Publications by authors named "Martin von Bergen"

281 Publications

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

Microbiome 2021 Feb 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.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1186/s40168-020-00981-zDOI Listing
February 2021

Wood emissions and asthma development: Results from an experimental mouse model and a prospective cohort study.

Environ Int 2021 Feb 18;151:106449. Epub 2021 Feb 18.

UFZ - Helmholtz Centre for Environmental Research Leipzig-Halle, Department of Environmental Immunology, Leipzig, Germany; Department of Dermatology, Venerology and Allergology, Leipzig University Medical Center, University of Leipzig, Leipzig, Germany. Electronic address:

Background: Increased use of renewable resources like sustainably produced wood in construction or for all sorts of long-lived products is considered to contribute to reducing society's carbon footprint. However, as a natural, biological material, wood and wood products emit specific volatile organic compounds (VOCs). Therefore, the evaluation of possible health effects due to wood emissions is of major interest.

Objectives: We investigated the effects of an exposure to multiple wood-related VOCs on asthma development.

Methods: A murine asthma model was used to evaluate possible allergic and inflammatory effects on the lung after short- or long-term and perinatal exposure to pinewood or oriented strand board (OSB). In addition, wood-related VOCs were measured within the German prospective mother-child cohort LINA and their joint effect on early wheezing or asthma development in children until the age of 10 was estimated by Bayesian kernel machine regression (BKMR) stratifying also for family history of atopy (FHA).

Results: Our experimental data show that neither pinewood nor OSB emissions even at high total VOC levels and a long-lasting exposure period induce significant inflammatory or asthma-promoting effects in sensitized or non-sensitized mice. Moreover, an exposure during the vulnerable time window around birth was also without effect. Consistently, in our mother-child cohort LINA, an exposure to multiple wood-related VOCs during pregnancy or the first year of life was not associated with early wheezing or asthma development in children independent from their FHA.

Conclusion: Our findings indicate that emissions from wood and wood products at levels commonly occurring in the living environment do not exert adverse effects concerning wheezing or asthma development.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.envint.2021.106449DOI Listing
February 2021

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

ISME J 2021 Jan 21. 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.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41396-020-00887-6DOI Listing
January 2021

The gut bacterium produces secondary bile acids and influences liver physiology in gnotobiotic mice.

Gut Microbes 2021 Jan-Dec;13(1):1-21

Functional Microbiome Research Group, Institute of Medical Microbiology, University Hospital of RWTH , Aachen, Germany.

is a newly described mouse gut bacterium which metabolizes cholic acid (CA) to deoxycholic acid (DCA) via 7α-dehydroxylation. Although bile acids influence metabolic and inflammatory responses, few models exist for studying their metabolism and impact on the host. Mice were colonized from birth with the simplified community Oligo-MM with or without . As the metabolism of bile acids is known to affect lipid homeostasis, mice were fed either a low- or high-fat diet for eight weeks before sampling and analyses targeting the gut and liver. Multiple Oligo-MM strains were capable of deconjugating primary bile acids produced DCA from CA either as pure compound or in mouse bile. This production was inducible by CA . Ursodeoxycholic, chenodeoxycholic, and β-muricholic acid were not metabolized under the conditions tested. All gnotobiotic mice were stably colonized with , which showed higher relative abundances after HF diet feeding. The presence of had minor, diet-dependent effects on Oligo-MM communities. The secondary bile acids DCA and surprisingly LCA and their taurine conjugates were detected exclusively in -colonized mice. colonization did not influence body weight, white adipose tissue mass, liver histopathology, hepatic aspartate aminotransferase, or blood levels of cholesterol, insulin, and paralytic peptide (PP). However, proteomics revealed shifts in hepatic pathways involved in amino acid, glucose, lipid, energy, and drug metabolism in -colonized mice. Liver fatty acid composition was substantially altered by dietary fat but not by In summary, stably colonized the gut of mice harboring a simplified community and produced secondary bile acids, which affected proteomes in the liver. This new gnotobiotic mouse model can now be used to study the pathophysiological role of secondary bile acids .
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1080/19490976.2020.1854008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7781625PMC
December 2020

Systematic Review of Multi-Omics Approaches to Investigate Toxicological Effects in Macrophages.

Int J Mol Sci 2020 Dec 9;21(24). Epub 2020 Dec 9.

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

Insights into the modes of action (MoAs) of xenobiotics are of utmost importance for the definition of adverse outcome pathways (AOPs), which are essential for a mechanism-based risk assessment. A well-established strategy to reveal MoAs of xenobiotics is the use of omics. However, often an even more comprehensive approach is needed, which can be achieved using multi-omics. Since the immune system plays a central role in the defense against foreign substances and pathogens, with the innate immune system building a first barrier, we systematically reviewed multi-omics studies investigating the effects of xenobiotics on macrophages. Surprisingly, only nine publications were identified, combining proteomics with transcriptomics or metabolomics. We summarized pathways and single proteins, transcripts, or metabolites, which were described to be affected upon treatment with xenobiotics in the reviewed studies, thus revealing a broad range of effects. In summary, we show that macrophages are a relevant model system to investigate the toxicological effects induced by xenobiotics. Furthermore, the multi-omics approaches led to a more comprehensive overview compared to only one omics layer with slight advantages for combinations that complement each other directly, e.g., proteome and metabolome.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3390/ijms21249371DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7764599PMC
December 2020

Comparison of quantitation methods in proteomics to define relevant toxicological information on AhR activation of HepG2 cells by BaP.

Toxicology 2021 Jan 2;448:152652. Epub 2020 Dec 2.

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

The application of quantitative proteomics provides a new and promising tool for standardized toxicological research. However, choosing a suitable quantitative method still puzzles many researchers because the optimal method needs to be determined. In this study, we investigated the advantages and limitations of two of the most commonly used global quantitative proteomics methods, namely label-free quantitation (LFQ) and tandem mass tags (TMT). As a case study, we exposed hepatocytes (HepG2) to the environmental contaminant benzo[a]pyrene (BaP) using a concentration of 2 μM. Our results revealed that both methods yield a similar proteome coverage, in which for LFQ a wider range of fold changes was observed but with less significant p-values compared to TMT. We detected 37 and 47 significantly enriched pathways by LFQ and TMT, respectively, with 17 overlapping pathways. To define the minimally required effort in proteomics as a benchmark, we artificially reduced the LFQ, and TMT data sets stepwise and compared the pathway enrichment. Thereby, we found that fewer proteins are necessary for detecting significant enrichment of pathways in TMT compared to LFQ, which might be explained by the higher reproducibility of the TMT data that was observed. In summary, we showed that the TMT approach is the preferable one when investigating toxicological questions because it offers a high reproducibility and sufficient proteome coverage in a comparably short time.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.tox.2020.152652DOI Listing
January 2021

Reduced lipolysis in lipoma phenocopies lipid accumulation in obesity.

Int J Obes (Lond) 2021 Mar 24;45(3):565-576. Epub 2020 Nov 24.

Division of Molecular Biochemistry, Rudolf Schönheimer Institute of Biochemistry, Medical Faculty, Leipzig University, 04103, Leipzig, Germany.

Background: Elucidation of lipid metabolism and accumulation mechanisms is of paramount importance to understanding obesity and unveiling therapeutic targets. In vitro cell models have been extensively used for these purposes, yet, they do not entirely reflect the in vivo setup. Conventional lipomas, characterized by the presence of mature adipocytes and increased adipogenesis, could overcome the drawbacks of cell cultures. Also, they have the unique advantage of easily accessible matched controls in the form of subcutaneous adipose tissue (SAT) from the same individual. We aimed to determine whether lipomas are a good model to understand lipid accumulation.

Methods: We histologically compared lipomas and control SAT, followed by assessment of the lipidome using high-resolution H NMR spectroscopy and ESI-IT mass spectrometry. RNA-sequencing was used to obtain the transcriptome of lipomas and the matched SAT.

Results: We found a significant increase of small-size (maximal axis < 70 µm) and very big (maximal axis > 150 µm) adipocytes within lipomas. This suggests both enhanced adipocyte proliferation and increased lipid accumulation. We further show that there is no significant change in the lipid composition compared to matched SAT. To better delineate the pathophysiology of lipid accumulation, we considered two groups with different genetic backgrounds: (1) lipomas with HMGA2 fusions and (2) without gene fusions. To reduce the search space for genes that are relevant for lipid pathophysiology, we focused on the overlapping differentially expressed (DE) genes between the two groups. Gene Ontology analysis revealed that DE genes are enriched in pathways related to lipid accumulation.

Conclusions: We show that the common shared lipid accumulation mechanism in lipoma is a reduction in lipolysis, with most gene dysregulations leading to a reduced cAMP in the adipocyte. Superficial lipomas could thus be used as a model for lipid accumulation through altered lipolysis as found in obese patients.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41366-020-00716-yDOI Listing
March 2021

The effect of green Mediterranean diet on cardiometabolic risk; a randomised controlled trial.

Heart 2020 Nov 23. Epub 2020 Nov 23.

Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel

Background: A Mediterranean diet is favourable for cardiometabolic risk.

Objective: To examine the residual effect of a green Mediterranean diet, further enriched with green plant-based foods and lower meat intake, on cardiometabolic risk.

Methods: For the DIRECT-PLUS parallel, randomised clinical trial we assigned individuals with abdominal obesity/dyslipidaemia 1:1:1 into three diet groups: healthy dietary guidance (HDG), Mediterranean and green Mediterranean diet, all combined with physical activity. The Mediterranean diets were equally energy restricted and included 28 g/day walnuts. The green Mediterranean diet further included green tea (3-4 cups/day) and a (Mankai strain; 100 g/day frozen cubes) plant-based protein shake, which partially substituted animal protein. We examined the effect of the 6-month dietary induction weight loss phase on cardiometabolic state.

Results: Participants (n=294; age 51 years; body mass index 31.3 kg/m; waist circumference 109.7 cm; 88% men; 10 year Framingham risk score 4.7%) had a 6-month retention rate of 98.3%. Both Mediterranean diets achieved similar weight loss ((green Mediterranean -6.2 kg; Mediterranean -5.4 kg) vs the HDG group -1.5 kg; p<0.001), but the green Mediterranean group had a greater reduction in waist circumference (-8.6 cm) than the Mediterranean (-6.8 cm; p=0.033) and HDG (-4.3 cm; p<0.001) groups. Stratification by gender showed that these differences were significant only among men. Within 6 months the green Mediterranean group achieved greater decrease in low-density lipoprotein cholesterol (LDL-C; green Mediterranean -6.1 mg/dL (-3.7%), -2.3 (-0.8%), HDG -0.2 mg/dL (+1.8%); p=0.012 between extreme groups), diastolic blood pressure (green Mediterranean -7.2 mm Hg, Mediterranean -5.2 mm Hg, HDG -3.4 mm Hg; p=0.005 between extreme groups), and homeostatic model assessment for insulin resistance (green Mediterranean -0.77, Mediterranean -0.46, HDG -0.27; p=0.020 between extreme groups). The LDL-C/high-density lipoprotein cholesterol (HDL-C) ratio decline was greater in the green Mediterranean group (-0.38) than in the Mediterranean (-0.21; p=0.021) and HDG (-0.14; p<0.001) groups. High-sensitivity C-reactive protein reduction was greater in the green Mediterranean group (-0.52 mg/L) than in the Mediterranean (-0.24 mg/L; p=0.023) and HDG (-0.15 mg/L; p=0.044) groups. The green Mediterranean group achieved a better improvement (-3.7% absolute risk reduction) in the 10-year Framingham Risk Score (Mediterranean-2.3%; p0.073, HDG-1.4%; p<0.001).

Conclusions: The green MED diet, supplemented with walnuts, green tea and Mankai and lower in meat/poultry, may amplify the beneficial cardiometabolic effects of Mediterranean diet.

Trial Registration Number: This study is registered under ClinicalTrials.gov Identifier no NCT03020186.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1136/heartjnl-2020-317802DOI Listing
November 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/.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1093/nar/gkaa1031DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7778935PMC
January 2021

Proteomics reveals sex-specific heat shock response of Baikal amphipod Eulimnogammarus cyaneus.

Sci Total Environ 2021 Apr 19;763:143008. Epub 2020 Oct 19.

Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research - UFZ, Permoserstr. 15, Leipzig, Germany; Fraunhofer Institute for Cell Therapy and Immunology, Dept. Cell Engineering, Perlickstr. 1, 04103 Leipzig, Germany; Institute of Bioanalysis, University of Applied Sciences and Arts of Coburg, Friedrich-Streib-Str. 2, 96450 Coburg, Germany.

The ancient Lake Baikal is the largest source of liquid freshwater on Earth and home to a unique fauna. Several hundred mostly cold-adapted endemic amphipod species inhabit Baikal, an ecosystem that is already being influenced by global change. In this study, we characterized the core proteome and heat stress-induced changes in a temperature-tolerant endemic amphipod, Eulimnogammarus cyaneus, using a proteogenomic approach (PRIDE dataset PXD013237) to unravel the molecular mechanisms of the observed adverse effects. As males were previously found to be much more tolerant to thermal stress, we placed special emphasis on differences between the sexes. For both sexes, we observed adaption of energy metabolism, cytoskeleton, lipid, and carbohydrate metabolism upon heat stress. In contrast, significant differences were determined in the molecular chaperone response. Females from the control conditions possessed significantly higher levels of heat shock proteins (HSP70, HSPb1, Hsc70-3), which, in contrast to males, were not further increased in response to heat stress. The inability of females to further increase heat shock protein synthesis in response to temperature stress may be due to sex-specific processes, such as egg production, requiring a large proportion of the available energy. As ovigerous females synthesize generally higher amounts of protein, they also need higher levels of molecular chaperones for the folding of these new proteins. Thus, the higher sensitivity of females to heat shock may be due to the lack of molecular chaperone molecules to counteract the heat-induced protein denaturation.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.scitotenv.2020.143008DOI Listing
April 2021

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.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3390/microorganisms8111694DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7716230PMC
October 2020

Multiplexed Quantitative Assessment of the Fate of Taurine and Sulfoquinovose in the Intestinal Microbiome.

Metabolites 2020 Oct 26;10(11). Epub 2020 Oct 26.

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

(1) Introduction: Sulfonates, which can be diet- or host-derived, are a class of compounds detected in the gut, are involved in host-microbiome interactions and have several health effects. Our aim was to develop a method to quantify five of the sulfonates in the intestine and apply it in a simplified human microbiome model. These were taurine, its metabolic precursor cysteate and one of its degradation products isethionate, as well as sulfoquinovose and one of its most relevant degradation products 2,3-dihydroxy-1-propanesulfonate. (2) Methods: An extraction and sample preparation method was developed, without the need for derivatization. To detect and quantify the extracted sulfonates, a multiplexed LC-MS/MS-MRM method was established. (3) Results: The accuracy and precision of the method were within GLP-accepted parameters (www.ema.europa.eu). To apply this method in a pilot study, we spiked either taurine or sulfoquinovose into an in vitro simplified human microbiota model with and without , a known sulfonate utilizer. The results revealed that only the culture with was able to degrade taurine, with isethionate as an intermediate. After spiking the communities with sulfoquinovose, the results revealed that the simplified human microbiome model was able to degrade sulfoquinovose to 2,3-dihydroxypropane-1-sulfonate, which was probably catalyzed by . In the community with , the 2,3-dihydroxypropane-1-sulfonate produced was further degraded by to sulfide. (4) Conclusions: We successfully developed a method for sulfonate quantification and applied it in a first pilot study.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3390/metabo10110430DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7692227PMC
October 2020

Accumulation of distinct persistent organic pollutants is associated with adipose tissue inflammation.

Sci Total Environ 2020 Dec 23;748:142458. Epub 2020 Sep 23.

Medical Department III - Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, Germany; Helmholtz Institute for Metabolic, Obesity and Vascular Research (HI-MAG) of the Helmholtz Zentrum München at the University of Leipzig and University Hospital, Leipzig, Germany. Electronic address:

Hydrophobic environmental chemicals bio-accumulate in adipose tissue (AT) in animals and humans, but their impact on diseases related to adipose tissue dysfunction remains unclear. Moreover, visceral rather than subcutaneous (SC) fat deposition is more closely associated with cardio-metabolic diseases such as type 2 diabetes, fatty liver and cardiovascular diseases. We therefore tested the hypotheses that environmental chemicals bio-accumulate in a fat depot specific pattern and that these patterns are related AT inflammation and obesity comorbidities. First, we developed an extraction method for detecting and quantifying a set of 9 persistent organic pollutants (POPs) in human AT. The quantified chemicals exhibit K coefficients from 4 to 7. Paired abdominal omental and SC AT samples were obtained from 54 individuals (30 women, 24 men) with a wide range of body mass index (BMI, 16-70 kg/m) during laparoscopic abdominal surgeries. Among the POPs are classical halogenated substances like Dichlorodiphenyldichloroethylene (DDE) and polychlorinated biphenyls (PCBs), but also fragrance substances. We find that AT concentrations of these chemicals are neither significantly different between visceral and SC fat depots nor between women and men. However, AT bio-accumulation of distinct POPs significantly correlates with AT macrophage infiltration, adipocyte size and parameters of glucose metabolism. In both fat depots, the strongest correlations of POPs (Ethyl- tetradecanoate, 4,4'-Diisopropylbiphenyl, 2-Phenyltetralin, 2,2',4,4',5,5'-Hexachlorobiphenyl, Hexachlorobenzene) and AT macrophage infiltration were detected in lean individuals. In men with obesity, abundance of POPs correlated with the duration of obesity. Additional significant associations between AT POPs and parameters of glycemia, insulin sensitivity, and inflammation suggest that specific environmental chemicals may contribute to AT dysfunction, adipocyte hypertrophy, impaired glucose metabolism, systemic inflammation and variation in fat distribution, but not to obesity.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.scitotenv.2020.142458DOI Listing
December 2020

Disturbed gut microbiota and bile homeostasis in -infected mice contributes to metabolic dysregulation and growth impairment.

Sci Transl Med 2020 10;12(565)

Institute of Medical Microbiology, RWTH University Hospital, 52074 Aachen, Germany.

Although infection with the human enteropathogen causes self-limited diarrhea in adults, infant populations in endemic areas experience persistent pathogen carriage in the absence of diarrhea. The persistence of this protozoan parasite in infants has been associated with reduced weight gain and linear growth (height-for-age). The mechanisms that support persistent infection and determine the different disease outcomes in the infant host are incompletely understood. Using a neonatal mouse model of persistent infection, we demonstrate that induced bile secretion and used the bile constituent phosphatidylcholine as a substrate for parasite growth. In addition, we show that infection altered the enteric microbiota composition, leading to enhanced bile acid deconjugation and increased expression of fibroblast growth factor 15. This resulted in elevated energy expenditure and dysregulated lipid metabolism with reduced adipose tissue, body weight gain, and growth in the infected mice. Our results indicate that this enteropathogen's modulation of bile acid metabolism and lipid metabolism in the neonatal mouse host led to an altered body composition, suggesting how infection could contribute to growth restriction in infants in endemic areas.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1126/scitranslmed.aay7019DOI Listing
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.
View Article and Find Full Text PDF

Download full-text PDF

Source
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.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3390/microorganisms8091436DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7564734PMC
September 2020

Mitochondrial Transfer by Human Mesenchymal Stromal Cells Ameliorates Hepatocyte Lipid Load in a Mouse Model of NASH.

Biomedicines 2020 Sep 14;8(9). Epub 2020 Sep 14.

Applied Molecular Hepatology Laboratory, Department of Visceral, Transplant, Thoracic and Vascular Surgery, University of Leipzig Medical Center, 04103 Leipzig, Germany.

Mesenchymal stromal cell (MSC) transplantation ameliorated hepatic lipid load; tissue inflammation; and fibrosis in rodent animal models of non-alcoholic steatohepatitis (NASH) by as yet largely unknown mechanism(s). In a mouse model of NASH; we transplanted bone marrow-derived MSCs into the livers; which were analyzed one week thereafter. Combined metabolomic and proteomic data were applied to weighted gene correlation network analysis (WGCNA) and subsequent identification of key drivers. Livers were analyzed histologically and biochemically. The mechanisms of MSC action on hepatocyte lipid accumulation were studied in co-cultures of hepatocytes and MSCs by quantitative image analysis and immunocytochemistry. WGCNA and key driver analysis revealed that NASH caused the impairment of central carbon; amino acid; and lipid metabolism associated with mitochondrial and peroxisomal dysfunction; which was reversed by MSC treatment. MSC improved hepatic lipid metabolism and tissue homeostasis. In co-cultures of hepatocytes and MSCs; the decrease of lipid load was associated with the transfer of mitochondria from the MSCs to the hepatocytes via tunneling nanotubes (TNTs). Hence; MSCs may ameliorate lipid load and tissue perturbance by the donation of mitochondria to the hepatocytes. Thereby; they may provide oxidative capacity for lipid breakdown and thus promote recovery from NASH-induced metabolic impairment and tissue injury.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3390/biomedicines8090350DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7554948PMC
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.
View Article and Find Full Text PDF

Download full-text PDF

Source
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.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1128/mBio.01259-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7448270PMC
August 2020

Bidirectional role of NLRP3 during acute and chronic cholestatic liver injury.

Hepatology 2020 Aug 4. Epub 2020 Aug 4.

Department of Internal Medicine III, University Hospital RWTH Aachen, Aachen, Germany.

Introduction: Cholestatic liver injury leads to cell death and subsequent inflammation and fibrosis. As shown for primary biliary cholangitis (PBC) the mechanisms and circuits between different cell death pathways leading to disease progression are incompletely defined. Ligation of the common bile duct (BDL) is a well-established murine model to mimic cholestatic liver injury. Here, we hypothesised that pyroptotic cell death by the Nlrp3 inflammasome plays an essential role during human and murine cholestasis.

Material & Methods: NLRP3 activation was analysed in humans with cholestatic liver injury. WT and Nlrp3 mice were subjected to BDL for 2 or 28 days.

Results: Chronic cholestasis in humans and mice is associated with NLRP3 activation and correlates with disease activity. Acute BDL in Nlrp3-deficient mice triggered increased inflammation as well as liver injury, associated with stronger apoptotic and necroptotic cell death. In contrast, NLRP3 deletion led to decreased liver injury and inflammation in chronic cholestasis. Moreover, bridging fibrosis was observed in WT, but not in NLRP3 knockout mice 28 days after BDL In contrast, lack of NLRP3 expression attenuated kidney injury and fibrosis after acute and chronic BDL. Importantly, MCC950 administration - a NLRP3 small molecule inhibitor - reduced BDL-induced disease progression in WT mice.

Conclusion: NLRP3 activation correlates with disease activity in PBC patients. NLRP3 has a differential role during acute and chronic cholestatic liver injury in contrast to kidney injury. Disease progression during chronic cholestasis can be targeted via small molecules and thus suggests a potential clinical benefit for humans, attenuating liver and kidney injury.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1002/hep.31494DOI Listing
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.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.scitotenv.2020.140932DOI Listing
November 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:

View Article and Find Full Text PDF

Download full-text PDF

Source
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.
View Article and Find Full Text PDF

Download full-text PDF

Source
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.
View Article and Find Full Text PDF

Download full-text PDF

Source
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.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3389/fmicb.2020.00755DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7189812PMC
April 2020

In Depth Quantitative Proteomic and Transcriptomic Characterization of Human Adipocyte Differentiation Using the SGBS Cell Line.

Proteomics 2020 May 8:e1900405. Epub 2020 May 8.

Center for Pediatric Research Leipzig (CPL), University Hospital for Children and Adolescents, Leipzig, Germany.

Most information on molecular processes accompanying and driving adipocyte differentiation are derived from rodent models. Here, we provide a comprehensive analysis of combined transcriptomic and proteomic alterations during adipocyte differentiation in Simpson-Golabi-Behmel Syndrome (SGBS) cells. The SGBS cells are a well-established and the most widely applied cell model to study human adipocyte differentiation and cell biology. However, the molecular alterations during human adipocyte differentiation in SGBS cells have not yet been described in a combined analysis of proteome and transcriptome. Here we present a global proteomic and transcriptomic data set comprising relative quantification of a total of 14372 mRNA transcripts and 2641 intracellular and secreted proteins. 1153 proteins and 313 genes were determined as differentially expressed between preadipocytes and the fully differentiated cells including adiponectin, lipoprotein lipase, fatty acid binding protein 4, fatty acid synthase, stearoyl-CoA desaturase and apolipoprotein E and many other proteins from the fatty acid synthesis, amino acid synthesis as well as glucose and lipid metabolic pathways. Preadipocyte markers, such as latexin, GATA6 and CXCL6, were found to be significantly downregulated at the protein and transcript level. This multi-omics data set provides a deep molecular profile of adipogenesis and will support future studies to understand adipocyte function. This article is protected by copyright. All rights reserved.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1002/pmic.201900405DOI Listing
May 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.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.jprot.2020.103791DOI Listing
June 2020

Adipose tissue derived bacteria are associated with inflammation in obesity and type 2 diabetes.

Gut 2020 Oct 21;69(10):1796-1806. Epub 2020 Apr 21.

Medical Department III - Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, Leipzig, Germany

Objective: Bacterial translocation to various organs including human adipose tissue (AT) due to increased intestinal permeability remains poorly understood. We hypothesised that: (1) bacterial presence is highly tissue specific and (2) related in composition and quantity to immune inflammatory and metabolic burden.

Design: We quantified and sequenced the bacterial 16S rRNA gene in blood and AT samples (omental, mesenteric and subcutaneous) of 75 subjects with obesity with or without type 2 diabetes (T2D) and used catalysed reporter deposition (CARD) - fluorescence in situ hybridisation (FISH) to detect bacteria in AT.

Results: Under stringent experimental and bioinformatic control for contaminants, bacterial DNA was detected in blood and omental, subcutaneous and mesenteric AT samples in the range of 0.1 to 5 pg/µg DNA isolate. Moreover, CARD-FISH allowed the detection of living, AT-borne bacteria. and were the predominant phyla, and bacterial quantity was associated with immune cell infiltration, inflammatory and metabolic parameters in a tissue-specific manner. Bacterial composition differed between subjects with and without T2D and was associated with related clinical measures, including systemic and tissues-specific inflammatory markers. Finally, treatment of adipocytes with bacterial DNA in vitro stimulated the expression of and .

Conclusions: Our study provides contaminant aware evidence for the presence of bacteria and bacterial DNA in several ATs in obesity and T2D and suggests an important role of bacteria in initiating and sustaining local AT subclinical inflammation and therefore impacting metabolic sequelae of obesity.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1136/gutjnl-2019-320118DOI Listing
October 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.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1080/14789450.2020.1738931DOI Listing
February 2020

Ethnomedicinal survey and in vitro confirmation of anti-inflammatory and antispasmodic properties of the termite strain Macrotermes bellicosus used in traditional medicine in the Republic of Benin.

J Ethnopharmacol 2020 May 22;254:112705. Epub 2020 Feb 22.

Leipzig University, Medical Faculty, Institute for Medical Physics and Biophysics, Leipzig, Germany. Electronic address:

Ethnopharmacological Relevance: Insects and insect-derived products play a vital role in traditional medicine in many parts of the world since ancient times. Among these insects, fungus-growing termites like Macrotermes bellicosus (M. bellicosus) are widely used in nutrition and traditional medicine in various societies of sub-Saharan Africa.

Aim Of The Study: Aim of the present study was to explore the traditional applications of M. bellicosus and subsequently investigate the anti-inflammatory and spasmolytic activity of samples collected in Benin.

Material And Methods: An ethnomedicinal survey with thirty active healers in Benin was conducted and the anti-inflammatory activity of an ethanolic extract of M. bellicosus was investigated. Thus, LPS-induced TNFα release from differentiated human macrophages (THP-1) and IL-8 release from cytokine (IL-1β/TNFα/IFNγ)-challenged human intestinal epithelial cells (Caco-2) was measured by enzyme-linked immunosorbent assay. Furthermore, the influence of M. bellicosus extract on basal tone and induced contractions in isolated rat small intestinal preparations was determined to examine the influence on intestinal motility.

Results: The survey of 30 active healers demonstrated that M. bellicosus and its products (termites' mound and fungus comb) are used in Benin for therapeutic purposes mainly to treat infectious and inflammatory diseases including digestive disorders, snake bites and diarrhea. It was found that M. bellicosus extract inhibited both LPS-induced TNFα release from human macrophages and cytokine-induced IL-8 release from intestinal epithelial cells comparable to budesonide. In addition, isometric contraction measurement with isolated rat small intestinal preparations demonstrated a mild spasmolytic effect of the termite extract in higher concentrations with a suppression of induced contractions and relaxation of basal tone.

Conclusion: M. bellicosus which is used in traditional medicine in Benin to treat infectious and inflammatory diseases showed anti-inflammatory activity by inhibiting pro-inflammatory cytokine release and a moderate influence on intestinal motility.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.jep.2020.112705DOI Listing
May 2020