221 results on '"Pieper DH"'
Search Results
2. The microbiome as a possible predictor for the formation of HNSCC
- Author
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Böse, B, additional, Oberste, M, additional, Beule, AG., additional, Pieper, DH., additional, and Rudack, C, additional
- Published
- 2021
- Full Text
- View/download PDF
3. Unterscheidet sich die mikrobielle Besiedlung je nach Lokalisation und Dignität (Malignom vs. Kontrollgruppe) im Kopf Hals Bereich? Eine prospektive Observationsstudie
- Author
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Böse, BE, Oberste, M, Beule, AG, Pieper, DH, and Rudack, C
- Subjects
ddc: 610 ,610 Medical sciences ,Medicine - Abstract
Einleitung: Die Kopf-Hals-Karzinome spielen als sechsthäufigste Krebserkrankung weltweit eine sehr große Rolle in der Gesellschaft. Insgesamt sind schon einige Risikofaktoren identifiziert worden (Nikotin, Alkohol, HPV), neuere Studien konzentrieren sich jedoch zunehmend auf die Bedeutung [zum vollständigen Text gelangen Sie über die oben angegebene URL], Jahrestagung der Vereinigung Westdeutscher Hals-Nasen-Ohren-Ärzte
- Published
- 2020
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4. Die Nasen-'WG': S. aureus und das nasale Mikrobiom
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Kaspar, U, Schaumburg, F, Rudack, C, Pieper, DH, and Becker, K
- Subjects
ddc: 610 ,610 Medical sciences ,Medicine - Abstract
Screening und Dekolonisierung sind unerlässliche Teile des Maßnahmenbündels zur Prävention und Kontrolle von MRSA (Methicillin-resistenter Staphylococcus aureus). Die menschliche Nasenhöhle als primäres Habitat des Erregers stellt Quelle und Risikofaktor für invasive[for full text, please go to the a.m. URL], Bad Honnef-Symposium 2015
- Published
- 2015
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5. Molecular characterization of a deletion/duplication rearrangement in tfd genes from ralstonia eutropha jmp134(pjp4) that improves growth on 3-chlorobenzoic acid but abolishes growth on 2,4-dichlorophenoxyacetic acid
- Author
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Clement, P, Pieper, DH, and Gonzalez, B
- Published
- 2001
6. Role of tfdc(i)d(i)e(i)f(i) and tfdd(ii)c(ii)e(ii)f(ii) gene modules in catabolism of 3-chlorobenzoate by ralstonia eutropha jmp134(pjp4)
- Author
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Perez-Pantoja, D, Guzman, L, Manzano, M, Pieper, DH, and Gonzalez, B
- Published
- 2000
7. Superior survival and degradation of dibenzo-p-dioxin and dibenzofuran in soil by soil-adapted Sphingomonas sp strain RW1
- Author
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Dietmar H. Pieper, Rolf-Michael Wittich, Kenneth N. Timmis, Rafael Blasco, Mallavarapu Megharaj, Wittich, RM, Blasco, R, Pieper, DH, and Timmis, KN
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biology ,Strain (chemistry) ,Substrate (chemistry) ,General Medicine ,Biodegradation ,biology.organism_classification ,Sphingomonas ,complex mixtures ,Applied Microbiology and Biotechnology ,Microbiology ,Dibenzofuran ,chemistry.chemical_compound ,chemistry ,Sphingomonas wittichii ,Soil water ,Food science ,Bacteria ,Biotechnology - Abstract
The dibenzo-p-dioxin(DD)- and dibenzofuran(DF)-degrading bacterium, Sphingomonas sp. strain RW1, was tagged by insertion of a mini-Tn5 lacZ transposon in order to follow its fate in complex laboratory soil systems. The tagged strain was tested for its ability to survive in soil and degrade DF and DD applied at a concentration of 1 mg/g. Bacteria pre-adapted to soil conditions were found to survive better in DF- and DD-amended soil and degrade the substrate more efficiently than bacteria that had not been subjected to pre-adaptation. The concentration of soil-applied DF and DD, individually and in combination, decreased to less than 2% of the original concentrations within 3 weeks of addition of the RW1 derivative, accompanied by a short, but significant exponential increase in RW1 viable cells. During the same period the native bacterial population in soil was stable while viable fungi declined.
- Published
- 1997
8. Evidence that formation of protoanemonin from metabolites of 4-chlorobiphenyl degradation negatively affects the survival of 4-chlorobiphenyl-cometabolizing microorganisms
- Author
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Blasco, R, Wittich, RM, Timmis, KN, and Pieper, DH
- Published
- 1997
9. From xenobiotic to antibiotic, formation of protoanemonin from 4-chlorocatechol by enzymes of the 3-oxoadipate pathway
- Author
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Dietmar H. Pieper, Rolf-Michael Wittich, Kenneth N. Timmis, Megharaj Mallavarapu, Rafael Blasco, Blasco, R, Wittich, RM, Timmis, KN, and Pieper, DH
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chemistry.chemical_classification ,Ecology ,Catabolism ,Decarboxylation ,Stereochemistry ,Adipates ,Microorganism ,Catechols ,Cell Biology ,Biochemistry ,Anti-Bacterial Agents ,chemistry.chemical_compound ,Enzyme ,chemistry ,Pseudomonas ,Antibiotic formation ,Furans ,Intramolecular Lyases ,Isomerases ,Xenobiotic ,Molecular Biology ,Protoanemonin - Abstract
Chloroaromatics, a major class of industrial pollutants, may be oxidatively metabolized to chlorocatechols by soil and water microorganisms that have evolved catabolic activities toward these xenobiotics. We show here that 4-chlorocatechol can be further transformed by enzymes of the ubiquitous 3-oxoadipate pathway. However, whereas chloromuconate cycloisomerases catalyze the dechlorination of 3-chloro-cis,cis-muconate to form cis-dienelactone, muconate cycloisomerases catalyze a novel reaction, i.e. the dechlorination and concomitant decarboxylation to form 4-methylenebut-2-en-4-olide (protoanemonin), an ordinarily plant-derived antibiotic that is toxic to microorganisms.
10. Screening Privileged Alkyl Guanidinium Motifs under Host-Mimicking Conditions Reveals a Novel Antibiotic with an Unconventional Mode of Action.
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Schum D, Elsen FAV, Ruddell S, Schorpp K, Junca H, Müsken M, Chen SY, Fiedler MK, Pickl T, Pieper DH, Hadian K, Zacharias M, and Sieber SA
- Abstract
Screening large molecule libraries against pathogenic bacteria is often challenged by a low hit rate due to limited uptake, underrepresentation of antibiotic structural motifs, and assays that do not resemble the infection conditions. To address these limitations, we present a screen of a focused library of alkyl guanidinium compounds, a structural motif associated with antibiotic activity and enhanced uptake, under host-mimicking infection conditions against a panel of disease-associated bacteria. Several hit molecules were identified with activities against Gram-positive and Gram-negative bacteria, highlighting the fidelity of the general concept. We selected one compound ( L15 ) for in-depth mode of action studies that exhibited bactericidal activity against methicillin-resistant Staphylococcus aureus USA300 with a minimum inhibitory concentration of 1.5 μM. Structure-activity relationship studies confirmed the necessity of the guanidinium motif for antibiotic activity. The mode of action was investigated using affinity-based protein profiling with an L15 probe and identified the signal peptidase IB (SpsB) as the most promising hit. Validation by activity assays, binding site identification, docking, and molecular dynamics simulations demonstrated SpsB activation by L15 , a recently described mechanism leading to the dysregulation of protein secretion and cell death. Overall, this study highlights the need for unconventional screening strategies to identify novel antibiotics., Competing Interests: The authors declare no competing financial interest., (© 2024 The Authors. Published by American Chemical Society.)
- Published
- 2024
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11. Isocyanides inhibit bacterial pathogens by covalent targeting of essential metabolic enzymes.
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Geißler A, Junca H, Kany AM, Daumann LJ, Hirsch AKH, Pieper DH, and Sieber SA
- Abstract
Isonitrile natural products, also known as isocyanides, demonstrate potent antimicrobial activities, yet our understanding of their molecular targets remains limited. Here, we focus on the so far neglected group of monoisonitriles to gain further insights into their antimicrobial mode of action (MoA). Screening a focused monoisonitrile library revealed a potent S. aureus growth inhibitor with a different MoA compared to previously described isonitrile antibiotics. Chemical proteomics via competitive cysteine reactivity profiling, uncovered covalent modifications of two essential metabolic enzymes involved in the fatty acid biosynthetic process (FabF) and the hexosamine pathway (GlmS) at their active site cysteines. In-depth studies with the recombinant enzymes demonstrated concentration-dependent labeling, covalent binding to the catalytic site and corresponding functional inhibition by the isocyanide. Thermal proteome profiling and full proteome studies of compound-treated S. aureus further highlighted the destabilization and dysregulation of proteins related to the targeted pathways. Cytotoxicity and the inhibition of cytochrome P450 enzymes require optimization of the hit molecule prior to therapeutic application. The here described novel, covalent isocyanide MoA highlights the versatility of the functional group, making it a useful tool and out-of-the-box starting point for the development of innovative antibiotics., Competing Interests: S. A. S is co-founder of Smartbax Limited., (This journal is © The Royal Society of Chemistry.)
- Published
- 2024
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12. Infection and antibiotic-associated changes in the fecal microbiota of C. rodentium ϕ stx2 dact -infected C57BL/6 mice.
- Author
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Mühlen S, Heroven AK, Elxnat B, Kahl S, Pieper DH, and Dersch P
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- Animals, Mice, Trimethoprim, Sulfamethoxazole Drug Combination therapeutic use, Trimethoprim, Sulfamethoxazole Drug Combination pharmacology, Enterohemorrhagic Escherichia coli drug effects, Enrofloxacin pharmacology, Enrofloxacin therapeutic use, Female, Disease Models, Animal, Dysbiosis microbiology, Citrobacter rodentium drug effects, Anti-Bacterial Agents pharmacology, Anti-Bacterial Agents therapeutic use, Anti-Bacterial Agents adverse effects, Feces microbiology, Mice, Inbred C57BL, Enterobacteriaceae Infections drug therapy, Enterobacteriaceae Infections microbiology, Gastrointestinal Microbiome drug effects
- Abstract
Enterohemorrhagic Escherichia coli causes watery to bloody diarrhea, which may progress to hemorrhagic colitis and hemolytic-uremic syndrome. While early studies suggested that antibiotic treatment may worsen the pathology of an enterohemorrhagic Escherichia coli (EHEC) infection, recent work has shown that certain non-Shiga toxin-inducing antibiotics avert disease progression. Unfortunately, both intestinal bacterial infections and antibiotic treatment are associated with dysbiosis. This can alleviate colonization resistance, facilitate secondary infections, and potentially lead to more severe illness. To address the consequences in the context of an EHEC infection, we used the established mouse infection model organism Citrobacter rodentium ϕ stx2
dact and monitored changes in fecal microbiota composition during infection and antibiotic treatment. C. rodentium ϕ stx2dact infection resulted in minor changes compared to antibiotic treatment. The infection caused clear alterations in the microbial community, leading mainly to a reduction of Muribaculaceae and a transient increase in Enterobacteriaceae distinct from Citrobacter . Antibiotic treatments of the infection resulted in marked and distinct variations in microbiota composition, diversity, and dispersion. Enrofloxacin and trimethoprim/sulfamethoxazole, which did not prevent Shiga toxin-mediated organ damage, had the least disruptive effects on the intestinal microbiota, while kanamycin and tetracycline, which rapidly cleared the infection without causing organ damage, caused a severe reduction in diversity. Kanamycin treatment resulted in the depletion of all but Bacteroidetes genera, whereas tetracycline effects on Clostridia were less severe. Together, these data highlight the need to address the impact of individual antibiotics in the clinical care of life-threatening infections and consider microbiota-regenerating therapies.IMPORTANCEUnderstanding the impact of antibiotic treatment on EHEC infections is crucial for appropriate clinical care. While discouraged by early studies, recent findings suggest certain antibiotics can impede disease progression. Here, we investigated the impact of individual antibiotics on the fecal microbiota in the context of an established EHEC mouse model using C. rodentium ϕ stx2dact . The infection caused significant variations in the microbiota, leading to a transient increase in Enterobacteriaceae distinct from Citrobacter . However, these effects were minor compared to those observed for antibiotic treatments. Indeed, antibiotics that most efficiently cleared the infection also had the most detrimental effect on the fecal microbiota, causing a substantial reduction in microbial diversity. Conversely, antibiotics showing adverse effects or incomplete bacterial clearance had a reduced impact on microbiota composition and diversity. Taken together, our findings emphasize the delicate balance required to weigh the harmful effects of infection and antibiosis in treatment., Competing Interests: The authors declare no conflict of interest.- Published
- 2024
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13. Next Generation Sequencing Outperforms Cultivation-Based Methods for Detection of Bacterial Genera in Bile After Liver Transplantation.
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Grobe B, Wellhöner F, Klein F, Chhatwal P, Vital M, Pieper DH, Voigtländer T, Lenzen H, Wedemeyer H, Solbach P, and Heidrich B
- Abstract
Background and Aims: Bacterial cholangitis is a common complication in patients with ischemic type biliary lesions and/or anastomotic strictures after liver transplantation (LTX). Patients frequently need antibiotics and endoscopic retrograde cholangiography (ERC) to improve the bile flow. Antibiotic treatment is based on findings in standard microbiological cultivation (SMC) of bile. However, the cultivation techniques are limited to a subset of bacteria easy-to-cultivate. Therefore, the aim of our study was to evaluate the value of next generation sequencing as an additional diagnostic tool to SMC in ischemic type biliary lesions and/or anastomotic strictures., Methods: We sequenced the V1-V2 region of the 16S rRNA gene in 242 stored bile samples in patients after LTX and compared the results with findings of SMC. SMC was performed in n = 135 (56%) fresh bile samples in addition to NGS. SMC was part of the clinical routine in these patients., Results: NGS detected bacterial genera in bile samples more often than SMC ( P = 5.42 × 10
-74 ). SMC showed insufficient discovery of bacterial genera compared to NGS with better performance in patients receiving antibiotics prior to ERC. SMC missed many bacterial genera detected by NGS., Conclusions: NGS was more sensitive in detecting bacteria in bile than SMC, no clinical parameters could be used to improve discovery rates in SMC and many genera were missed by SMC. Therefore, NGS should be used in a combined approach with SMC for improved diagnostics to achieve more specific and targeted antibiotic treatments., (© 2023 Indian National Association for Study of the Liver. Published by Elsevier B.V. All rights reserved.)- Published
- 2024
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14. Effects of squamous cell carcinoma and smoking status on oropharyngeal and laryngeal microbial communities.
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Oberste M, Böse BE, Dos Anjos Borges LG, Junca H, Plumeier I, Kahl S, Simon F, Beule AG, Rudack C, and Pieper DH
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- Humans, RNA, Ribosomal, 16S genetics, Smoking adverse effects, Oropharynx pathology, Laryngeal Neoplasms, Carcinoma, Squamous Cell pathology, Larynx pathology, Microbiota, Oropharyngeal Neoplasms pathology, Head and Neck Neoplasms
- Abstract
Background: Still, little is known about microbial dysbiosis in oropharyngeal and laryngeal tissue as risk factor for development of local squamous cell carcinoma. The site-specific microbiota at these regions in healthy and cancer tissue and their modulation by environmental factors need to be defined., Methods: The local microbiota of cancer tissue and healthy controls was profiled by 16S rRNA gene amplicon sequencing and statistical analysis using 111 oropharyngeal and 72 laryngeal intraoperative swabs., Results: Oropharynx and larynx harbor distinct microbial communities. Clear effects of both smoking and cancer were seen in the oropharynx whereas effects in the larynx were minor., Conclusion: The distinct microbial communities at larynx and oropharynx partially explain why the effects of cancer and smoking were distinct at those sites. Thus, the use of microbiota supposed to mirror community changes in another target location should be avoided and more studies on the actual cancerous environment are necessary., (© 2023 The Authors. Head & Neck published by Wiley Periodicals LLC.)
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- 2024
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15. Engraftment of essential functions through multiple fecal microbiota transplants in chronic antibiotic-resistant pouchitis-a case study using metatranscriptomics.
- Author
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Deng ZL, Pieper DH, Stallmach A, Steube A, Vital M, Reck M, and Wagner-Döbler I
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- Humans, Fecal Microbiota Transplantation, Anti-Bacterial Agents therapeutic use, Feces microbiology, Butyrates analysis, Pouchitis therapy, Pouchitis diagnosis, Pouchitis microbiology, Microbiota, Colitis, Ulcerative surgery
- Abstract
Background: Ileal pouch-anal anastomosis (IPAA) is the standard of care after total proctocolectomy for ulcerative colitis (UC). Around 50% of patients will experience pouchitis, an idiopathic inflammatory condition. Antibiotics are the backbone of treatment of pouchitis; however, antibiotic-resistant pouchitis develops in 5-10% of those patients. It has been shown that fecal microbiota transplantation (FMT) is an effective treatment for UC, but results for FMT antibiotic-resistant pouchitis are inconsistent., Methods: To uncover which metabolic activities were transferred to the recipients during FMT and helped the remission, we performed a longitudinal case study of the gut metatranscriptomes from three patients and their donors. The patients were treated by two to three FMTs, and stool samples were analyzed for up to 140 days., Results: Reduced expression in pouchitis patients compared to healthy donors was observed for genes involved in biosynthesis of amino acids, cofactors, and B vitamins. An independent metatranscriptome dataset of UC patients showed a similar result. Other functions including biosynthesis of butyrate, metabolism of bile acids, and tryptophan were also much lower expressed in pouchitis. After FMT, these activities transiently increased, and the overall metatranscriptome profiles closely mirrored those of the respective donors with notable fluctuations during the subsequent weeks. The levels of the clinical marker fecal calprotectin were concordant with the metatranscriptome data. Faecalibacterium prausnitzii represented the most active species contributing to butyrate synthesis via the acetyl-CoA pathway. Remission occurred after the last FMT in all patients and was characterized by a microbiota activity profile distinct from donors in two of the patients., Conclusions: Our study demonstrates the clear but short-lived activity engraftment of donor microbiota, particularly the butyrate biosynthesis after each FMT. The data suggest that FMT triggers shifts in the activity of patient microbiota towards health which need to be repeated to reach critical thresholds. As a case study, these insights warrant cautious interpretation, and validation in larger cohorts is necessary for generalized applications. In the long run, probiotics with high taxonomic diversity consisting of well characterized strains could replace FMT to avoid the costly screening of donors and the risk of transferring unwanted genetic material. Video Abstract., (© 2023. The Author(s).)
- Published
- 2023
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16. The 2-methylpropene degradation pathway in Mycobacteriaceae family strains.
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Helbich S, Barrantes I, Dos Anjos Borges LG, Pieper DH, Vainshtein Y, Sohn K, and Engesser KH
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- Sewage, Carbon, Alkenes metabolism, Intramolecular Transferases genetics, Intramolecular Transferases metabolism
- Abstract
Mycolicibacterium gadium IBE100 and Mycobacterium paragordonae IBE200 are aerobic, chemoorganoheterotrophic bacteria isolated from activated sludge from a wastewater treatment plant. They use 2-methylpropene (isobutene, 2-MP) as the sole source of carbon and energy. Here, we postulate a degradation pathway of 2-methylpropene derived from whole genome sequencing, differential expression analysis and peptide-mass fingerprinting. Key genes identified are coding for a 4-component soluble diiron monooxygenase with epoxidase activity, an epoxide hydrolase, and a 2-hydroxyisobutyryl-CoA mutase. In both strains, involved genes are arranged in clusters of 61.0 and 58.5 kbp, respectively, which also contain the genes coding for parts of the aerobic pathway of adenosylcobalamin synthesis. This vitamin is essential for the carbon rearrangement reaction catalysed by the mutase. These findings provide data for the identification of potential 2-methylpropene degraders., (© 2023 The Authors. Environmental Microbiology published by Applied Microbiology International and John Wiley & Sons Ltd.)
- Published
- 2023
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17. Gender-specific changes of the gut microbiome correlate with tumor development in murine models of pancreatic cancer.
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Kaune T, Griesmann H, Theuerkorn K, Hämmerle M, Laumen H, Krug S, Plumeier I, Kahl S, Junca H, Gustavo Dos Anjos Borges L, Michl P, Pieper DH, and Rosendahl J
- Abstract
Pancreatic ductal adenocarcinoma (PDAC) is a devastating disease with a dismal outcome. To improve understanding of sequential microbiome changes during PDAC development we analyzed mouse models of pancreatic carcinogenesis (KC mice recapitulating pre-invasive PanIN formation, as well as KPC mice recapitulating invasive PDAC) during early tumor development and subsequent tumor progression. Diversity and community composition were analyzed depending on genotype, age, and gender. Both mouse models demonstrated concordant abundance changes of several genera influenced by one or more of the investigated factors. Abundance was significantly impacted by gender, highlighting the need to further elucidate the impact of gender differences. The findings underline the importance of the microbiome in PDAC development and indicate that microbiological screening of patients at risk and targeting the microbiome in PDAC development may be feasible in future., Competing Interests: The authors declare that they have no competing interests., (© 2023 The Author(s).)
- Published
- 2023
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18. Correction to: Biochemical and genetic characterization comparison of four extradiol dioxygenases in Rhizorhabdus wittichii RW1.
- Author
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Hassan HA, D Enza M, Armengaud J, and Pieper DH
- Published
- 2023
- Full Text
- View/download PDF
19. Vaginal and neonatal microbiota in pregnant women with preterm premature rupture of membranes and consecutive early onset neonatal sepsis.
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Dos Anjos Borges LG, Pastuschek J, Heimann Y, Dawczynski K, Schleußner E, Pieper DH, and Zöllkau J
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- Infant, Newborn, Female, Pregnancy, Humans, Pregnant Women, Cohort Studies, Prospective Studies, RNA, Ribosomal, 16S genetics, Anti-Bacterial Agents, Neonatal Sepsis, Premature Birth, Microbiota
- Abstract
Background: Preterm premature rupture of membranes (PPROM), which is associated with vaginal dysbiosis, is responsible for up to one-third of all preterm births. Consecutive ascending colonization, infection, and inflammation may lead to relevant neonatal morbidity including early-onset neonatal sepsis (EONS). The present study aims to assess the vaginal microbial composition of PPROM patients and its development under standard antibiotic therapy and to evaluate the usefulness of the vaginal microbiota for the prediction of EONS. It moreover aims to decipher neonatal microbiota at birth as possible mirror of the in utero microbiota., Methods: As part of the PEONS prospective multicenter cohort study, 78 women with PPROM and their 89 neonates were recruited. Maternal vaginal and neonatal pharyngeal, rectal, umbilical cord blood, and meconium microbiota were analyzed by 16S rRNA gene sequencing. Significant differences between the sample groups were evaluated using permutational multivariate analysis of variance and differently distributed taxa by the Mann-Whitney test. Potential biomarkers for the prediction of EONS were analyzed using the MetaboAnalyst platform., Results: Vaginal microbiota at admission after PPROM were dominated by Lactobacillus spp. Standard antibiotic treatment triggers significant changes in microbial community (relative depletion of Lactobacillus spp. and relative enrichment of Ureaplasma parvum) accompanied by an increase in bacterial diversity, evenness and richness. The neonatal microbiota showed a heterogeneous microbial composition where meconium samples were characterized by specific taxa enriched in this niche. The vaginal microbiota at birth was shown to have the potential to predict EONS with Escherichia/Shigella and Facklamia as risk taxa and Anaerococcus obesiensis and Campylobacter ureolyticus as protective taxa. EONS cases could also be predicted at a reasonable rate from neonatal meconium communities with the protective taxa Bifidobacterium longum, Agathobacter rectale, and S. epidermidis as features., Conclusions: Vaginal and neonatal microbiota analysis by 16S rRNA gene sequencing after PPROM may form the basis of individualized risk assessment for consecutive EONS. Further studies on extended cohorts are necessary to evaluate how far this technique may in future close a diagnostic gap to optimize and personalize the clinical management of PPROM patients., Trial Registration: NCT03819192, ClinicalTrials.gov. Registered on January 28, 2019., (© 2023. The Author(s).)
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- 2023
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20. Coupled C, H, N, S and Fe biogeochemical cycles operating in the continental deep subsurface of the Iberian Pyrite Belt.
- Author
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Amils R, Escudero C, Oggerin M, Puente Sánchez F, Arce Rodríguez A, Fernández Remolar D, Rodríguez N, García Villadangos M, Sanz JL, Briones C, Sánchez-Román M, Gómez F, Leandro T, Moreno-Paz M, Prieto-Ballesteros O, Molina A, Tornos F, Sánchez-Andrea I, Timmis K, Pieper DH, and Parro V
- Subjects
- In Situ Hybridization, Fluorescence, Iron metabolism, Oxidation-Reduction, Bacteria metabolism, Microbiota genetics
- Abstract
Microbial activity is a major contributor to the biogeochemical cycles that make up the life support system of planet Earth. A 613 m deep geomicrobiological perforation and a systematic multi-analytical characterization revealed an unexpected diversity associated with the rock matrix microbiome that operates in the subsurface of the Iberian Pyrite Belt (IPB). Members of 1 class and 16 genera were deemed the most representative microorganisms of the IPB deep subsurface and selected for a deeper analysis. The use of fluorescence in situ hybridization allowed not only the identification of microorganisms but also the detection of novel activities in the subsurface such as anaerobic ammonium oxidation (ANAMMOX) and anaerobic methane oxidation, the co-occurrence of microorganisms able to maintain complementary metabolic activities and the existence of biofilms. The use of enrichment cultures sensed the presence of five different complementary metabolic activities along the length of the borehole and isolated 29 bacterial species. Genomic analysis of nine isolates identified the genes involved in the complete operation of the light-independent coupled C, H, N, S and Fe biogeochemical cycles. This study revealed the importance of nitrate reduction microorganisms in the oxidation of iron in the anoxic conditions existing in the subsurface of the IPB., (© 2022 The Authors. Environmental Microbiology published by Applied Microbiology International and John Wiley & Sons Ltd.)
- Published
- 2023
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21. Out of the blue: the independent activity of sulfur-oxidizers and diatoms mediate the sudden color shift of a tropical river.
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Arce-Rodríguez A, Libby E, Castellón E, Avendaño R, Cambronero JC, Vargas M, Pieper DH, Bertilsson S, Chavarría M, and Puente-Sánchez F
- Abstract
Background: Río Celeste ("Sky-Blue River") is a river located in the Tenorio National Park (Costa Rica) that has become an important hotspot for eco-tourism due to its striking sky-blue color. A previous study indicated that this color is not caused by dissolved chemical species, but by formation of light-scattering aluminosilicate particles at the mixing point of two colorless streams, the acidic Quebrada Agria and the neutral Río Buenavista., Results: We now present microbiological information on Río Celeste and its two tributaries, as well as a more detailed characterization of the particles that occur at the mixing point. Our results overturn the previous belief that the light scattering particles are formed by the aggregation of smaller particles coming from Río Buenavista, and rather point to chemical formation of hydroxyaluminosilicate colloids when Quebrada Agria is partially neutralized by Río Buenavista, which also contributes silica to the reaction. The process is mediated by the activities of different microorganisms in both streams. In Quebrada Agria, sulfur-oxidizing bacteria generate an acidic environment, which in turn cause dissolution and mobilization of aluminum and other metals. In Río Buenavista, the growth of diatoms transforms dissolved silicon into colloidal biogenic forms which may facilitate particle precipitation., Conclusions: We show how the sky-blue color of Río Celeste arises from the tight interaction between chemical and biological processes, in what constitutes a textbook example of emergent behavior in environmental microbiology., (© 2023. The Author(s).)
- Published
- 2023
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22. Diversity of Myxobacteria Isolated from Indonesian Mangroves and Their Potential for New Antimicrobial Sources.
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Octaviana S, Primahana G, Mozef T, Borges LGA, Pieper DH, and Wink J
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- Humans, Ecosystem, Soil Microbiology, Indonesia, RNA, Ribosomal, 16S genetics, Phylogeny, Myxococcales genetics, Anti-Infective Agents
- Abstract
Mangroves are unique intertidal ecosystems that provide ecological niches to different microbes, which play various roles in nutrient recycling and diverse environmental activities. The association between myxobacteria and mangroves are hitherto poorly understood. The aim of our study was to evaluate the myxobacterial community composition as well as isolate myxobacteria and to characterize the antimicrobial activity of myxobacteria isolates from Indonesian mangroves. Twenty-five cultivable myxobacteria were affiliated in six genera: Myxococcus, Corallococcus, Archangium, Chondromyces, Racemicystis and Nannocystis of the order Myxococcales based on partial 16S rRNA gene sequences. Thirteen crude extracts showed moderate activities against at least one of human pathogenic microorganisms. The crude extract of Racemicystis sp. strain 503MSO indicated a novel compound, which has not been reported in the database yet and the identification of this compound needs further study. The myxobacterial communities of three different sampling sites were analyzed using primers adapted for the myxobacteria group identification. The results showed that myxobacterial communities are more diverse than assumed. Therefore, our study has highlighted the importance of the mangrove habitat as promising harbor of myxobacteria as well as novel antimicrobial compounds with activity against pathogenic microorganisms., (© 2022. The Author(s).)
- Published
- 2022
- Full Text
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23. Hundreds of Novel DNA Viruses From a Single Healthy Patient: Biomarker Potential for Colorectal Cancer.
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Junca H and Pieper DH
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- Biomarkers, Biomarkers, Tumor genetics, DNA Methylation, DNA Viruses, Humans, Colorectal Neoplasms diagnosis, Colorectal Neoplasms genetics
- Published
- 2022
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24. Biochemical and genetic characterization comparison of four extradiol dioxygenases in Rhizorhabdus wittichii RW1.
- Author
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Hassan HA, D Enza M, Armengaud J, and Pieper DH
- Subjects
- Dibenzofurans, Kinetics, Oxygenases, Dioxygenases, Sphingomonas
- Abstract
Rhizorhabdus (previously Sphingomonas) wittichii RW1 uses a diverse array of aromatic organic compounds as energy and carbon sources, including some extremely recalcitrant compounds such as dibenzo-p-dioxin and dibenzofuran. Extradiol dioxygenases play a key role in the metabolism of dibenzofuran (DBF), dibenzo-p-dioxin (DBD), PCBs, and various other aromatic compounds. In this study, a detailed kinetic analysis of four extradiol dioxygenases identified in R. wittichii RW1 (DbfB, Edo2, Edo3, and Edo4) showed all of them to be typical 2,3dihydroxybiphenyl (DHB) dioxygenases with DHB as preferred substrate (k
cat /Km values of 0.13-188 (µM-1 s-1 )) and only slightly lower activity against trihydroxybiphenyl (THB) whereas monocyclic substrates were, to different extents, poor substrates due to high km values. All extradiol dioxygenases analyzed were subject to mechanism-based inactivation by 2,2`,3-trihydroxybiphenylether (THBE) the intermediate of DBD degradation. However, Edo4 was superior as reflected by the relatively high partition ratio and the comparably low efficiency of inactivation. Significant differences were observed with respect to their inactivation by 3-chlorocatechol. The absence of any significant mechanism-based inactivation makes Edo3 a perfect candidate for being recruited for chlorobiphenyl degradation where inactivation of extradiol dioxygenases by this intermediate creates significant metabolic problems. KEY POINTS: • Characterization of additional extradiol dioxygenases encoded by RW1 • Identification of differences in 2,2`,3-trihydroxybiphenylether transformation • Identification of differences in inhibition by 3-chlorocatechol., (© 2022. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)- Published
- 2022
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25. The biliary microbiome in ischaemic-type biliary lesions can be shaped by stenting but is resilient to antibiotic treatment.
- Author
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Klein F, Wellhöner F, Plumeier I, Kahl S, Chhatwal P, Vital M, Voigtländer T, Pieper DH, Manns MP, Lenzen H, Solbach P, and Heidrich B
- Subjects
- Anti-Bacterial Agents therapeutic use, Humans, Ischemia, RNA, Ribosomal, 16S, Biliary Tract, Microbiota
- Abstract
This study aims to characterize the biliary microbiome as neglected factor in patients with ischaemic-type biliary lesions (ITBL) after liver transplantation. Therefore, the V1-V2 region of the 16S rRNA gene was sequenced in 175 bile samples. Samples from patients with anastomotic strictures (AS) served as controls. Multivariate analysis and in silico metagenomics were applied cross-sectionally and longitudinally. The microbial community differed significantly between ITBL and AS in terms of alpha and beta diversity. Both, antibiotic treatment and stenting were associated independently with differences in the microbial community structure. In contrast to AS, in ITBL stenting was associated with pronounced differences in the biliary microbiome, whereas no differences associated with antibiotic treatment could be observed in ITBL contrasting the pronounced differences found in AS. Bacterial pathways involved in the production of antibacterial metabolites were increased in ITBL with antibiotic treatment. After liver transplantation, the biliary tract harbours a complex microbial community with significant differences between ITBL and AS. Fundamental changes in the microbial community in ITBL can be achieved with biliary stenting. However, the effect of antibiotic treatment in ITBL was minimal. Therefore, antibiotics should be administered wisely in order to reduce emerging resistance of the biliary microbiome towards external antibiotics., (© 2022 The Authors. Liver International published by John Wiley & Sons Ltd.)
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- 2022
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26. Transfer of FRozen Encapsulated multi-donor Stool filtrate for active ulcerative Colitis (FRESCO): study protocol for a prospective, multicenter, double-blind, randomized, controlled trial.
- Author
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Stallmach A, Grunert P, Stallhofer J, Löffler B, Baier M, Rödel J, Kiehntopf M, Neugebauer S, Pieper DH, Junca H, Tannapfel A, Merkel U, Schumacher U, Breternitz-Gruhne M, Heller T, Schauer A, Hartmann M, and Steube A
- Subjects
- Double-Blind Method, Fecal Microbiota Transplantation adverse effects, Fecal Microbiota Transplantation methods, Feces, Humans, Multicenter Studies as Topic, Prospective Studies, Randomized Controlled Trials as Topic, Treatment Outcome, Colitis, Ulcerative diagnosis, Colitis, Ulcerative therapy
- Abstract
Background: Ulcerative colitis (UC) is a chronic inflammatory bowel disease with significant morbidity and mortality. Although the precise cause remains unknown, disturbances in the intestinal microbial community have been linked to its pathogenesis. Randomized controlled trials in UC and relapsing Clostridioides difficile infection (CDI) have established fecal microbiota (FM) transfer (FMT) as an effective therapy. In this context, preliminary results indicated that the transfer of sterile fecal microbiota filtrates (<0.2 μm; FMF, FMFT) of donor stool also drives gastrointestinal microbiota changes and eliminates symptoms in CDI patients. However, along with the success of FMT, regulatory agencies issued safety alerts following reports of serious adverse events due to transmission of enteric pathogens through FMT. To reduce this risk, we established an extensive test protocol for our donors and quarantine regulations for the produced capsules, but alternative concepts are desirable., Methods: Our project is a randomized, controlled, longitudinal, prospective, three-arm, multicenter, double-blind study to determine the safety and efficacy of repeated long-term, multi-donor FM or FMF transfers compared to placebo using oral, frozen capsules in 174 randomized patients with mild to moderate active UC. The primary outcome will be clinical remission at week 12., Discussion: This proposal aims to examine (a) the efficacy of encapsulated transfer of FM and FMF as a therapy for mild to moderate UC, (b) the short- and long-term safety of FMT and FMFT in patients with UC, and (c) the microbial and immunologic changes that occur after FMT and FMFT to help understand how and why it affects inflammatory bowel disease., Trial Registration: ClinicalTrials.gov NCT03843385 . DRKS (Deutsches Register für Klinische Studien) DRKS00020471., (© 2022. The Author(s).)
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- 2022
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27. The emerging potential of microbiome transplantation on human health interventions.
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Junca H, Pieper DH, and Medina E
- Abstract
The human microbiome has been the subject of intense research over the past few decades, in particular as a promising area for new clinical interventions. The microbiota colonizing the different body surfaces are of benefit for multiple physiological and metabolic processes of the human host and increasing evidence suggests an association between disturbances in the composition and functionality of the microbiota and several pathological conditions. This has provided a rationale for beneficial modulation of the microbiome. One approach being explored for modulating the microbiota in diseased individuals is transferring microbiota or microbiota constituents from healthy donors via microbiome transplantation. The great success of fecal microbiome transplantation for the treatment of Clostridioides difficile infections has encouraged the application of this procedure for the treatment of other diseases such as vaginal disorders via transplantation of vaginal microbiota, or of skin pathologies via the transplantation of skin microbiota. Microbiome modulation could even become a novel strategy for improving the efficacy of cancer therapies. This review discusses the principle, advantages and limitations of microbiome transplantation as well as different clinical contexts where microbiome transplantation has been applied., Competing Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (© 2022 The Author(s).)
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- 2022
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28. Higher Trimethylamine- N -Oxide Plasma Levels with Increasing Age Are Mediated by Diet and Trimethylamine-Forming Bacteria.
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Rath S, Rox K, Kleine Bardenhorst S, Schminke U, Dörr M, Mayerle J, Frost F, Lerch MM, Karch A, Brönstrup M, Pieper DH, and Vital M
- Abstract
The gut microbiota-dependent metabolite trimethylamine- N -oxide (TMAO) is linked to an increased risk for cardiovascular diseases. Trimethylamine (TMA), which is subsequently oxidized to TMAO in the liver, is formed by intestinal bacteria via distinct biochemical routes from dietary precursors that are enriched in animal product-based foods. To get a full picture of the entire process of the diet > gut microbiota > TMAO axis, we quantified potential TMA-forming gut bacteria and plasma metabolites using gene-targeted assays and targeted metabolomics on a subsample ( n = 425) of a German population-based cohort study. We specifically compared persons reporting daily meat intake with those that rarely or never consume meat. While meat intake did not predict TMAO plasma levels in our study, two major bacterial TMA-forming pathways were linked to the metabolite's concentration. Furthermore, advancing age was strongly associated with TMAO. Construction of a structural equation model allowed us to disentangle the different routes that promote higher TMAO levels with increasing age, demonstrating, for the first time, a functional role of gut microbiota in the process, where specific food items augmented abundances of TMA-forming bacteria that were associated with higher TMAO plasma concentrations. Analyses stratified by age showed an association between carotid intima-media thickness and TMAO only in individuals >65 of age, indicating that this group is particularly affected by the metabolite. IMPORTANCE Many cohort studies have investigated the link between diet and plasma TMAO levels, reporting incongruent results, while gut microbiota were only recently included into analyses. In these studies, taxonomic data were recorded that are not a good proxy for TMA formation, as specific members of various taxa exhibit genes catalyzing this reaction, demanding function-based technologies for accurate quantification of TMA-synthesizing bacteria. Using this approach, we demonstrated that abundances of the main components leading to TMAO formation, i.e., TMA precursors and TMA-forming bacteria, are uncoupled and not governed by the same (dietary) factors. Results emphasize that all levels leading to TMA(O) formation should be considered for accurate risk assessment, rejecting the simple view that diets rich in TMA precursors directly lead to increased plasma levels of this hazardous compound. The results can assist in developing strategies to reduce TMAO levels, specifically in the elderly, who are prone to TMAO-associated diseases.
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- 2021
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29. Free human DNA attenuates the activity of antimicrobial peptides in atopic dermatitis.
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Kopfnagel V, Dreyer S, Zeitvogel J, Pieper DH, Buch A, Sodeik B, Rademacher F, Harder J, and Werfel T
- Subjects
- Antimicrobial Cationic Peptides, DNA, Humans, Pore Forming Cytotoxic Proteins, Skin, Dermatitis, Atopic drug therapy
- Abstract
Background: The high susceptibility of AD patients to microbial skin infections has been attributed to a deficient antimicrobial peptide (AMP) expression, which is contradicted by a growing amount of recent studies clearly demonstrating that AMP expression is not impaired in lesional skin of AD patients. The reasons for the high susceptibility of AD patients to microbial infections are still unknown., Methods: The influence of self-DNA on the antimicrobial activity of RNase 7, LL-37, and hBD2 has been investigated using antibacterial and antiviral assays. The amount of self-DNA on skin has been analyzed by skin rinsings and subsequent quantification using dsDNA assays. DNA source was identified by qPCR., Results: Complex formation of the AMPs with self-DNA significantly impaired their antibacterial activity against Staphylococcus aureus and their antiviral activity against HSV-1. The inhibition of the antibacterial activity was dependent on the DNA concentration but not on the length of the DNA molecules. Of note, we detected significant higher amounts of cell-free self-DNA in skin rinses taken from lesional AD skin compared to skin rinses from non-lesional skin and from normal skin of healthy donors. Consequently, rinse solution from AD lesional skin prevented antibacterial activity of LL-37., Conclusion: Our study indicates that extracellular self-DNA is released in considerable amounts in AD skin lesions and AMP-self-DNA-complex formation leads to a significant loss of antibacterial and antiviral activity in atopic dermatitis. Studies on strategies to reduce the amount of extracellular DNA in AD are needed to identify possible methods relevant in clinical settings., (© 2021 EAACI and John Wiley and Sons A/S. Published by John Wiley and Sons Ltd.)
- Published
- 2021
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30. An Innovative Protocol for Metaproteomic Analyses of Microbial Pathogens in Cystic Fibrosis Sputum.
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Graf AC, Striesow J, Pané-Farré J, Sura T, Wurster M, Lalk M, Pieper DH, Becher D, Kahl BC, and Riedel K
- Subjects
- Bacteria genetics, Humans, Lung, Sputum, Cystic Fibrosis complications, Microbiota
- Abstract
Hallmarks of cystic fibrosis (CF) are increased viscosity of mucus and impaired mucociliary clearance within the airways due to mutations of the cystic fibrosis conductance regulator gene. This facilitates the colonization of the lung by microbial pathogens and the concomitant establishment of chronic infections leading to tissue damage, reduced lung function, and decreased life expectancy. Although the interplay between key CF pathogens plays a major role during disease progression, the pathophysiology of the microbial community in CF lungs remains poorly understood. Particular challenges in the analysis of the microbial population present in CF sputum is (I) the inhomogeneous, viscous, and slimy consistence of CF sputum, and (II) the high number of human proteins masking comparably low abundant microbial proteins. To address these challenges, we used 21 CF sputum samples to develop a reliable, reproducible and widely applicable protocol for sputum processing, microbial enrichment, cell disruption, protein extraction and subsequent metaproteomic analyses. As a proof of concept, we selected three sputum samples for detailed metaproteome analyses and complemented and validated metaproteome data by 16S sequencing, metabolomic as well as microscopic analyses. Applying our protocol, the number of bacterial proteins/protein groups increased from 199-425 to 392-868 in enriched samples compared to nonenriched controls. These early microbial metaproteome data suggest that the arginine deiminase pathway and multiple proteases and peptidases identified from various bacterial genera could so far be underappreciated in their contribution to the CF pathophysiology. By providing a standardized and effective protocol for sputum processing and microbial enrichment, our study represents an important basis for future studies investigating the physiology of microbial pathogens in CF in vivo - an important prerequisite for the development of novel antimicrobial therapies to combat chronic recurrent airway infection in CF., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 Graf, Striesow, Pané-Farré, Sura, Wurster, Lalk, Pieper, Becher, Kahl and Riedel.)
- Published
- 2021
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31. A simplified LC-MS/MS method for the quantification of the cardiovascular disease biomarker trimethylamine- N -oxide and its precursors.
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Rox K, Rath S, Pieper DH, Vital M, and Brönstrup M
- Abstract
Trimethylamine- N -oxide (TMAO) has emerged as a potential biomarker for atherosclerosis and the development of cardiovascular diseases (CVDs). Although several clinical studies have shown striking associations of TMAO levels with atherosclerosis and CVDs, TMAO determinations are not clinical routine yet. The current methodology relies on isotope-labeled internal standards, which adds to pre-analytical complexity and costs for the quantification of TMAO and its precursors carnitine, betaine or choline. Here, we report a liquid chromatography-tandem mass spectrometry based method that is fast (throughput up to 240 samples/day), consumes low sample volumes (e.g., from a finger prick), and does not require isotope-labeled standards. We circumvented the analytical problem posed by the presence of endogenous TMAO and its precursors in human plasma by using an artificial plasma matrix for calibration. We cross-validated the results obtained using an artificial matrix with those using mouse plasma matrix and demonstrated that TMAO, carnitine, betaine and choline were accurately quantified in 'real-life' human plasma samples from healthy volunteers, obtained either from a finger prick or from venous puncture. Additionally, we assessed the stability of samples stored at -20 °C and room temperature. Whereas all metabolites were stable at -20 °C, increasing concentrations of choline were determined when stored at room temperature. Our method will facilitate the establishment of TMAO as a routine clinical biomarker in hematology in order to assess the risk for CVDs development, or to monitor disease progression and intervention effects., Competing Interests: The authors declare that there are no conflicts of interest., (© 2021 Xi'an Jiaotong University. Production and hosting by Elsevier B.V.)
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- 2021
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32. Lethal Neonatal Respiratory Failure by Perinatal Transmission of Ureaplasma Parvum after Maternal PPROM.
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Zöllkau J, Pieper DH, Pastuschek J, Makarewicz O, Mentzel HJ, Dawczynski K, and Schleußner E
- Subjects
- Cesarean Section, Female, Gestational Age, Humans, Infant, Newborn, Infant, Premature, Infectious Disease Transmission, Vertical prevention & control, Pregnancy, Ureaplasma genetics, Fetal Membranes, Premature Rupture diagnosis, Respiratory Insufficiency
- Abstract
A primiparous pregnant woman was admitted due to preterm premature rupture of membranes (PPROM) at 27+0 week of gestational age (WGA). Conventional vaginal microbiological analysis had no pathological finding. Management decisions based on national guidelines included antenatal corticoids, tocolytics and antibiotics. Unstoppable efforts of preterm labor in 28+0 WGA and supposed amniotic infection syndrome necessitated emergency cesarean section. The preterm infant underwent NICU therapy, developed an early-onset neonatal sepsis and therapy-refractory pulmonary insufficiency with consecutive right heart failure, resulting in death on the 36
th day of life. Microbiota analyses by 16Sr DNA sequencing was performed from maternal vaginal swabs and from neonatal pharyngeal swabs. Maternal antibiotic treatment resulted in depletion of physiological vaginal colonization with Lactobacillus crispatus . Ureaplasma parvum became the dominant vaginal microorganism at delivery and was detected in high relative abundance in the neonatal specimen. Progressive radiological air-space changes and interstitial pathologies associated with Ureaplasma infection (bronchopulmonary dysplasia type III) were seen early at the 3rd and distinctly from 14th day of life. This clearly demonstrates the need of vaginal colonization diagnostics in PPROM patients and awareness of the consecutive risks in the preterm. Vaginal microbiome analysis may allow individualized and targeted maternal and fetal diagnostic, prophylactic and therapeutic strategies to identify, protect and treat the high-risk neonates after PPROM., Competing Interests: The authors declare that they have no conflict of interest., (Thieme. All rights reserved.)- Published
- 2021
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33. Eradication of Chronic HCV Infection: Improvement of Dysbiosis Only in Patients Without Liver Cirrhosis.
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Wellhöner F, Döscher N, Woelfl F, Vital M, Plumeier I, Kahl S, Potthoff A, Manns MP, Pieper DH, Cornberg M, Wedemeyer H, and Heidrich B
- Subjects
- Adult, Aged, Aged, 80 and over, Dysbiosis immunology, Dysbiosis microbiology, Elasticity Imaging Techniques, Female, Hepacivirus immunology, Hepacivirus isolation & purification, Hepatitis C, Chronic immunology, Hepatitis C, Chronic pathology, Hepatitis C, Chronic virology, Humans, Liver diagnostic imaging, Liver pathology, Liver virology, Liver Cirrhosis immunology, Liver Cirrhosis pathology, Liver Cirrhosis virology, Male, Middle Aged, Prospective Studies, Sustained Virologic Response, Antiviral Agents therapeutic use, Dysbiosis diagnosis, Gastrointestinal Microbiome immunology, Hepatitis C, Chronic drug therapy, Liver Cirrhosis diagnosis
- Abstract
Background and Aims: It is well accepted that liver diseases and their outcomes are associated with intestinal microbiota, but causality is difficult to establish. The intestinal microbiota are altered in patients with hepatitis C. As chronic HCV infection can now be cured in almost all patients, it is an ideal model to study the influence of liver disease on the microbiota., Approach and Results: We aimed to prospectively analyze the changes in the gut microbiome in patients who received direct-acting antivirals (DAA) and achieved sustained virological response (SVR). Amplicon sequencing of the V1-V2 region in the 16S ribosomal RNA gene was performed in stool samples of patients with chronic hepatitis C. Patients in the treatment group received DAA (n = 65), whereas in the control group, no DAA were given (n = 33). Only patients achieving SVR were included. The alpha diversity increased numerically but not significantly from baseline to SVR at week 24 or 48 (SVR24/48; 2.784 ± 0.248 vs. 2.846 ± 0.224; P = 0.057). When stratifying for the presence of liver cirrhosis, a significant increase in diversity was only seen in patients without cirrhosis. Differences in the microbial community structure induced by the achievement of SVR were only observed in patients without liver cirrhosis. In patients with liver cirrhosis and in the control group, no significant differences were observed., Conclusions: In conclusion, the achievement of SVR24/48 in patients with chronic HCV was associated with changes in the intestinal microbiota. However, these changes were only seen in patients without liver cirrhosis. A major role of liver remodeling on the intestinal microbiota is indicated by the dynamics of the intestinal microbial community structure depending on the stage of fibrosis in patients resolving chronic hepatitis C., (© 2021 The Authors. Hepatology published by Wiley Periodicals LLC on behalf of American Association for the Study of Liver Diseases.)
- Published
- 2021
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34. Broad Spectrum Antibiotic Xanthocillin X Effectively Kills Acinetobacter baumannii via Dysregulation of Heme Biosynthesis.
- Author
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Hübner I, Shapiro JA, Hoßmann J, Drechsel J, Hacker SM, Rather PN, Pieper DH, Wuest WM, and Sieber SA
- Abstract
Isonitrile natural products exhibit promising antibacterial activities. However, their mechanism of action (MoA) remains largely unknown. Based on the nanomolar potency of xanthocillin X ( Xan ) against diverse difficult-to-treat Gram-negative bacteria, including the critical priority pathogen Acinetobacter baumannii , we performed in-depth studies to decipher its MoA. While neither metal binding nor cellular protein targets were detected as relevant for Xan 's antibiotic effects, sequencing of resistant strains revealed a conserved mutation in the heme biosynthesis enzyme porphobilinogen synthase (PbgS). This mutation caused impaired enzymatic efficiency indicative of reduced heme production. This discovery led to the validation of an untapped mechanism, by which direct heme sequestration of Xan prevents its binding into cognate enzyme pockets resulting in uncontrolled cofactor biosynthesis, accumulation of porphyrins, and corresponding stress with deleterious effects for bacterial viability. Thus, Xan represents a promising antibiotic displaying activity even against multidrug resistant strains, while exhibiting low toxicity to human cells., Competing Interests: The authors declare no competing financial interest., (© 2021 The Authors. Published by American Chemical Society.)
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- 2021
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35. Temperature and elemental sulfur shape microbial communities in two extremely acidic aquatic volcanic environments.
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Rojas-Gätjens D, Arce-Rodríguez A, Puente-Sánchez F, Avendaño R, Libby E, Mora-Amador R, Rojas-Jimenez K, Fuentes-Schweizer P, Pieper DH, and Chavarría M
- Subjects
- Acids, Archaea classification, Bacteria classification, Costa Rica, Hydrogen-Ion Concentration, RNA, Ribosomal, 16S genetics, Rivers, Volcanic Eruptions, Hot Temperature, Microbiota, Phylogeny, Sulfur
- Abstract
Aquatic environments of volcanic origin provide an exceptional opportunity to study the adaptations of microorganisms to early planet life conditions. Here, we characterized the prokaryotic communities and physicochemical properties of seepage sites at the bottom of the Poas Volcano crater and the Agrio River, two geologically related extremely acidic environments located in Costa Rica. Both locations hold a low pH (1.79-2.20) and have high sulfate and iron concentrations (Fe = 47-206 mg/L, SO
4 2- = 1170-2460 mg/L), but significant differences in their temperature (90.0-95.0 ºC in the seepages at Poas Volcano, 19.1-26.6 ºC in Agrio River) and in the elemental sulfur content. Based on the analysis of 16S rRNA gene sequences, we determined that Sulfobacillus spp. represented more than half of the sequences in Poas Volcano seepage sites, while Agrio River was dominated by Leptospirillum and members of the archaeal order Thermoplasmatales. Both environments share some chemical characteristics and part of their microbiota, however, the temperature and the reduced sulfur are likely the main distinguishing features, ultimately shaping their microbial communities. Our data suggest that in the Poas Volcano-Agrio River system there is a common metabolism but with specialization of species that adapt to the physicochemical conditions of each environment.- Published
- 2021
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36. Impact of healthy aging on active bacterial assemblages throughout the gastrointestinal tract.
- Author
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Schütte K, Schulz C, Vilchez-Vargas R, Vasapolli R, Palm F, Simon B, Schomburg D, Lux A, Geffers R, Pieper DH, Link A, and Malfertheiner P
- Subjects
- Adult, Aged, Aged, 80 and over, Bacteria genetics, Bacteria isolation & purification, DNA, Bacterial genetics, Feces microbiology, Female, Humans, Male, Middle Aged, Probiotics analysis, Prospective Studies, RNA, Ribosomal, 16S genetics, Saliva microbiology, Aging, Bacteria classification, Gastrointestinal Microbiome physiology, Host Microbial Interactions physiology, Intestinal Mucosa microbiology
- Abstract
The adaption of gut microbiota (GM) throughout human life is a key factor in maintaining health. Interventions to restore a healthy GM composition may have the potential to improve health and disease outcomes in the elderly. We performed a comprehensive characterization of changes in the luminal and mucosa-associated microbiota composition in elderly compared with younger healthy individuals. Samples from saliva and feces, and biopsies from the upper and lower gastrointestinal tract (UGIT, LGIT), were collected from 59 asymptomatic individuals grouped by age: 40-55, 56-70, and 71-85 years). All underwent anthropometric, geriatric, and nutritional assessment. RNA was extracted and reverse-transcribed into complementary DNA; the V1-V2 regions of 16S ribosomal RNA genes were amplified and sequenced. Abundances of the taxa in all taxonomic ranks in each sample type were used to construct sample-similarity matrices by the Bray-Curtis algorithm. Significant differences between defined groups were assessed by analysis of similarity. The bacterial community showed strong interindividual variations and a clear distinction between samples from UGIT, LGIT, and feces. While in saliva some taxa were affected by aging, this number was considerably greater in UGIT and was subsequently higher in LGIT. Unexpectedly, aging scarcely influenced the bacterial community of feces over the age range of 40-85 years. The development of interventions to preserve and restore human health with increased age by establishing a healthy gut microbiome should not rely solely on data from fecal analysis, as the intestinal mucosa is affected by more significant changes, which differ from those observed in fecal analyses.
- Published
- 2021
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37. Microbial Community Structure Along a Horizontal Oxygen Gradient in a Costa Rican Volcanic Influenced Acid Rock Drainage System.
- Author
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Arce-Rodríguez A, Puente-Sánchez F, Avendaño R, Libby E, Mora-Amador R, Rojas-Jimenez K, Martínez M, Pieper DH, and Chavarría M
- Subjects
- Costa Rica, Hydrogen-Ion Concentration, RNA, Archaeal analysis, RNA, Bacterial analysis, RNA, Ribosomal, 16S analysis, Rivers, Volcanic Eruptions, Archaea isolation & purification, Bacteria isolation & purification, Microbiota physiology, Oxygen analysis
- Abstract
We describe the geochemistry and microbial diversity of a pristine environment that resembles an acid rock drainage (ARD) but it is actually the result of hydrothermal and volcanic influences. We designate this environment, and other comparable sites, as volcanic influenced acid rock drainage (VARD) systems. The metal content and sulfuric acid in this ecosystem stem from the volcanic milieu and not from the product of pyrite oxidation. Based on the analysis of 16S rRNA gene amplicons, we report the microbial community structure in the pristine San Cayetano Costa Rican VARD environment (pH = 2.94-3.06, sulfate ~ 0.87-1.19 g L
-1 , iron ~ 35-61 mg L-1 (waters), and ~ 8-293 g kg-1 (sediments)). San Cayetano was found to be dominated by microorganisms involved in the geochemical cycling of iron, sulfur, and nitrogen; however, the identity and abundance of the species changed with the oxygen content (0.40-6.06 mg L-1 ) along the river course. The hypoxic source of San Cayetano is dominated by a putative anaerobic sulfate-reducing Deltaproteobacterium. Sulfur-oxidizing bacteria such as Acidithiobacillus or Sulfobacillus are found in smaller proportions with respect to typical ARD. In the oxic downstream, we identified aerobic iron-oxidizers (Leptospirillum, Acidithrix, Ferrovum) and heterotrophic bacteria (Burkholderiaceae bacterium, Trichococcus, Acidocella). Thermoplasmatales archaea closely related to environmental phylotypes found in other ARD niches were also observed throughout the entire ecosystem. Overall, our study shows the differences and similarities in the diversity and distribution of the microbial communities between an ARD and a VARD system at the source and along the oxygen gradient that establishes on the course of the river.- Published
- 2020
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38. Importance of superoxide dismutases A and M for protection of Staphylococcus aureus in the oxidative stressful environment of cystic fibrosis airways.
- Author
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Treffon J, Chaves-Moreno D, Niemann S, Pieper DH, Vogl T, Roth J, and Kahl BC
- Subjects
- A549 Cells, Bacterial Proteins genetics, Epithelial Cells microbiology, Fibrosis, Gene Expression Regulation, Bacterial, Humans, Superoxide Dismutase genetics, Transcriptome, Virulence, Virulence Factors, Bacterial Proteins metabolism, Cystic Fibrosis microbiology, Oxidative Stress, Respiratory System microbiology, Staphylococcus aureus enzymology, Superoxide Dismutase metabolism
- Abstract
Staphylococcus aureus is one of the earliest pathogens that persists the airways of cystic fibrosis (CF) patients and contributes to increased inflammation and decreased lung function. In contrast to other staphylococci, S. aureus possesses two superoxide dismutases (SODs), SodA and SodM, with SodM being unique to S. aureus. Both SODs arm S. aureus for its fight against oxidative stress, a by-product of inflammatory reactions. Despite complex investigations, it is still unclear if both enzymes are crucial for the special pathogenicity of S. aureus. To investigate the role of both SODs during staphylococcal persistence in CF airways, we analysed survival and gene expression of S. aureus CF isolates and laboratory strains in different CF-related in vitro and ex vivo settings. Bacteria located in inflammatory and oxidised CF sputum transcribed high levels of sodA and sodM. Especially expression values of sodM were remarkably higher in CF sputum than in bacterial in vitro cultures. Interestingly, also S. aureus located in airway epithelial cells expressed elevated transcript numbers of both SODs, indicating that S. aureus is exposed to oxidative stress at various sites within CF airways. Both enzymes promoted survival of S. aureus during polymorphonuclear leukocyte killing and seem to act compensatory, thereby giving evidence that the interwoven interaction of SodA and SodM contributes to S. aureus virulence and facilitates S. aureus persistence within CF airways., (© 2020 The Authors. Cellular Microbiology published by John Wiley & Sons Ltd.)
- Published
- 2020
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39. A combination of genetics and microbiota influences the severity of the obesity phenotype in diet-induced obesity.
- Author
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Smoczek M, Vital M, Wedekind D, Basic M, Zschemisch NH, Pieper DH, Siebert A, Bleich A, and Buettner M
- Subjects
- Animals, Diet, High-Fat adverse effects, Male, Mice, Mice, Inbred C57BL, Obesity etiology, Obesity microbiology, Obesity pathology, Gastrointestinal Microbiome, Genotype, Obesity genetics, Phenotype
- Abstract
Obesity has emerged as a major global health problem and is associated with various diseases, such as metabolic syndrome, type 2 diabetes mellitus, and cardiovascular diseases. The inbred C57BL/6 mouse strain is often used for various experimental investigations, such as metabolic research. However, over time, genetically distinguishable C57BL/6 substrains have evolved. The manifestation of genetic alterations has resulted in behavioral and metabolic differences. In this study, a comparison of diet-induced obesity in C57BL/6JHanZtm, C57BL/6NCrl and C57BL/6 J mice revealed several metabolic and immunological differences such as blood glucose level and cytokine expression, respectively, among these C57BL/6 substrains. For example, C57BL/6NCrl mice developed the most pronounced adiposity, whereas C57BL/6 J mice showed the highest impairment in glucose tolerance. Moreover, our results indicated that the immunological phenotype depends on the intestinal microbiota, as the cell subset composition of the colon was similar in obese ex-GF B6NRj
B6JHanZtm and obese B6JHanZtm mice. Phenotypic differences between C57BL/6 substrains are caused by a complex combination of genetic and microbial alterations. Therefore, in performing metabolic research, considering substrain-specific characteristics, which can influence the course of study, is important. Moreover, for unbiased comparison of data, the entire strain name should be shared with the scientific community.- Published
- 2020
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40. Toward Biorecycling: Isolation of a Soil Bacterium That Grows on a Polyurethane Oligomer and Monomer.
- Author
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Espinosa MJC, Blanco AC, Schmidgall T, Atanasoff-Kardjalieff AK, Kappelmeyer U, Tischler D, Pieper DH, Heipieper HJ, and Eberlein C
- Abstract
The fate of plastic waste and a sustainable use of synthetic polymers is one of the major challenges of the twenty first century. Waste valorization strategies can contribute to the solution of this problem. Besides chemical recycling, biological degradation could be a promising tool. Among the high diversity of synthetic polymers, polyurethanes are widely used as foams and insulation materials. In order to examine bacterial biodegradability of polyurethanes, a soil bacterium was isolated from a site rich in brittle plastic waste. The strain, identified as Pseudomonas sp. by 16S rRNA gene sequencing and membrane fatty acid profile, was able to grow on a PU-diol solution, a polyurethane oligomer, as the sole source of carbon and energy. In addition, the strain was able to use 2,4-diaminotoluene, a common precursor and putative degradation intermediate of polyurethanes, respectively, as sole source of energy, carbon, and nitrogen. Whole genome sequencing of the strain revealed the presence of numerus catabolic genes for aromatic compounds. Growth on potential intermediates of 2,4-diaminotoluene degradation, other aromatic growth substrates and a comparison with a protein data base of oxygenases present in the genome, led to the proposal of a degradation pathway., (Copyright © 2020 Cárdenas Espinosa, Colina Blanco, Schmidgall, Atanasoff-Kardjalieff, Kappelmeyer, Tischler, Pieper, Heipieper and Eberlein.)
- Published
- 2020
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41. Repurposing human kinase inhibitors to create an antibiotic active against drug-resistant Staphylococcus aureus, persisters and biofilms.
- Author
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Le P, Kunold E, Macsics R, Rox K, Jennings MC, Ugur I, Reinecke M, Chaves-Moreno D, Hackl MW, Fetzer C, Mandl FAM, Lehmann J, Korotkov VS, Hacker SM, Kuster B, Antes I, Pieper DH, Rohde M, Wuest WM, Medina E, and Sieber SA
- Subjects
- Animals, Anti-Bacterial Agents chemical synthesis, Anti-Bacterial Agents pharmacokinetics, Autolysis chemically induced, Benzodioxoles chemical synthesis, Benzodioxoles pharmacokinetics, Biofilms drug effects, Cell Line, Tumor, Female, Humans, Male, Methicillin-Resistant Staphylococcus aureus physiology, Mice, Inbred C57BL, Microbial Sensitivity Tests, Molecular Dynamics Simulation, Molecular Structure, Protein Kinase Inhibitors chemistry, Sorafenib pharmacokinetics, Structure-Activity Relationship, Anti-Bacterial Agents therapeutic use, Benzodioxoles therapeutic use, Drug Repositioning, Methicillin-Resistant Staphylococcus aureus drug effects, Protein Kinase Inhibitors pharmacology, Sorafenib analogs & derivatives, Sorafenib therapeutic use
- Abstract
New drugs are desperately needed to combat methicillin-resistant Staphylococcus aureus (MRSA) infections. Here, we report screening commercial kinase inhibitors for antibacterial activity and found the anticancer drug sorafenib as major hit that effectively kills MRSA strains. Varying the key structural features led to the identification of a potent analogue, PK150, that showed antibacterial activity against several pathogenic strains at submicromolar concentrations. Furthermore, this antibiotic eliminated challenging persisters as well as established biofilms. PK150 holds promising therapeutic potential as it did not induce in vitro resistance, and shows oral bioavailability and in vivo efficacy. Analysis of the mode of action using chemical proteomics revealed several targets, which included interference with menaquinone biosynthesis by inhibiting demethylmenaquinone methyltransferase and the stimulation of protein secretion by altering the activity of signal peptidase IB. Reduced endogenous menaquinone levels along with enhanced levels of extracellular proteins of PK150-treated bacteria support this target hypothesis. The associated antibiotic effects, especially the lack of resistance development, probably stem from the compound's polypharmacology.
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- 2020
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42. Identification of benzene-degrading Proteobacteria in a constructed wetland by employing in situ microcosms and RNA-stable isotope probing.
- Author
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Nitz H, Duarte M, Jauregui R, Pieper DH, Müller JA, and Kästner M
- Subjects
- Carbon Isotopes, Proteobacteria isolation & purification, RNA, Bacterial genetics, RNA, Ribosomal, 16S genetics, Benzene metabolism, Proteobacteria classification, Proteobacteria metabolism, Wetlands
- Abstract
Constructed wetlands (CWs) are effective ecological remediation technologies for various contaminated water bodies. Here, we queried for benzene-degrading microbes in a horizontal subsurface flow CW with reducing conditions in the pore water and fed with benzene-contaminated groundwater. For identification of relevant microbes, we employed in situ microcosms (BACTRAPs, which are made from granulated activated carbon) coupled with
13 C-stable isotope probing and Illumina sequencing of 16S rRNA amplicons. A significant incorporation of13 C was detected in RNA isolated from BACTRAPs loaded with13 C-benzene and exposed in the CW for 28 days. A shorter incubation time did not result in detectable13 C incorporation. After 28 days, members from four genera, namely Dechloromonas, Hydrogenophaga, and Zoogloea from the Betaproteobacteria and Arcobacter from the Epsilonproteobacteria were significantly labeled with13 C and were abundant in the bacterial community on the BACTRAPs. Sequences affiliated to Geobacter were also numerous on the BACTRAPs but apparently those microbes did not metabolize benzene as no13 C label incorporation was detected. Instead, they may have metabolized plant-derived organic compounds while using the BACTRAPs as electron sink. In representative wetland samples, sequences affiliated with Dechloromonas, Zoogloea, and Hydrogenophaga were present at relative proportions of up to a few percent. Sequences affiliated with Arcobacter were present at < 0.01% in wetland samples. In conclusion, we identified microbes of likely significance for benzene degradation in a CW used for remediation of contaminated water.- Published
- 2020
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43. Potential TMA-Producing Bacteria Are Ubiquitously Found in Mammalia.
- Author
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Rath S, Rud T, Pieper DH, and Vital M
- Abstract
Human gut bacteria metabolize dietary components such as choline and carnitine to trimethylamine (TMA) that is subsequently oxidized to trimethylamine- N -oxide (TMAO) by hepatic enzymes. Increased plasma levels of TMAO are associated with the development of cardiovascular and renal disease. In this study, we applied gene-targeted assays in order to quantify (qPCR) and characterize (MiSeq) bacterial genes encoding enzymes responsible for TMA production, namely choline-TMA lyase ( CutC ), carnitine oxygenase ( CntA ) and betaine reductase ( GrdH ) in 89 fecal samples derived from various mammals spanning three dietary groups (carnivores, omnivores and herbivores) and four host orders (Carnivora, Primates, Artiodactyla and Perissodactyla). All samples contained potential TMA-producing bacteria, however, at low abundances (<1.2% of total community). The cutC gene was more abundant in omnivores and carnivores compared with herbivores. C ntA was almost absent from herbivores and grdH showed lowest average abundance of all three genes. Bacteria harboring cutC and grdH displayed high diversities where sequence types affiliated with various taxa within Firmicutes dominated, whereas cntA comprised sequences primarily linked to Escherichia . Composition of TMA-forming communities was strongly influenced by diet and host taxonomy and despite their high correlation, both factors contributed uniquely to community structure. Furthermore, Random Forest (RF) models could differentiate between groups at high accuracies. This study gives a comprehensive overview of potential TMA-producing bacteria in the mammalian gut demonstrating that both diet and host taxonomy govern their abundance and composition. It highlights the role of functional redundancy sustaining potential TMA formation in distinct gut environments., (Copyright © 2020 Rath, Rud, Pieper and Vital.)
- Published
- 2020
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44. Development and validation of the Simulator of the Canine Intestinal Microbial Ecosystem (SCIME)1.
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Duysburgh C, Ossieur WP, De Paepe K, Van den Abbeele P, Vichez-Vargas R, Vital M, Pieper DH, Van de Wiele T, Hesta M, Possemiers S, and Marzorati M
- Subjects
- Animals, Bacteria isolation & purification, Feces microbiology, Gastrointestinal Tract microbiology, Humans, Intestines microbiology, Bacteria classification, Dogs microbiology, Gastrointestinal Microbiome, Lactobacillus physiology, Probiotics analysis
- Abstract
Whereas a wide variety of in vitro models have been developed and validated to assess the effect of specific food ingredients on the human gut microbiome, such models have only been developed and applied to a limited extent for companion animals. Since the use of pre- and probiotics to improve gut health is an emerging research topic in the field of companion animals and as dogs are often used as laboratory animals in developing and testing of pharmaceuticals, the current study aimed to establish an adequate canine in vitro model. This consisted of a four-stage reactor composed of a stomach and small intestinal compartment followed by a proximal and distal colon. This semi-continuous gastrointestinal tract model allowed a long-term, region-dependent, and pH-controlled simulation of the colon-associated microbial community of dogs. Upon reaching a functional steady state, the simulated canine microbial community composition proved to be representative of the in vivo situation. Indeed, the predominant bacterial phyla present in the in vitro proximal and distal colon corresponded with the main bacterial phyla detected in the fecal material of the dogs, resulting in an average community composition along the simulated canine gastrointestinal tract of 50.5% Firmicutes, 34.5% Bacteroidetes, 7.4% Fusobacteria, 4.9% Actinobacteria, and 2.7% Proteobacteria. A parallel in vivo-in vitro comparison assessing the effects of fructooligosaccharides (FOS) on the canine microbial community composition showed a consistent stimulation of Lactobacillus concentrations in the in vivo fecal samples as well as in the in vitro canine gut model. Furthermore, the in vitro platform provided additional insights about the prebiotic effect of FOS supplementation of dogs, such as a reduced abundance of Megamonas spp. which are only present in very low abundance in in vivo fecal samples, indicating an interesting application potential of the developed canine in vitro model in research related to gastrointestinal health of dogs., (© The Author(s) 2019. Published by Oxford University Press on behalf of the American Society of Animal Science. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)
- Published
- 2020
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45. Prothrombotic and Proinflammatory Activities of the β-Hemolytic Group B Streptococcal Pigment.
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Siemens N, Oehmcke-Hecht S, Hoßmann J, Skorka SB, Nijhuis RHT, Ruppen C, Skrede S, Rohde M, Schultz D, Lalk M, Itzek A, Pieper DH, van den Bout CJ, Claas ECJ, Kuijper EJ, Mauritz R, Sendi P, Wunderink HF, and Norrby-Teglund A
- Subjects
- Bacterial Toxins genetics, Bacterial Toxins immunology, Hemolysis immunology, Humans, Interleukin-1beta immunology, Interleukin-6 immunology, Leukocytes microbiology, Leukocytes pathology, Pigments, Biological genetics, Pigments, Biological immunology, Streptococcal Infections genetics, Streptococcal Infections pathology, Streptococcus agalactiae genetics, Thrombosis genetics, Thrombosis microbiology, Thrombosis pathology, Bacterial Toxins toxicity, Leukocytes immunology, Pigments, Biological toxicity, Streptococcal Infections immunology, Streptococcus agalactiae immunology, Streptococcus agalactiae pathogenicity, Thrombosis immunology
- Abstract
A prominent feature of severe streptococcal infections is the profound inflammatory response that contributes to systemic toxicity. In sepsis the dysregulated host response involves both immunological and nonimmunological pathways. Here, we report a fatal case of an immunocompetent healthy female presenting with toxic shock and purpura fulminans caused by group B streptococcus (GBS; serotype III, CC19). The strain (LUMC16) was pigmented and hyperhemolytic. Stimulation of human primary cells with hyperhemolytic LUMC16 and STSS/NF-HH strains and pigment toxin resulted in a release of proinflammatory mediators, including tumor necrosis factor, interleukin (IL)-1β, and IL-6. In addition, LUMC16 induced blood clotting and showed factor XII activity on its surface, which was linked to the presence of the pigment. The expression of pigment was not linked to a mutation within the CovR/S region. In conclusion, our study shows that the hemolytic lipid toxin contributes to the ability of GBS to cause systemic hyperinflammation and interferes with the coagulation system., (© 2019 The Author(s) Published by S. Karger AG, Basel.)
- Published
- 2020
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46. High Nuclease Activity of Long Persisting Staphylococcus aureus Isolates Within the Airways of Cystic Fibrosis Patients Protects Against NET-Mediated Killing.
- Author
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Herzog S, Dach F, de Buhr N, Niemann S, Schlagowski J, Chaves-Moreno D, Neumann C, Goretzko J, Schwierzeck V, Mellmann A, Dübbers A, Küster P, Schültingkemper H, Rescher U, Pieper DH, von Köckritz-Blickwede M, and Kahl BC
- Subjects
- Bacterial Proteins genetics, Cystic Fibrosis microbiology, Deoxyribonucleases genetics, Humans, Sputum immunology, Staphylococcal Infections microbiology, Staphylococcus aureus genetics, Bacterial Proteins immunology, Cystic Fibrosis immunology, Deoxyribonucleases immunology, Extracellular Traps immunology, Staphylococcal Infections immunology, Staphylococcus aureus enzymology
- Abstract
Staphylococcus aureus is one of the first and most prevalent pathogens cultured from the airways of cystic fibrosis (CF) patients, which can persist there for extended periods. Airway infections in CF patients are characterized by a strong inflammatory response of highly recruited neutrophils. One killing mechanism of neutrophils is the formation of neutrophil extracellular traps (NETs), which capture and eradicate bacteria by extracellular fibers of neutrophil chromatin decorated with antimicrobial granule proteins. S. aureus secretes nuclease, which can degrade NETs. We hypothesized, that S. aureus adapts to the airways of CF patients during persistent infection by escaping from NET-mediated killing via an increase of nuclease activity. Sputum samples of CF patients with chronic S. aureus infection were visualized by confocal microscopy after immuno-fluorescence staining for NET-specific markers, S. aureus bacteria and overall DNA structures. Nuclease activity was analyzed in sequential isogenic long persisting S. aureus isolates, as confirmed by whole genome sequencing, from an individual CF patient using a FRET-based nuclease activity assay. Additionally, some of these isolates were selected and analyzed by qRT-PCR to determine the expression of nuc1 and regulators of interest. NET-killing assays were performed with clinical S. aureus isolates to evaluate killing and bacterial survival depending on nuclease activity. To confirm the role of nuclease during NET-mediated killing, a clinical isolate with low nuclease activity was transformed with a nuclease expression vector (pCM28 nuc ). Furthermore, two sputa from an individual CF patient were subjected to RNA-sequence analysis to evaluate the activity of nuclease in vivo . In sputa, S. aureus was associated to extracellular DNA structures. Nuclease activity in clinical S. aureus isolates increased in a time-and phenotype-dependent manner. In the clinical isolates, the expression of nuc 1 was inversely correlated to the activity of agr and was independent of saeS . NET-mediated killing was significantly higher in S. aureus isolates with low compared to isolates with high nuclease activity. Importantly, transformation of the clinical isolate with low nuclease activity with pCM28 nuc conferred protection against NET-mediated killing confirming the beneficial role of nuclease for protection against NETs. Also, nuclease expression in in vivo sputa was high, which underlines the important role of nuclease within the highly inflamed CF airways. In conclusion, our data show that S. aureus adapts to the neutrophil-rich environment of CF airways with increasing nuclease expression most likely to avoid NET-killing during long-term persistence., (Copyright © 2019 Herzog, Dach, de Buhr, Niemann, Schlagowski, Chaves-Moreno, Neumann, Goretzko, Schwierzeck, Mellmann, Dübbers, Küster, Schültingkemper, Rescher, Pieper, von Köckritz-Blickwede and Kahl.)
- Published
- 2019
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47. Long-term Multidonor Faecal Microbiota Transfer by Oral Capsules for Active Ulcerative Colitis.
- Author
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Steube A, Vital M, Grunert P, Pieper DH, and Stallmach A
- Subjects
- Capsules, Fecal Microbiota Transplantation, Feces, Humans, Pilot Projects, Colitis, Ulcerative, Microbiota
- Published
- 2019
- Full Text
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48. Analysis of Transcriptionally Active Bacteria Throughout the Gastrointestinal Tract of Healthy Individuals.
- Author
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Vasapolli R, Schütte K, Schulz C, Vital M, Schomburg D, Pieper DH, Vilchez-Vargas R, and Malfertheiner P
- Subjects
- Aged, Bacteria classification, Feces microbiology, Female, Gastric Mucosa microbiology, Germany, Healthy Volunteers, High-Throughput Nucleotide Sequencing, Humans, Intestinal Mucosa microbiology, Male, Middle Aged, Phylogeny, Ribotyping, Saliva microbiology, Bacteria genetics, DNA, Bacterial genetics, Gastrointestinal Microbiome, Gastrointestinal Tract microbiology, Gene Expression Regulation, Bacterial, RNA, Ribosomal, 16S genetics, Transcriptional Activation
- Abstract
Background & Aims: The microbiome varies along the human gastrointestinal (GI) tract with exposure to luminal and mucosal factors. We analyzed active bacterial communities at 8 locations along the GI tract using high-throughput sequencing techniques., Methods: We collected saliva, mucosal, and fecal samples from healthy adults (10 men and 11 women; mean age, 59 ± 12.3 years) who underwent upper and lower GI tract endoscopy in Germany from December 2015 through September 2016. Biopsies were taken from stomach, antrum, corpus, duodenum, terminal ileum, ascending colon, and descending colon. RNA was extracted from all samples and reverse transcribed into complementary DNA; V1-V2 regions of 16S ribosomal RNA genes were amplified and sequenced on an Illumina MiSeq platform. Abundances of the taxa in all taxonomic ranks in each sample type were used to construct sample-similarity matrices with the Bray-Curtis algorithm. Significant differences between a priori-defined groups were evaluated using analysis of similarity., Results: After taxonomic annotation, 4045 phylotypes, belonging to 169 genera and 14 different phyla, were identified. Each subject had a different bacterial community. We identified distinct microbial consortia in saliva, upper GI tract, lower GI tract, and fecal samples. The predominant genera in the upper GI tract (Gemella, Veillonella, Neisseria, Fusobacterium, Streptococcus, Prevotella, Pseudomonas, and Actinomyces) were almost absent from the lower GI tract, where the microbial communities mainly comprised Faecalibacterium, Ruminococcus, and Bacteroides. The bacterial communities in the upper GI tract were characterized by greater richness and heterogeneity (measured by the Shannon index) than those in the lower GI tract. We detected Helicobacter pylori in only the upper GI tract., Conclusions: In an analysis of saliva, mucosal, and fecal samples from 21 healthy adults, we found each individual, and each GI region, to have a different bacterial community. The fecal microbiome is not representative of the mucosal microbiome. We propose a systematic method to analyze the bacterial communities of the GI tract., (Copyright © 2019 AGA Institute. Published by Elsevier Inc. All rights reserved.)
- Published
- 2019
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49. Molecular profiling of tissue biopsies reveals unique signatures associated with streptococcal necrotizing soft tissue infections.
- Author
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Thänert R, Itzek A, Hoßmann J, Hamisch D, Madsen MB, Hyldegaard O, Skrede S, Bruun T, Norrby-Teglund A, Medina E, and Pieper DH
- Subjects
- Adult, Aged, Bacterial Typing Techniques, Bacteroides genetics, Bacteroides isolation & purification, Bacteroides metabolism, Biopsy, Coinfection diagnosis, Coinfection microbiology, DNA, Bacterial isolation & purification, Escherichia genetics, Escherichia isolation & purification, Escherichia metabolism, Female, Humans, Male, Microbiota genetics, Middle Aged, Necrosis diagnosis, Necrosis microbiology, Necrosis pathology, RNA, Ribosomal, 16S genetics, RNA-Seq, Soft Tissue Infections diagnosis, Soft Tissue Infections microbiology, Staphylococcus genetics, Staphylococcus isolation & purification, Staphylococcus metabolism, Streptococcal Infections diagnosis, Streptococcal Infections microbiology, Streptococcus genetics, Streptococcus isolation & purification, Streptococcus metabolism, Virulence Factors genetics, Coinfection pathology, Soft Tissue Infections pathology, Streptococcal Infections pathology, Virulence Factors metabolism
- Abstract
Necrotizing soft tissue infections (NSTIs) are devastating infections caused by either a single pathogen, predominantly Streptococcus pyogenes, or by multiple bacterial species. A better understanding of the pathogenic mechanisms underlying these different NSTI types could facilitate faster diagnostic and more effective therapeutic strategies. Here, we integrate microbial community profiling with host and pathogen(s) transcriptional analysis in patient biopsies to dissect the pathophysiology of streptococcal and polymicrobial NSTIs. We observe that the pathogenicity of polymicrobial communities is mediated by synergistic interactions between community members, fueling a cycle of bacterial colonization and inflammatory tissue destruction. In S. pyogenes NSTIs, expression of specialized virulence factors underlies infection pathophysiology. Furthermore, we identify a strong interferon-related response specific to S. pyogenes NSTIs that could be exploited as a potential diagnostic biomarker. Our study provides insights into the pathophysiology of mono- and polymicrobial NSTIs and highlights the potential of host-derived signatures for microbial diagnosis of NSTIs.
- Published
- 2019
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50. The impact of proton pump inhibitors on the intestinal microbiota in chronic hepatitis C patients.
- Author
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Wellhöner F, Döscher N, Tergast TL, Vital M, Plumeier I, Kahl S, Potthoff A, Manns MP, Maasoumy B, Wedemeyer H, Cornberg M, Pieper DH, and Heidrich B
- Subjects
- Adult, Aged, Aged, 80 and over, Cohort Studies, Female, Gastrointestinal Tract microbiology, Hepacivirus, Hepatitis C, Chronic diagnosis, Hepatitis C, Chronic virology, Humans, Liver Cirrhosis diagnosis, Liver Cirrhosis virology, Male, Middle Aged, Proton Pump Inhibitors therapeutic use, Risk Factors, Bacteria classification, Gastrointestinal Microbiome drug effects, Hepatitis C, Chronic microbiology, Liver Cirrhosis microbiology, Proton Pump Inhibitors pharmacology
- Abstract
Objectives: Proton pump inhibitors (PPI), a class of drugs commonly used, are known to be associated with changes in the intestinal microbiota. Published studies were done in heterogeneous cohorts which could hamper conclusions drawn as effects of diseases were not taken into consideration. We aimed to elucidate differences in the intestinal microbiota being associated to the use of PPI in a cohort study of patients with chronic hepatitis C. Material and Methods: The 16S rDNA gene was analyzed in stool samples of patients with and without PPI use. Patients with concomitant medication influencing the microbiota were excluded. Results were compared with the clinical course of hepatitis C patients with decompensated liver cirrhosis. Results: No differences in alpha diversity could be observed, while the microbial community structure differed significantly, especially in patients with liver cirrhosis. The relative abundance of Streptococcus spp ., Enterobacter spp . and Haemophilus spp . was significantly increased in patients with PPI use irrespectively of the stage of liver disease. Finally, in patients with decompensated liver cirrhosis due to chronic HCV infection only in these using PPI bacterial phylotypes were isolated. Conclusions: PPI use was associated with significant alterations in the microbial community in patients with chronic hepatitis C, which were even pronounced in patients with liver cirrhosis. In patients with decompensated liver cirrhosis due to chronic HCV infection, the use of PPI may promote infections either directly or indirectly through changes in the microbial community structure. Future studies should further investigate long-term impact on the microbiota and the clinical outcome.
- Published
- 2019
- Full Text
- View/download PDF
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