33 results on '"Javier Ramiro-Garcia"'
Search Results
2. Microbial Community Redundancy and Resilience Underpins High-Rate Anaerobic Treatment of Dairy-Processing Wastewater at Ambient Temperatures
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Lara M. Paulo, Juan Castilla-Archilla, Javier Ramiro-Garcia, José Antonio Escamez-Picón, Dermot Hughes, Thérèse Mahony, Michael Murray, Paul Wilmes, and Vincent O'Flaherty
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ambient temperature anaerobic digestion ,biogas ,dairy wastewater ,microbial community ,perturbations ,Biotechnology ,TP248.13-248.65 - Abstract
High-rate anaerobic digestion (AD) is a reliable, efficient process to treat wastewaters and is often operated at temperatures exceeding 30°C, involving energy consumption of biogas in temperate regions, where wastewaters are often discharged at variable temperatures generally below 20°C. High-rate ambient temperature AD, without temperature control, is an economically attractive alternative that has been proven to be feasible at laboratory-scale. In this study, an ambient temperature pilot scale anaerobic reactor (2 m3) was employed to treat real dairy wastewater in situ at a milk processing plant, at organic loading rates of 1.3 ± 0.6 to 10.6 ± 3.7 kg COD/m3/day and hydraulic retention times (HRT) ranging from 36 to 6 h. Consistent high levels of COD removal efficiencies, ranging from 50 to 70% for total COD removal and 70 to 84% for soluble COD removal, were achieved during the trial. Within the reactor biomass, stable active archaeal populations were observed, consisting mainly of Methanothrix (previously Methanosaeta) species, which represented up to 47% of the relative abundant active species in the reactor. The decrease in HRT, combined with increases in the loading rate had a clear effect on shaping the structure and composition of the bacterial fraction of the microbial community, however, without affecting reactor performance. On the other hand, perturbances in influent pH had a strong impact, especially when pH went higher than 8.5, inducing shifts in the microbial community composition and, in some cases, affecting negatively the performance of the reactor in terms of COD removal and biogas methane content. For example, the main pH shock led to a drop in the methane content to 15%, COD removals decreased to 0%, while the archaeal population decreased to ~11% both at DNA and cDNA levels. Functional redundancy in the microbial community underpinned stable reactor performance and rapid reactor recovery after perturbations.
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- 2020
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3. Integrated In Vitro and In Silico Modeling Delineates the Molecular Effects of a Synbiotic Regimen on Colorectal-Cancer-Derived Cells
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Kacy Greenhalgh, Javier Ramiro-Garcia, Almut Heinken, Pit Ullmann, Tamara Bintener, Maria Pires Pacheco, Joanna Baginska, Pranjul Shah, Audrey Frachet, Rashi Halder, Joëlle V. Fritz, Thomas Sauter, Ines Thiele, Serge Haan, Elisabeth Letellier, and Paul Wilmes
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Biology (General) ,QH301-705.5 - Abstract
Summary: By modulating the human gut microbiome, prebiotics and probiotics (combinations of which are called synbiotics) may be used to treat diseases such as colorectal cancer (CRC). Methodological limitations have prevented determining the potential combinatorial mechanisms of action of such regimens. We expanded our HuMiX gut-on-a-chip model to co-culture CRC-derived epithelial cells with a model probiotic under a simulated prebiotic regimen, and we integrated the multi-omic results with in silico metabolic modeling. In contrast to individual prebiotic or probiotic treatments, the synbiotic regimen caused downregulation of genes involved in procarcinogenic pathways and drug resistance, and reduced levels of the oncometabolite lactate. Distinct ratios of organic and short-chain fatty acids were produced during the simulated regimens. Treatment of primary CRC-derived cells with a molecular cocktail reflecting the synbiotic regimen attenuated self-renewal capacity. Our integrated approach demonstrates the potential of modeling for rationally formulating synbiotics-based treatments in the future. : The use of specific diets that promote the growth of beneficial microorganisms together with such microorganisms may help treat such diseases as colorectal cancer. Greenhalgh et al. show that one such synbiotic regimen induces downregulation of pro-carcinogenic and drug resistance genes as well as metabolic changes that affect the growth of cancer cells. Keywords: gut-on-a-chip, modeling, gut microbiome, prebiotic, probiotic, symbiotic, colorectal cancer, nutritional therapy
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- 2019
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4. NG-Tax, a highly accurate and validated pipeline for analysis of 16S rRNA amplicons from complex biomes [version 2; referees: 2 approved, 1 approved with reservations, 1 not approved]
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Javier Ramiro-Garcia, Gerben D. A. Hermes, Christos Giatsis, Detmer Sipkema, Erwin G. Zoetendal, Peter J. Schaap, and Hauke Smidt
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Bioinformatics ,Genomics ,Microbial Evolution & Genomics ,Medicine ,Science - Abstract
Background: Massive high-throughput sequencing of short, hypervariable segments of the 16S ribosomal RNA (rRNA) gene has transformed the methodological landscape describing microbial diversity within and across complex biomes. However, several studies have shown that the methodology rather than the biological variation is responsible for the observed sample composition and distribution. This compromises meta-analyses, although this fact is often disregarded. Results: To facilitate true meta-analysis of microbiome studies, we developed NG-Tax, a pipeline for 16S rRNA gene amplicon sequence analysis that was validated with different mock communities and benchmarked against QIIME as a frequently used pipeline. The microbial composition of 49 independently amplified mock samples was characterized by sequencing two variable 16S rRNA gene regions, V4 and V5-V6, in three separate sequencing runs on Illumina’s HiSeq2000 platform. This allowed for the evaluation of important causes of technical bias in taxonomic classification: 1) run-to-run sequencing variation, 2) PCR–error, and 3) region/primer specific amplification bias. Despite the short read length (~140 nt) and all technical biases, the average specificity of the taxonomic assignment for the phylotypes included in the mock communities was 97.78%. On average 99.95% and 88.43% of the reads could be assigned to at least family or genus level, respectively, while assignment to ‘spurious genera’ represented on average only 0.21% of the reads per sample. Analysis of α- and β-diversity confirmed conclusions guided by biology rather than the aforementioned methodological aspects, which was not achieved with QIIME. Conclusions: Different biological outcomes are commonly observed due to 16S rRNA region-specific performance. NG-Tax demonstrated high robustness against choice of region and other technical biases associated with 16S rRNA gene amplicon sequencing studies, diminishing their impact and providing accurate qualitative and quantitative representation of the true sample composition. This will improve comparability between studies and facilitate efforts towards standardization.
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- 2018
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5. Metagenomic- and Cultivation-Based Exploration of Anaerobic Chloroform Biotransformation in Hypersaline Sediments as Natural Source of Chloromethanes
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Peng Peng, Yue Lu, Tom N.P. Bosma, Ivonne Nijenhuis, Bart Nijsse, Sudarshan A. Shetty, Alexander Ruecker, Alexander Umanets, Javier Ramiro-Garcia, Andreas Kappler, Detmer Sipkema, Hauke Smidt, and Siavash Atashgahi
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hypersaline lakes ,chloroform ,biotransformation ,metagenome ,Biology (General) ,QH301-705.5 - Abstract
Chloroform (CF) is an environmental contaminant that can be naturally formed in various environments ranging from forest soils to salt lakes. Here we investigated CF removal potential in sediments obtained from hypersaline lakes in Western Australia. Reductive dechlorination of CF to dichloromethane (DCM) was observed in enrichment cultures derived from sediments of Lake Strawbridge, which has been reported as a natural source of CF. No CF removal was observed in abiotic control cultures without artificial electron donors, indicating biotic CF dechlorination in the enrichment cultures. Increasing vitamin B12 concentration from 0.04 to 4 µM in enrichment cultures enhanced CF removal and reduced DCM formation. In cultures amended with 4 µM vitamin B12 and 13C labelled CF, formation of 13CO2 was detected. Known organohalide-respiring bacteria and reductive dehalogenase genes were neither detected using quantitative PCR nor metagenomic analysis of the enrichment cultures. Rather, members of the order Clostridiales, known to co-metabolically transform CF to DCM and CO2, were detected. Accordingly, metagenome-assembled genomes of Clostridiales encoded enzymatic repertoires for the Wood-Ljungdahl pathway and cobalamin biosynthesis, which are known to be involved in fortuitous and nonspecific CF transformation. This study indicates that hypersaline lake microbiomes may act as a filter to reduce CF emission to the atmosphere.
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- 2020
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6. Effect of Nickel and Cobalt on Methanogenic Enrichment Cultures and Role of Biogenic Sulfide in Metal Toxicity Attenuation
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Lara M. Paulo, Javier Ramiro-Garcia, Simon van Mourik, Alfons J. M. Stams, and Diana Z. Sousa
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heavy metals ,anaerobic sludge ,sulfate ,sulfide ,inhibition ,stimulation ,Microbiology ,QR1-502 - Abstract
Metals play an important role in microbial metabolism by acting as cofactors for many enzymes. Supplementation of biological processes with metals may result in improved performance, but high metal concentrations are often toxic to microorganisms. In this work, methanogenic enrichment cultures growing on H2/CO2 or acetate were supplemented with trace concentrations of nickel (Ni) and cobalt (Co), but no significant increase in methane production was observed in most of the tested conditions. However, high concentrations of these metals were detrimental to methanogenic activity of the cultures. Cumulative methane production (after 6 days of incubation) from H2/CO2 was 40% lower in the presence of 8 mM of Ni or 30 mM of Co, compared to controls without metal supplementation. When acetate was used as substrate, cumulative methane production was also reduced: by 18% with 8 mM of Ni and by 53% with 30 mM of Co (after 6 days of incubation). Metal precipitation with sulfide was further tested as a possible method to alleviate metal toxicity. Anaerobic sludge was incubated with Co (30 mM) and Ni (8 mM) in the presence of sulfate or sulfide. The addition of sulfide helped to mitigate the toxic effect of the metals. Methane production from H2/CO2 was negatively affected in the presence of sulfate, possibly due to competition of hydrogenotrophic methanogens by sulfate-reducing bacteria. However, in the enrichment cultures growing on acetate, biogenically produced sulfide had a positive effect and more methane was produced in these incubations than in similar assays without sulfate addition. The outcome of competition between methanogens and sulfate-reducing bacteria is a determinant factor for the success of using biogenic sulfide as detoxification method.
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- 2017
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7. Dietary protein sources differentially affect microbiota, mTOR activity and transcription of mTOR signaling pathways in the small intestine.
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Soumya K Kar, Alfons J M Jansman, Nirupama Benis, Javier Ramiro-Garcia, Dirkjan Schokker, Leo Kruijt, Ellen H Stolte, Johanna J Taverne-Thiele, Mari A Smits, and Jerry M Wells
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Medicine ,Science - Abstract
Dietary protein sources can have profound effects on host-microbe interactions in the gut that are critically important for immune resilience. However more knowledge is needed to assess the impact of different protein sources on gut and animal health. Thirty-six wildtype male C57BL/6J mice of 35 d age (n = 6/group; mean ± SEM body weight 21.9 ± 0.25 g) were randomly assigned to groups fed for four weeks with semi synthetic diets prepared with one of the following protein sources containing (300 g/kg as fed basis): soybean meal (SBM), casein, partially delactosed whey powder, spray dried plasma protein, wheat gluten meal and yellow meal worm. At the end of the experiment, mice were sacrificed to collect ileal tissue to acquire gene expression data, and mammalian (mechanistic) target of rapamycin (mTOR) activity, ileal digesta to study changes in microbiota and serum to measure cytokines and chemokines. By genome-wide transcriptome analysis, we identified fourteen high level regulatory genes that are strongly affected in SBM-fed mice compared to the other experimental groups. They mostly related to the mTOR pathway. In addition, an increased (P < 0.05) concentration of granulocyte colony-stimulating factor was observed in serum of SBM-fed mice compared to other dietary groups. Moreover, by 16S rRNA sequencing, we observed that SBM-fed mice had higher (P < 0.05) abundances of Bacteroidales family S24-7, compared to the other dietary groups. We showed that measurements of genome-wide expression and microbiota composition in the mouse ileum reveal divergent responses to diets containing different protein sources, in particular for a diet based on SBM.
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- 2017
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8. Psychrophilic and Mesophilic Anaerobic Digestion of Dairy Wastewater with Long Chain Fatty Acids: Process Performances and Microbial Community Dynamics
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Yu-Chen Liu, Javier Ramiro-Garcia, Lara M. Paulo, Camilla Maria Braguglia, Maria Cristina Gagliano, and Vincent O'Flaherty
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History ,Polymers and Plastics ,Business and International Management ,Industrial and Manufacturing Engineering - Published
- 2023
9. Psychrophilic and mesophilic anaerobic treatment of synthetic dairy wastewater with long chain fatty acids: Process performances and microbial community dynamics
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Yu-Chen Liu, Javier Ramiro-Garcia, Lara M. Paulo, Camilla Maria Braguglia, Maria Cristina Gagliano, Vincent O'Flaherty, Enterprise Ireland, Science Foundation Ireland, and European Commission
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Environmental Engineering ,Renewable Energy, Sustainability and the Environment ,Biofilm ,Fungi ,Bioengineering ,Core microbiome ,Wastewater treatment ,General Medicine ,Lipid ,Waste Management and Disposal - Abstract
9 Páginas.-- 4 Figuras.-- 1 Tabla, Facilitating the anaerobic degradation of long chain fatty acids (LCFA) is the key to unlock the energy potential of lipids-rich wastewater. In this study, the feasibility of psychrophilic anaerobic treatment of LCFA-containing dairy wastewater was assessed and compared to mesophilic anaerobic treatment. The results showed that psychrophilic treatment at 15 ℃ was feasible for LCFA-containing dairy wastewater, with high removal rates of soluble COD (>90%) and LCFA (∼100%). However, efficient long-term treatment required prior acclimation of the biomass to psychrophilic temperatures. The microbial community analysis revealed that putative syntrophic fatty acid bacteria and Methanocorpusculum played a crucial role in LCFA degradation during both mesophilic and psychrophilic treatments. Additionally, a fungal-bacterial biofilm was found to be important during the psychrophilic treatment. Overall, these findings demonstrate the potential of psychrophilic anaerobic treatment for industrial wastewaters and highlight the importance of understanding the microbial communities involved in the process., The authors thank Arrabawn Dairies and Dairygold Co-Operative Society for providing the inoculum; Sandra O’Connor, Alison Graham, and Andrew Bartle for assisting reactor operations and Dr Anna Christine Trego for scientific discussions. The authors acknowledge the facilities and scientific and technical assistance of the Centre for Microscopy & Imaging at University of Galway (www.imaging.universityofgalway.ie). This work was supported by the Enterprise Ireland Technology Centres Programme (TC/2014/0016) and Science Foundation Ireland (19/FFP/6746 and 16/RC/3889), as well as the European Union's Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant agreement N° 101033411
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- 2023
10. NG-Tax, a highly accurate and validated pipeline for analysis of 16S rRNA amplicons from complex biomes [version 1; referees: 2 approved with reservations, 1 not approved]
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Javier Ramiro-Garcia, Gerben D. A. Hermes, Christos Giatsis, Detmer Sipkema, Erwin G. Zoetendal, Peter J. Schaap, and Hauke Smidt
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Research Article ,Articles ,Bioinformatics ,Genomics ,Microbial Evolution & Genomics ,16S rRNA amplicon analysis ,microbial community analysis ,microbial ecology ,next-generation sequencing ,bioinformatic pipeline - Abstract
Background Massive high-throughput sequencing of short, hypervariable segments of the 16S ribosomal RNA (rRNA) gene has transformed the methodological landscape describing microbial diversity within and across complex biomes. However, several studies have shown that the methodology rather than the biological variation is responsible for the observed sample composition and distribution. This compromises true meta-analyses, although this fact is often disregarded. Results To facilitate true meta-analysis of microbiome studies, we developed NG-Tax, a pipeline for 16S rRNA gene amplicon sequence analysis that was validated with different mock communities and benchmarked against QIIME as the currently most frequently used pipeline. The microbial composition of 49 independently amplified mock samples was characterized by sequencing two variable 16S rRNA gene regions, V4 and V5-V6, in three separate sequencing runs on Illumina’s HiSeq2000 platform. This allowed evaluating important factors of technical bias in taxonomic classification: 1) run-to-run sequencing variation, 2) PCR–error, and 3) region/primer specific amplification bias. Despite the short read length (~140 nt) and all technical biases, the average specificity of the taxonomic assignment for the phylotypes included in the mock communities was 96%. On average 99.94% and 92.02% of the reads could be assigned to at least family or genus level, respectively, while assignment to ‘spurious genera’ represented on average only 0.02% of the reads per sample. Analysis of α- and β-diversity confirmed conclusions guided by biology rather than the aforementioned methodological aspects, which was not the case when samples were analysed using QIIME. Conclusions Different biological outcomes are commonly observed due to 16S rRNA region-specific performance. NG-Tax demonstrated high robustness against choice of region and other technical biases associated with 16S rRNA gene amplicon sequencing studies, diminishing their impact and providing accurate qualitative and quantitative representation of the true sample composition. This will improve comparability between studies and facilitate efforts towards standardization.
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- 2016
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11. An archaeal compound as a driver of Parkinson’s disease pathogenesis
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Paul Wilmes, Jean-Pierre Trezzi, Velma Aho, Christian Jäger, Sebastian Schade, Annette Janzen, Oskar Hickl, Benoit Kunath, Mélanie Thomas, Kristopher Schmit, Pierre Garcia, Alessia Sciortino, Camille Martin-Gallausiaux, Rashi Halder, Oihane Uriarte Huarte, Tony Heurtaux, Ursula Heins-Marroquin, Gemma Gomez-Giro, Katrin Weidenbach, Léa Delacour, Cédric Laczny, Polina Novikova, Javier Ramiro-Garcia, Randolph Singh, Begoña Talavera Andújar, Laura Lebrun, Annegrait Daujeumont, Janine Habier, Xiangyi Dong, Floriane Gavotto, Anna Heintz-Buschart, Jochen Schneider, Nico Jehmlich, Martin von Bergen, Emma Schymanski, Ruth Schmitz, Jens Schwamborn, Enrico Glaab, Carole Linster, Toshimori Kitami, Manuel Buttini, Patrick May, Claudia Trenkwalder, Wolfgang Oertel, Brit Mollenhauer, Fonds National de la Recherche - FnR [sponsor], European Research Council (ERC) [sponsor], Michael J. Fox Foundation (MJFF) [sponsor], Luxembourg Centre for Systems Biomedicine (LCSB): Eco-Systems Biology (Wilmes Group) [research center], Luxembourg Centre for Systems Biomedicine (LCSB): Enzymology & Metabolism (Linster Group) [research center], Luxembourg Centre for Systems Biomedicine (LCSB): Bioinformatics Core (R. Schneider Group) [research center], Luxembourg Centre for Systems Biomedicine (LCSB): Biomedical Data Science (Glaab Group) [research center], Luxembourg Centre for Systems Biomedicine (LCSB) [research center], Luxembourg Institute of Health - LIH [research center], Luxembourg Centre for Systems Biomedicine (LCSB): Medical Translational Research (J. Schneider Group) [research center], Luxembourg Centre for Systems Biomedicine (LCSB): Environmental Cheminformatics (Schymanski Group) [research center], and Luxembourg Centre for Systems Biomedicine (LCSB): Developmental and Cellular Biology (Schwamborn Group) [research center]
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Environmental sciences & ecology [F08] [Life sciences] ,Sciences de l'environnement & écologie [F08] [Sciences du vivant] ,Microbiologie [F11] [Sciences du vivant] ,Neurologie [D14] [Sciences de la santé humaine] ,Neurology [D14] [Human health sciences] ,Microbiology [F11] [Life sciences] ,Genetics & genetic processes [F10] [Life sciences] ,Biochemistry, biophysics & molecular biology [F05] [Life sciences] ,Biochimie, biophysique & biologie moléculaire [F05] [Sciences du vivant] ,Génétique & processus génétiques [F10] [Sciences du vivant] - Abstract
Patients with Parkinson’s disease (PD) exhibit differences in their gut microbiomes compared to healthy individuals. Although differences have most commonly been described in the abundances of bacterial taxa, changes to viral and archaeal populations have also been observed. Mechanistic links between gut microbes and PD pathogenesis remain elusive but could involve molecules that promote α-synuclein aggregation. Here, we show that 2-hydroxypyridine (2-HP) represents a key molecule for the pathogenesis of PD. We observe significantly elevated 2-HP levels in faecal samples from patients with PD or its prodrome, idiopathic REM sleep behaviour disorder (iRBD), compared to healthy controls. 2-HP is correlated with the archaeal species Methanobrevibacter smithii and with genes involved in methane metabolism, and it is detectable in isolate cultures of M. smithii. We demonstrate that 2-HP is selectively toxic to transgenic α-synuclein overexpressing yeast and increases α-synuclein aggregation in a yeast model as well as in human induced pluripotent stem cell derived enteric neurons. It also exacerbates PD-related motor symptoms, α-synuclein aggregation, and striatal degeneration when injected intrastriatally in transgenic mice overexpressing human α-synuclein. Our results highlight the effect of an archaeal molecule in relation to the gut-brain axis, which is critical for the diagnosis, prognosis, and treatment of PD.
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- 2022
12. Caractérisation systémique des molécules sécrétées par le microbiome intestinal humain via l'intégration de données omiques
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Bianca De Saedeleer, Antoine Malabirade, Javier Ramiro-Garcia, Janine Habier, Jean-Pierre Trezzi, Samantha L. Peters, Annegrät Daujeumont, Rashi Halder, Christian Jäger, Susheel Bhanu Busi, Patrick May, Wolfgang Oertel, Brit Mollenhauer, Cédric C. Laczny, Robert L. Hettich, Paul Wilmes, Luxembourg Centre For Systems Biomedicine (LCSB), University of Luxembourg [Luxembourg], Université du Luxembourg (Uni.lu), Luxembourg Institute of Health (LIH), Oak Ridge National Laboratory [Oak Ridge] (ORNL), UT-Battelle, LLC, Philipps Universität Marburg = Philipps University of Marburg, Department of Neurology, University Medical Center Goettingen, Paracelsus-Elena-Klinik, Kassel, Germany., This work was further supported by the Luxembourg National Research Fund (FNR, CORE/16/BM/11333923 and CORE/15/BM/10404093), and the Michael J. Fox Foundation under grant No. 14701 to PW. SBB was supported by a Synergia grant (CRSII5_180241) through the Swiss National Science Foundation. The mass spectrometry-based proteome measurements at ORNL were supported by U.S. National Institutes of Health grant 1R01-GM-103600. Oak Ridge National Laboratory is managed by University of Tennessee-Battelle LLC for the Department of Energy under contract DOE-AC05-00OR22725., and European Project: 863664,ERC-2019-COG-ExpoBiome
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Microbiologie [F11] [Sciences du vivant] ,[SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology ,[SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN] ,[SDV.MHEP.HEG]Life Sciences [q-bio]/Human health and pathology/Hépatology and Gastroenterology ,Microbiology [F11] [Life sciences] ,General Medicine ,[SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM] ,Article ,microbiome ,multi-omics ,human gut microbiome ,secreted molecules - Abstract
The human gut microbiome produces a complex mixture of biomolecules that interact with human physiology and play essential roles in health and disease. Crosstalk between micro-organisms and host cells is enabled by different direct contacts, but also by the export of molecules through secretion systems and extracellular vesicles. The resulting molecular network, comprised of various biomolecular moieties, has so far eluded systematic study. Here we present a methodological framework, optimized for the extraction of the microbiome-derived, extracellular biomolecular complement, including nucleic acids, (poly)peptides, and metabolites, from flash-frozen stool samples of healthy human individuals. Our method allows simultaneous isolation of individual biomolecular fractions from the same original stool sample, followed by specialized omic analyses. The resulting multi-omics data enable coherent data integration for the systematic characterization of this molecular complex. Our results demonstrate the distinctiveness of the different extracellular biomolecular fractions, both in terms of their taxonomic and functional composition. This highlights the challenge of inferring the extracellular biomolecular complement of the gut microbiome based on single-omic data. The developed methodological framework provides the foundation for systematically investigating mechanistic links between microbiome-secreted molecules, including those that are typically vesicle-associated, and their impact on host physiology in health and disease.
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- 2021
13. Development of an enhanced chain elongation process for caproic acid production from waste-derived lactic acid and butyric acid
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Corine orline Nzeteu, Fabiana Coelho, Anna Christine Trego, Florence Abram, Javier Ramiro-Garcia, Lara Paulo, and Vincent O'Flaherty
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Renewable Energy, Sustainability and the Environment ,Strategy and Management ,Building and Construction ,Industrial and Manufacturing Engineering ,General Environmental Science - Published
- 2022
14. Dechlorination of three tetrachlorobenzene isomers by contaminated harbor sludge-derived enrichment cultures follows thermodynamically favorable reactions
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Javier Ramiro-Garcia, Steffi Herrmann, Siavash Atashgahi, Hauke Smidt, Yue Lu, Pieter Vandermeeren, Danuta Cichocka, and Dirk Springael
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0301 basic medicine ,DNA, Bacterial ,Thermodynamically favorable reactions ,Microbial Consortia ,Dehalobacter ,010501 environmental sciences ,Desulfitobacterium ,Chlorobenzenes ,01 natural sciences ,Applied Microbiology and Biotechnology ,Microbiology ,03 medical and health sciences ,Environmental Biotechnology ,Tetrachlorobenzenes ,Microbiologie ,Organohalide respiration ,Reductive dechlorination ,Humans ,Dehalococcoides mccartyi ,0105 earth and related environmental sciences ,VLAG ,Dehalococcoides ,WIMEK ,biology ,Sewage ,Ecology ,Stereoisomerism ,General Medicine ,Chloroflexi ,biology.organism_classification ,Anoxic waters ,030104 developmental biology ,Biodegradation, Environmental ,Environmental chemistry ,Peptococcaceae ,Thermodynamics ,Chlorine ,Microcosm ,Geobacter ,Bacteria ,Water Pollutants, Chemical ,Biotechnology - Abstract
Dechlorination patterns of three tetrachlorobenzene isomers, 1,2,3,4-, 1,2,3,5-, and 1,2,4,5-TeCB, were studied in anoxic microcosms derived from contaminated harbor sludge. The removal of doubly, singly, and un-flanked chlorine atoms was noted in 1,2,3,4- and 1,2,3,5-TeCB fed microcosms, whereas only singly flanked chlorine was removed in 1,2,4,5-TeCB microcosms. The thermodynamically more favorable reactions were selectively followed by the enriched cultures with di- and/or mono-chlorobenzene as the main end products of the reductive dechlorination of all three isomers. Based on quantitative PCR analysis targeting 16S rRNA genes of known organohalide-respiring bacteria, the growth of Dehalococcoides was found to be associated with the reductive dechlorination of all three isomers, while growth of Dehalobacter, another known TeCB dechlorinator, was only observed in one 1,2,3,5-TeCB enriched microcosm among biological triplicates. Numbers of Desulfitobacterium and Geobacter as facultative dechlorinators were rather stable suggesting that they were not (directly) involved in the observed TeCB dechlorination. Bacterial community profiling suggested bacteria belonging to the phylum Bacteroidetes and the order Clostridiales as well as sulfate-reducing members of the class Deltaproteobacteria as putative stimulating guilds that provide electron donor and/or organic cofactors to fastidious dechlorinators. Our results provide a better understanding of thermodynamically preferred TeCB dechlorinating pathways in harbor environments and microbial guilds enriched and active in anoxic TeCB dechlorinating microcosms. Electronic supplementary material The online version of this article (doi:10.1007/s00253-016-8004-8) contains supplementary material, which is available to authorized users.
- Published
- 2017
15. Geochemical and microbial community determinants of reductive dechlorination at a site biostimulated with glycerol
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Ying Zheng, Heinrich Eisenmann, Yue Lu, Maria Suarez-Diez, Winnie Dejonghe, Martin Elsner, Edoardo Saccenti, Hauke Smidt, Dirk Springael, Javier Ramiro-Garcia, Siavash Atashgahi, and Alfons J. M. Stams
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0301 basic medicine ,2. Zero hunger ,Ecology ,Microbial metabolism ,010501 environmental sciences ,Biology ,Deltaproteobacteria ,biology.organism_classification ,01 natural sciences ,Microbiology ,Anoxic waters ,6. Clean water ,Biostimulation ,03 medical and health sciences ,chemistry.chemical_compound ,030104 developmental biology ,Bioremediation ,chemistry ,13. Climate action ,Environmental chemistry ,Reductive dechlorination ,Sulfate-reducing bacteria ,Sulfate ,Ecology, Evolution, Behavior and Systematics ,0105 earth and related environmental sciences - Abstract
Biostimulation is widely used to enhance reductive dechlorination of chlorinated ethenes in contaminated aquifers. However, the knowledge on corresponding biogeochemical responses is limited. In this study, glycerol was injected in an aquifer contaminated with cis-dichloroethene (cDCE), and geochemical and microbial shifts were followed for 265 days. Consistent with anoxic conditions and sulfate reduction after biostimulation, MiSeq 16S rRNA gene sequencing revealed temporarily increased relative abundance of Firmicutes, Bacteriodetes and sulfate reducing Deltaproteobacteria. In line with 13 C cDCE enrichment and increased Dehalococcoides mccartyi (Dcm) numbers, dechlorination was observed toward the end of the field experiment, albeit being incomplete with accumulation of vinyl chloride. This was concurrent with (i) decreased concentrations of dissolved organic carbon (DOC), reduced relative abundances of fermenting and sulfate reducing bacteria that have been suggested to promote Dcm growth by providing electron donor (H2 ) and essential corrinoid cofactors, (ii) increased sulfate concentration and increased relative abundance of Epsilonproteobacteria and Deferribacteres as putative oxidizers of reduced sulfur compounds. Strong correlations of DOC, relative abundance of fermenters and sulfate reducers, and dechlorination imply the importance of syntrophic interactions to sustain robust dechlorination. Tracking microbial and environmental parameters that promote/preclude enhanced reductive dechlorination should aid development of sustainable bioremediation strategies.
- Published
- 2016
16. Integrated In Vitro and In Silico Modeling Delineates the Molecular Effects of a Synbiotic Regimen on Colorectal-Cancer-Derived Cells
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Joëlle V. Fritz, Almut Heinken, Joanna Baginska, Ines Thiele, Thomas Sauter, Kacy Greenhalgh, Maria Irene Pires Pacheco, Pit Ullmann, Pranjul Shah, Paul Wilmes, Elisabeth Letellier, Tamara Jean Rita Bintener, Rashi Halder, Serge Haan, Audrey Frachet, Javier Ramiro-Garcia, Fonds National de la Recherche Luxembourg, and Horizon 2020
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0301 basic medicine ,Synbiotics ,Colorectal cancer ,In silico ,medicine.medical_treatment ,gut microbiome ,colorectal cancer ,Pharmacology ,Biology ,General Biochemistry, Genetics and Molecular Biology ,law.invention ,03 medical and health sciences ,Probiotic ,0302 clinical medicine ,Downregulation and upregulation ,law ,medicine ,Humans ,Computer Simulation ,Microbiome ,Intestinal Mucosa ,lcsh:QH301-705.5 ,Cells, Cultured ,2. Zero hunger ,Lacticaseibacillus rhamnosus ,Prebiotic ,Probiotics ,modeling ,medicine.disease ,3. Good health ,Gastrointestinal Microbiome ,Regimen ,030104 developmental biology ,Prebiotics ,lcsh:Biology (General) ,gut-on-a-chip ,Host-Pathogen Interactions ,prebiotic ,symbiotic ,Caco-2 Cells ,Colorectal Neoplasms ,nutritional therapy ,030217 neurology & neurosurgery ,probiotic - Abstract
By modulating the human gut microbiome, prebiotics and probiotics (combinations of which are called synbiotics) may be used to treat diseases such as colorectal cancer (CRC). Methodological limitations have prevented determining the potential combinatorial mechanisms of action of such regimens. We expanded our HuMiX gut-on-a-chip model to co-culture CRC-derived epithelial cells with a model probiotic under a simulated prebiotic regimen, and we integrated the multi-omic results with in silico metabolic modeling. In contrast to individual prebiotic or probiotic treatments, the synbiotic regimen caused downregulation of genes involved in procarcinogenic pathways and drug resistance, and reduced levels of the oncometabolite lactate. Distinct ratios of organic and short-chain fatty acids were produced during the simulated regimens. Treatment of primary CRC-derived cells with a molecular cocktail reflecting the synbiotic regimen attenuated self-renewal capacity. Our integrated approach demonstrates the potential of modeling for rationally formulating synbiotics-based treatments in the future. The authors would like to thank Dr. Christian Jäger at the LCSB Metabolomics Platform for helpful discussions and metabolite quantification, and Martine Schmitz for RT-PCR validation analysis. We thank the contributing surgeons from the Centre Hospitalier Emile Mayrisch in Esch-sur-Alzette and the nurses of the Clinical and Epidemiological Investigation Center of the Luxembourg Institute of Health for collecting samples for research purposes. The authors wish to thank Frutarom for providing the SoyLife prebiotic. K.G. was supported by an AFR PhD fellowship from the Luxembourg National Research Fund (FNR; AFR/PHD/9964547 ). This work was supported by a Luxembourg Personalised Medicine Consortium pump-prime grant (PerPreProBioCRC) and a proof-of-concept grant ( PoC/15/11014639 ) from the FNR , awarded to P.W. The project was also supported through an internal research project grant (IRP; MiDiCa) from the University of Luxembourg to S.H. and P.W., and two CORE Junior grants ( C14/BM/8066232 and C16/BM/11282028 ) awarded to J.F. and E.L., respectively. This work was further supported by an ATTRACT Programme grant ( FNR/A12/01 ) awarded to I.T., a European Research Council (ERC) grant under the European Union’s Horizon 2020 research and innovation programme (grant agreement No. 757922 ) awarded to I.T., and an FNR grant ( PRIDE15/10675146/CANBIO ) to T.B. peer-reviewed
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- 2019
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17. NG-Tax, a highly accurate and validated pipeline for analysis of 16S rRNA amplicons from complex biomes
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Christos Giatsis, Peter J. Schaap, Detmer Sipkema, Javier Ramiro-Garcia, Gerben D. A. Hermes, Erwin G. Zoetendal, and Hauke Smidt
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0301 basic medicine ,16S rRNA amplicon analysis ,bioinformatic pipeline ,Sequence analysis ,Bioinformatics ,030106 microbiology ,Computational biology ,Biology ,microbial ecology ,Microbiology ,General Biochemistry, Genetics and Molecular Biology ,DNA sequencing ,Microbial ecology ,03 medical and health sciences ,0302 clinical medicine ,Aquaculture and Fisheries ,Microbiologie ,Systems and Synthetic Biology ,Microbiome ,microbial community analysis ,General Pharmacology, Toxicology and Pharmaceutics ,Gene ,Microbial community analysis ,VLAG ,Systeem en Synthetische Biologie ,General Immunology and Microbiology ,Aquacultuur en Visserij ,Robustness (evolution) ,Microbial Evolution & Genomics ,General Medicine ,Articles ,Genomics ,Ribosomal RNA ,Amplicon ,16S ribosomal RNA ,030104 developmental biology ,Next-generation sequencing ,WIAS ,Bioinformatic pipeline ,next-generation sequencing ,030217 neurology & neurosurgery ,Research Article - Abstract
Background Massive high-throughput sequencing of short, hypervariable segments of the 16S ribosomal RNA (rRNA) gene has transformed the methodological landscape describing microbial diversity within and across complex biomes. However, several studies have shown that the methodology rather than the biological variation is responsible for the observed sample composition and distribution. This compromises true meta-analyses, although this fact is often disregarded. Results To facilitate true meta-analysis of microbiome studies, we developed NG-Tax, a pipeline for 16S rRNA gene amplicon sequence analysis that was validated with different mock communities and benchmarked against QIIME as the currently most frequently used pipeline. The microbial composition of 49 independently amplified mock samples was characterized by sequencing two variable 16S rRNA gene regions, V4 and V5-V6, in three separate sequencing runs on Illumina’s HiSeq2000 platform. This allowed evaluating important factors of technical bias in taxonomic classification: 1) run-to-run sequencing variation, 2) PCR–error, and 3) region/primer specific amplification bias. Despite the short read length (~140 nt) and all technical biases, the average specificity of the taxonomic assignment for the phylotypes included in the mock communities was 96%. On average 99.94% and 92.02% of the reads could be assigned to at least family or genus level, respectively, while assignment to ‘spurious genera’ represented on average only 0.02% of the reads per sample. Analysis of α- and β-diversity confirmed conclusions guided by biology rather than the aforementioned methodological aspects, which was not the case when samples were analysed using QIIME. Conclusions Different biological outcomes are commonly observed due to 16S rRNA region-specific performance. NG-Tax demonstrated high robustness against choice of region and other technical biases associated with 16S rRNA gene amplicon sequencing studies, diminishing their impact and providing accurate qualitative and quantitative representation of the true sample composition. This will improve comparability between studies and facilitate efforts towards standardization.
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- 2018
18. New Insights into Microbial Diversity of the Traditional Packed Table Olives Aloreña de Málaga through Metataxonomic Analysis
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Antonio Benítez-Cabello, Francisco Noé Arroyo-López, Francisco Rodríguez-Gómez, Javier Ramiro-Garcia, Verónica Romero-Gil, Elio López-García, and Ministerio de Ciencia, Innovación y Universidades (España)
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Microbiology (medical) ,Population ,Biology ,Shelf life ,Microbiology ,Metagenomic analysis ,Food safety ,microbial evolution ,03 medical and health sciences ,Brining ,Virology ,Food science ,education ,lcsh:QH301-705.5 ,Table olives ,030304 developmental biology ,0303 health sciences ,education.field_of_study ,Shelf-life ,Microbial evolution ,030306 microbiology ,metagenomic analysis ,biology.organism_classification ,shelf-life ,food safety ,table olives ,lcsh:Biology (General) ,Penicillium ,Fermentation ,Pediococcus ,Bacteria ,Mesophile - Abstract
12 Páginas, Aloreña de Málaga is a table olive especially characterised by its natural freshness and short shelf-life. In this work, we applied a metataxonomic approach to unravel the microbial diversity of bacterial and fungi populations through the shelf-life of traditionally packed Aloreña de Málaga. A significant increase in lactic acid bacteria and mesophilic aerobic populations was observed during shelf-life, reaching the maximum population levels (4–5 log10 CFU) at the end of the study (260 days). On the contrary, a rapid reduction in yeast and mould populations was reported. The use of a metataxonomic analysis based on the amplification of 16S (bacteria) and internal transcribed spacer (ITS) region (fungi) regions revealed a low diversity for both microbial groups. Lactiplantibacillus (65.05 ± 8.65% in brine vs. 58.70 ± 15.70% in fruit), Pediococcus (28.17 ± 7.36% in brine vs. 27.20 ± 15.95% in fruit), and Celerinatantimonas (4.64 ± 1.08% in brine vs. 11.82 ± 18.17% in fruit) were the main genera found among bacteria, and an increase in Lactiplantibacillus and a reduction in Celerinatantimonas populations during the shelf-life were observed. On the other hand, Citeromyces was the dominant fungi genus (54.11 ± 2.00% in brine vs. 50.91 ± 16.14% in fruit), followed by Candida (8.80 ± 2.57% in brine vs. 12.32 ± 8.61% in fruit) and Penicillium (6.48 ± 1.87% vs. 8.48 ± 4.43% in fruit). No food-borne pathogen genera were detected in any of the samples analysed, indicating the high level of food safety found in this ready-to-eat fermented vegetable. Data obtained in this work will help in the design of new strategies for the control of microbial populations during the shelf-life of Aloreña de Málaga., This research was funded by the Spanish Government through the TOBE project (RTI2018-100883-B-I00).
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- 2021
19. Abstract A09: Understanding the role of colorectal cancer-associated microbes in colorectal cancer
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Kacy Greenhalgh, Diana Kuhn, Eric Koncina, Léa Grandmougin, Javier Ramiro Garcia, Dominik Ternes, Paul Wilmes, Mina Tsenkova, Serge Haan, Jessica Karta, Aurélien Ginolhac, Martine Schmitz, and Elisabeth Letellier
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Cancer Research ,Colorectal cancer ,In silico ,Fusobacteria ,Disease ,Biology ,medicine.disease ,biology.organism_classification ,Transcriptome ,Oncology ,medicine ,Cancer research ,Sample collection ,Microbiome ,Dysbiosis - Abstract
Accumulating evidence suggests that dysbiosis, a state of pathologic imbalance in the human gut microbiome, is present in patients suffering from colorectal cancer (CRC). Several microbiome studies identified specific bacteria that are associated with CRC, among which Fusobacteria were shown to directly interact with cancer or immune cells of their host. However, only a limited number of CRC-associated microbes have been studied for host-microbial interactions; hence, the role of bacteria in the etiology of the disease remains unknown. Accordingly, our work aims at the development of a methodologic workflow for studying CRC-associated bacteria and their role in colon cancer tumor initiation and progression. In a first step, we identified CRC-associated bacteria that are enriched at the tumor site of CRC patients. Therefore, we used publicly available datasets and an in-house patient sample collection. Then, we predicted and optimized bacterial growth in silico by using a genome-scale metabolic reconstruction model combined with a constraint-based modeling approach. Finally, we implemented CRC-associated bacteria together with established primary CRC patient cultures into the microfluidics-based human-microbial crosstalk model (HuMiX). Our workflow allowed to analyze host-microbial interaction mechanisms of CRC-associated bacteria on a transcriptomic, proteomic, and metabolomic level. Citation Format: Dominik Ternes, Martine Schmitz, Léa Grandmougin, Mina Tsenkova, Eric Koncina, Aurélien Ginolhac, Jessica Karta, Diana Kuhn, Javier Ramiro Garcia, Kacy Greenhalgh, Paul Wilmes, Elisabeth Letellier, Serge Haan. Understanding the role of colorectal cancer-associated microbes in colorectal cancer [abstract]. In: Proceedings of the AACR Special Conference on the Microbiome, Viruses, and Cancer; 2020 Feb 21-24; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2020;80(8 Suppl):Abstract nr A09.
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- 2020
20. Occupancy strongly influences faecal microbial composition of wild lemurs
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Iris de Winter, Javier Ramiro-Garcia, Pim van Hooft, Alexander Umanets, Hauke Smidt, Freek IJdema, Ignas M. A. Heitkönig, and Herbert H. T. Prins
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0301 basic medicine ,Male ,Occupancy ,Firmicutes ,Climate ,Population ,Lemur ,Zoology ,Animals, Wild ,Biology ,Forests ,Environment ,Applied Microbiology and Biotechnology ,Microbiology ,Eulemur ,03 medical and health sciences ,Feces ,Microbiologie ,biology.animal ,Madagascar ,Animals ,Microbiome ,education ,Ecosystem ,VLAG ,education.field_of_study ,Ecology ,Bacteria ,Gastro-intestinal tract ,Microbiota ,Bacteroidetes ,biology.organism_classification ,PE&RC ,Multivariate statistics ,Gastrointestinal Microbiome ,030104 developmental biology ,Sympatric speciation ,Wildlife Ecology and Conservation ,Female ,Adaptation - Abstract
The microbiota of the mammalian gut is a complex ecosystem, the composition of which is greatly influenced by host genetics and environmental factors. In this study, we aim to investigate the influence of occupancy (a geographical area of habitation), species, age and sex on intestinal microbiota composition of the three lemur species: Eulemur fulvus, E. rubriventer and E. rufifrons. Faecal samples were collected from a total of 138 wild lemurs across Madagascar, and microbial composition was determined using next-generation sequencing of PCR-amplified 16S rRNA gene fragments. Consistent with reports from other primate species, the predominant phyla were Firmicutes (43 ± 6.4% [s.d.]) and Bacteroidetes (30.3 ± 5.3%). The microbial composition was strongly associated with occupancy in the E. fulvus population, with up to 19.9% of the total variation in microbial composition being explained by this factor. In turn, geographical differences observed in faecal microbiota of sympatric lemur species were less pronounced, as was the impact of the factors sex and age. Our findings showed that among the studied factors occupancy had the strongest influence on intestinal microbiota of congeneric lemur species. This suggests adaptation of microbiota to differences in forest composition, climate variations and correspondingly available diet in different geographical locations of Madagascar.
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- 2018
21. Integrated in Vitro and in Silico Modelling Delineates the Molecular Effects of a Symbiotic Regimen on Colorectal Cancer-Derived Cells
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Maria Irene Pires Pacheco, Audrey Frachet, Tamara Jean Rita Bintener, Joëlle V. Fritz, Serge Haan, Pranjul Shah, Thomas Sauter, Elisabeth Letellier, Javier Ramiro-Garcia, Kacy Greenhalgh, Rashi Halder, Pit Ullmann, Paul Wilmes, Joanna Baginska, Almut Heinken, and Ines Thiele
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Colorectal cancer ,Synbiotics ,In silico ,Prebiotic ,medicine.medical_treatment ,Pharmacology ,Biology ,medicine.disease ,law.invention ,Probiotic ,Regimen ,Downregulation and upregulation ,law ,medicine ,Microbiome - Abstract
By modulating the human gut microbiome, prebiotics and probiotics (combinations of which are called synbiotics) may be used to treat diseases such as colorectal cancer (CRC). Methodological limitations have prevented determining the potential combinatorial mechanisms of action of such regimens. We expanded our HuMiX gut-ona- chip model to co-culture CRC-derived epithelial cells with a model probiotic under a simulated prebiotic regimen, and integrated the multi-omic results with in silico metabolic modelling. In contrast to individual prebiotic or probiotic treatments, the synbiotic regimen caused downregulation of genes involved in procarcinogenic pathways and drug resistance, and reduced levels of the oncometabolite lactate. Distinct ratios of organic and short-chain fatty acids were produced during the simulated regimens. Treatment of primary CRC-derived cells with a molecular cocktail reflecting the synbiotic regimen attenuated self-renewal capacity. Our integrated approach demonstrates the potential of modelling for rationally formulating synbiotics-based treatments in the future.
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- 2018
22. Birth mode is associated with earliest strain-conferred gut microbiome functions and immunostimulatory potential
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Javier Ramiro-Garcia, Angela Hogan, Anna Heintz-Buschart, Shaman Narayanasamy, Janine Habier, Malte Herold, Jean Bottu, Anders F. Andersson, Linda Wampach, Patrick May, Rashi Halder, Lutz Bindl, Anne Kaysen, Carine de Beaufort, Conny Sjöqvist, Joëlle V. Fritz, Paul Wilmes, and Fonds National de la Recherche - FnR [sponsor]
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0301 basic medicine ,Lipopolysaccharides ,Microbiologie [F11] [Sciences du vivant] ,Lipopolysaccharide ,Science ,medicine.medical_treatment ,General Physics and Astronomy ,Stimulation ,Biology ,In Vitro Techniques ,digestive system ,General Biochemistry, Genetics and Molecular Biology ,Article ,03 medical and health sciences ,chemistry.chemical_compound ,0302 clinical medicine ,Immune system ,fluids and secretions ,Pregnancy ,Blood plasma ,medicine ,Humans ,Caesarean section ,Microbiology [F11] [Life sciences] ,Microbiome ,lcsh:Science ,reproductive and urinary physiology ,Multidisciplinary ,Cesarean Section ,Tumor Necrosis Factor-alpha ,Infant, Newborn ,Interleukin-18 ,General Chemistry ,medicine.disease ,Delivery, Obstetric ,Infectious Disease Transmission, Vertical ,female genital diseases and pregnancy complications ,Gastrointestinal Microbiome ,stomatognathic diseases ,030104 developmental biology ,chemistry ,Immunology ,Interleukin 18 ,Female ,lcsh:Q ,Metagenomics ,030217 neurology & neurosurgery - Abstract
The rate of caesarean section delivery (CSD) is increasing worldwide. It remains unclear whether disruption of mother-to-neonate transmission of microbiota through CSD occurs and whether it affects human physiology. Here we perform metagenomic analysis of earliest gut microbial community structures and functions. We identify differences in encoded functions between microbiomes of vaginally delivered (VD) and CSD neonates. Several functional pathways are over-represented in VD neonates, including lipopolysaccharide (LPS) biosynthesis. We link these enriched functions to individual-specific strains, which are transmitted from mothers to neonates in case of VD. The stimulation of primary human immune cells with LPS isolated from early stool samples of VD neonates results in higher levels of tumour necrosis factor (TNF-α) and interleukin 18 (IL-18). Accordingly, the observed levels of TNF-α and IL-18 in neonatal blood plasma are higher after VD. Taken together, our results support that CSD disrupts mother-to-neonate transmission of specific microbial strains, linked functional repertoires and immune-stimulatory potential during a critical window for neonatal immune system priming., The effects of caesarean section delivery on mother-to-neonate transmission of microbiota are unclear. Here the authors show that caesarean section delivery can affect the transmission of specific microbial strains and the immunomodulatory potential of the microbiota.
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- 2018
23. Gene probing reveals the widespread distribution, diversity and abundance of isoprene-degrading bacteria in the environment
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Muhammad Farhan Ul Haque, J. Colin Murrell, Lisa Gibson, Terry J. McGenity, Ornella Carrión, Nasmille L Larke-Mejía, and Javier Ramiro-Garcia
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0301 basic medicine ,Microbiology (medical) ,010504 meteorology & atmospheric sciences ,Isoprene ,Climate ,Biology ,01 natural sciences ,Microbiology ,lcsh:Microbial ecology ,Mixed Function Oxygenases ,Molecular ecology ,Comamonadaceae ,03 medical and health sciences ,chemistry.chemical_compound ,Hemiterpenes ,Bacterial Proteins ,Microbial ecology ,Botany ,Butadienes ,Rhodococcus ,Isoprene monooxygenase ,Gene probes ,14. Life underwater ,Phylogeny ,Soil Microbiology ,DNA Primers ,0105 earth and related environmental sciences ,Bacteria ,Research ,isoA ,Sequence Analysis, DNA ,Variovorax ,15. Life on land ,biology.organism_classification ,Sphingomonadaceae ,Sphingopyxis ,Biodegradation, Environmental ,030104 developmental biology ,chemistry ,13. Climate action ,lcsh:QR100-130 ,Phyllosphere - Abstract
Background Approximately 500 Tg of isoprene are emitted to the atmosphere annually, an amount similar to that of methane, and despite its significant effects on the climate, very little is known about the biological degradation of isoprene in the environment. Isolation and characterisation of isoprene degraders at the molecular level has allowed the development of probes targeting isoA encoding the α-subunit of the isoprene monooxygenase. This enzyme belongs to the soluble diiron centre monooxygenase family and catalyses the first step in the isoprene degradation pathway. The use of probes targeting key metabolic genes is a successful approach in molecular ecology to study specific groups of bacteria in complex environments. Here, we developed and tested a novel isoA PCR primer set to study the distribution, abundance, and diversity of isoprene degraders in a wide range of environments. Results The new isoA probes specifically amplified isoA genes from taxonomically diverse isoprene-degrading bacteria including members of the genera Rhodococcus, Variovorax, and Sphingopyxis. There was no cross-reactivity with genes encoding related oxygenases from non-isoprene degraders. Sequencing of isoA amplicons from DNA extracted from environmental samples enriched with isoprene revealed that most environments tested harboured a considerable variety of isoA sequences, with poplar leaf enrichments containing more phylogenetically diverse isoA genes. Quantification by qPCR using these isoA probes revealed that isoprene degraders are widespread in the phyllosphere, terrestrial, freshwater and marine environments. Specifically, soils in the vicinity of high isoprene-emitting trees contained the highest number of isoprene-degrading bacteria. Conclusion This study provides the molecular ecology tools to broaden our knowledge of the distribution, abundance and diversity of isoprene degraders in the environment, which is a fundamental step necessary to assess the impact that microbes have in mitigating the effects of this important climate-active gas. Electronic supplementary material The online version of this article (10.1186/s40168-018-0607-0) contains supplementary material, which is available to authorized users.
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- 2018
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24. Effect of Nickel and Cobalt on Methanogenic Enrichment Cultures and Role of Biogenic Sulfide in Metal Toxicity Attenuation
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Alfons J. M. Stams, Javier Ramiro-Garcia, Lara M. Paulo, Diana Z. Sousa, Simon van Mourik, and Universidade do Minho
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0301 basic medicine ,Microbiology (medical) ,Sulfide ,Microorganism ,lcsh:QR1-502 ,Microbial metabolism ,chemistry.chemical_element ,Farm Technology ,Metal toxicity ,sulfate ,010501 environmental sciences ,stimulation ,01 natural sciences ,Microbiology ,lcsh:Microbiology ,Methane ,03 medical and health sciences ,chemistry.chemical_compound ,anaerobic sludge ,Microbiologie ,Sulfate ,heavy metals ,Original Research ,Inhibition ,0105 earth and related environmental sciences ,chemistry.chemical_classification ,WIMEK ,Science & Technology ,sulfide ,Chemistry ,inhibition ,3. Good health ,Nickel ,030104 developmental biology ,Heavy metals ,Environmental chemistry ,Anaerobic sludge ,Stimulation ,WIAS ,Agrarische Bedrijfstechnologie ,Cobalt - Abstract
The Supplementary Material for this article can be found online at: http://journal.frontiersin.org/article/10.3389/fmicb. 2017.01341/full#supplementary-material, Metals play an important role in microbial metabolism by acting as cofactors for many enzymes. Supplementation of biological processes with metals may result in improved performance, but high metal concentrations are often toxic to microorganisms. In this work, methanogenic enrichment cultures growing on H2/CO2 or acetate were supplemented with trace concentrations of nickel (Ni) and cobalt (Co), but no significant increase in methane production was observed in most of the tested conditions. However, high concentrations of these metals were detrimental to methanogenic activity of the cultures. Cumulative methane production (after 6 days of incubation) from H2/CO2 was 40% lower in the presence of 8 mM of Ni or 30 mM of Co, compared to controls without metal supplementation. When acetate was used as substrate, cumulative methane production was also reduced: by 18% with 8 mM of Ni and by 53% with 30 mM of Co (after 6 days of incubation). Metal precipitation with sulphide was further tested as a possible method to alleviate metal toxicity. Anaerobic sludge was incubated with Co (30 mM) and Ni (8 mM) in the presence of sulphate or sulphide. The addition of sulphide helped to mitigate the toxic effect of the metals. Methane production from H2/CO2 was negatively affected in the presence of sulphate, possibly due to competition of hydrogenotrophic methanogens by sulphate-reducing bacteria. However, in the enrichment cultures growing on acetate, biogenically produced sulphide had a positive effect and more methane was produced in these incubations than in similar assays without sulphate addition. The outcome of competition between methanogens and sulphate-reducing bacteria is a determinant factor for the success of using biogenic sulphide as detoxification method., The research was financially supported by the People Program (Marie Curie Actions) of the European Union's Seventh Framework Programme FP7/2007-2013 under REA agreement 289193. Research of AS and DS is supported by a ERC grant (project 323009) of the European Union Seventh Framework Program FP7 and a Gravitation grant (project 024.002.002) of the Netherlands Ministry of Education, Culture and Science and the Netherlands Science Foundation (NWO)., info:eu-repo/semantics/publishedVersion
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- 2017
25. Geochemical Parameters and Reductive Dechlorination Determine Aerobic Cometabolic vs Aerobic Metabolic Vinyl Chloride Biodegradation at Oxic/Anoxic Interface of Hyporheic Zones
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Siavash Atashgahi, Peng Peng, Javier Ramiro-Garcia, Farai Maphosa, Yue Lu, Detmer Sipkema, Dirk Springael, Hauke Smidt, and Winnie Dejonghe
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0301 basic medicine ,030106 microbiology ,Vinyl Chloride ,010501 environmental sciences ,01 natural sciences ,Redox ,Microbiology ,Vinyl chloride ,03 medical and health sciences ,chemistry.chemical_compound ,Microbiologie ,Reductive dechlorination ,Life Science ,Environmental Chemistry ,Groundwater ,Phylogeny ,0105 earth and related environmental sciences ,VLAG ,Total organic carbon ,WIMEK ,Chemistry ,General Chemistry ,Biodegradation ,Anoxic waters ,6. Clean water ,Biodegradation, Environmental ,13. Climate action ,Environmental chemistry ,Microcosm ,Oxidation-Reduction ,Anaerobic exercise - Abstract
Hyporheic zones mediate vinyl chloride (VC) biodegradation in groundwater discharging into surface waters. At the oxic/anoxic interface (OAI) of hyporheic zones subjected to redox oscillations, VC is degraded via coexisting aerobic ethenotrophic and anaerobic reductive dechlorination pathways. However, the identity of aerobic VC degradation pathways (cometabolic vs metabolic) and their interactions with reductive dechlorination in relation to riverbed sediment geochemistry remain ill-defined. We addressed this using microcosms containing OAI sediments incubated under fluctuating oxic/anoxic atmosphere. Under oxic atmosphere, aerobic metabolic VC oxidation was absent in sediments with high total organic carbon (TOC) and VC was reductively dechlorinated to ethene. Ethene was oxidized by ethenotrophs that can degrade VC cometabolically. Contrastingly, VC was metabolically oxidized by ethenotrophs in low-TOC sediments with low reductive dechlorination potential. Accordingly, enrichment and isolation of metabolic VC-oxidizing ethenotrophs was successful only from the low-TOC sediment. Sequence analysis of etnE genes from the microcosms as well phylogenetic typing of the isolates showed that ethenotrophs in the sediments were facultative anaerobic Proteobacteria capable of coping with OAI-associated redox fluctuations. Our results suggest that local sediment heterogeneity supports/selects divergent VC degradation processes at the OAI and that high reductive dechlorination potential suppresses development of aerobic metabolic VC oxidation potential.
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- 2017
26. Dietary protein sources differentially affect microbiota, mTOR activity and transcription of mTOR signaling pathways in the small intestine
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L. Kruijt, Dirkjan Schokker, Jerry M. Wells, Nirupama Benis, Mari A. Smits, Javier Ramiro-Garcia, Ellen H. Stolte, Soumya K. Kar, J.J. Taverne-Thiele, and Alfons J. M. Jansman
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Male ,0301 basic medicine ,Animal Nutrition ,Physiology ,Soybean meal ,lcsh:Medicine ,Transcriptome ,White Blood Cells ,Mice ,Animal Cells ,Microbiologie ,Immune Physiology ,Casein ,Genes, Regulator ,Granulocyte Colony-Stimulating Factor ,Gene expression ,Medicine and Health Sciences ,Gene Regulatory Networks ,Systems and Synthetic Biology ,lcsh:Science ,Regulator gene ,Innate Immune System ,Meal ,Systeem en Synthetische Biologie ,Multidisciplinary ,T Cells ,TOR Serine-Threonine Kinases ,Bacteriologie ,Caseins ,Agriculture ,Bacteriology, Host Pathogen Interaction & Diagnostics ,Genomics ,Blood Proteins ,Diervoeding ,medicine.anatomical_structure ,Physiological Parameters ,Biochemistry ,Medical Microbiology ,Cytokines ,Dietary Proteins ,Cellular Types ,Anatomy ,Research Article ,Animal Breeding & Genomics ,medicine.medical_specialty ,Glutens ,Immune Cells ,Immunology ,Crops ,Microbial Genomics ,Biology ,Microbiology ,03 medical and health sciences ,Ileum ,Internal medicine ,Genetics ,medicine ,Animals ,Life Science ,Host-Microbe Interactomics ,Fokkerij & Genomica ,PI3K/AKT/mTOR pathway ,Nutrition ,VLAG ,Food, Formulated ,Host Pathogen Interaction & Diagnostics ,Blood Cells ,Bacteria ,Body Weight ,lcsh:R ,Biology and Life Sciences ,Bacteriology ,Cell Biology ,Nutrients ,Molecular Development ,Small intestine ,Host Pathogen Interactie & Diagnostiek ,Diet ,Gastrointestinal Microbiome ,Gastrointestinal Tract ,Mice, Inbred C57BL ,Whey Proteins ,030104 developmental biology ,Endocrinology ,Immune System ,Bacteriologie, Host Pathogen Interactie & Diagnostiek ,WIAS ,lcsh:Q ,Microbiome ,Soybeans ,Soybean ,Digestive System ,Developmental Biology ,Crop Science - Abstract
Dietary protein sources can have profound effects on host-microbe interactions in the gut that are critically important for immune resilience. However more knowledge is needed to assess the impact of different protein sources on gut and animal health. Thirty-six wildtype male C57BL/6J mice of 35 d age (n = 6/group; mean ± SEM body weight 21.9 ± 0.25 g) were randomly assigned to groups fed for four weeks with semi synthetic diets prepared with one of the following protein sources containing (300 g/kg as fed basis): soybean meal (SBM), casein, partially delactosed whey powder, spray dried plasma protein, wheat gluten meal and yellow meal worm. At the end of the experiment, mice were sacrificed to collect ileal tissue to acquire gene expression data, and mammalian (mechanistic) target of rapamycin (mTOR) activity, ileal digesta to study changes in microbiota and serum to measure cytokines and chemokines. By genome-wide transcriptome analysis, we identified fourteen high level regulatory genes that are strongly affected in SBM-fed mice compared to the other experimental groups. They mostly related to the mTOR pathway. In addition, an increased (P < 0.05) concentration of granulocyte colony-stimulating factor was observed in serum of SBM-fed mice compared to other dietary groups. Moreover, by 16S rRNA sequencing, we observed that SBM-fed mice had higher (P < 0.05) abundances of Bacteroidales family S24-7, compared to the other dietary groups. We showed that measurements of genome-wide expression and microbiota composition in the mouse ileum reveal divergent responses to diets containing different protein sources, in particular for a diet based on SBM.
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- 2017
27. To pool or not to pool? Impact of the use of individual and pooled fecal samples for in vitro fermentation studies
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Marisol Aguirre, Marjorie E. Koenen, Javier Ramiro-Garcia, Koen Venema, Humane Biologie, RS: NUTRIM - R1 - Metabolic Syndrome, and RS: NUTRIM - HB/BW section A
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Male ,Pooling ,Time Factors ,Unclassified drug ,Prevotella ,Biomedical Innovation ,Acetates ,In vitro model ,Feces ,Clostridium ,fluids and secretions ,Life ,Microbiologie ,Food science ,bacteria ,Phylogeny ,Intestine flora ,Microbiota ,starch ,Short chain fatty acid ,core ,Biodiversity ,Middle Aged ,Branched chain fatty acids ,Normal human ,Actinobacteria ,Butyrates ,products ,Biochemistry ,Human experiment ,Female ,Healthy Living ,Fecal inoculum preparation ,human large-intestine ,Human ,Microbiology (medical) ,Adult ,Branched chain fatty acid ,Firmicutes ,Fermentation technique ,Gut microbiota ,In Vitro Techniques ,Biology ,Isobutyric acid ,Microbiology ,Turicibacter ,Sample ,Inoculation ,Verrucomicrobia ,oligosaccharides ,Microbial community ,Proteobacteria ,Humans ,In vitro study ,patterns ,Molecular Biology ,VLAG ,model ,Genus ,gut microbiota ,Bacteroidetes ,biology.organism_classification ,Fatty acid ,Nonhuman ,In vitro ,MSB - Microbiology and Systems Biology ,Fermentation ,Metagenome ,ELSS - Earth, Life and Social Sciences ,Propionates ,Isovaleric acid ,Controlled study ,metabolism - Abstract
This study investigated the stability and the activity of the microbiota from a single and a pool of donors in the TNO in vitro model of the colon (TIM-2 system). Our findings demonstrate the suitability of the preparation of a pool of fecal sample to be used for fermentation experiments. Chemicals/CAS: isobutyric acid, 5711-69-3, 79-31-2; isovaleric acid, 503-74-2, 539-66-2
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- 2014
28. Probiotic legacy effects on gut microbial assembly in tilapia larvae
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Christos Giatsis, Marc C.J. Verdegem, Javier Ramiro-Garcia, Johan A.J. Verreth, Jason Abernathy, Detmer Sipkema, Hauke Smidt, and Gianina M. Bacanu
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0301 basic medicine ,food.ingredient ,Bacillus subtilis ,Gut flora ,Microbiology ,digestive system ,Article ,law.invention ,03 medical and health sciences ,Probiotic ,food ,Aquaculture and Fisheries ,Microbiologie ,law ,Life Science ,Colonization ,Axenic ,VLAG ,Larva ,Multidisciplinary ,biology ,Aquacultuur en Visserij ,Tilapia ,biology.organism_classification ,16S ribosomal RNA ,030104 developmental biology ,WIAS - Abstract
The exposure of fish to environmental free-living microbes and its effect on early colonization in the gut have been studied in recent years. However, little is known regarding how the host and environment interact to shape gut communities during early life. Here, we tested whether the early microbial exposure of tilapia larvae affects the gut microbiota at later life stages. The experimental period was divided into three stages: axenic, probiotic and active suspension. Axenic tilapia larvae were reared either under conventional conditions (active suspension systems) or exposed to a single strain probiotic (Bacillus subtilis) added to the water. Microbial characterization by Illumina HiSeq sequencing of 16S rRNA gene amplicons showed the presence of B. subtilis in the gut during the seven days of probiotic application. Although B. subtilis was no longer detected in the guts of fish exposed to the probiotic after day 7, gut microbiota of the exposed tilapia larvae remained significantly different from that of the control treatment. Compared with the control, fish gut microbiota under probiotic treatment was less affected by spatial differences resulting from tank replication, suggesting that the early probiotic contact contributed to the subsequent observation of low inter-individual variation.
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- 2016
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29. A novel biomarker panel for irritable bowel syndrome and the application in the general population
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Cisca Wijmenga, Agnieszka Baranska, Javier Ramiro-Garcia, Daisy Jonkers, Agnieszka Smolinska, Zlatan Mujagic, Morris A. Swertz, Ettje F. Tigchelaar, Thomas Ludwig, Frederik J. van Schooten, Ad A.M. Masclee, Alexandra Zhernakova, MUMC+: MA Med Staf Artsass Interne Geneeskunde (9), Promovendi NTM, Interne Geneeskunde, Farmacologie en Toxicologie, RS: NUTRIM - R4 - Gene-environment interaction, MUMC+: MA Maag Darm Lever (9), RS: NUTRIM - R2 - Gut-liver homeostasis, Groningen Institute for Gastro Intestinal Genetics and Immunology (3GI), and Translational Immunology Groningen (TRIGR)
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0301 basic medicine ,Male ,SYMPTOMS ,CHROMOGRANIN-A ,Gastroenterology ,Irritable Bowel Syndrome ,0302 clinical medicine ,Microbiologie ,Mass Screening ,Young adult ,Irritable bowel syndrome ,education.field_of_study ,Multidisciplinary ,INDUCTION ,Middle Aged ,Area Under Curve ,Cohort ,030211 gastroenterology & hepatology ,Female ,CITRULLINE ,Adult ,medicine.medical_specialty ,Population ,General Population Cohort ,Biomarker panel ,DIAGNOSIS ,Microbiology ,Article ,03 medical and health sciences ,Young Adult ,INFLAMMATION ,Internal medicine ,IBS ,medicine ,Life Science ,Humans ,PERMEABILITY ,education ,Mass screening ,METAANALYSIS ,business.industry ,Case-control study ,medicine.disease ,030104 developmental biology ,ROC Curve ,Case-Control Studies ,Immunology ,CELLS ,business ,Biomarkers - Abstract
Biological markers that measure gut health and diagnose functional gastro-intestinal (GI) disorders, such as irritable bowel syndrome (IBS), are lacking. The objective was to identify and validate a biomarker panel associated with the pathophysiology of IBS that discriminates IBS from healthy controls (HC) and correlates with GI symptom severity. In a case-control design, various plasma and fecal markers were measured in a cohort of 196 clinical IBS patients and 160 HC without GI symptoms. A combination of biomarkers, which best discriminates between IBS and HC was identified and validated in an independent internal validation set and by permutation testing. The correlation between the biomarker panel and GI symptom severity was tested in IBS patients and in a general population cohort of 958 subjects. A set of 8 biomarker panel was identified to discriminate IBS from HC with high sensitivity (88.1%) and specificity (86.5%). The results for the IBS subtypes were comparable. Moreover, a moderate correlation was found between the biomarker panel and GI symptom scores in the IBS (r = 0.59, p r = 0.51, p = 0.003). A novel multi-domain biomarker panel has been identified and validated, which correlated moderately to GI symptom severity in IBS and general population subjects.
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- 2016
30. A comprehensive metatranscriptome analysis pipeline and its validation using human small intestine microbiota datasets
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Milkha M. Leimena, Erwin G. Zoetendal, Michiel Kleerebezem, Mark Davids, Jos Boekhorst, Hauke Smidt, Bartholomeus van den Bogert, Eddy J. Smid, Peter J. Schaap, and Javier Ramiro-Garcia
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Single-end reads ,Levensmiddelenmicrobiologie ,Microbiologie ,Databases, Genetic ,Intestine, Small ,Paired-end reads ,Systems and Synthetic Biology ,bacteria ,Phylogeny ,Genetics ,Systeem en Synthetische Biologie ,Phylogenetic tree ,Human small intestine microbiota ,Illumina sequencing ,ribosomal-rna ,Middle Aged ,Reference Standards ,identities ,communities ,Metabolic pathways ,quality ,KEGG ,Bioinformatic pipeline ,Female ,DNA microarray ,Metabolic Networks and Pathways ,Research Article ,Biotechnology ,Metatranscriptome ,Energy and redox metabolism [NCMLS 4] ,Computational biology ,Biology ,Microbiology ,DNA sequencing ,diversity ,seq ,COG ,transcriptomes ,Humans ,RNA, Messenger ,Host-Microbe Interactomics ,Illumina dye sequencing ,Aged ,VLAG ,metagenomics ,Sequence Analysis, RNA ,Gene Expression Profiling ,Computational Biology ,Ribosomal RNA ,gene-expression ,Metagenomics ,WIAS ,Food Microbiology ,Metagenome ,Pyrosequencing - Abstract
Background Next generation sequencing (NGS) technologies can be applied in complex microbial ecosystems for metatranscriptome analysis by employing direct cDNA sequencing, which is known as RNA sequencing (RNA-seq). RNA-seq generates large datasets of great complexity, the comprehensive interpretation of which requires a reliable bioinformatic pipeline. In this study, we focus on the development of such a metatranscriptome pipeline, which we validate using Illumina RNA-seq datasets derived from the small intestine microbiota of two individuals with an ileostomy. Results The metatranscriptome pipeline developed here enabled effective removal of rRNA derived sequences, followed by confident assignment of the predicted function and taxonomic origin of the mRNA reads. Phylogenetic analysis of the small intestine metatranscriptome datasets revealed a strong similarity with the community composition profiles obtained from 16S rDNA and rRNA pyrosequencing, indicating considerable congruency between community composition (rDNA), and the taxonomic distribution of overall (rRNA) and specific (mRNA) activity among its microbial members. Reproducibility of the metatranscriptome sequencing approach was established by independent duplicate experiments. In addition, comparison of metatranscriptome analysis employing single- or paired-end sequencing methods indicated that the latter approach does not provide improved functional or phylogenetic insights. Metatranscriptome functional-mapping allowed the analysis of global, and genus specific activity of the microbiota, and illustrated the potential of these approaches to unravel syntrophic interactions in microbial ecosystems. Conclusions A reliable pipeline for metatransciptome data analysis was developed and evaluated using RNA-seq datasets obtained for the human small intestine microbiota. The set-up of the pipeline is very generic and can be applied for (bacterial) metatranscriptome analysis in any chosen niche.
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- 2013
31. In Silico Evidence of the Multifunctional Features of Lactiplantibacillus pentosus LPG1, a Natural Fermenting Agent Isolated from Table Olive Biofilms
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Elio López-García, Antonio Benítez-Cabello, Javier Ramiro-García, Victor Ladero, and Francisco Noé Arroyo-López
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probiotic ,starter culture ,genome overview ,fermented vegetables ,whole-genome sequencing ,Chemical technology ,TP1-1185 - Abstract
In recent years, there has been a growing interest in obtaining probiotic bacteria from plant origins. This is the case of Lactiplantibacillus pentosus LPG1, a lactic acid bacterial strain isolated from table olive biofilms with proven multifunctional features. In this work, we have sequenced and closed the complete genome of L. pentosus LPG1 using both Illumina and PacBio technologies. Our intention is to carry out a comprehensive bioinformatics analysis and whole-genome annotation for a further complete evaluation of the safety and functionality of this microorganism. The chromosomic genome had a size of 3,619,252 bp, with a GC (Guanine-Citosine) content of 46.34%. L. pentosus LPG1 also had two plasmids, designated as pl1LPG1 and pl2LPG1, with lengths of 72,578 and 8713 bp (base pair), respectively. Genome annotation revealed that the sequenced genome consisted of 3345 coding genes and 89 non-coding sequences (73 tRNA and 16 rRNA genes). Taxonomy was confirmed by Average Nucleotide Identity analysis, which grouped L. pentosus LPG1 with other sequenced L. pentosus genomes. Moreover, the pan-genome analysis showed that L. pentosus LPG1 was closely related to the L. pentosus strains IG8, IG9, IG11, and IG12, all of which were isolated from table olive biofilms. Resistome analysis reported the absence of antibiotic resistance genes, whilst PathogenFinder tool classified the strain as a non-human pathogen. Finally, in silico analysis of L. pentosus LPG1 showed that many of its previously reported technological and probiotic phenotypes corresponded with the presence of functional genes. In light of these results, we can conclude that L. pentosus LPG1 is a safe microorganism and a potential human probiotic with a plant origin and application as a starter culture for vegetable fermentations.
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- 2023
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32. Gene probing reveals the widespread distribution, diversity and abundance of isoprene-degrading bacteria in the environment
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Ornella Carrión, Nasmille L. Larke-Mejía, Lisa Gibson, Muhammad Farhan Ul Haque, Javier Ramiro-García, Terry J. McGenity, and J. Colin Murrell
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Isoprene ,Climate ,Isoprene monooxygenase ,isoA ,Gene probes ,Microbial ecology ,QR100-130 - Abstract
Abstract Background Approximately 500 Tg of isoprene are emitted to the atmosphere annually, an amount similar to that of methane, and despite its significant effects on the climate, very little is known about the biological degradation of isoprene in the environment. Isolation and characterisation of isoprene degraders at the molecular level has allowed the development of probes targeting isoA encoding the α-subunit of the isoprene monooxygenase. This enzyme belongs to the soluble diiron centre monooxygenase family and catalyses the first step in the isoprene degradation pathway. The use of probes targeting key metabolic genes is a successful approach in molecular ecology to study specific groups of bacteria in complex environments. Here, we developed and tested a novel isoA PCR primer set to study the distribution, abundance, and diversity of isoprene degraders in a wide range of environments. Results The new isoA probes specifically amplified isoA genes from taxonomically diverse isoprene-degrading bacteria including members of the genera Rhodococcus, Variovorax, and Sphingopyxis. There was no cross-reactivity with genes encoding related oxygenases from non-isoprene degraders. Sequencing of isoA amplicons from DNA extracted from environmental samples enriched with isoprene revealed that most environments tested harboured a considerable variety of isoA sequences, with poplar leaf enrichments containing more phylogenetically diverse isoA genes. Quantification by qPCR using these isoA probes revealed that isoprene degraders are widespread in the phyllosphere, terrestrial, freshwater and marine environments. Specifically, soils in the vicinity of high isoprene-emitting trees contained the highest number of isoprene-degrading bacteria. Conclusion This study provides the molecular ecology tools to broaden our knowledge of the distribution, abundance and diversity of isoprene degraders in the environment, which is a fundamental step necessary to assess the impact that microbes have in mitigating the effects of this important climate-active gas.
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- 2018
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33. New Insights into Microbial Diversity of the Traditional Packed Table Olives Aloreña de Málaga through Metataxonomic Analysis
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Elio López-García, Antonio Benítez-Cabello, Javier Ramiro-García, Verónica Romero-Gil, Francisco Rodríguez-Gómez, and Francisco Noé Arroyo-López
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shelf-life ,table olives ,microbial evolution ,metagenomic analysis ,food safety ,Biology (General) ,QH301-705.5 - Abstract
Aloreña de Málaga is a table olive especially characterised by its natural freshness and short shelf-life. In this work, we applied a metataxonomic approach to unravel the microbial diversity of bacterial and fungi populations through the shelf-life of traditionally packed Aloreña de Málaga. A significant increase in lactic acid bacteria and mesophilic aerobic populations was observed during shelf-life, reaching the maximum population levels (4–5 log10 CFU) at the end of the study (260 days). On the contrary, a rapid reduction in yeast and mould populations was reported. The use of a metataxonomic analysis based on the amplification of 16S (bacteria) and internal transcribed spacer (ITS) region (fungi) regions revealed a low diversity for both microbial groups. Lactiplantibacillus (65.05 ± 8.65% in brine vs. 58.70 ± 15.70% in fruit), Pediococcus (28.17 ± 7.36% in brine vs. 27.20 ± 15.95% in fruit), and Celerinatantimonas (4.64 ± 1.08% in brine vs. 11.82 ± 18.17% in fruit) were the main genera found among bacteria, and an increase in Lactiplantibacillus and a reduction in Celerinatantimonas populations during the shelf-life were observed. On the other hand, Citeromyces was the dominant fungi genus (54.11 ± 2.00% in brine vs. 50.91 ± 16.14% in fruit), followed by Candida (8.80 ± 2.57% in brine vs. 12.32 ± 8.61% in fruit) and Penicillium (6.48 ± 1.87% vs. 8.48 ± 4.43% in fruit). No food-borne pathogen genera were detected in any of the samples analysed, indicating the high level of food safety found in this ready-to-eat fermented vegetable. Data obtained in this work will help in the design of new strategies for the control of microbial populations during the shelf-life of Aloreña de Málaga.
- Published
- 2021
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