pesticide. However, the mechanism of bioremediation of pesticide (lindane) and multimetal [mixture of cadmium (Cd), chromium (Cr), copper (Cu), nickel (Ni), lead (Pb), zinc (Zn)] by a fungus is little understood. In the present study, Aspergillus fumigatus, a filamentous fungus was found to accumulate heavy metals in the order [Zn(98%)>Pb(95%)>Cd(63%)>Cr(62%)>Ni(46%)>Cu(37%)] from a cocktail of 30 mg L multimetal and lindane (30 mg L) in a composite media amended with 1% glucose. Particularly, Pb and Zn uptake was enhanced in presence of lindane. Remarkably, lindane was degraded to 1.92 ± 0.01 mg L in 72 h which is below the permissible limit value (2.0 mg L) for the discharge of lindane into the aquatic bodies as prescribed by European Community legislation. The utilization of lindane as a cometabolite from the complex environment was evident by the phenomenal growth of the fungal pellet biomass (5.89 ± 0.03 g L) at 72 h with cube root growth constant of fungus (0.0211 g L h) compared to the biomasses obtained in case of the biotic control as well as in presence of multimetal complex without lindane. The different analytical techniques revealed the various stress coping strategies adopted by A. fumigatus for multimetal uptake in the simultaneous presence of multimetal and pesticide. From the Transmission electron microscope coupled energy dispersive X-ray analysis (TEM-EDAX) results, uptake of the metals Cd, Cu and Pb in the cytoplasmic membrane and the accumulation of the metals Cr, Ni and Zn in the cytoplasm of the fungus were deduced. Fourier-transform infrared spectroscopy (FTIR) revealed involvement of carboxyl/amide group of fungal cell wall in metal chelation. Thus A. fumigatus exhibited biosorption and bioaccumulation as the mechanisms involved in detoxification of multimetals.
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http://dx.doi.org/10.1016/j.envpol.2020.114255DOI Listing
July 2020

Benzylsuccinate Synthase is Post-Transcriptionally Regulated in the Toluene-Degrading Denitrifier sp. Strain 15-1.

Microorganisms 2020 May 7;8(5). Epub 2020 May 7.

Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research - UFZ, Permoserstr. 15, 04318 Leipzig, Germany.

The facultative denitrifying alphaproteobacterium sp strain 15-1 had been isolated from the hypoxic rhizosphere of a constructed wetland model fed with toluene. This bacterium can catabolize toluene anaerobically but not aerobically. Here, we used strain 15-1 to investigate regulation of expression of the highly oxygen-sensitive glycyl radical enzyme benzylsuccinate synthase, which catalyzes the first step in anaerobic toluene degradation. In cells growing aerobically with benzoate, the addition of toluene resulted in a ~20-fold increased transcription of , encoding for the catalytically active subunit of the enzyme. Under anoxic conditions, mRNA copy numbers were up to 129-fold higher in cells growing with toluene as compared to cells growing with benzoate. Proteomics showed that abundance of benzylsuccinate synthase increased in cells growing anaerobically with toluene. In contrast, peptides of this enzyme were never detected in oxic conditions. These findings show that synthesis of benzylsuccinate synthase was under stringent post-transcriptional control in the presence of oxygen, which is a novel level of regulation for glycyl radical enzymes.
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http://dx.doi.org/10.3390/microorganisms8050681DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7285207PMC
May 2020

The Activation of Mucosal-Associated Invariant T (MAIT) Cells Is Affected by Microbial Diversity and Riboflavin Utilization .

Front Microbiol 2020 22;11:755. Epub 2020 Apr 22.

Department of Environmental Immunology, Helmholtz-Centre for Environmental Research - UFZ Leipzig, Germany.

Recent research has demonstrated that MAIT cells are activated by individual bacterial or yeasts species that possess the riboflavin biosynthesis pathway. However, little is known about the MAIT cell activating potential of microbial communities and the contribution of individual community members. Here, we analyze the MAIT cell activating potential of a human intestinal model community (SIHUMIx) as well as intestinal microbiota after bioreactor cultivation. We determined the contribution of individual SIHUMIx community members to the MAIT cell activating potential and investigated whether microbial stress can influence their MAIT cell activating potential. The MAIT cell activating potential of SIHUMIx was directly related to the relative species abundances in the community. We therefore suggest an additive relationship between the species abundances and their MAIT cell activating potential. In diverse microbial communities, we found that a low MAIT cell activating potential was associated with high microbial diversity and a high level of riboflavin demand and vice versa. We suggest that microbial diversity might affect MAIT cell activation via riboflavin utilization within the community. Microbial acid stress significantly reduced the MAIT cell activating potential of SIHUMIx by impairing riboflavin availability through increasing the riboflavin demand. We show that MAIT cells can perceive microbial stress due to changes in riboflavin utilization and that riboflavin availability might also play a central role for the MAIT cell activating potential of diverse microbiota.
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http://dx.doi.org/10.3389/fmicb.2020.00755DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7189812PMC
April 2020

Actinobacterial Degradation of 2-Hydroxyisobutyric Acid Proceeds via Acetone and Formyl-CoA by Employing a Thiamine-Dependent Lyase Reaction.

Front Microbiol 2020 15;11:691. Epub 2020 Apr 15.

Institute of Water Research, University of Granada, Granada, Spain.

The tertiary branched short-chain 2-hydroxyisobutyric acid (2-HIBA) has been associated with several metabolic diseases and lysine 2-hydroxyisobutyrylation seems to be a common eukaryotic as well as prokaryotic post-translational modification in proteins. In contrast, the underlying 2-HIBA metabolism has thus far only been detected in a few microorganisms, such as the betaproteobacterium L108 and the group bacterium DSM 2912. In these strains, 2-HIBA can be specifically activated to the corresponding CoA thioester by the 2-HIBA-CoA ligase (HCL) and is then isomerized to 3-hydroxybutyryl-CoA in a reversible and B-dependent mutase reaction. Here, we demonstrate that the actinobacterial strain DSM 45062 degrades 2-HIBA and also its precursor 2-methylpropane-1,2-diol via acetone and formic acid by employing a thiamine pyrophosphate-dependent lyase. The corresponding gene is located directly upstream of , which has previously been found only in operonic association with the 2-hydroxyisobutyryl-CoA mutase genes in other bacteria. Heterologous expression of the lyase gene from DSM 45062 in established a 2-hydroxyisobutyryl-CoA lyase activity in the latter. In line with this, analysis of the DSM 45062 proteome reveals a strong induction of the lyase-HCL gene cluster on 2-HIBA. Acetone is likely degraded via hydroxylation to acetol catalyzed by a MimABCD-related binuclear iron monooxygenase and formic acid appears to be oxidized to CO by selenium-dependent dehydrogenases. The presence of the lyase-HCL gene cluster in isoprene-degrading strains and associated with tropical leafcutter ant species points to a role in degradation of biogenic short-chain ketones and highly branched organic compounds.
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http://dx.doi.org/10.3389/fmicb.2020.00691DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7176365PMC
April 2020

Tracing incorporation of heavy water into proteins for species-specific metabolic activity in complex communities.

J Proteomics 2020 06 23;222:103791. Epub 2020 Apr 23.

Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research - UFZ, Leipzig, Germany; Institute of Biochemistry, Faculty of Biosciences, Pharmacy and Psychology, University of Leipzig, Leipzig, Germany. Electronic address:

Stable isotope probing (SIP) approaches are a suitable tool to identify active organisms in bacterial communities, but adding isotopically labeled substrate can alter both the structure and the functionality of the community. Here, we validated and demonstrated a substrate-independent protein-SIP protocol using isotopically labeled water that captures the entire microbial activity of a community. We found that O yielded a higher incorporation rate into peptides and thus comprised a higher sensitivity. We then applied the method to an in vitro model of a human distal gut microbial ecosystem grown in two medium formulations, to evaluate changes in microbial activity between a high-fiber and high-protein diet. We showed that only little changes are seen in the community structure but the functionality varied between the diets. In conclusion, our approach can detect species-specific metabolic activity in complex bacterial communities and more specifically to quantify the amount of amino acid synthesis. Heavy water makes possible to analyze the activity of bacterial communities for which adding an isotopically labeled energy and nutrient sources is not easily feasible. SIGNIFICANCE: Heavy stable isotopes allow for the detection of active key players in complex ecosystems where many organisms are thought to be dormant. Opposed to the labelling with energy or nutrient sources, heavy water could be a suitable replacement to trace activity, which has been shown for DNA and RNA. Here we validate, quantify and compare the incorporation of heavy water either labeled with deuterium or 18‑oxygen into proteins of Escherichia coli K12 and of an in vitro model of a human gut microbial ecosystem. The significance of our research is in providing a freely available pipeline to analyze the incorporation of deuterium and 18‑oxygen into proteins together with the validation of the applicability of tracing heavy water as a proxy for activity. Our approach unveils the relative functional contribution of microbiota in complex ecosystems, which will improve our understanding of both animal- and environment-associated microbiomes and in vitro models.
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http://dx.doi.org/10.1016/j.jprot.2020.103791DOI Listing
June 2020

Function is what counts: how microbial community complexity affects species, proteome and pathway coverage in metaproteomics.

Expert Rev Proteomics 2020 02 15;17(2):163-173. Epub 2020 Mar 15.

Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research - UFZ, Leipzig, Germany.

: Metaproteomics is an established method to obtain a comprehensive taxonomic and functional view of microbial communities. After more than a decade, we are now able to describe the promise, reality, and perspectives of metaproteomics and provide useful information about the choice of method, applications, and potential improvement strategies.: In this article, we will discuss current challenges of species and proteome coverage, and also highlight functional aspects of metaproteomics analysis of microbial communities with different levels of complexity. To do this, we re-analyzed data from microbial communities with low to high complexity (8, 72, 200 and >300 species). High species diversity leads to a reduced number of protein group identifications in a complex community, and thus the number of species resolved is underestimated. Ultimately, low abundance species remain undiscovered in complex communities. However, we observed that the main functional categories were better represented within complex microbiomes when compared to species coverage.: Our findings showed that even with low species coverage, metaproteomics has the potential to reveal habitat-specific functional features. Finally, we exploit this information to highlight future research avenues that are urgently needed to enhance our understanding of taxonomic composition and functions of complex microbiomes.
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http://dx.doi.org/10.1080/14789450.2020.1738931DOI Listing
February 2020

Microbial metaproteome data from decayed beech dead wood.

Data Brief 2020 Apr 14;29:105285. Epub 2020 Feb 14.

Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research GmbH - UFZ, Permoserstraße 15, 04318, Leipzig, Germany.

Wood-decomposition in terrestrial ecosystems is a very important process with huge ecologic consequences. This decomposition process is a combination of biological respiration, leaching and fragmentation, mainly triggered by organismic activities. In order to gain a deeper insight into these microbial communities and their role in deadwood decay, we used metaproteomics. Metaproteomics is an important tool and offers the ability to characterize the protein complement of environmental microbiota at a given point in time. In this dataset, we provide data of an exemplary beech wood log and applied different extraction methods to provide the proteome profile of beech dead wood and their corresponding fungal-bacterial community.
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http://dx.doi.org/10.1016/j.dib.2020.105285DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7038588PMC
April 2020

Explorative Meta-Analysis of 377 Extant Fungal Genomes Predicted a Total Mycobiome Functionality of 42.4 Million KEGG Functions.

Front Microbiol 2020 6;11:143. Epub 2020 Feb 6.

Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czechia.

Unveiling the relationship between taxonomy and function of the microbiome is crucial to determine its contribution to ecosystem functioning. However, while there is a considerable amount of information on microbial taxonomic diversity, our understanding of its relationship to functional diversity is still scarce. Here, we used a meta-analysis of completely annotated extant genomes of 377 taxonomically distinct fungal species to predict the total fungal microbiome functionality on Earth with accumulation curves (ACs) of all known functions from the level 3 of KEGG Orthology using both parametric and non-parametric estimates in an explorative data-mining approach. The unsaturated model extrapolating functional diversity as a function of species richness described the ACs significantly better than the saturated model that assumed a limited total number of functions, which suggested the presence of widespread and rare functions. Based on previous estimates of 3.8 million fungal species on Earth, we propagated the unsaturated model to predict a total of 42.4 ± 0.5 million KEGG level 3 functions of which only 0.06% are known today. Our approach not only highlights the presence of widespread and rare functions but points toward the necessity of novel and more sophisticated methods to unveil the entirety of functions to fully understand the involvement of the fungal microbiome in ecosystem functioning.
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http://dx.doi.org/10.3389/fmicb.2020.00143DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7015973PMC
February 2020

Metabolomics reveals impact of seven functional foods on metabolic pathways in a gut microbiota model.

J Adv Res 2020 May 3;23:47-59. Epub 2020 Jan 3.

Helmholtz-Centre for Environmental Research - UFZ GmbH, Department of Molecular Systems Biology, Leipzig, Germany.

Functional food defined as dietary supplements that in addition to their nutritional values, can beneficially modulate body functions becomes more and more popular but the reaction of the intestinal microbiota to it is largely unknown. In order to analyse the impact of functional food on the microbiota itself it is necessary to focus on the physiology of the microbiota, which can be assessed in a whole by untargeted metabolomics. Obtaining a detailed description of the gut microbiota reaction to food ingredients can be a key to understand how these organisms regulate and bioprocess many of these food components. Extracts prepared from seven chief functional foods, namely green tea, black tea, (prickly pear, cactus pear), black coffee, green coffee, pomegranate, and sumac were administered to a gut consortium culture encompassing 8 microbes which are resembling, to a large extent, the metabolic activities found in the human gut. Samples were harvested at 0.5 and 24 h post addition of functional food extract and from blank culture in parallel and analysed for its metabolites composition using gas chromatography coupled to mass spectrometry detection (GC-MS). A total of 131 metabolites were identified belonging to organic acids, alcohols, amino acids, fatty acids, inorganic compounds, nitrogenous compounds, nucleic acids, phenolics, steroids and sugars, with amino acids as the most abundant class in cultures. Considering the complexity of such datasets, multivariate data analyses were employed to classify samples and investigate how functional foods influence gut microbiota metabolisms. Results from this study provided a first insights regarding how functional foods alter gut metabolism through either induction or inhibition of certain metabolic pathways, i.e. GABA production in the presence of higher acidity induced by functional food metabolites such as polyphenols. Likewise, functional food metabolites ., purine alkaloids acted themselves as direct substrate in microbiota metabolism.
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http://dx.doi.org/10.1016/j.jare.2020.01.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7016031PMC
May 2020

Gastric bypass surgery in a rat model alters the community structure and functional composition of the intestinal microbiota independently of weight loss.

Microbiome 2020 02 7;8(1):13. Epub 2020 Feb 7.

Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany.

Background: Roux-en-Y gastric bypass (RYGB) surgery is a last-resort treatment to induce substantial and sustained weight loss in cases of severe obesity. This anatomical rearrangement affects the intestinal microbiota, but so far, little information is available on how it interferes with microbial functionality and microbial-host interactions independently of weight loss.

Methods: A rat model was employed where the RYGB-surgery cohort is compared to sham-operated controls which were kept at a matched body weight by food restriction. We investigated the microbial taxonomy and functional activity using 16S rRNA amplicon gene sequencing, metaproteomics, and metabolomics on samples collected from theileum, the cecum, and the colon, and separately analysed the lumen and mucus-associated microbiota.

Results: Altered gut architecture in RYGB increased the relative occurrence of Actinobacteria, especially Bifidobacteriaceae and Proteobacteria, while in general, Firmicutes were decreased although Streptococcaceae and Clostridium perfringens were observed at relative higher abundances independent of weight loss. A decrease of conjugated and secondary bile acids was observed in the RYGB-gut lumen. The arginine biosynthesis pathway in the microbiota was altered, as indicated by the changes in the abundance of upstream metabolites and enzymes, resulting in lower levels of arginine and higher levels of aspartate in the colon after RYGB.

Conclusion: The anatomical rearrangement in RYGB affects microbiota composition and functionality as well as changes in amino acid and bile acid metabolism independently of weight loss. The shift in the taxonomic structure of the microbiota after RYGB may be mediated by the resulting change in the composition of the bile acid pool in the gut and by changes in the composition of nutrients in the gut. Video abstract.
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http://dx.doi.org/10.1186/s40168-020-0788-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7007695PMC
February 2020

Quantification of glyphosate and aminomethylphosphonic acid from microbiome reactor fluids.

Rapid Commun Mass Spectrom 2020 Apr;34(7):e8668

Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany.

Rationale: Glyphosate is one of the most widely used herbicides and it is suspected to affect the intestinal microbiota through inhibition of aromatic amino acid synthesis via the shikimate pathway. In vitro microbiome bioreactors are increasingly used as model systems to investigate effects on intestinal microbiota and consequently methods for the quantitation of glyphosate and its degradation product aminomethylphosphonic acid (AMPA) in microbiome model systems are required.

Methods: An optimized protocol enables the analysis of both glyphosate and AMPA by simple extraction with methanol:acetonitrile:water (2:3:1) without further enrichment steps. Glyphosate and AMPA are separated by liquid chromatography on an amide column and identified and quantified with a targeted tandem mass spectrometry method using a QTRAP 5500 system (AB Sciex).

Results: Our method has a limit of detection (LOD) in extracted water samples of <2 ng/mL for both glyphosate and AMPA. In complex intestinal medium, the LOD is 2 and 5 ng/mL for glyphosate and AMPA, respectively. These LODs allow for measurement at exposure-relevant concentrations. Glyphosate levels in a bioreactor model of porcine colon were determined and consequently it was verified whether AMPA was produced by porcine gut microbiota.

Conclusions: The method presented here allows quantitation of glyphosate and AMPA in complex bioreactor fluids and thus enables studies of the impact of glyphosate and its metabolism on intestinal microbiota. In addition, the extraction protocol is compatible with an untargeted metabolomics analysis, thus allowing one to look for other perturbations caused by glyphosate in the same sample.
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http://dx.doi.org/10.1002/rcm.8668DOI Listing
April 2020

Following the community development of SIHUMIx - a new intestinal model for bioreactor use.

Gut Microbes 2020 07 10;11(4):1116-1129. Epub 2020 Jan 10.

Department of Environmental Immunology, Helmholtz Centre for Environmental Research - UFZ , Leipzig, German.

Diverse intestinal microbiota is frequently used in bioreactor models to study the effects of diet, chemical contaminations, or medication. However, the reproducible cultivation of fecal microbiota is challenging and the resultant communities behave highly dynamic. To approach the issue of reproducibility in models, we established an intestinal microbiota model community of reduced complexity, SIHUMIx, as a valuable model for use. The development of the SIHUMIx community was monitored over time with methods covering the cellular and the molecular level. We used microbial flow cytometry, intact protein profiling and terminal restriction fragment length polymorphism analysis to assess community structure. In parallel, we analyzed the functional level by targeted analysis of short-chain fatty acids and untargeted metabolomics. The stability properties constancy, resistance, and resilience were approached both on the structural and functional level of the community. We show that the SIHUMIx community is highly reproducible and constant since day 5 of cultivation. Furthermore, SIHUMIx has the ability to resist and recover from a pulsed perturbation, with changes in community structure recovered earlier than functional changes. Since community structure and function changed divergently, both levels need to be monitored at the same time to gain a full overview of the community development. All five methods are highly suitable to follow the community dynamics of SIHUMIx and indicated stability on day five. This makes SIHUMIx a suitable model to investigate the effects of e.g. medical, chemical, or dietary interventions.
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http://dx.doi.org/10.1080/19490976.2019.1702431DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7524388PMC
July 2020

Mucosal-associated invariant T-Cell (MAIT) activation is altered by chlorpyrifos- and glyphosate-treated commensal gut bacteria.

J Immunotoxicol 2020 12;17(1):10-20

Department of Environmental Immunology, Helmholtz Centre for Environmental Research Leipzig - UFZ, Leipzig, Germany.

Mucosal-associated invariant T-cells (MAIT) can react to metabolites of the vitamins riboflavin and folate which are produced by the human gut microbiota. Since several studies showed that the pesticide chlorpyrifos (CPF) and glyphosate (GLP) can impair the gut microbiota, the present study was undertaken to investigate the impact of CPF and GLP treatment on the metabolism of gut microbiota and the resulting bacteria-mediated modulation of MAIT cell activity. Here, (), (), and () were treated with CPF (50-200 µM) or GLP (75-300 mg/L) and then used in MAIT cell stimulation assays as well as in vitamin and proteome analyses. All three bacteria were nonpathogenic and chosen as representatives of a healthy human gut microflora. The results showed that activated MAIT cells whereas and inhibited MAIT cell activation. CPF treatment significantly increased -mediated MAIT cell activation. Treatment of and with CPF and GLP weakened the inhibition of MAIT cell activation. Riboflavin and folate production by the test bacteria was influenced by CPF treatment, whereas GLP had only minor effects. Proteomic analysis of CPF-treated revealed changes in the riboflavin and folate biosynthesis pathways. The findings here suggest that the metabolism of the analyzed bacteria could be altered by exposure to CPF and GLP, leading to an increased pro-inflammatory immune response.
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http://dx.doi.org/10.1080/1547691X.2019.1706672DOI Listing
December 2020
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