131 results on '"Pieper DH"'
Search Results
2. Die Nasen-'WG': S. aureus und das nasale Mikrobiom
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Kaspar, U, Schaumburg, F, Rudack, C, Pieper, DH, and Becker, K
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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
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- 2015
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3. 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
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Clement, P, Pieper, DH, and Gonzalez, B
- Published
- 2001
4. 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
5. From xenobiotic to antibiotic, formation of protoanemonin from 4-chlorocatechol by enzymes of the 3-oxoadipate pathway
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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.
6. 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.)
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- 2024
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7. 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.)
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- 2024
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8. Engraftment of essential functions through multiple fecal microbiota transplants in chronic antibiotic-resistant pouchitis-a case study using metatranscriptomics.
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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).)
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- 2023
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9. 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).)
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- 2023
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10. 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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11. 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).)
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- 2023
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12. 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
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- 2022
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13. Transfer of FRozen Encapsulated multi-donor Stool filtrate for active ulcerative Colitis (FRESCO): study protocol for a prospective, multicenter, double-blind, randomized, controlled trial.
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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
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- 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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14. The emerging potential of microbiome transplantation on human health interventions.
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Junca H, Pieper DH, and Medina E
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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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15. 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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16. 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
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- 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.)
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- 2021
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17. A simplified LC-MS/MS method for the quantification of the cardiovascular disease biomarker trimethylamine- N -oxide and its precursors.
- Author
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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.)
- Published
- 2021
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18. Broad Spectrum Antibiotic Xanthocillin X Effectively Kills Acinetobacter baumannii via Dysregulation of Heme Biosynthesis.
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Hübner I, Shapiro JA, Hoßmann J, Drechsel J, Hacker SM, Rather PN, Pieper DH, Wuest WM, and Sieber SA
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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.)
- Published
- 2021
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19. Impact of healthy aging on active bacterial assemblages throughout the gastrointestinal tract.
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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
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- 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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20. Importance of superoxide dismutases A and M for protection of Staphylococcus aureus in the oxidative stressful environment of cystic fibrosis airways.
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Treffon J, Chaves-Moreno D, Niemann S, Pieper DH, Vogl T, Roth J, and Kahl BC
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- 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.)
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- 2020
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21. A combination of genetics and microbiota influences the severity of the obesity phenotype in diet-induced obesity.
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Smoczek M, Vital M, Wedekind D, Basic M, Zschemisch NH, Pieper DH, Siebert A, Bleich A, and Buettner M
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- 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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22. Toward Biorecycling: Isolation of a Soil Bacterium That Grows on a Polyurethane Oligomer and Monomer.
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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.)
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- 2020
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23. Potential TMA-Producing Bacteria Are Ubiquitously Found in Mammalia.
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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.)
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- 2020
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24. 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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25. 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.)
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- 2020
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26. High Nuclease Activity of Long Persisting Staphylococcus aureus Isolates Within the Airways of Cystic Fibrosis Patients Protects Against NET-Mediated Killing.
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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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27. Analysis of Transcriptionally Active Bacteria Throughout the Gastrointestinal Tract of Healthy Individuals.
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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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28. Molecular profiling of tissue biopsies reveals unique signatures associated with streptococcal necrotizing soft tissue infections.
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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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29. Cohort profile: The LoewenKIDS Study - life-course perspective on infections, the microbiome and the development of the immune system in early childhood.
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Gottschick C, Raupach-Rosin H, Langer S, Hassan L, Horn J, Dorendorf E, Caputo M, Bittner M, Beier L, Rübsamen N, Schlinkmann K, Zoch B, Guzman CA, Hansen G, Heselich V, Holzapfel E, Hübner J, Pietschmann T, Pieper DH, Pletz M, Riese P, Schmidt-Pokrzywniak A, Hartwig S, von Kaisenberg C, Aydogdu M, Buhles M, Dressler F, Eberl W, Haase R, von Koch FE, Feidicker S, Frambach T, Franz HGB, Guthmann F, Koch HG, Seeger S, Oberhoff C, Pauker W, Petry KU, Schild RL, Tchirikov M, Röhrig E, Karch A, and Mikolajczyk R
- Published
- 2019
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30. Diversity of Bacteria Exhibiting Bile Acid-inducible 7α-dehydroxylation Genes in the Human Gut.
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Vital M, Rud T, Rath S, Pieper DH, and Schlüter D
- Abstract
The secondary bile acids deoxycholic acid (DCA) and lithocholic acid (LCA), formed by gut microbiota from primary bile acids via a multi-step 7α-dehydroxylation reaction, have wide-ranging effects on host metabolism and play an important role in health and disease. A few 7α-dehydroxylating strains have been isolated, where bile acid-inducible ( bai ) genes were organized in a gene cluster and encoded major enzymes involved. However, only little is known on diversity and abundance of intestinal bacteria catalysing DCA/LCA formation in the human gut in situ . In this study, we took the opportunity to screen metagenome-assembled genomes (MAGs) from sequence data of stool samples provided by two recent studies along with newly available gut-derived isolates for the presence of the bai gene cluster. We revealed in total 765 and 620 MAGs encoding the potential to form DCA/LCA that grouped into 21 and 26 metagenomic species, respectively. The majority of MAGs (92.4 and 90.3%) were associated with a Ruminococcaceae clade that still lacks an isolate, whereas less MAGs belonged to Lachnospiraceae along with eight new isolates (n total = 11) that contained the bai genes. Only a few MAGs were linked to Peptostreptococcaceae . Signatures for horizontal transfer of bai genes were observed. This study gives a comprehensive overview of the diversity of bai -exhibiting bacteria in the human gut highlighting the application of metagenomics to unravel potential functions hidden from current isolates. Eventually, isolates of the identified main MAG clade are required in order to prove their capability of 7α-dehydroxylating primary bile acids., Competing Interests: There is no conflict of interest.
- Published
- 2019
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31. Analysis of Cdcs1 colitogenic effects in the hematopoietic compartment reveals distinct microbiome interaction and a new subcongenic interval active in T cells.
- Author
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Bruesch I, Meier P, Vital M, Pieper DH, Selke K, Böhlen S, Basic M, Meier M, Glage S, Hundrieser J, Wedekind D, Buettner M, and Bleich A
- Subjects
- Adoptive Transfer, Animals, Bone Marrow Transplantation, Cells, Cultured, Colitis genetics, Disease Models, Animal, Hematopoiesis, Humans, Interleukin-10 genetics, Mice, Mice, Knockout, Mutation genetics, Colitis immunology, Inflammatory Bowel Diseases immunology, Microbiota immunology, T-Lymphocytes immunology
- Abstract
Disease activity in Interleukin-10-deficient (Il10
-/- ) mice, a model for IBD, depends on genetic background and microbiome composition. B6.129P2/JZtm-Il10tm1Cgn (B6-Il10-/- ) mice are partially resistant to colitis, whereas mice carrying the Cdcs1C3Bir haplotype on chromosome 3, B6.Cg-Il10tm1Cgn MMU3(D3Mit11-D3Mit348)/JZtm (BC-R3-Il10-/- ), are susceptible. This study was performed to clarify Cdcs1 and candidate gene effects on the colitogenic potential of hematopoietic cells using bone marrow (BM) and T-cell transfer models. Acute and chronic graft versus host reaction was excluded by high-density genotyping, in vitro and in vivo approaches. BM-chimeras were created with animals housed in two barriers (I and II) with distinct microbiota composition as identified by sequencing. BM-chimeras of all groups developed comparable moderate-to-severe colitis in Barrier I, however, in Barrier II only recipients of BC-R3-Il10-/- BM. Subsequent adoptive T cell transfers pointed to a new subcongenic interval within Cdcs1 affecting their colitogenic potential. Transfers excluded Larp7 and Alpk1 but highlighted Ifi44 as potential candidate genes. In this model-system, colitis development after cell transfer heavily depends on microbiome, though Cdcs1 acts mainly independently in hematopoietic cells. A new subcongenic interval, provisionally named Cdcs1.4, modifies colitogenic T cell function. Within this locus, Ifi44 represents an important candidate gene for colitis expression.- Published
- 2019
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32. Spermidine and Voluntary Activity Exert Differential Effects on Sucrose- Compared with Fat-Induced Systemic Changes in Male Mice.
- Author
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Schipke J, Vital M, Schnapper-Isl A, Pieper DH, and Mühlfeld C
- Subjects
- Animal Feed, Animals, Blood Glucose, Diet, Energy Intake, Gastrointestinal Microbiome, Glucose metabolism, Homeostasis, Lipids blood, Male, Mice, Motor Activity, Dietary Carbohydrates adverse effects, Dietary Fats adverse effects, Spermidine pharmacology, Sucrose adverse effects
- Abstract
Background: Excess dietary fat and sugar are linked to obesity and metabolic syndrome. Polyamines such as spermidine are implicated in fat accumulation and may support activity-induced weight loss., Objective: This study tested interventional spermidine supplementation and voluntary activity against fat- and sucrose-induced systemic and gut microbiota changes., Methods: A 3-factorial study design (3 × 2 × 2) was used to test the factors diet, activity, and spermidine. Male 6-wk-old C57BL/6N mice were fed a control diet (CD; carbohydrate:protein:fat, 70%:20%:10% of energy; 7% sucrose), a high-fat diet (HFD; carbohydrate:protein:fat, 20%:20%:60% of energy; 7% sucrose), or a high-sucrose diet (HSD; carbohydrate:protein:fat, 70%:20%:10% of energy; 35% sucrose). Diet groups were left untreated (+0) or had unlimited access to running wheels (+A) or were supplemented with 3 mM spermidine via drinking water (+S) or a combination of both (+A+S) for 30 wk (n = 7-10)., Results: In comparison to the CD, the HFD enhanced body weights (by 36%, P < 0.001), plasma lipids (cholesterol by 24%, P < 0.001; triglycerides by 27%, P = 0.004), and glucose concentrations (by 18%, P < 0.001), whereas the HSD increased weight by 13% (P < 0.001) and fasting glucose by 17% (P < 0.001) but did not increase plasma lipids. Microbiota taxonomic composition changed upon the HFD and HSD (both P < 0.001); however, only the HSD increased microbial diversity (P < 0.001) compared with the CD. Activity influenced microbiota composition (P < 0.01) and reduced glucose concentrations in HSD-fed (P = 0.021) and HFD-fed (P < 0.001) mice compared with nonactive mice. The combination of activity and spermidine affected energy intake (P-interaction = 0.037) and reduced body weights of HSD+A+S mice compared with HSD+0 mice (P = 0.024)., Conclusions: In male C57BL/6N mice, dietary sucrose and fat caused diverse metabolic and microbiota changes that were differentially susceptible to physical exercise. Spermidine has the potential to augment activity-induced beneficial effects, particularly for sucrose-induced obesity., (© 2019 American Society for Nutrition.)
- Published
- 2019
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33. Bacterial community structure and effects of picornavirus infection on the anterior nares microbiome in early childhood.
- Author
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Caputo M, Zoch-Lesniak B, Karch A, Vital M, Meyer F, Klawonn F, Baillot A, Pieper DH, and Mikolajczyk RT
- Subjects
- Child, Preschool, Female, Genetic Variation, Humans, Infant, Male, RNA, Ribosomal, 16S genetics, Time Factors, Biodiversity, Microbiota, Nasal Cavity microbiology, Picornaviridae Infections microbiology
- Abstract
Background: Little is known regarding the nasal microbiome in early childhood and the impact of respiratory infection on the infants' nasal microbial composition. Here we investigated the temporal dynamics and diversity of the bacterial composition in the anterior nares in children attending daycare centers., Results: For our investigation, we considered 76 parental-taken nasal swabs of 26 children (aged 13 to 36 months) collected over a study period of 3 months. Overall, there was no significant age-specific effect or seasonal shift in the nasal bacterial community structure. In a sub-sample of 14 healthy children the relative abundance of individual taxa as well as the overall diversity did not reveal relevant changes, indicating a stable community structure over the entire study period. Moreover, the nasal bacterial profiles clustered subject-specific with Bray-Curtis similarities being elevated in intra-subject calculations compared to between-subject calculations. The remaining subset of 12 children provided samples taken during picornavirus infection (PVI) and either before or after a PVI. We detected an association between the relative abundance of members of the genus Streptococcus and PV when comparing both (i) samples taken during PVI with samples out of 14 healthy children and (ii) samples taken during PVI with samples taken after PVI within the same individual. In addition, the diversity was higher during PVI than after infection., Conclusions: Our findings suggest that a personalized structure of the nasal bacterial community is established already in early childhood and could be detected over a timeframe of 3 months. Studies following infants over a longer time with frequent swab sampling would allow investigating whether certain parameter of the bacterial community, such as the temporal variability, could be related to viral infection.
- Published
- 2019
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34. Determining lineage-specific bacterial growth curves with a novel approach based on amplicon reads normalization using internal standard (ARNIS).
- Author
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Piwosz K, Shabarova T, Tomasch J, Šimek K, Kopejtka K, Kahl S, Pieper DH, and Koblížek M
- Subjects
- Bacteria genetics, Food Chain, Fresh Water microbiology, Microbiota, Reference Standards, Bacteria growth & development, High-Throughput Nucleotide Sequencing standards, Sequence Analysis, DNA standards
- Abstract
The growth rate is a fundamental characteristic of bacterial species, determining its contributions to the microbial community and carbon flow. High-throughput sequencing can reveal bacterial diversity, but its quantitative inaccuracy precludes estimation of abundances and growth rates from the read numbers. Here, we overcame this limitation by normalizing Illumina-derived amplicon reads using an internal standard: a constant amount of Escherichia coli cells added to samples just before biomass collection. This approach made it possible to reconstruct growth curves for 319 individual OTUs during the grazer-removal experiment conducted in a freshwater reservoir Římov. The high resolution data signalize significant functional heterogeneity inside the commonly investigated bacterial groups. For instance, many Actinobacterial phylotypes, a group considered to harbor slow-growing defense specialists, grew rapidly upon grazers' removal, demonstrating their considerable importance in carbon flow through food webs, while most Verrucomicrobial phylotypes were particle associated. Such differences indicate distinct life strategies and roles in food webs of specific bacterial phylotypes and groups. The impact of grazers on the specific growth rate distributions supports the hypothesis that bacterivory reduces competition and allows existence of diverse bacterial communities. It suggests that the community changes were driven mainly by abundant, fast, or moderately growing, and not by rare fast growing, phylotypes. We believe amplicon read normalization using internal standard (ARNIS) can shed new light on in situ growth dynamics of both abundant and rare bacteria.
- Published
- 2018
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35. Viable cyanobacteria in the deep continental subsurface.
- Author
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Puente-Sánchez F, Arce-Rodríguez A, Oggerin M, García-Villadangos M, Moreno-Paz M, Blanco Y, Rodríguez N, Bird L, Lincoln SA, Tornos F, Prieto-Ballesteros O, Freeman KH, Pieper DH, Timmis KN, Amils R, and Parro V
- Subjects
- Biological Evolution, Cyanobacteria genetics, Cyanobacteria metabolism, Cyanobacteria growth & development, Ecosystem, Geologic Sediments analysis, Metagenomics, Microscopy, Fluorescence, Protein Array Analysis
- Abstract
Cyanobacteria are ecologically versatile microorganisms inhabiting most environments, ranging from marine systems to arid deserts. Although they possess several pathways for light-independent energy generation, until now their ecological range appeared to be restricted to environments with at least occasional exposure to sunlight. Here we present molecular, microscopic, and metagenomic evidence that cyanobacteria predominate in deep subsurface rock samples from the Iberian Pyrite Belt Mars analog (southwestern Spain). Metagenomics showed the potential for a hydrogen-based lithoautotrophic cyanobacterial metabolism. Collectively, our results suggest that they may play an important role as primary producers within the deep-Earth biosphere. Our description of this previously unknown ecological niche for cyanobacteria paves the way for models on their origin and evolution, as well as on their potential presence in current or primitive biospheres in other planetary bodies, and on the extant, primitive, and putative extraterrestrial biospheres., Competing Interests: The authors declare no conflict of interest., (Copyright © 2018 the Author(s). Published by PNAS.)
- Published
- 2018
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36. Pathogenic functions of host microbiota.
- Author
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Rath S, Rud T, Karch A, Pieper DH, and Vital M
- Subjects
- Bacterial Infections microbiology, Bacterial Physiological Phenomena genetics, Bile Acids and Salts biosynthesis, Humans, Hydrogen Sulfide metabolism, Methylamines metabolism, Bacteria genetics, Bacteria metabolism, Bacterial Infections pathology, Gastrointestinal Microbiome genetics
- Abstract
Background: It is becoming evident that certain features of human microbiota, encoded by distinct autochthonous taxa, promote disease. As a result, borders between the so-called opportunistic pathogens, pathobionts, and commensals are increasingly blurred, and specific targets for manipulating microbiota to improve host health are becoming elusive., Results: In this study, we focus on the functions of host bacterial communities that have the potential to cause disease, proposing the term "pathogenic function (pathofunction)". The concept is presented via three distinct examples, namely, the formation of (i) trimethylamine, (ii) secondary bile acids, and (iii) hydrogen sulfide, which represent metabolites of the gut microbiota linked to the development of non-communicable diseases. Using publicly available metagenomic and metatranscriptomic data (n = 2975), we quantified those pathofunctions in health and disease and exposed the key players. Pathofunctions were ubiquitously present with increased abundances in patient groups. Overall, the three pathofunctions were detected at low mean concentrations (< 1% of total bacteria carried respective genes) and encompassed various taxa, including uncultured members., Conclusions: We outline how this function-centric approach, where all members of a community exhibiting a particular pathofunction are redundant, can contribute to risk assessment and the development of precision treatment directing gut microbiota to increase host health.
- Published
- 2018
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37. Neonatally imprinted stromal cell subsets induce tolerogenic dendritic cells in mesenteric lymph nodes.
- Author
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Pezoldt J, Pasztoi M, Zou M, Wiechers C, Beckstette M, Thierry GR, Vafadarnejad E, Floess S, Arampatzi P, Buettner M, Schweer J, Fleissner D, Vital M, Pieper DH, Basic M, Dersch P, Strowig T, Hornef M, Bleich A, Bode U, Pabst O, Bajénoff M, Saliba AE, and Huehn J
- Subjects
- Animals, Animals, Newborn, Cellular Microenvironment genetics, Cellular Microenvironment immunology, Dendritic Cells metabolism, Forkhead Transcription Factors immunology, Forkhead Transcription Factors metabolism, Gene Expression Profiling, Immune Tolerance genetics, Lymph Nodes metabolism, Lymph Nodes transplantation, Mesentery immunology, Mice, Inbred BALB C, Mice, Inbred C57BL, Mice, Knockout, Mice, Transgenic, Stromal Cells metabolism, T-Lymphocytes, Regulatory immunology, T-Lymphocytes, Regulatory metabolism, Dendritic Cells immunology, Immune Tolerance immunology, Lymph Nodes immunology, Stromal Cells immunology
- Abstract
Gut-draining mesenteric lymph nodes (mLNs) are important for inducing peripheral tolerance towards food and commensal antigens by providing an optimal microenvironment for de novo generation of Foxp3
+ regulatory T cells (Tregs). We previously identified microbiota-imprinted mLN stromal cells as a critical component in tolerance induction. Here we show that this imprinting process already takes place in the neonatal phase, and renders the mLN stromal cell compartment resistant to inflammatory perturbations later in life. LN transplantation and single-cell RNA-seq uncover stably imprinted expression signatures in mLN fibroblastic stromal cells. Subsetting common stromal cells across gut-draining mLNs and skin-draining LNs further refine their location-specific immunomodulatory functions, such as subset-specific expression of Aldh1a2/3. Finally, we demonstrate that mLN stromal cells shape resident dendritic cells to attain high Treg-inducing capacity in a Bmp2-dependent manner. Thus, crosstalk between mLN stromal and resident dendritic cells provides a robust regulatory mechanism for the maintenance of intestinal tolerance.- Published
- 2018
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38. Delftia sp. LCW, a strain isolated from a constructed wetland shows novel properties for dimethylphenol isomers degradation.
- Author
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Vásquez-Piñeros MA, Martínez-Lavanchy PM, Jehmlich N, Pieper DH, Rincón CA, Harms H, Junca H, and Heipieper HJ
- Subjects
- Bacterial Proteins genetics, Bacterial Proteins metabolism, Biodegradation, Environmental, Delftia classification, Delftia genetics, Delftia isolation & purification, Isomerism, Mixed Function Oxygenases genetics, Mixed Function Oxygenases metabolism, Phylogeny, Soil Microbiology, Wetlands, Delftia metabolism, Phenols chemistry, Phenols metabolism
- Abstract
Background: Dimethylphenols (DMP) are toxic compounds with high environmental mobility in water and one of the main constituents of effluents from petro- and carbochemical industry. Over the last few decades, the use of constructed wetlands (CW) has been extended from domestic to industrial wastewater treatments, including petro-carbochemical effluents. In these systems, the main role during the transformation and mineralization of organic pollutants is played by microorganisms. Therefore, understanding the bacterial degradation processes of isolated strains from CWs is an important approach to further improvements of biodegradation processes in these treatment systems., Results: In this study, bacterial isolation from a pilot scale constructed wetland fed with phenols led to the identification of Delftia sp. LCW as a DMP degrading strain. The strain was able to use the o-xylenols 3,4-DMP and 2,3-DMP as sole carbon and energy sources. In addition, 3,4-DMP provided as a co-substrate had an effect on the transformation of other four DMP isomers. Based on the detection of the genes, proteins, and the inferred phylogenetic relationships of the detected genes with other reported functional proteins, we found that the phenol hydroxylase of Delftia sp. LCW is induced by 3,4-DMP and it is responsible for the first oxidation of the aromatic ring of 3,4-, 2,3-, 2,4-, 2,5- and 3,5-DMP. The enzyme may also catalyze both monooxygenation reactions during the degradation of benzene. Proteome data led to the identification of catechol meta cleavage pathway enzymes during the growth on ortho DMP, and validated that cleavage of the aromatic rings of 2,5- and 3,5-DMPs does not result in mineralization. In addition, the tolerance of the strain to high concentrations of DMP, especially to 3,4-DMP was higher than that of other reported microorganisms from activated sludge treating phenols., Conclusions: LCW strain was able to degraded complex aromatics compounds. DMPs and benzene are reported for the first time to be degraded by a member of Delftia genus. In addition, LCW degraded DMPs with a first oxidation of the aromatic rings by a phenol hydroxylase, followed by a further meta cleavage pathway. The higher resistance to DMP toxicity, the ability to degrade and transform DMP isomers and the origin as a rhizosphere bacterium from wastewater systems, make LCW a suitable candidate to be used in bioremediation of complex DMP mixtures in CWs systems.
- Published
- 2018
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39. Chronic rhinosinusitis with nasal polyps is characterized by dysbacteriosis of the nasal microbiota.
- Author
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Chalermwatanachai T, Vilchez-Vargas R, Holtappels G, Lacoere T, Jáuregui R, Kerckhof FM, Pieper DH, Van de Wiele T, Vaneechoutte M, Van Zele T, and Bachert C
- Subjects
- Adult, Asthma physiopathology, Case-Control Studies, Chronic Disease, Female, Humans, Inflammation etiology, Male, Middle Aged, Bacteria isolation & purification, Bacterial Infections microbiology, Dysbiosis microbiology, Nasal Polyps microbiology, Nose microbiology, Rhinitis microbiology, Sinusitis microbiology
- Abstract
Chronic rhinosinusitis with nasal polyp (CRSwNP) patients are often characterized by asthma comorbidity and a type-2 inflammation of the sinonasal mucosa. The mucosal microbiota has been suggested to be implicated in the persistence of inflammation, but associations have not been well defined. To compare the bacterial communities of healthy subjects with CRSwNP patients, we collected nasal swabs from 17 healthy subjects, 21 CRSwNP patients without asthma (CRSwNP-A), and 20 CRSwNP patients with co-morbid asthma (CRSwNP+A). We analysed the microbiota using high-throughput sequencing of the bacterial 16S rRNA. Bacterial communities were different between the three groups. Haemophilus influenzae was significantly enriched in CRSwNP patients, Propionibacterium acnes in the healthy group; Staphylococcus aureus was abundant in the CRSwNP-A group, even though present in 57% of patients. Escherichia coli was found in high amounts in CRSwNP+A patients. Nasal tissues of CRSwNP+A patients expressed significantly higher concentrations of IgE, SE-IgE, and IL-5 compared to those of CRSwNP-A patients. Co-cultivation demonstrated that P. acnes growth was inhibited by H. influenzae, E. coli and S. aureus. The nasal microbiota of healthy subjects are different from those of CRSwNP-A and CRSwNP+A patients. However, the most abundant species in healthy status could not inhibit those in CRSwNP disease.
- Published
- 2018
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40. Initial evenness determines diversity and cell density dynamics in synthetic microbial ecosystems.
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Ehsani E, Hernandez-Sanabria E, Kerckhof FM, Props R, Vilchez-Vargas R, Vital M, Pieper DH, and Boon N
- Subjects
- Metagenome, Metagenomics methods, Models, Theoretical, Phenotype, Biodiversity, Ecosystem, Microbiota
- Abstract
The effect of initial evenness on the temporal trajectory of synthetic communities in comprehensive, low-volume microcosm studies remains unknown. We used flow cytometric fingerprinting and 16S rRNA gene amplicon sequencing to assess the impact of time on community structure in one hundred synthetic ecosystems of fixed richness but varying initial evenness. Both methodologies uncovered a similar reduction in diversity within synthetic communities of medium and high initial evenness classes. However, the results of amplicon sequencing showed that there were no significant differences between and within the communities in all evenness groups at the end of the experiment. Nevertheless, initial evenness significantly impacted the cell density of the community after five medium transfers. Highly even communities retained the highest cell densities at the end of the experiment. The relative abundances of individual species could be associated to particular evenness groups, suggesting that their presence was dependent on the initial evenness of the synthetic community. Our results reveal that using synthetic communities for testing ecological hypotheses requires prior assessment of initial evenness, as it impacts temporal dynamics.
- Published
- 2018
- Full Text
- View/download PDF
41. Colonic Butyrate-Producing Communities in Humans: an Overview Using Omics Data.
- Author
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Vital M, Karch A, and Pieper DH
- Abstract
Given the key role of butyrate for host health, understanding the ecology of intestinal butyrate-producing communities is a top priority for gut microbiota research. To this end, we performed a pooled analysis on 2,387 metagenomic/transcriptomic samples from 15 publicly available data sets that originated from three continents and encompassed eight diseases as well as specific interventions. For analyses, a gene catalogue was constructed from gene-targeted assemblies of all genes from butyrate synthesis pathways of all samples and from an updated reference database derived from genome screenings. We demonstrate that butyrate producers establish themselves within the first year of life and display high abundances (>20% of total bacterial community) in adults regardless of origin. Various bacteria form this functional group, exhibiting a biochemical diversity including different pathways and terminal enzymes, where one carbohydrate-fueled pathway was dominant with butyryl coenzyme A (CoA):acetate CoA transferase as the main terminal enzyme. Subjects displayed a high richness of butyrate producers, and 17 taxa, primarily members of the Lachnospiraceae and Ruminococcaceae along with some Bacteroidetes , were detected in >70% of individuals, encompassing ~85% of the total butyrate-producing potential. Most of these key taxa were also found to express genes for butyrate formation, indicating that butyrate producers occupy various niches in the gut ecosystem, concurrently synthesizing that compound. Furthermore, results from longitudinal analyses propose that diversity supports functional stability during ordinary life disturbances and during interventions such as antibiotic treatment. A reduction of the butyrate-producing potential along with community alterations was detected in various diseases, where patients suffering from cardiometabolic disorders were particularly affected. IMPORTANCE Studies focusing on taxonomic compositions of the gut microbiota are plentiful, whereas its functional capabilities are still poorly understood. Specific key functions deserve detailed investigations, as they regulate microbiota-host interactions and promote host health and disease. The production of butyrate is among the top targets since depletion of this microbe-derived metabolite is linked to several emerging noncommunicable diseases and was shown to facilitate establishment of enteric pathogens by disrupting colonization resistance. In this study, we established a workflow to investigate in detail the composition of the polyphyletic butyrate-producing community from omics data extracting its biochemical and taxonomic diversity. By combining information from various publicly available data sets, we identified universal ecological key features of this functional group and shed light on its role in health and disease. Our results will assist the development of precision medicine to combat functional dysbiosis.
- Published
- 2017
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42. Treatment of biofilms in bacterial vaginosis by an amphoteric tenside pessary-clinical study and microbiota analysis.
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Gottschick C, Deng ZL, Vital M, Masur C, Abels C, Pieper DH, Rohde M, Mendling W, and Wagner-Döbler I
- Subjects
- Adult, Female, Gardnerella vaginalis drug effects, Gardnerella vaginalis genetics, High-Throughput Nucleotide Sequencing, Humans, Lactobacillus drug effects, Lactobacillus genetics, Lactobacillus crispatus drug effects, Lactobacillus crispatus genetics, Lactobacillus crispatus isolation & purification, Metronidazole therapeutic use, Microbiota genetics, Middle Aged, Pessaries, Prevotella drug effects, Prevotella genetics, RNA, Ribosomal, 16S genetics, Vagina drug effects, Vaginosis, Bacterial microbiology, Young Adult, Anti-Bacterial Agents administration & dosage, Biofilms drug effects, Microbiota drug effects, Surface-Active Agents administration & dosage, Vagina microbiology, Vaginosis, Bacterial drug therapy
- Abstract
Background: Bacterial vaginosis (BV) is the most common vaginal syndrome among women in their reproductive years. It is associated with an increased risk of acquiring sexually transmitted infections and complications like preterm labor. BV is characterized by a high recurrence rate for which biofilms frequently found on vaginal epithelial cells may be a reason., Results: Here, we report a controlled randomized clinical trial that tested the safety and effectiveness of a newly developed pessary containing an amphoteric tenside (WO3191) to disrupt biofilms after metronidazole treatment of BV. Pessaries containing lactic acid were provided to the control group, and microbial community composition was determined via Illumina sequencing of the V1-V2 region of the 16S rRNA gene. The most common community state type (CST) in healthy women was characterized by Lactobacillus crispatus. In BV, diversity was high with communities dominated by either Lactobacillus iners, Prevotella bivia, Sneathia amnii, or Prevotella amnii. Women with BV and proven biofilms had an increased abundance of Sneathia sanguinegens and a decreased abundance of Gardnerella vaginalis. Following metronidazole treatment, clinical symptoms cleared, Nugent score shifted to Lactobacillus dominance, biofilms disappeared, and diversity (Shannon index) was reduced in most women. Most of the patients responding to therapy exhibited a L. iners CST. Treatment with WO 3191 reduced biofilms but did not prevent recurrence. Women with high diversity after antibiotic treatment were more likely to develop recurrence., Conclusions: Stabilizing the low diversity healthy flora by promoting growth of health-associated Lactobacillus sp. such as L. crispatus may be beneficial for long-term female health., Trial Registration: ClinicalTrials.gov NCT02687789.
- Published
- 2017
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43. The urinary microbiota of men and women and its changes in women during bacterial vaginosis and antibiotic treatment.
- Author
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Gottschick C, Deng ZL, Vital M, Masur C, Abels C, Pieper DH, and Wagner-Döbler I
- Subjects
- Actinobacteria genetics, Actinobacteria isolation & purification, Adult, Anti-Bacterial Agents administration & dosage, Anti-Bacterial Agents adverse effects, Female, Gardnerella vaginalis genetics, Gardnerella vaginalis isolation & purification, Healthy Volunteers, High-Throughput Nucleotide Sequencing, Humans, Lactobacillus genetics, Lactobacillus isolation & purification, Male, Metronidazole administration & dosage, Metronidazole therapeutic use, Microbiota physiology, Middle Aged, RNA, Ribosomal, 16S, Urethra microbiology, Urinary Bladder microbiology, Vagina microbiology, Young Adult, Anti-Bacterial Agents therapeutic use, Microbiota drug effects, Microbiota genetics, Urine microbiology, Vaginosis, Bacterial drug therapy, Vaginosis, Bacterial microbiology
- Abstract
Background: The urinary microbiota is similarly complex as the vaginal and penile microbiota, yet its role as a reservoir for pathogens and for recurrent polymicrobial biofilm diseases like bacterial vaginosis (BV) is not clear., Results: Here, we analysed the urinary microbiota of healthy men and women and compared it with that of women during BV and after antibiotic treatment using next-generation sequencing of the 16S rRNA gene V1-V2 regions. Eight different community types, so called urotypes (UT), were identified in healthy humans, all of which were shared between men and women, except UT 7, dominated in relative abundance by Lactobacillus crispatus, which was found in healthy women only. Orally applied metronidazole significantly reduced Shannon diversity and the mean relative abundance of Gardnerella vaginalis, Atopobium vaginae, and Sneathia amnii, while L. iners increased to levels twofold higher than those found in healthy women. Although individual urine microbial profiles strongly responded to the antibiotic, the healthy community could not be restored. The correlation between urinary and vaginal fluid microbiota was generally weak and depending on UT and BV status. It was highest in UT 1 in acute BV (59% of samples), but after metronidazole treatment, only 3 out of 35 women showed a significant correlation between their urinary and vaginal microbiota composition., Conclusions: Urethra and bladder thus harbor microbial communities distinct from the vagina. The high abundance of BV related species in the urine of both men and women suggests that urine may act as a reservoir of pathogens and contribute to recurrence., Trial Registration: ClinicalTrials.gov, NCT02687789.
- Published
- 2017
- Full Text
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44. Fusobacterium and colorectal cancer: causal factor or passenger? Results from a large colorectal cancer screening study.
- Author
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Amitay EL, Werner S, Vital M, Pieper DH, Höfler D, Gierse IJ, Butt J, Balavarca Y, Cuk K, and Brenner H
- Subjects
- Aged, Colorectal Neoplasms genetics, Colorectal Neoplasms pathology, Early Detection of Cancer, Feces microbiology, Female, Fusobacterium genetics, Fusobacterium pathogenicity, Humans, Male, Middle Aged, RNA, Ribosomal, 16S genetics, Colorectal Neoplasms microbiology, Fusobacterium isolation & purification, Gastrointestinal Microbiome genetics
- Abstract
Colorectal cancer is a leading cause of morbidity and mortality worldwide in both men and women. The gut microbiome is increasingly recognized as having an important role in human health and disease. Fusobacterium has been identified in former studies as a leading gut bacterium associated with colorectal cancer, but it is still not clear if it plays an oncogenic role. In the current study, fecal samples were collected prior to bowel preparation from participants of screening colonoscopy in the German BliTz study. Using 16S rRNA gene analysis, we examined the presence and relative abundance of Fusobacterium in fecal samples from 500 participants, including 46, 113, 110 and 231 individuals with colorectal cancer, advanced adenomas, non-advanced adenomas and without any neoplasms, respectively. We found that the abundance of Fusobacterium in feces was strongly associated with the presence of colorectal cancer (P-value < 0.0001). This was confirmed by PCR at the species level for Fusobacterium nucleatum. However, no association was seen with the presence of advanced adenomas (P-value = 0.80) or non-advanced adenomas (P-value = 0.80), nor were there any associations observed with dietary or lifestyle habits. Although a causal role cannot be ruled out, our observations, based on fecal microbiome, support the hypothesis that Fusobacterium is a passenger that multiplies in the more favorable conditions caused by the malignant tumor rather than a causal factor in colorectal cancer development., (© The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.)
- Published
- 2017
- Full Text
- View/download PDF
45. Uncovering the trimethylamine-producing bacteria of the human gut microbiota.
- Author
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Rath S, Heidrich B, Pieper DH, and Vital M
- Subjects
- Bacteria enzymology, Bacteria isolation & purification, Bacteria metabolism, Bacterial Proteins genetics, Biosynthetic Pathways, Feces microbiology, Humans, Multilocus Sequence Typing, Phylogeny, Sequence Analysis, DNA methods, Bacteria classification, Gastrointestinal Microbiome, Metagenomics methods, Methylamines metabolism
- Abstract
Background: Trimethylamine (TMA), produced by the gut microbiota from dietary quaternary amines (mainly choline and carnitine), is associated with atherosclerosis and severe cardiovascular disease. Currently, little information on the composition of TMA producers in the gut is available due to their low abundance and the requirement of specific functional-based detection methods as many taxa show disparate abilities to produce that compound., Results: In order to examine the TMA-forming potential of microbial communities, we established databases for the key genes of the main TMA-synthesis pathways, encoding choline TMA-lyase (cutC) and carnitine oxygenase (cntA), using a multi-level screening approach on 67,134 genomes revealing 1107 and 6738 candidates to exhibit cutC and cntA, respectively. Gene-targeted assays enumerating the TMA-producing community by quantitative PCR and characterizing its composition via Illumina sequencing were developed and applied on human fecal samples (n = 50) where all samples contained potential TMA producers (cutC was detected in all individuals, whereas only 26% harbored cntA) constituting, however, only a minor part of the total community (below 1% in most samples). Obtained cutC amplicons were associated with various taxa, in particular with Clostridium XIVa strains and Eubacterium sp. strain AB3007, though a bulk of sequences displayed low nucleotide identities to references (average 86% ± 7%) indicating that key human TMA producers are yet to be isolated. Co-occurrence analysis revealed specific groups governing the community structure of cutC-exhibiting taxa across samples. CntA amplicons displayed high identities (~99%) to Gammaproteobacteria-derived references, primarily from Escherichia coli. Metagenomic analysis of samples provided by the Human Microbiome Project (n = 154) confirmed the abundance patterns as well as overall taxonomic compositions obtained with our assays, though at much lower resolution, whereas 16S ribosomal RNA gene sequence analysis could not adequately uncover the TMA-producing potential., Conclusions: In this study, we developed a diagnostic framework that enabled the quantification and comprehensive characterization of the TMA-producing potential in human fecal samples. The key players were identified, and together with predictions on their environmental niches using functional genomics on most closely related reference strains, we provide crucial information for the development of specific treatment strategies to restrain TMA producers and limit their proliferation.
- Published
- 2017
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46. Determination of nasal and oropharyngeal microbiomes in a multicenter population-based study - findings from Pretest 1 of the German National Cohort.
- Author
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Akmatov MK, Koch N, Vital M, Ahrens W, Flesch-Janys D, Fricke J, Gatzemeier A, Greiser H, Günther K, Illig T, Kaaks R, Krone B, Kühn A, Linseisen J, Meisinger C, Michels K, Moebus S, Nieters A, Obi N, Schultze A, Six-Merker J, Pieper DH, and Pessler F
- Subjects
- Cohort Studies, Germany epidemiology, Humans, Microbiota, Nasal Cavity microbiology, Oropharynx microbiology, Public Health Surveillance
- Abstract
We examined acceptability, preference and feasibility of collecting nasal and oropharyngeal swabs, followed by microbiome analysis, in a population-based study with 524 participants. Anterior nasal and oropharyngeal swabs were collected by certified personnel. In addition, participants self-collected nasal swabs at home four weeks later. Four swab types were compared regarding (1) participants' satisfaction and acceptance and (2) detection of microbial community structures based on deep sequencing of the 16 S rRNA gene V1-V2 variable regions. All swabbing methods were highly accepted. Microbial community structure analysis revealed 846 phylotypes, 46 of which were unique to oropharynx and 164 unique to nares. The calcium alginate tipped swab was found unsuitable for microbiome determinations. Among the remaining three swab types, there were no differences in oropharyngeal microbiomes detected and only marginal differences in nasal microbiomes. Microbial community structures did not differ between staff-collected and self-collected nasal swabs. These results suggest (1) that nasal and oropharyngeal swabbing are highly feasible methods for human population-based studies that include the characterization of microbial community structures in these important ecological niches, and (2) that self-collection of nasal swabs at home can be used to reduce cost and resources needed, particularly when serial measurements are to be taken.
- Published
- 2017
- Full Text
- View/download PDF
47. Draft Genome Sequence of Streptococcus dysgalactiae subsp. equisimilis Strain C161L1 Isolated in Vellore, India.
- Author
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Babbar A, Nitsche-Schmitz DP, Pieper DH, and Barrantes I
- Abstract
Streptococcus dysgalactiae subsp. equisimilis belongs to the β-hemolytic group C and G pyogenic group of streptococci. Here, we report the draft genome of the S. dysgalactiae subsp. equisimilis strain C161L1 from Vellore, a region in southern India with a high incidence rate of S. dysgalactiae subsp. equisimilis infection. This genome is 2.1 Mb long, with a 39.82% G+C content, and encodes 2,022 genes., (Copyright © 2017 Babbar et al.)
- Published
- 2017
- Full Text
- View/download PDF
48. Ursodeoxycholic Acid and Its Taurine- or Glycine-Conjugated Species Reduce Colitogenic Dysbiosis and Equally Suppress Experimental Colitis in Mice.
- Author
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Van den Bossche L, Hindryckx P, Devisscher L, Devriese S, Van Welden S, Holvoet T, Vilchez-Vargas R, Vital M, Pieper DH, Vanden Bussche J, Vanhaecke L, Van de Wiele T, De Vos M, and Laukens D
- Subjects
- Animals, Bacteroides drug effects, Colon microbiology, Dextran Sulfate administration & dosage, Disease Models, Animal, Feces microbiology, Firmicutes drug effects, Humans, Mice, Taurine chemistry, Taurochenodeoxycholic Acid administration & dosage, Ursodeoxycholic Acid administration & dosage, Ursodeoxycholic Acid chemistry, Dysbiosis drug therapy, Gastrointestinal Microbiome drug effects, Inflammatory Bowel Diseases drug therapy, Taurochenodeoxycholic Acid therapeutic use, Ursodeoxycholic Acid analogs & derivatives, Ursodeoxycholic Acid therapeutic use
- Abstract
The promising results seen in studies of secondary bile acids in experimental colitis suggest that they may represent an attractive and safe class of drugs for the treatment of inflammatory bowel diseases (IBD). However, the exact mechanism by which bile acid therapy confers protection from colitogenesis is currently unknown. Since the gut microbiota plays a crucial role in the pathogenesis of IBD, and exogenous bile acid administration may affect the community structure of the microbiota, we examined the impact of the secondary bile acid ursodeoxycholic acid (UDCA) and its taurine or glycine conjugates on the fecal microbial community structure during experimental colitis. Daily oral administration of UDCA, tauroursodeoxycholic acid (TUDCA), or glycoursodeoxycholic acid (GUDCA) equally lowered the severity of dextran sodium sulfate-induced colitis in mice, as evidenced by reduced body weight loss, colonic shortening, and expression of inflammatory cytokines. Illumina sequencing demonstrated that bile acid therapy during colitis did not restore fecal bacterial richness and diversity. However, bile acid therapy normalized the colitis-associated increased ratio of Firmicutes to Bacteroidetes Interestingly, administration of bile acids prevented the loss of Clostridium cluster XIVa and increased the abundance of Akkermansia muciniphila , bacterial species known to be particularly decreased in IBD patients. We conclude that UDCA, which is an FDA-approved drug for cholestatic liver disorders, could be an attractive treatment option to reduce dysbiosis and ameliorate inflammation in human IBD. IMPORTANCE Secondary bile acids are emerging as attractive candidates for the treatment of inflammatory bowel disease. Although bile acids may affect the intestinal microbial community structure, which significantly contributes to the course of these inflammatory disorders, the impact of bile acid therapy on the fecal microbiota during colitis has not yet been considered. Here, we studied the alterations in the fecal microbial abundance in colitic mice following the administration of secondary bile acids. Our results show that secondary bile acids reduce the severity of colitis and ameliorate colitis-associated fecal dysbiosis at the phylum level. This study indicates that secondary bile acids might act as a safe and effective drug for inflammatory bowel disease., (Copyright © 2017 American Society for Microbiology.)
- Published
- 2017
- Full Text
- View/download PDF
49. Presence does not imply activity: DNA and RNA patterns differ in response to salt perturbation in anaerobic digestion.
- Author
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De Vrieze J, Regueiro L, Props R, Vilchez-Vargas R, Jáuregui R, Pieper DH, Lema JM, and Carballa M
- Abstract
Background: The microbial community in anaerobic digestion is mainly monitored by means of DNA-based methods. This may lead to incorrect interpretation of the community parameters, because microbial abundance does not necessarily reflect activity. In this research, the difference between microbial community response on DNA (total community) and RNA (active community) based on the 16S rRNA (gene) with respect to salt concentration and response time was evaluated., Results: The application of higher NaCl concentrations resulted in a decrease in methane production. A stronger and faster response to salt concentration was observed on RNA level. This was reflected in terms of microbial community composition and organization, as richness, evenness, and overall diversity were differentially impacted. A higher divergence of community structure was observed on RNA level as well, indicating that total community composition depends on deterministic processes, while the active community is determined by stochastic processes. Methanosaeta was identified as the most abundant methanogen on DNA level, but its relative abundance decreased on RNA level, related to salt perturbation., Conclusions: This research demonstrated the need for RNA-based community screening to obtain reliable information on actual community parameters and to identify key species that determine process stability.
- Published
- 2016
- Full Text
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50. Draft Genome Sequence of the Deep-Subsurface Actinobacterium Tessaracoccus lapidicaptus IPBSL-7T.
- Author
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Puente-Sánchez F, Pieper DH, and Arce-Rodríguez A
- Abstract
The type strain of Tessaracoccus lapidicaptus was isolated from the deep subsurface of the Iberian Pyrite Belt (southwest Spain). Here, we report its draft genome, consisting of 27 contigs with a ~3.1-Mb genome size. The annotation revealed 2,905 coding DNA sequences, 45 tRNA genes, and three rRNA genes., (Copyright © 2016 Puente-Sánchez et al.)
- Published
- 2016
- Full Text
- View/download PDF
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